diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 00000000..36f23cc4 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,9 @@ +include hicexplorer/trained_models/10kb_model_cleanlab_proteins_obs_exp.BIN +include hicexplorer/trained_models/25kb_model_cleanlab_proteins_obs_exp.BIN +include hicexplorer/trained_models/50kb_model_cleanlab_proteins_obs_exp.BIN +include hicexplorer/trained_models/100kb_model_cleanlab_proteins_obs_exp.BIN +include hicexplorer/trained_models/10kb_model_cleanlab_proteins_range.BIN +include hicexplorer/trained_models/25kb_model_cleanlab_proteins_range.BIN +include hicexplorer/trained_models/50kb_model_cleanlab_proteins_range.BIN +include hicexplorer/trained_models/100kb_model_cleanlab_proteins_range.BIN + diff --git a/azure-pipelines.yml b/azure-pipelines.yml index e78ac771..f5faacf8 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -43,7 +43,9 @@ jobs: displayName: doc_test_and_number_of_cases - script: | source activate hicexplorer - py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 + py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 --ignore=hicexplorer/test/general/test_hicTADClassifier.py --ignore=hicexplorer/test/general/test_hicTrainTADClassifier.py + py.test hicexplorer/test/general/test_hicTADClassifier.py + py.test hicexplorer/test/general/test_hicTrainTADClassifier.py displayName: pytest - job: 'OSX' @@ -86,5 +88,7 @@ jobs: displayName: doc_test_and_number_of_cases - script: | source activate hicexplorer - py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 + py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 --ignore=hicexplorer/test/general/test_hicTADClassifier.py --ignore=hicexplorer/test/general/test_hicTrainTADClassifier.py + py.test hicexplorer/test/general/test_hicTADClassifier.py + py.test hicexplorer/test/general/test_hicTrainTADClassifier.py displayName: pytest \ No newline at end of file diff --git a/bin/chicExportData b/bin/chicExportData new file mode 100644 index 00000000..136b71f7 --- /dev/null +++ b/bin/chicExportData @@ -0,0 +1,8 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +from hicexplorer.chicExportData import main + +if __name__ == "__main__": + main() + diff --git a/bin/hicInterIntraTAD b/bin/hicInterIntraTAD new file mode 100644 index 00000000..a23212d2 --- /dev/null +++ b/bin/hicInterIntraTAD @@ -0,0 +1,7 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +from hicexplorer.hicInterIntraTAD import main + +if __name__ == "__main__": + main() diff --git a/bin/hicTADClassifier b/bin/hicTADClassifier new file mode 100644 index 00000000..8abcfda6 --- /dev/null +++ b/bin/hicTADClassifier @@ -0,0 +1,7 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +from hicexplorer.hicTADClassifier import main + +if __name__ == "__main__": + main() diff --git a/bin/hicTrainTADClassifier b/bin/hicTrainTADClassifier new file mode 100644 index 00000000..7bfb82f9 --- /dev/null +++ b/bin/hicTrainTADClassifier @@ -0,0 +1,7 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +from hicexplorer.hicTrainTADClassifier import main + +if __name__ == "__main__": + main() diff --git a/docs/conf.py b/docs/conf.py index 099a780f..2a3a9e3f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -28,9 +28,12 @@ 'matplotlib', 'matplotlib.pyplot', 'matplotlib.gridspec', 'matplotlib.ticker', 'matplotlib.textpath', 'matplotlib.patches', 'matplotlib.colors', 'matplotlib.cm', 'mpl_toolkits', 'mpl_toolkits.axisartist', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid1', - 'Bio', 'Bio.Seq', 'Bio.Alphabet', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins', + 'Bio.Seq', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins', 'future.utils', 'cooler', 'logging', 'unidecode', 'hic2cool', 'hicmatrix', 'hicmatrix.HiCMatrix', - 'hicmatrix.lib', 'krbalancing', 'fit_nbinom', 'pybedtools', 'graphviz', 'hyperopt', 'sklearn', 'sklearn.cluster'] + 'hicmatrix.lib', 'krbalancing', 'fit_nbinom', 'pybedtools', 'graphviz', 'hyperopt', 'sklearn', 'sklearn.cluster', + 'h5py', 'numpy.random', 'sklearn', 'sklearn.model_selection', 'matplotlib.backends', 'sklearn.preprocessing', + 'matplotlib.backends.backend_agg', 'cleanlab.classification', 'imblearn.under_sampling', 'sklearn.ensemble', + 'sklearn.metrics', 'sklearn.impute', 'tarfile'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() diff --git a/docs/content/News.rst b/docs/content/News.rst index e830a588..1d9d55ed 100644 --- a/docs/content/News.rst +++ b/docs/content/News.rst @@ -2,6 +2,41 @@ News and Developments ===================== +Release 3.7 +----------- +**27 July 2021** + +- A new TAD prediction method: `hicTADClassifier` and a method to train own classifiers `hicTrainTADClassifier`. Thanks @AlbertLidel for the design and implementation. +- New file formats for capture Hi-C modules. `chicViewpoint`, `chicSignificantInteractions`, `chicAggregateStatistic` and `chicDifferentialTest` use now HDF5 based files. A new export script `chicExportData` is provided to retrieve text files from these HDF5 files. +- Implementing a few feature requests: + - `hicPlotMatrix`: TADs can be visualized with hicPlotMatrix + - `hicAdjustMatrix` is able to remove intra- or inter-chromosomal contacts (#664, #704) + - `hicValidateLocations`: An option to validate TADs and to use additional data stored in `cool` matrices + - `hicPCA`: Adding a function to select which eigenvector should be used for the output (#669) + - `hicConvertFormat`: Adding the function to export hicpro file format and to import `2D-text` files. + - `hicFindRestSites`: Support of multiple restriction cut sequences (#659) + - `hicPlotMatrix`: Option for loop locations spanning more than one bin to define if the start, center or end should be used for plotting (#640) + - `hicInterIntraTAD`: A new script to compute the ratio of inter and intra TAD. ($404) + - `hicAggregateContacts`: Option to consider the strand orientation (#633) + - `hicAverageRegions`: Option to consider the strand orientation (#633) + - `hicCompareMatrices`: An option to not normalize the matrices before the computation. (#677, #645) Thanks @lldelisle + - `hicDifferentialTAD`: Adding rank sum statistics to the output (#728, #727). Thanks @dawe + - `hicPlotDistVsCounts`: Adding a function to plot the counts vs distance in TAD regions. (#696) Thanks @lldelisle +- Bug fixes: + - `hicCorrectMatrix`: A bug that lead to wrong correction factors for the KR correction for `cool` files (#724) + - `hicDifferentialTAD`: Solved multicore issue related to skipping data at the start and end of chromosomes (#725, #685) + - `hicHyperoptDetectLoops`: Added an option to set if the `chr` prefix should be added or removed (#723) + - `hicPCA`: Solving an issue if the region defined by the gene track is larger the region stored in the interaction matrix (#655, #710, #716, #719) + - `hicPCA`: Fixing a bug where the masking of bins was automatically applied which lead to differing matrix dimensions for the e.g. the Pearson correlation matrices (#618) + - `hicBuildMatrix`: Solving a bug if multiple restriction cut sites have the same dangling ends (#720) + - `hicBuildMatrix`: Solving a bug that the parameter `--removeSelfLigations` was always set to true. Changed parameter name to `--keepSelfLigations` to keep the functionality. If the parameter is not set, the self ligations are removed. + - `hicBuildMatrix`: If a region is specified, only the restrictionCutSite file information for that region is loaded to save memory (#646) + - `hicConvertFormat`: Fixing a bug to copy the genome annotation information in the case of a `cool` to `cool` file conversion (#657) + - `hicCorrelate`: Correcting the range of colors for the heatmap (#585) + - `hicCompartmentalization`: Fixed index bug (#635, #637) Thanks @LeilyR +- Updating `hicBuildMatrix` to be able to work with biopython versions > 1.77. Thanks @lldelisle (#691) + + Release 3.6 ----------- **10 November 2020** @@ -113,7 +148,7 @@ Release 3.4.2 Preprint -------- -**6 March 2020* +**6 March 2020** The preprint of the loop detection algorithm is online via biorXiv: ``_ diff --git a/docs/content/capture-Hi-C.rst b/docs/content/capture-Hi-C.rst index 950daf39..d1e88195 100644 --- a/docs/content/capture-Hi-C.rst +++ b/docs/content/capture-Hi-C.rst @@ -6,6 +6,8 @@ How we use HiCExplorer to analyse cHi-C data This How-to is based on the published dataset from `Andrey et al. 2017 `__. For the tutorial, we use the samples FL-E13.5 and MB-E-10.5. +**Disclaimer**: With HiCExplorer 3.7 all data is stored in hdf5 based files to make the handling easier. Please check your version of HiCExplorer to make sure you use the latest version. Commands of older HiCExplorer version do not work with the introduced changes! + Download the raw data --------------------- @@ -150,48 +152,34 @@ Viewpoint computation In this step the viewpoints for each reference point listed in a `reference_points.bed`-file is extracted from the interaction matrix, using the quality controlled file created by `chicQualityControl`. The up- and downstream range can be given via `--range upstream downstream`. Please use the same value for `--fixateRange` as in the background model computation. For each relative distance the x-fold over the average value of this relative distance is computed and each location is assigned a p-value based on the background negative binomial distribution for this relative distance. -For each viewpoint one viewpoint file is created and stored in the folder given by the parameter `--outputFolder`. +The output is one hdf5 based file containing all the data. .. code:: bash - chicViewpoint -m FL-E13-5.cool MB-E10-5.cool --averageContactBin 5 --range 1000000 1000000 -rp referencePoints.bed -bmf background_model.txt --writeFileNamesToFile interactionFiles.txt --outputFolder interactionFilesFolder --fixateRange 500000 --threads 20 - - -The name of each viewpoint file starts with its sample name (given by the name of the matrix), the -exact location and the gene / promoter name. For example, the viewpoint `chr1 4487435 4487435 Sox17` from `MB-E10-5.cool` matrix will be called `MB-E10-5_chr1_4487435_4487435_Sox17.txt` and looks like the following: - -.. code:: text + chicViewpoint -m FL-E13-5.cool MB-E10-5.cool --averageContactBin 5 --range 1000000 1000000 -rp referencePoints.bed -bmf background_model.txt --outFileName interactions.hdf5 --fixateRange 500000 --threads 20 - # Interaction file, created with HiCExplorer's chicViewpoint version 3.2 - # MB-E10-5.cool chr1_4487435_4487435 3.49 Mbp 5.49 Mbp Sox17 Sum of interactions in fixate range: 978.0 - # Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw - # - chr1 3487000 3488000 Sox17 978.0 -1000000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3488000 3489000 Sox17 978.0 -999000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3489000 3490000 Sox17 978.0 -998000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3490000 3491000 Sox17 978.0 -997000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3491000 3492000 Sox17 978.0 -996000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3492000 3493000 Sox17 978.0 -995000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3493000 3494000 Sox17 978.0 -994000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3494000 3495000 Sox17 978.0 -993000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3495000 3496000 Sox17 978.0 -992000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 - chr1 3496000 3497000 Sox17 978.0 -991000 0.000000000000 0.894286365313 0.000000000000 0.000000000000 +.. code:: bash + chicExportData --file interactions.hdf5 --outputMode all -o interactions.tar.gz -t 16 -Each file contains a header with information about the HiCExplorer version used, the sample, the viewpoint and the content of the different columns. +The text files for each matrix and viewpoint have the following structure: -If the parameter `--writeFileNamesToFile` is set, the viewpoint file names are written to a file which can be used for batch processing in the later steps. Each sample is combined with every other sample for each viewpoint to enable the batch processing -for the differential analysis. Example: matrices `FL-E13-5.cool` and `MB-E10-5.cool` with the three reference points: +.. code:: text -.. code:: bash + # Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw + chr1 14167000 14168000 Eya1 673.000000000000 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14168000 14169000 Eya1 673.000000000000 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14169000 14170000 Eya1 673.000000000000 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14170000 14171000 Eya1 673.000000000000 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14171000 14172000 Eya1 673.000000000000 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14172000 14173000 Eya1 673.000000000000 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14173000 14174000 Eya1 673.000000000000 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14174000 14175000 Eya1 673.000000000000 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 + chr1 14175000 14176000 Eya1 673.000000000000 -125000 0.000297176820 0.042850447268 0.916568982282 0.200000000000 + chr1 14176000 14177000 Eya1 673.000000000000 -124000 0.000297176820 0.042850447268 0.908160092485 0.200000000000 - FL-E13-5_chr1_4487435_4487435_Sox17.txt - MB-E10-5_chr1_4487435_4487435_Sox17.txt - FL-E13-5_chr1_14300280_14300280_Eya1.txt - MB-E10-5_chr1_14300280_14300280_Eya1.txt - FL-E13-5_chr1_19093103_19093103_Tfap2d.txt - MB-E10-5_chr1_19093103_19093103_Tfap2d.txt +Each file contains a header with information about content of the different columns. @@ -202,102 +190,76 @@ Significant interactions detection To detect significant interactions and to prepare a target file for each viewpoint which will be used for the differential analysis, the script `chicSignificantInteractions` is used. It offers two modes: either the user can specify an x-fold value or a loose p-value. The first one considers all interactions with a minimum x-fold over the average background for its relative distribution as a candidate or secondly, all interactions with a loose p-value or less are considered. These are pre-selection steps to be able to detect wider peaks in the same way as sharp ones. All detected candidates are merged to one peak if they are direct neighbors, and the sum of all interaction values of this neighborhood -is used to compute a new p-value. The p-value is computed based on the relative distance negative binomial distribution of the interaction with the original highest interaction value. All peaks considered are accepted as significant interactions if +is used to compute a new p-value. The p-value is computed based on the relative distance continuous negative binomial distribution of the interaction with the original highest interaction value. All peaks considered are accepted as significant interactions if their p-value is as small as the threshold `--pvalue`. To exclude interactions with an interaction value smaller than desired the parameter `--peakInteractionsThreshold` can be set. -In this example we use the reference point Mstn at location chr1 53118507, a loose p-value of 0.1 and p-value of 0.01: +In this example we use the created interactions.hdf5 file of chicViewpoint, a loose p-value of 0.1 and p-value of 0.01. For all stored locations the significant interactions are computed: .. code:: bash - chicSignificantInteractions --interactionFile interactionFilesFolder/FL-E13-5_chr1_53118507_53118507_Mstn.txt -bmf background_model.txt --range 1000000 1000000 --pValue 0.01 --loosePValue 0.1 + chicSignificantInteractions --interactionFile interactions.hdf5 -bmf background_model.txt --range 1000000 1000000 --pValue 0.01 --loosePValue 0.1 --outFileNameSignificant significant.hdf5 --outFileNameTarget target.hdf5 --combinationMode dual -This creates two files: +This creates two files, a file storing all significant interactions, significant.hdf5, and a target file, target.hdf5. The content of the two files can be export via chicExport: .. code:: bash - FL-E13-5_chr1_53118507_53118507_Mstn_target.txt - FL-E13-5_chr1_53118507_53118507_Mstn__significant_interactions.txt + chicExportData --file significant.hdf5 --outputMode all -o targets.tar.gz -t 16 + chicExportData --file target.hdf5 --outputMode all -o targets.tar.gz -t 16 -These files are stored in the folders given by the parameters `--targetFolder` and `--outputFolder`. - -The significant interaction files looks like the following: +For all tools it is also possible to just extract one gene by the gene name as it was given in the fourth column of the reference file. For each name, the data for all stored matrices is extracted. This mode works also on the interactions, target, aggregated and differential files. .. code:: bash - # FL-E13-5.cool chr1_53118507_53118507 52.12 Mbp 54.12 Mbp Mstn Sum of interactions in fixate range: 1517.0 - #Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target - chr1 53318000 53321000 Mstn 1517.0 200000 0.00395517468600000040 0.00000145009991170397 8.37043994897500098773 6.00000000000000000000 - chr1 53329000 53334000 Mstn 1517.0 212000 0.01081081081000000166 0.00000000000000188738 22.37661518795599846499 16.39999999999999857891 - chr1 53348000 53350000 Mstn 1517.0 231000 0.00329597890600000004 0.00001463968364323609 7.37204640642899988734 5.00000000000000000000 - chr1 53351000 53359000 Mstn 1517.0 239000 0.01437046802899999941 0.00000000000000099920 34.20972383882499912033 21.80000000000000071054 - chr1 53393000 53401000 Mstn 1517.0 278000 0.01793012524599999977 0.00000000000000044409 48.20518935066399990319 27.19999999999999928946 - chr1 53408000 53420000 Mstn 1517.0 294000 0.02307185234000000418 0.00000000000001743050 68.05162660125500906361 35.00000000000000000000 + chicExportData --file significant.hdf5 --outputMode geneName --outputModeName Eya1 -t 16 -The target file looks like: +The significant interaction files looks like the following: .. code:: bash - # Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev - # targetFolder/FL-E13-5_chr1_53118507_53118507_Mstn_target.txt - # Mode: loose p-value with 0.1 - # Used p-value: 0.01 - # - chr1 53318000 53321000 - chr1 53329000 53334000 - chr1 53348000 53359000 - chr1 53393000 53401000 - chr1 53408000 53420000 - + # Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw + chr1 14274000 14278000 Eya1 673.000000000000 -26000 0.008320950966 0.007037698679 7.811125758170 5.600000000000 + chr1 14296000 14298000 Eya1 673.000000000000 -3000 0.057949479941 0.104215728599 3.781355935916 39.000000000000 + chr1 14314000 14316000 Eya1 673.000000000000 14000 0.015156017831 0.048507853154 3.190333935010 10.200000000000 + chr1 14317000 14319000 Eya1 673.000000000000 17000 0.014561664190 0.034914431882 3.517090338584 9.800000000000 + chr1 14480000 14488000 Eya1 673.000000000000 184000 0.011292719168 0.000000010481 19.285082946462 7.600000000000 + chr1 14491000 14501000 Eya1 673.000000000000 200000 0.030683506686 0.000000000000 56.967824833429 20.650000000000 -Batch mode -~~~~~~~~~~ -The batch mode supports the computation of many viewpoints at once and is able to create one target list for the same viewpoint and two (or n) samples. To do the batch computation the -parameter `--batchMode` needs to be added and the folder of the viewpoint files needs to be defined. In addition, the list of viewpoints created by `chicViewpoint` with `--writeFileNamesToFile` needs to be -used as input. One target file is created for n consecutive lines and can be defined via the `--computeSampleNumber` parameter. However, for the differential test where the target file is needed, only -two samples and one target file is supported. +The target file looks like: .. code:: bash - chicSignificantInteractions --interactionFile interactionFiles.txt --interactionFileFolder interactionFilesFolder/ -bmf background_model.txt --range 1000000 1000000 --pValue 0.01 --loosePValue 0.1 --batchMode - -The output is: + chr1 14274000 14278000 + chr1 14295000 14298000 + chr1 14314000 14319000 + chr1 14426000 14432000 + chr1 14447000 14455000 + chr1 14460000 14465000 + chr1 14480000 14488000 + chr1 14491000 14501000 -- A folder containing all target files, name defined by `--targetFolder`, default value is `targetFolder` -- A folder with all significant interaction files, name defined by `--outputFolder`, default value is `significantFiles` -- A list containing the file names of all target files, name defined by `--targetFileList`, default value is `targetList.txt` -- A list containing the file names of all significant interaction files, name defined by `--writeFileNamesToFile`, default value is `significantFilesBatch.txt` +The parameter `--combinationMode` has the options `single` and `dual`. This parameter is important if a differential analysis should be computed, either a target region is only for one gene of one matrix, or the regions of one gene of two matrices are combined. +For example: +- `dual` combines as follows: `[[matrix1_gene1, matrix2_gene1], [matrix2_gene1, matrix3_gene1],[matrix1_gene2, matrix2_gene2], ...]` +- `single` combines as follows: `[matrix1_gene1, matrix1_gene2, matrix2_gene1, ...]` Aggregate data for differential test ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The process to aggregate data is only necessary if the differential test is used. Either two files and one target list are used to generate the files for the differential test -or the batch mode can be used. `chicAggregateStatistic` takes the created viewpoint files from `chicViewpoint` as input and either the target files per two samples created by `chicSignificantInteractions` +The process to aggregate data is only necessary if the differential test is used. `chicAggregateStatistic` takes the created interaction file from `chicViewpoint` as input and either the target file created by `chicSignificantInteractions` or one target file which applies for all viewpoints. .. code:: bash - chicAggregateStatistic --interactionFile interactionFilesFolder/FL-E13-5_chr1_53118507_53118507_Mstn.txt interactionFilesFolder/MB-E10-5_chr1_53118507_53118507_Mstn.txt --targetFile targetFolder/FL-E13-5_MB-E10-5_chr1_53118507_53118507_Mstn_target.txt - -It selects the original data based on the target locations and returns one file per sample which is used for the differential test. - -Batch mode -~~~~~~~~~~ - -In the batch mode the interaction file is the file containing the viewpoint file names, the folder needs to be defined by `--interactionFileFolder`, the same applies to the target file and folder. -Two viewpoint files are match with one target file created by `chicSignificantInteractions` or one target file for all viewpoints. Please notice the output files are written to the folder name -defined by `--outputFolder`, the default is `aggregatedFiles` and it is recommended to write the file names for further batch processing with `hicDifferentialTest` to `--writeFileNamesToFile`. All output files -get the suffix defined by `--outFileNameSuffix`, default value is `_aggregate_target.txt`. - -.. code:: bash - - chicAggregateStatistic --interactionFile interactionFiles.txt --interactionFileFolder interactionFilesFolder --targetFile targetList.txt --targetFileFolder targetFolder --batchMode + chicAggregateStatistic --interactionFile interaction.hdf5 --targetFile target.hdf5 --outFileName aggregate.hdf5 -t 16 + chicAggregateStatistic --interactionFile interaction.hdf5 --targetFile regions_of_interest.bed --outFileName aggregate.hdf5 -t 16 +It selects the original data based on the target locations and returns one hdf5 based file. Differential test @@ -306,101 +268,58 @@ Differential test The differential test tests the interaction value of the reference point and the interaction value of the target of two samples for a differential expression. To achieve this, either Fisher's test or the chi-squared test can be used. H0 is defined as 'both locations are equal', meaning the differential expressed targets can be found in the H0 rejected file. -This can be computed per sample: - .. code:: bash - chicDifferentialTest --interactionFile aggregatedFiles/FL-E13-5_chr1_53118507_53118507_Mstn__aggregate_target.txt aggregatedFiles/MB-E10-5_chr1_53118507_53118507_Mstn__aggregate_target.txt --alpha 0.05 --statisticTest fisher + chicDifferentialTest --aggregatedFile aggregate.hdf5 --alpha 0.05 --statisticTest fisher --outFileName differential.hdf5 -t 16 -Or via batch mode: -.. code:: bash - - chicDifferentialTest --interactionFile aggregatedFilesBatch.txt --interactionFileFolder aggregatedFiles --alpha 0.05 --statisticTest fisher --batchMode --threads 20 - -In both cases it is important to set the desired alpha value and the output is written to `--outputFolder` (default `differentialResults`). For each sample three files are created: +It is important to set the desired alpha value and the output is written to one hdf5 based file. For each sample three internal datasets are created: - H0 rejected targets - H0 accepted targets - one file containing both -In the batch mode, the file `--rejectedFileNamesToFile` is also written and contains the file names of the rejected files. This can be used for the batch processing mode of `chicPlotViewpoint`. +The data can be exported via `chicExportData`: .. code:: bash - # Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev - # This file contains the p-values computed by fisher test - # To test the smoothed (float) values they were rounded up to the next integer - # - # Alpha level 0.05 - # Degrees of freedom 1 - # - # FL-E13-5.cool chr1_53118507_53118507 52.12 Mbp 54.12 Mbp Mstn Sum of interactions in fixate range: 1517.0 - # MB-E10-5.cool chr1_53118507_53118507 52.12 Mbp 54.12 Mbp Mstn Sum of interactions in fixate range: 1670.0 - #Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value - chr1 53089000 53091000 Mstn -28000 1517.00000 5.00000 1670.00000 10.40000 0.21800 - chr1 53131000 53133000 Mstn 14000 1517.00000 18.20000 1670.00000 23.60000 0.75900 - chr1 53156000 53158000 Mstn 39000 1517.00000 3.00000 1670.00000 10.80000 0.06117 - chr1 53251000 53254000 Mstn 135000 1517.00000 4.00000 1670.00000 9.60000 0.18614 - chr1 53287000 53291000 Mstn 172000 1517.00000 7.20000 1670.00000 15.00000 0.29506 - chr1 53305000 53309000 Mstn 190000 1517.00000 6.20000 1670.00000 12.40000 0.36952 - chr1 53318000 53321000 Mstn 202000 1517.00000 6.00000 1670.00000 3.20000 0.53309 - chr1 53326000 53334000 Mstn 215000 1517.00000 25.80000 1670.00000 22.60000 0.47374 - chr1 53346000 53359000 Mstn 240000 1517.00000 31.60000 1670.00000 22.20000 0.13464 - chr1 53408000 53421000 Mstn 302000 1517.00000 36.40000 1670.00000 28.20000 0.21290 + chicExportData --file differential.hdf5 --outputMode all -o differential.tar.gz -t 16 +The created tar.gz file contains for each tested regions the three files `rejected`, 'accepted' and a file containing both information. It is also possible to extract only one gene: .. code:: bash - # Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev - # This file contains the p-values computed by fisher test - # To test the smoothed (float) values they were rounded up to the next integer - # - # Alpha level 0.05 - # Degrees of freedom 1 - # - # FL-E13-5.cool chr1_53118507_53118507 52.12 Mbp 54.12 Mbp Mstn Sum of interactions in fixate range: 1517.0 - # MB-E10-5.cool chr1_53118507_53118507 52.12 Mbp 54.12 Mbp Mstn Sum of interactions in fixate range: 1670.0 - #Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value - chr1 53393000 53401000 Mstn 282000 1517.00000 27.20000 1670.00000 6.40000 0.00012 + chicExportData --file differential.hdf5 --outputMode geneName --outputModeName Eya1 -o differential_one -t 16 + +In case of the single extraction, the output file name serves only to determine the folder to save the data. The names are based on the gene name. + .. code:: bash - # Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev - # This file contains the p-values computed by fisher test - # To test the smoothed (float) values they were rounded up to the next integer - # - # Alpha level 0.05 - # Degrees of freedom 1 - # - # FL-E13-5.cool chr1_53118507_53118507 52.12 Mbp 54.12 Mbp Mstn Sum of interactions in fixate range: 1517.0 - # MB-E10-5.cool chr1_53118507_53118507 52.12 Mbp 54.12 Mbp Mstn Sum of interactions in fixate range: 1670.0 - #Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value - chr1 53089000 53091000 Mstn -28000 1517.00000 5.00000 1670.00000 10.40000 0.21800 - chr1 53131000 53133000 Mstn 14000 1517.00000 18.20000 1670.00000 23.60000 0.75900 - chr1 53156000 53158000 Mstn 39000 1517.00000 3.00000 1670.00000 10.80000 0.06117 - chr1 53251000 53254000 Mstn 135000 1517.00000 4.00000 1670.00000 9.60000 0.18614 - chr1 53287000 53291000 Mstn 172000 1517.00000 7.20000 1670.00000 15.00000 0.29506 - chr1 53305000 53309000 Mstn 190000 1517.00000 6.20000 1670.00000 12.40000 0.36952 - chr1 53318000 53321000 Mstn 202000 1517.00000 6.00000 1670.00000 3.20000 0.53309 - chr1 53326000 53334000 Mstn 215000 1517.00000 25.80000 1670.00000 22.60000 0.47374 - chr1 53346000 53359000 Mstn 240000 1517.00000 31.60000 1670.00000 22.20000 0.13464 - chr1 53393000 53401000 Mstn 282000 1517.00000 27.20000 1670.00000 6.40000 0.00012 - chr1 53408000 53421000 Mstn 302000 1517.00000 36.40000 1670.00000 28.20000 0.21290 + # Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value + chr1 14274000 14278000 Eya1 -23000 673.000000000000 5.600000000000 832.000000000000 0.000000000000 0.008134451704 + chr1 14295000 14298000 Eya1 -3000 673.000000000000 44.400000000000 832.000000000000 49.800000000000 0.670801771179 + chr1 14314000 14319000 Eya1 18000 673.000000000000 24.200000000000 832.000000000000 23.400000000000 0.385952554141 + chr1 14426000 14432000 Eya1 131000 673.000000000000 2.400000000000 832.000000000000 9.000000000000 0.245228952263 + chr1 14447000 14455000 Eya1 154000 673.000000000000 4.400000000000 832.000000000000 12.400000000000 0.232102031454 + chr1 14460000 14465000 Eya1 164000 673.000000000000 3.200000000000 832.000000000000 7.600000000000 0.564250349826 + chr1 14480000 14488000 Eya1 187000 673.000000000000 7.600000000000 832.000000000000 3.200000000000 0.151571165731 + chr1 14491000 14501000 Eya1 200000 673.000000000000 20.650000000000 832.000000000000 18.750000000000 0.338670136491 + Plotting of Viewpoints ^^^^^^^^^^^^^^^^^^^^^^ -`chicPlotViewpoint` can plot `n` viewpoints in one plot, add the mean background, show the p-value per relative distance per sample as an additional heatmap bar and highlight significant interactions or differential expressed regions. +`chicPlotViewpoint` can plot viewpoints of one gene in one plot, add the mean background, show the p-value per relative distance per sample as an additional heatmap bar and highlight significant interactions or differential expressed regions. One viewpoint: .. code:: bash - chicPlotViewpoint --interactionFile interactionFilesFolder/FL-E13-5_chr1_53118507_53118507_Mstn.txt --range 200000 200000 -o single_plot.png + chicPlotViewpoint --interactionFile interactions.hdf5 --combinationMode oneGene --combinationName Eya1 --range 200000 200000 -o single_plot.tar.gz --outputFormat png .. image:: ../images/chic/single_plot.png @@ -408,8 +327,9 @@ Two viewpoints, background, differential expression and p-values: .. code:: bash - chicPlotViewpoint --interactionFile interactionFilesFolder/FL-E13-5_chr1_53118507_53118507_Mstn.txt interactionFilesFolder/MB-E10-5_chr1_53118507_53118507_Mstn.txt --range 300000 300000 --pValue --differentialTestResult differentialResults/FL-E13-5_MB-E10-5_chr1_53118507_53118507_Mstn__H0_rejected.txt --backgroundModelFile background_model.txt -o differential_background_pvalue.png + chicPlotViewpoint --interactionFile interactions.hdf5 --combinationMode dual --range 300000 300000 --pValue --differentialTestResult differential.hdf5 --backgroundModelFile background_model.txt -o differential_background_pvalue.tar.gz +This command plots two viewpoints of two different matrices of the same gene in a plot and highlights the differential regions. .. image:: ../images/chic/differential_background_pvalue.png @@ -417,19 +337,7 @@ Two viewpoints, background, significant interactions and p-values: .. code:: bash - chicPlotViewpoint --interactionFile interactionFilesFolder/FL-E13-5_chr1_53118507_53118507_Mstn.txt interactionFilesFolder/MB-E10-5_chr1_53118507_53118507_Mstn.txt --range 300000 300000 --pValue --significantInteractions significantFiles/FL-E13-5_chr1_53118507_53118507_Mstn__significant_interactions.txt significantFiles/MB-E10-5_chr1_53118507_53118507_Mstn__significant_interactions.txt --backgroundModelFile background_model.txt -o significant_background_pvalue.png + chicPlotViewpoint --interactionFile interaction.hdf5 --combinationMode dual --range 300000 300000 --pValue --significantInteractions significant.hdf5 --plotSignificantInteractions --backgroundModelFile background_model.txt -o significant_background_pvalue.tar.gz .. image:: ../images/chic/significant_background_pvalue.png - -Batch mode -~~~~~~~~~~ - -The batch mode is able to plot files under the same parameter setting for multiple viewpoints. These viewpoints are given by the file created by `chicViewpoint` with `--writeFileNamesToFile` parameter. -The number of consecutive lines which should be plotted to one image can be defined using `--plotSampleNumber`. If the differentially expressed regions should be highlighted, setting this parameter to 2 is recommended. - -For all modes the principle of a file containing the file names and a folder containing them applies for the plotting too, and using all cores available is highly recommended. - -.. code:: bash - - chicPlotViewpoint --interactionFile interactionFiles.txt --interactionFileFolder interactionFilesFolder/ --range 300000 300000 --pValue --significantInteractions significantFilesBatch.txt --significantInteractionFileFolder significantFiles --backgroundModelFile background_model.txt --outputFolder plots --threads 20 --batchMode \ No newline at end of file diff --git a/docs/content/installation.rst b/docs/content/installation.rst index f750d7ee..daa555d2 100644 --- a/docs/content/installation.rst +++ b/docs/content/installation.rst @@ -14,7 +14,7 @@ Requirements * ipykernel >= 5.3.0 * pysam >= 0.16.* * intervaltree >= 3.1.* -* biopython < 1.77 +* biopython * pytables >= 3.6.* * pandas >= 1.1.* * pybigwig >= 0.3.* diff --git a/docs/content/list-of-tools.rst b/docs/content/list-of-tools.rst index dc66843b..6cd92433 100644 --- a/docs/content/list-of-tools.rst +++ b/docs/content/list-of-tools.rst @@ -50,6 +50,10 @@ Tools for TADs processing tools/hicMergeDomains tools/hicDifferentialTAD tools/hicMergeTADbins + tools/hicInterIntraTAD + tools/hicTrainTADClassifier + tools/hicTADClassifier + Tools for Hi-C and TADs visualization ------------------------------------- @@ -113,6 +117,12 @@ For single-cell Hi-C data analysis please use `scHiCExplorer = 1 and pOneTarget == False: - if pArgs.targetFileFolder != '.': - target_file = pArgs.targetFileFolder + '/' + pTargetList[i] - log.debug('194') - else: - target_file = pTargetList[i] - log.debug('197') - - elif pArgs.batchMode and len(pTargetList) == 1 and pOneTarget == True: - target_file = None - log.debug('201') + interaction_data, interaction_file_data, _ = pViewpointObj.readInteractionFile(pArgs.interactionFile, sample) + if pOneTarget == True: + target_file = None else: target_file = pTargetList[i] - log.debug('205') - - accepted_scores = filter_scores_target_list(interaction_file_data, pTargetList=target_file, pTargetIntervalTree=target_regions_intervaltree) - - if len(accepted_scores) == 0: - # do not call 'break' or 'continue' - # with this an empty file is written and no track of 'no significant interactions' detected files needs to be recorded. - if pArgs.batchMode: - with open('errorLog.txt', 'a+') as errorlog: - errorlog.write('Failed for: {} and {}.\n'.format(interactionFile[0], interactionFile[1])) - else: - log.info('No target regions found') - outFileName = '.'.join(sample.split('/')[-1].split('.')[:-1]) + '_' + pArgs.outFileNameSuffix - - if pArgs.batchMode: - outfile_names.append(outFileName) - if pArgs.outputFolder != '.': - outFileName = pArgs.outputFolder + '/' + outFileName - - write(outFileName, header, accepted_scores, - interaction_file_data) + + accepted_scores = filter_scores_target_list(interaction_file_data, pTargetList=target_file, pTargetIntervalTree=target_regions_intervaltree, pTargetFile=pArgs.targetFile) + + outfile_names_list_intern.append(sample) + accepted_scores_list_intern.append(accepted_scores) + outfile_names_list.append(outfile_names_list_intern) + accepted_scores_list.append(accepted_scores_list_intern) + except Exception as exp: pQueue.put('Fail: ' + str(exp) + traceback.format_exc()) return if pQueue is None: return - pQueue.put(outfile_names) + counter = 0 + for item in accepted_scores_list_intern: + if len(item) == 0: + counter += 1 + pQueue.put([outfile_names_list, accepted_scores_list]) return def call_multi_core(pInteractionFilesList, pTargetFileList, pFunctionName, pArgs, pViewpointObj): if len(pInteractionFilesList) < pArgs.threads: pArgs.threads = len(pInteractionFilesList) - outfile_names = [None] * pArgs.threads + outfile_names_list = [None] * pArgs.threads + accepted_scores_list = [None] * pArgs.threads + interactionFilesPerThread = len(pInteractionFilesList) // pArgs.threads all_data_collected = False @@ -260,13 +258,13 @@ def call_multi_core(pInteractionFilesList, pTargetFileList, pFunctionName, pArgs if i < pArgs.threads - 1: interactionFileListThread = pInteractionFilesList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] if len(pTargetFileList) == 1: - targetFileListThread = pTargetFileList + targetFileListThread = pTargetFileList[0] else: targetFileListThread = pTargetFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] else: interactionFileListThread = pInteractionFilesList[i * interactionFilesPerThread:] if len(pTargetFileList) == 1: - targetFileListThread = pTargetFileList + targetFileListThread = pTargetFileList[0] else: targetFileListThread = pTargetFileList[i * interactionFilesPerThread:] @@ -290,7 +288,8 @@ def call_multi_core(pInteractionFilesList, pTargetFileList, pFunctionName, pArgs if 'Fail:' in background_data_thread: fail_flag = True fail_message = background_data_thread[6:] - outfile_names[i] = background_data_thread + else: + outfile_names_list[i], accepted_scores_list[i] = background_data_thread queue[i] = None process[i].join() process[i].terminate() @@ -304,59 +303,67 @@ def call_multi_core(pInteractionFilesList, pTargetFileList, pFunctionName, pArgs if fail_flag: log.error(fail_message) exit(1) - outfile_names = [item for sublist in outfile_names for item in sublist] - return outfile_names + outfile_names_list = [item for sublist in outfile_names_list for item in sublist] + accepted_scores_list = [item for sublist in accepted_scores_list for item in sublist] + + return outfile_names_list, accepted_scores_list def main(args=None): args = parse_arguments().parse_args(args) viewpointObj = Viewpoint() - outfile_names = [] - if not os.path.exists(args.outputFolder): - try: - os.makedirs(args.outputFolder) - except OSError as exc: # Guard against race condition - if exc.errno != errno.EEXIST: - raise - - interactionFileList = [] - targetFileList = [] - - if args.batchMode: - with open(args.interactionFile[0], 'r') as interactionFile: - file_ = True - while file_: - file_ = interactionFile.readline().strip() - file2_ = interactionFile.readline().strip() - if file_ != '' and file2_ != '': - interactionFileList.append((file_, file2_)) - - if len(args.targetFile) == 1 and args.targetFileFolder: - - with open(args.targetFile[0], 'r') as targetFile: - file_ = True - while file_: - file_ = targetFile.readline().strip() - if file_ != '': - targetFileList.append(file_) - else: - targetFileList = args.targetFile - outfile_names = call_multi_core(interactionFileList, targetFileList, run_target_list_compilation, args, viewpointObj) + + interactionList = [] + interactionDict = {} + + targetList = [] + present_genes = {} + # read hdf file + interactionFileHDF5Object = h5py.File(args.interactionFile, 'r') + keys_interactionFile = list(interactionFileHDF5Object.keys()) + + if h5py.is_hdf5(args.targetFile): + + targetDict, present_genes = viewpointObj.readTargetHDFFile(args.targetFile) else: - targetFileList = args.targetFile - if len(args.interactionFile) % 2 == 0: - i = 0 - while i < len(args.interactionFile): - interactionFileList.append( - (args.interactionFile[i], args.interactionFile[i + 1])) - i += 2 - else: - log.error('Number of interaction files needs to be even: {}'.format( - len(args.interactionFile))) - exit(1) - run_target_list_compilation(interactionFileList, targetFileList, args, viewpointObj) - - if args.batchMode: - with open(args.writeFileNamesToFile, 'w') as nameListFile: - nameListFile.write('\n'.join(outfile_names)) + targetList = [args.targetFile] + + if len(keys_interactionFile) > 1: + + for i, sample in enumerate(keys_interactionFile): + for sample2 in keys_interactionFile[i + 1:]: + + matrix_obj1 = interactionFileHDF5Object[sample] + matrix_obj2 = interactionFileHDF5Object[sample2] + + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList2 = sorted(list(matrix_obj2.keys())) + chromosomeList1.remove('genes') + chromosomeList2.remove('genes') + for chromosome1, chromosome2 in zip(chromosomeList1, chromosomeList2): + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + geneList2 = sorted(list(matrix_obj2[chromosome2].keys())) + + for gene1, gene2 in zip(geneList1, geneList2): + if h5py.is_hdf5(args.targetFile): + if gene1 in present_genes[sample][sample2]: + interactionDict[gene1] = [[sample, chromosome1, gene1], [sample2, chromosome2, gene2]] + else: + interactionList.append([[sample, chromosome1, gene1], [sample2, chromosome2, gene2]]) + else: + log.error('To aggregate and prepare the data for the differential test, at least two matrices need to be stored, but only one is present.') + + interactionFileHDF5Object.close() + + if h5py.is_hdf5(args.targetFile): + key_outer_matrix = present_genes.keys() + for keys_outer in key_outer_matrix: + keys_inner_matrix = present_genes[keys_outer].keys() + for keys_inner in keys_inner_matrix: + for gene in present_genes[keys_outer][keys_inner]: + interactionList.append(interactionDict[gene]) + targetList.append(targetDict[gene]) + + outfile_names_list, accepted_scores_list = call_multi_core(interactionList, targetList, run_target_list_compilation, args, viewpointObj) + writeAggregateHDF(args.outFileName, outfile_names_list, accepted_scores_list, args) diff --git a/hicexplorer/chicDifferentialTest.py b/hicexplorer/chicDifferentialTest.py index b66995e2..4bd0f418 100644 --- a/hicexplorer/chicDifferentialTest.py +++ b/hicexplorer/chicDifferentialTest.py @@ -10,6 +10,7 @@ import numpy as np from scipy import stats +import h5py import hicmatrix.HiCMatrix as hm from hicexplorer import utilities @@ -22,33 +23,16 @@ def parse_arguments(args=None): formatter_class=argparse.RawDescriptionHelpFormatter, description=""" chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. For this either Fisher's test or the chi2 contingency test can be used. -The files that are accepted for this test can be created with `chicAggregateStatistic`. H0 assumes the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected. +The file that is accepted for this test can be created with `chicAggregateStatistic`. H0 assumes the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected. - -An example usage is: - -`$ chicDifferentialTest --interactionFile viewpoint1_aggregated.txt viewpoint2_aggregated.txt --alpha 0.05 --statisticTest fisher --outputFolder differentialResults` - -and this will create three files: `viewpoint1_viewpoint2_aggregated_H0_accepted.txt`, `viewpoint1_viewpoint2_aggregated_H0_rejected.txt`, `viewpoint1_viewpoint2_aggregated_results.txt` - -The first file contains all locations where H0 was accepted, the second file all locations where H0 was rejected and the third one all locations with the test result. - - - -A second mode is the batch processing mode. For this you need a file containing the names of the aggregated files (generated by chicAggregateStatistic via --writeFileNamesToFile and the batch mode): - -`$ chicDifferentialTest --statisticTest fisher --alpha 0.05 --interactionFile aggregatedFilesBatch.txt --interactionFileFolder aggregatedFilesFolder --batchMode --threads 20 --outputFolder differentialResults` - -This will create, as in the non-batch mode, three files per aggregated file and writes the file name to the file given by `--rejectedFileNamesToFile`. This last file can be used to plot the differential interactions per viewpoint in batch mode, using chicPlotViewpoint. """ ) parserRequired = parser.add_argument_group('Required arguments') - parserRequired.add_argument('--interactionFile', '-if', - help='path to the interaction files which should be used for the differential test.', - required=True, - nargs='+') + parserRequired.add_argument('--aggregatedFile', '-af', + help='path to the aggregated files which should be used for the differential test.', + required=True) parserRequired.add_argument('--alpha', '-a', help='define a significance level (alpha) for accepting samples', @@ -57,25 +41,16 @@ def parse_arguments(args=None): parserOpt = parser.add_argument_group('Optional arguments') - parserOpt.add_argument('--interactionFileFolder', '-iff', - help='Folder where the interaction files are stored. Applies only for batch mode' + parserOpt.add_argument('--outFileName', '-o', + help='Output file for the differential results' ' (Default: %(default)s).', required=False, - default='.') - parserOpt.add_argument('--outputFolder', '-o', - help='Output folder of the files' - ' (Default: %(default)s).', - required=False, - default='differentialResults') + default='differentialResults.hdf5') parserOpt.add_argument('--statisticTest', help='Type of test used: fisher\'s exact test or chi2 contingency' ' (Default: %(default)s).', choices=['fisher', 'chi2'], default='fisher') - parserOpt.add_argument('--batchMode', '-bm', - help='turn on batch mode. The given file for --interactionFile and or --targetFile contain a list of the to be processed files.', - required=False, - action='store_true') parserOpt.add_argument('--threads', '-t', help='Number of threads (uses the python multiprocessing module)' ' (Default: %(default)s).', @@ -83,10 +58,6 @@ def parse_arguments(args=None): default=4, type=int ) - parserOpt.add_argument('--rejectedFileNamesToFile', '-r', - help='Writes the names of the rejected H0 (therefore containing the differential interactions) to file. Can be used for batch processing mode of chicPlotViewpoint.' - ' (Default: %(default)s).', - default='rejected_H0.txt') parserOpt.add_argument("--help", "-h", action="help", help="show this help message and exit") parserOpt.add_argument('--version', action='version', @@ -210,50 +181,110 @@ def writeResult(pOutFileName, pData, pHeaderOld, pHeaderNew, pAlpha, pTest): file.write(line) -def run_statistical_tests(pInteractionFilesList, pArgs, pQueue=None): - rejected_names = [] - try: - for interactionFile in pInteractionFilesList: +def writeResultHDF(pOutFileName, pAcceptedData, pRejectedData, pAllResultData, pInputData, pAlpha, pTest): + resultFileH5Object = h5py.File(pOutFileName, 'w') + resultFileH5Object.attrs['type'] = "differential" + resultFileH5Object.attrs['version'] = __version__ - sample_prefix = interactionFile[0].split( - '/')[-1].split('_')[0] + '_' + interactionFile[1].split('/')[-1].split('_')[0] + resultFileH5Object.attrs['alpha'] = pAlpha + resultFileH5Object.attrs['test'] = pTest - region_prefix = '_'.join( - interactionFile[0].split('/')[-1].split('_')[1:6]) + all_data_dict = {'accepted': pAcceptedData, 'rejected': pRejectedData, 'all': pAllResultData} + for i, inputData in enumerate(pInputData): + matrix1_name = inputData[0][1] + matrix2_name = inputData[1][1] + chromosome = inputData[0][2] + gene_name = inputData[0][3] - outFileName = sample_prefix + '_' + region_prefix - rejected_name_output_file = outFileName + '_H0_rejected.txt' + if matrix1_name not in resultFileH5Object: + matrix1_object = resultFileH5Object.create_group(matrix1_name) + else: + matrix1_object = resultFileH5Object[matrix1_name] - if pArgs.outputFolder != '.': - outFileName_accepted = pArgs.outputFolder + \ - '/' + outFileName + '_H0_accepted.txt' - outFileName_rejected = pArgs.outputFolder + \ - '/' + outFileName + '_H0_rejected.txt' - outFileName = pArgs.outputFolder + '/' + outFileName + '_results.txt' - else: - outFileName_accepted = outFileName + '_H0_accepted.txt' - outFileName_rejected = outFileName + '_H0_rejected.txt' - outFileName = outFileName + '_results.txt' + if matrix2_name not in matrix1_object: + matrix2_object = matrix1_object.create_group(matrix2_name) + else: + matrix2_object = matrix1_object[matrix2_name] - if pArgs.interactionFileFolder != '.': - absolute_sample_path1 = pArgs.interactionFileFolder + '/' + interactionFile[0] - absolute_sample_path2 = pArgs.interactionFileFolder + '/' + interactionFile[1] + if 'genes' not in matrix2_object: + geneGroup = matrix2_object.create_group('genes') + else: + geneGroup = matrix2_object['genes'] - else: - absolute_sample_path1 = interactionFile[0] - absolute_sample_path2 = interactionFile[1] + if chromosome not in matrix2_object: + chromosome_object = matrix2_object.create_group(chromosome) + else: + chromosome_object = matrix2_object[chromosome] + + gene_object = chromosome_object.create_group(gene_name) + + gene_object.create_group('accepted') + gene_object.create_group('rejected') + gene_object.create_group('all') + + for category in ['accepted', 'rejected', 'all']: + write_object = gene_object[category] + data_object = all_data_dict[category][i] + if len(data_object) == 0: + continue + chromosome = None + start_list = [] + end_list = [] + sum_of_interactions_1 = None + sum_of_interactions_2 = None + + relative_distance_list = [] + pvalue_list = [] + + raw_target_list_1 = [] + raw_target_list_2 = [] + + for data in data_object: + + chromosome = data[0][0] + start_list.append(data[0][1]) + end_list.append(data[0][2]) - header1, line_content1, data1 = readInteractionFile(absolute_sample_path1) - header2, line_content2, data2 = readInteractionFile(absolute_sample_path2) + relative_distance_list.append(data[0][5]) + + sum_of_interactions_1 = float(data[3][0]) + sum_of_interactions_2 = float(data[4][0]) + + raw_target_list_1.append(data[3][1]) + raw_target_list_2.append(data[4][1]) + pvalue_list.append(data[2]) + + write_object["chromosome"] = str(chromosome) + write_object.create_dataset("start_list", data=start_list, compression="gzip", compression_opts=9) + write_object.create_dataset("end_list", data=end_list, compression="gzip", compression_opts=9) + write_object["gene"] = str(gene_name) + write_object.create_dataset("relative_distance_list", data=relative_distance_list, compression="gzip", compression_opts=9) + + write_object["sum_of_interactions_1"] = float(sum_of_interactions_1) + write_object["sum_of_interactions_2"] = float(sum_of_interactions_2) + + write_object.create_dataset("raw_target_list_1", data=raw_target_list_1, compression="gzip", compression_opts=9) + write_object.create_dataset("raw_target_list_2", data=raw_target_list_2, compression="gzip", compression_opts=9) + write_object.create_dataset("pvalue_list", data=pvalue_list, compression="gzip", compression_opts=9) + + try: + geneGroup[gene_name] = chromosome_object[gene_name] + except Exception as exp: + log.debug('exception {}'.format(str(exp))) + resultFileH5Object.close() + + +def run_statistical_tests(pInteractionFilesList, pArgs, pViewpointObject, pQueue=None): + accepted_list = [] + rejected_list = [] + all_results_list = [] + try: + for interactionFile in pInteractionFilesList: + + line_content1, data1 = pViewpointObject.readAggregatedFileHDF(pArgs.aggregatedFile, interactionFile[0]) + line_content2, data2 = pViewpointObject.readAggregatedFileHDF(pArgs.aggregatedFile, interactionFile[1]) if len(line_content1) == 0 or len(line_content2) == 0: - writeResult(outFileName, None, header1, header2, - pArgs.alpha, pArgs.statisticTest) - writeResult(outFileName_accepted, None, header1, header2, - pArgs.alpha, pArgs.statisticTest) - writeResult(outFileName_rejected, None, header1, header2, - pArgs.alpha, pArgs.statisticTest) - rejected_names.append(rejected_name_output_file) continue if pArgs.statisticTest == 'chi2': test_result, accepted, rejected = chisquare_test( @@ -277,13 +308,9 @@ def run_statistical_tests(pInteractionFilesList, pArgs, pQueue=None): write_out_lines_rejected.append( [line_content1[result[0]], line_content2[result[0]], result[1], data1[result[0]], data2[result[0]]]) - writeResult(outFileName, write_out_lines, header1, header2, - pArgs.alpha, pArgs.statisticTest) - writeResult(outFileName_accepted, write_out_lines_accepted, header1, header2, - pArgs.alpha, pArgs.statisticTest) - writeResult(outFileName_rejected, write_out_lines_rejected, header1, header2, - pArgs.alpha, pArgs.statisticTest) - rejected_names.append(rejected_name_output_file) + accepted_list.append(write_out_lines_accepted) + rejected_list.append(write_out_lines_rejected) + all_results_list.append(write_out_lines) except Exception as exp: pQueue.put('Fail: ' + str(exp)) @@ -291,93 +318,102 @@ def run_statistical_tests(pInteractionFilesList, pArgs, pQueue=None): if pQueue is None: return - pQueue.put(rejected_names) + pQueue.put([accepted_list, rejected_list, all_results_list]) return def main(args=None): args = parse_arguments().parse_args(args) - if not os.path.exists(args.outputFolder): - try: - os.makedirs(args.outputFolder) - except OSError as exc: # Guard against race condition - if exc.errno != errno.EEXIST: - raise - interactionFileList = [] - if args.batchMode: - with open(args.interactionFile[0], 'r') as interactionFile: - file_ = True - while file_: - # for line in fh.readlines(): - file_ = interactionFile.readline().strip() - file2_ = interactionFile.readline().strip() - if file_ != '' and file2_ != '': - interactionFileList.append((file_, file2_)) - log.debug('len(interactionFileList) {}'.format(len(interactionFileList))) - else: - if len(args.interactionFile) % 2 == 0: - - i = 0 - while i < len(args.interactionFile): - interactionFileList.append( - (args.interactionFile[i], args.interactionFile[i + 1])) - i += 2 + + viewpointObj = Viewpoint() + + aggregatedList = [] + + aggregatedFileHDF5Object = h5py.File(args.aggregatedFile, 'r') + if aggregatedFileHDF5Object.attrs['type'] != 'aggregate': + log.error('Please provide a file created by chicAggregateStatistic for the parameter --aggregatedFile.') + exit(1) + + keys_aggregatedFile = list(aggregatedFileHDF5Object.keys()) + + for i, combinationOfMatrix in enumerate(keys_aggregatedFile): + keys_matrix_intern = list(aggregatedFileHDF5Object[combinationOfMatrix].keys()) + if len(keys_matrix_intern) == 0: + continue + + matrix1 = keys_matrix_intern[0] + matrix2 = keys_matrix_intern[1] + + matrix_obj1 = aggregatedFileHDF5Object[combinationOfMatrix + '/' + matrix1] + matrix_obj2 = aggregatedFileHDF5Object[combinationOfMatrix + '/' + matrix2] + + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList2 = sorted(list(matrix_obj2.keys())) + chromosomeList1.remove('genes') + chromosomeList2.remove('genes') + for chromosome1, chromosome2 in zip(chromosomeList1, chromosomeList2): + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + geneList2 = sorted(list(matrix_obj2[chromosome2].keys())) + + for gene1, gene2 in zip(geneList1, geneList2): + aggregatedList.append([[combinationOfMatrix, matrix1, chromosome1, gene1], [combinationOfMatrix, matrix2, chromosome2, gene2]]) + + aggregatedFileHDF5Object.close() fail_flag = False fail_message = '' - if args.batchMode: - rejected_file_names = [None] * args.threads - interactionFilesPerThread = len(interactionFileList) // args.threads - all_data_collected = False - queue = [None] * args.threads - process = [None] * args.threads - thread_done = [False] * args.threads - length_of_threads = 0 + all_data = [None] * args.threads + accepted_data = [None] * args.threads + rejected_data = [None] * args.threads + + aggregatedListPerThread = len(aggregatedList) // args.threads + all_data_collected = False + queue = [None] * args.threads + process = [None] * args.threads + thread_done = [False] * args.threads + length_of_threads = 0 + for i in range(args.threads): + + if i < args.threads - 1: + aggregatedListThread = aggregatedList[i * aggregatedListPerThread:(i + 1) * aggregatedListPerThread] + else: + aggregatedListThread = aggregatedList[i * aggregatedListPerThread:] + length_of_threads += len(aggregatedListThread) + queue[i] = Queue() + process[i] = Process(target=run_statistical_tests, kwargs=dict( + pInteractionFilesList=aggregatedListThread, + pArgs=args, + pViewpointObject=viewpointObj, + pQueue=queue[i] + ) + ) + + process[i].start() + while not all_data_collected: for i in range(args.threads): - - if i < args.threads - 1: - interactionFileListThread = interactionFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] - else: - interactionFileListThread = interactionFileList[i * interactionFilesPerThread:] - length_of_threads += len(interactionFileListThread) - queue[i] = Queue() - process[i] = Process(target=run_statistical_tests, kwargs=dict( - pInteractionFilesList=interactionFileListThread, - pArgs=args, - pQueue=queue[i] - ) - ) - - process[i].start() - log.debug('length_of_threads {}'.format(length_of_threads)) - while not all_data_collected: - for i in range(args.threads): - if queue[i] is not None and not queue[i].empty(): - background_data_thread = queue[i].get() - if 'Fail:' in background_data_thread: - fail_flag = True - fail_message = background_data_thread[6:] - rejected_file_names[i] = background_data_thread - queue[i] = None - process[i].join() - process[i].terminate() - process[i] = None - thread_done[i] = True - all_data_collected = True - for thread in thread_done: - if not thread: - all_data_collected = False - time.sleep(1) - if fail_flag: - log.error(fail_message) - exit(1) - else: - run_statistical_tests(interactionFileList, args) - - if args.batchMode: - log.debug('rejected_file_names {}'.format(len(rejected_file_names))) - rejected_file_names = [item for sublist in rejected_file_names for item in sublist] - log.debug('rejected_file_names II {}'.format(len(rejected_file_names))) - - with open(args.rejectedFileNamesToFile, 'w') as nameListFile: - nameListFile.write('\n'.join(rejected_file_names)) + if queue[i] is not None and not queue[i].empty(): + background_data_thread = queue[i].get() + if 'Fail:' in background_data_thread: + fail_flag = True + fail_message = background_data_thread[6:] + else: + accepted_data[i], rejected_data[i], all_data[i] = background_data_thread + queue[i] = None + process[i].join() + process[i].terminate() + process[i] = None + thread_done[i] = True + all_data_collected = True + for thread in thread_done: + if not thread: + all_data_collected = False + time.sleep(1) + if fail_flag: + log.error(fail_message) + exit(1) + + accepted_data = [item for sublist in accepted_data for item in sublist] + rejected_data = [item for sublist in rejected_data for item in sublist] + all_data = [item for sublist in all_data for item in sublist] + + writeResultHDF(args.outFileName, accepted_data, rejected_data, all_data, aggregatedList, args.alpha, args.statisticTest) diff --git a/hicexplorer/chicExportData.py b/hicexplorer/chicExportData.py new file mode 100644 index 00000000..380c556c --- /dev/null +++ b/hicexplorer/chicExportData.py @@ -0,0 +1,565 @@ +import argparse +import sys +import os +import errno +import math +from multiprocessing import Process, Queue +import time +import traceback + +import logging +log = logging.getLogger(__name__) + +import numpy as np +# import matplotlib +# matplotlib.use('Agg') +# import matplotlib.pyplot as plt +# import matplotlib.gridspec as gridspec +# from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas + +import hicmatrix.HiCMatrix as hm +from hicexplorer import utilities +from hicexplorer._version import __version__ +from .lib import Viewpoint + +import h5py +import io +import tarfile +from contextlib import closing +import pyBigWig +from collections import OrderedDict + +from tempfile import mkdtemp +import shutil + + +def parse_arguments(args=None): + parser = argparse.ArgumentParser(add_help=False, + formatter_class=argparse.RawDescriptionHelpFormatter, + description=""" +chicExportData exports the data stored in the intermediate hdf5 files to text files per reference point. + +""" + ) + parserRequired = parser.add_argument_group('Required arguments') + + parserRequired.add_argument('--file', '-f', + help='path to the file which should be used for data export', + required=True) + + parserOpt = parser.add_argument_group('Optional arguments') + + parserOpt.add_argument('--outFileName', '-o', + help='Output tar.gz of the files. In case of --outputMode == geneName it is ignored.' + ' (Default: %(default)s).', + required=False, + default='data.tar.gz') + + parserOpt.add_argument('--outputFileType', + '-oft', + help='Output file type can be set for all file types to txt; except \'interaction\' supports also bigwig' + ' (Default: %(default)s).', + default='txt', + choices=['txt', 'bigwig'] + ) + parserOpt.add_argument('--outputMode', + '-om', + help='Output mode: Either all date is written or a gene name must be specified.' + ' (Default: %(default)s).', + default='all', + choices=['all', 'geneName'] + ) + parserOpt.add_argument('--outputModeName', + '-omn', + help='ONLY valid if --outputMode geneName! Define the name of the gene' + ) + parserOpt.add_argument('--decimalPlaces', + help='Decimal places for all output floating numbers in the viewpoint files' + ' (Default: %(default)s).', + type=int, + default=12) + parserOpt.add_argument('--chromosomeSizes', '-cs', + help=('File with the chromosome sizes for your genome. A tab-delimited two column layout \"chr_name size\" is expected' + 'Usually the sizes can be determined from the SAM/BAM input files, however, ' + 'for cHi-C or scHi-C it can be that at the start or end no data is present. ' + 'Please consider that this option causes that only reads are considered which are on the listed chromosomes.' + 'Use this option to guarantee fixed sizes. An example file is available via UCSC: ' + 'http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes'), + type=argparse.FileType('r'), + metavar='txt file') + parserOpt.add_argument('--backgroundModelFile', '-bmf', + help='Path to the background model file. Required only for fileType=interactions and outputFileTypeBigwig.', + required=False) + parserOpt.add_argument('--oneTargetFile', '-otf', + help='Compile all target files to one. Applies only if --fileType is target', + required=False, + action='store_true') + parserOpt.add_argument('--range', + help='Defines the region upstream and downstream of a reference point which should be included. ' + 'Format is --range upstream downstream, e.g.: --range 500000 500000 plots 500kb up- and 500kb downstream. ' + 'This value should not exceed the range used in the other chic-tools. Applies only for interaction files in the combination with bigwig and a background model file!', + required=False, + type=int, + nargs=2) + parserOpt.add_argument('--outputValueBigwig', + '-ovb', + help='Select which value the bigwig file should contain: \'relative-interactions\', \'p-value\', \'x-fold\', \'raw\'' + ' (Default: %(default)s).', + default='relative-interactions', + choices=['relative-interactions', 'p-value', 'x-fold', 'raw'] + ) + parserOpt.add_argument('--threads', '-t', + help='Number of threads (uses the python multiprocessing module)' + ' (Default: %(default)s).', + required=False, + default=4, + type=int + ) + parserOpt.add_argument("--help", "-h", action="help", help="show this help message and exit") + + parserOpt.add_argument('--version', action='version', + version='%(prog)s {}'.format(__version__)) + return parser + + +def exportData(pFileList, pArgs, pViewpointObject, pDecimalPlace, pChromosomeSizes, pBackgroundData, pFileType, pQueue): + + file_list = [] + file_content_list = [] + + file_ending = '.txt' if pArgs.outputFileType == 'txt' else '.bigwig' + try: + if pFileType == 'interactions' or pFileType == 'significant': + header_information = '# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n' + + for file in pFileList: + + if pArgs.outputFileType == 'bigwig': + chromosome_name = [] + start = [] + end = [] + values = [] + relative_distance = {} + for sample in file: + data = pViewpointObject.readInteractionFile(pArgs.file, sample) + key_list = sorted(list(data[1].keys())) + + if pArgs.outputFileType == 'txt': + + file_content_string = header_information + for key in key_list: + file_content_string += '\t'.join('{:.{decimal_places}f}'.format(x, decimal_places=pDecimalPlace) if isinstance(x, np.float) else str(x) for x in data[1][key]) + '\n' + else: + for key in key_list: + chromosome_name.append(str(data[1][key][0])) + start.append(int(data[1][key][1])) + end.append(int(data[1][key][2])) + if pArgs.outputValueBigwig == 'relative-interactions': + values.append(float(data[1][key][6])) + elif pArgs.outputValueBigwig == 'p-value': + values.append(float(data[1][key][7])) + elif pArgs.outputValueBigwig == 'x-fold': + values.append(float(data[1][key][8])) + elif pArgs.outputValueBigwig == 'raw': + values.append(float(data[1][key][9])) + + relative_distance[data[1][key][5]] = [str(data[1][key][0]), int(data[1][key][1]), int(data[1][key][2])] + header = [(chromosome_name[0], pChromosomeSizes[chromosome_name[0]])] + + if pArgs.backgroundModelFile is not None: + key_list_background = sorted(list(pBackgroundData.keys())) + chromosome_name_background = [] + start_background = [] + end_background = [] + value_background = [] + + for key in key_list_background: + if key in relative_distance: + chromosome_name_background.append(relative_distance[key][0]) + start_background.append(relative_distance[key][1]) + end_background.append(relative_distance[key][2]) + value_background.append(float(pBackgroundData[key][0])) + + if pArgs.outputFileType == 'txt': + file_content_list.append(file_content_string) + file_name = '_'.join(sample) + '_' + pFileType + file_ending + else: + if pArgs.backgroundModelFile is not None: + file_content_list.append([[header, chromosome_name, start, end, values], [header, chromosome_name_background, start_background, end_background, value_background]]) + + file_name = ['_'.join(sample) + file_ending, 'background_' + '_'.join(sample) + '_' + pFileType + file_ending] + + else: + file_content_list.append([[header, chromosome_name, start, end, values]]) + file_name = ['_'.join(sample) + '_' + pFileType + file_ending] + + file_list.append(file_name) + elif pFileType == 'target': + # targetList, present_genes = pViewpointObject.readTargetHDFFile(pArgs.file) + # header_information = '# Chromosome\tStart\tEnd\n' + + for targetFile in pFileList: + targetFileHDF5Object = h5py.File(pArgs.file, 'r') + target_object = targetFileHDF5Object['/'.join(targetFile)] + chromosome = target_object.get('chromosome')[()] + start_list = list(target_object['start_list'][:]) + end_list = list(target_object['end_list'][:]) + targetFileHDF5Object.close() + chromosome = [chromosome] * len(start_list) + + target_regions = list(zip(chromosome, start_list, end_list)) + file_content_string = '' + # key_list = sorted(list(data[1].keys())) + for region in target_regions: + file_content_string += '\t'.join(x.decode('utf-8') for x in region) + '\n' + file_content_list.append(file_content_string) + file_name = '_'.join(targetFile) + '_' + pFileType + '.txt' + file_list.append(file_name) + + elif pFileType == 'aggregate': + header_information = '# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRaw\n' + + for file in pFileList: + for sample in file: + line_content, data = pViewpointObject.readAggregatedFileHDF(pArgs.file, sample) + file_content_string = header_information + for line in line_content: + file_content_string += '\t'.join('{:.{decimal_places}f}'.format(x, decimal_places=pDecimalPlace) if isinstance(x, np.float) else str(x) for x in line) + '\n' + file_content_list.append(file_content_string) + + file_name = '_'.join(sample) + '_' + pFileType + '.txt' + file_list.append(file_name) + + elif pFileType == 'differential': + header_information = '# Chromosome\tStart\tEnd\tGene\tRelative distance\tsum of interactions 1\ttarget_1 raw\tsum of interactions 2\ttarget_2 raw\tp-value\n' + + for file in pFileList: + # accepted_list, all_list, rejected_list + item_classification = ['accepted', 'all', 'rejected'] + line_content = pViewpointObject.readDifferentialFile(pArgs.file, file) + for i, item in enumerate(line_content): + file_content_string = header_information + + for line in item: + file_content_string += '\t'.join('{:.{decimal_places}f}'.format(x, decimal_places=pDecimalPlace) if isinstance(x, np.float) else str(x) for x in line) + '\n' + file_content_list.append(file_content_string) + file_name = '_'.join(file) + '_' + item_classification[i] + '_' + pFileType + '.txt' + file_list.append(file_name) + + except Exception as exp: + pQueue.put('Fail: ' + str(exp) + traceback.format_exc()) + return + + pQueue.put([file_list, file_content_list]) + return + + +def main(args=None): + args = parse_arguments().parse_args(args) + viewpointObj = Viewpoint() + + fileList = [] + chromosome_sizes = None + background_dict = None + # read hdf file + fileHDF5Object = h5py.File(args.file, 'r') + + fileType = fileHDF5Object.attrs['type'] + + if args.outputMode == 'geneName' and args.outputModeName is None: + log.error('Output mode is \'geneName\'. Please specify a gene name via --outputModeName too!') + exit(1) + + if args.outputFileType == 'bigwig': + if fileType != 'interactions': + log.error('Only file type \'interactions\' supports bigwig. Exiting.') + exit(1) + if args.range is None: + log.error('Bigwig files require the argument \'--range upstream downstream\'. Exiting.') + exit(1) + if args.backgroundModelFile is not None: + if args.backgroundModelFile: + background_dict = viewpointObj.readBackgroundDataFile(args.backgroundModelFile, args.range, args.range[1], pMean=True) + else: + log.error('Please define a background file via --backgroundModelFile.') + exit(1) + if args.chromosomeSizes is not None: + chromosome_sizes = OrderedDict() + with open(args.chromosomeSizes.name, 'r') as file: + file_ = True + while file_: + file_ = file.readline().strip() + if file_ != '': + line_split = file_.split('\t') + chromosome_sizes[line_split[0]] = int(line_split[1]) + else: + log.error('Bigwig files require the argument \'--chromosomeSizes\'. Exiting.') + exit(1) + + # read hdf file + keys_file = list(fileHDF5Object.keys()) + if fileType == 'interactions' or fileType == 'significant': + if args.outputMode == 'all': + for i, sample in enumerate(keys_file): + matrix_obj1 = fileHDF5Object[sample] + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList1.remove('genes') + for chromosome1 in chromosomeList1: + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + for gene1 in geneList1: + fileList.append([[sample, chromosome1, gene1]]) + else: + for i, sample in enumerate(keys_file): + matrix_obj1 = fileHDF5Object[sample]['genes'] + chromosomeList1 = sorted(list(matrix_obj1.keys())) + gene_name = args.outputModeName + counter = 1 + while gene_name in chromosomeList1: + fileList.append([[sample, 'genes', gene_name]]) + gene_name = args.outputModeName + '_' + str(counter) + counter += 1 + elif fileType == 'target': + if fileHDF5Object.attrs['combinationMode'] == 'dual': + if args.outputMode == 'all': + for outer_matrix in keys_file: + inner_matrix_object = fileHDF5Object[outer_matrix] + keys_inner_matrices = list(inner_matrix_object.keys()) + for inner_matrix in keys_inner_matrices: + inner_object = inner_matrix_object[inner_matrix] + gene_object = inner_object['genes'] + keys_genes = list(gene_object.keys()) + for gen in keys_genes: + fileList.append([outer_matrix, inner_matrix, 'genes', gen]) + else: + for outer_matrix in keys_file: + inner_matrix_object = fileHDF5Object[outer_matrix] + keys_inner_matrices = list(inner_matrix_object.keys()) + for inner_matrix in keys_inner_matrices: + inner_object = inner_matrix_object[inner_matrix]['genes'] + keys_genes = list(inner_object.keys()) + gene_name = args.outputModeName + counter = 1 + while gene_name in keys_genes: + fileList.append([outer_matrix, inner_matrix, 'genes', gene_name]) + gene_name = args.outputModeName + '_' + str(counter) + counter += 1 + elif fileHDF5Object.attrs['combinationMode'] == 'single': + + if args.outputMode == 'all': + for outer_matrix in keys_file: + gene_object = fileHDF5Object[outer_matrix]['genes'] + keys_genes = list(gene_object.keys()) + for gen in keys_genes: + fileList.append([outer_matrix, 'genes', gen]) + else: + for outer_matrix in keys_file: + keys_genes = list(fileHDF5Object[outer_matrix]['genes'].keys()) + gene_name = args.outputModeName + counter = 1 + while gene_name in keys_genes: + fileList.append([outer_matrix, 'genes', gene_name]) + gene_name = args.outputModeName + '_' + str(counter) + counter += 1 + + elif fileType == 'aggregate': + if args.outputMode == 'all': + for i, combinationOfMatrix in enumerate(keys_file): + keys_matrix_intern = list(fileHDF5Object[combinationOfMatrix].keys()) + if len(keys_matrix_intern) == 0: + continue + matrix1 = keys_matrix_intern[0] + matrix2 = keys_matrix_intern[1] + + matrix_obj1 = fileHDF5Object[combinationOfMatrix + '/' + matrix1] + matrix_obj2 = fileHDF5Object[combinationOfMatrix + '/' + matrix2] + + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList2 = sorted(list(matrix_obj2.keys())) + chromosomeList1.remove('genes') + chromosomeList2.remove('genes') + for chromosome1, chromosome2 in zip(chromosomeList1, chromosomeList2): + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + geneList2 = sorted(list(matrix_obj2[chromosome2].keys())) + + for gene1, gene2 in zip(geneList1, geneList2): + fileList.append([[combinationOfMatrix, matrix1, chromosome1, gene1], [combinationOfMatrix, matrix2, chromosome2, gene2]]) + else: + for i, combinationOfMatrix in enumerate(keys_file): + keys_matrix_intern = list(fileHDF5Object[combinationOfMatrix].keys()) + if len(keys_matrix_intern) == 0: + continue + matrix1 = keys_matrix_intern[0] + matrix2 = keys_matrix_intern[1] + + matrix_obj1 = fileHDF5Object[combinationOfMatrix + '/' + matrix1]['genes'] + matrix_obj2 = fileHDF5Object[combinationOfMatrix + '/' + matrix2]['genes'] + + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList2 = sorted(list(matrix_obj2.keys())) + # chromosomeList1.remove('genes') + # chromosomeList2.remove('genes') + gene_name = args.outputModeName + counter = 1 + while gene_name in chromosomeList1 and gene_name in chromosomeList2: + fileList.append([[combinationOfMatrix, matrix1, 'genes', gene_name], [combinationOfMatrix, matrix2, 'genes', gene_name]]) + gene_name = args.outputModeName + '_' + str(counter) + counter += 1 + + elif fileType == 'differential': + if args.outputMode == 'all': + for outer_matrix in keys_file: + inner_matrix_object = fileHDF5Object[outer_matrix] + keys_inner_matrices = list(inner_matrix_object.keys()) + for inner_matrix in keys_inner_matrices: + inner_object = inner_matrix_object[inner_matrix] + chromosomeList = sorted(list(inner_object.keys())) + chromosomeList.remove('genes') + for chromosome in chromosomeList: + geneList = sorted(list(inner_object[chromosome].keys())) + + for gene in geneList: + fileList.append([outer_matrix, inner_matrix, chromosome, gene]) + else: + for outer_matrix in keys_file: + inner_matrix_object = fileHDF5Object[outer_matrix] + keys_inner_matrices = list(inner_matrix_object.keys()) + for inner_matrix in keys_inner_matrices: + inner_object = inner_matrix_object[inner_matrix]['genes'] + chromosomeList = sorted(list(inner_object.keys())) + gene_name = args.outputModeName + counter = 1 + while gene_name in chromosomeList: + fileList.append([outer_matrix, inner_matrix, 'genes', gene_name]) + # fileList.append([outer_matrix, inner_matrix, 'genes', gene_name]) + gene_name = args.outputModeName + '_' + str(counter) + counter += 1 + + fileHDF5Object.close() + + filesPerThread = len(fileList) // args.threads + + all_data_collected = False + thread_data = [None] * args.threads + file_name_list = [None] * args.threads + + queue = [None] * args.threads + process = [None] * args.threads + thread_done = [False] * args.threads + fail_flag = False + fail_message = '' + + for i in range(args.threads): + + if i < args.threads - 1: + fileListPerThread = fileList[i * filesPerThread:(i + 1) * filesPerThread] + else: + fileListPerThread = fileList[i * filesPerThread:] + queue[i] = Queue() + + process[i] = Process(target=exportData, kwargs=dict( + pFileList=fileListPerThread, + pArgs=args, + pViewpointObject=viewpointObj, + pDecimalPlace=args.decimalPlaces, + pChromosomeSizes=chromosome_sizes, + pBackgroundData=background_dict, + pFileType=fileType, + pQueue=queue[i] + ) + ) + + process[i].start() + + while not all_data_collected: + for i in range(args.threads): + if queue[i] is not None and not queue[i].empty(): + return_content = queue[i].get() + if 'Fail:' in return_content: + fail_flag = True + fail_message = return_content[6:] + else: + file_name_list[i], thread_data[i] = return_content + + queue[i] = None + process[i].join() + process[i].terminate() + process[i] = None + thread_done[i] = True + all_data_collected = True + for thread in thread_done: + if not thread: + all_data_collected = False + time.sleep(1) + if fail_flag: + log.error(fail_message) + exit(1) + + thread_data = [item for sublist in thread_data for item in sublist] + file_name_list = [item for sublist in file_name_list for item in sublist] + + if len(thread_data) == 0: + log.error('Contains not the requested data!') + exit(1) + if args.outputFileType == 'txt': + if args.outputMode == 'geneName': + basepath = os.path.dirname(args.outFileName) + for i, file_content_string in enumerate(thread_data): + with open(basepath + '/' + file_name_list[i], "w") as file: + file.write(file_content_string) + else: + with tarfile.open(args.outFileName, "w:gz") as tar: + + if args.oneTargetFile and fileType == 'target': + tar_info = tarfile.TarInfo(name='targets.tsv') + tar_info.mtime = time.time() + file_content_string_all = '' + for i, file_content_string in enumerate(thread_data): + + file_content_string_all += file_content_string + + file_content_string_all = file_content_string_all.encode('utf-8') + tar_info.size = len(file_content_string_all) + file = io.BytesIO(file_content_string_all) + tar.addfile(tarinfo=tar_info, fileobj=file) + else: + for i, file_content_string in enumerate(thread_data): + + tar_info = tarfile.TarInfo(name=file_name_list[i]) + tar_info.mtime = time.time() + file_content_string = file_content_string.encode('utf-8') + tar_info.size = len(file_content_string) + file = io.BytesIO(file_content_string) + tar.addfile(tarinfo=tar_info, fileobj=file) + + elif args.outputFileType == 'bigwig': + if args.outputMode == 'geneName': + bigwig_folder = os.path.dirname(args.outFileName) + # bigwig_folder = '.' + else: + bigwig_folder = mkdtemp(prefix="bigwig_folder") + for i, file_content in enumerate(thread_data): + + for j, file_list in enumerate(file_content): + + bw = pyBigWig.open(bigwig_folder + '/' + file_name_list[i][j], 'w') + # # set big wig header + bw.addHeader(file_list[0]) + + bw.addEntries(file_list[1], file_list[2], ends=file_list[3], values=file_list[4]) + bw.close() + + if args.outputMode == 'all': + if not args.outFileName.endswith('.tar.gz'): + args.outFileName = args.outFileName + '.tar.gz' + with tarfile.open(args.outFileName, "w:gz") as tar_handle: + for root, dirs, files in os.walk(bigwig_folder): + for file in files: + # tar_handle.addfile(tarfile.TarInfo(file), os.path.join(root, file)) + # tar_handle.add(os.path.join(root, file)) + tar_handle.add(os.path.join(root, file), arcname=file) + + if os.path.exists(bigwig_folder): + try: + shutil.rmtree(bigwig_folder) + except OSError as e: + log.error("Error: %s - %s." % (e.filename, e.strerror)) diff --git a/hicexplorer/chicPlotViewpoint.py b/hicexplorer/chicPlotViewpoint.py index 9be7a4cd..f89be658 100644 --- a/hicexplorer/chicPlotViewpoint.py +++ b/hicexplorer/chicPlotViewpoint.py @@ -5,6 +5,8 @@ import math from multiprocessing import Process, Queue import time +import traceback + import logging log = logging.getLogger(__name__) @@ -13,12 +15,18 @@ matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec - +from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas +import matplotlib as mpl import hicmatrix.HiCMatrix as hm from hicexplorer import utilities from hicexplorer._version import __version__ from .lib import Viewpoint +import h5py +import io +import tarfile +from contextlib import closing + def parse_arguments(args=None): parser = argparse.ArgumentParser(add_help=False, @@ -26,23 +34,13 @@ def parse_arguments(args=None): description=""" chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. In addition, it can highlight differential interactions of two samples and/or significant regions. -An example usage is: - -`$ chicPlotViewpoint --interactionFile viewpoint1.txt viewpoint2.txt --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.png --dpi 300` - - -In batch mode the list of file names and the folders containing the files need to be given: - -`$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outputFolder plotsFOlder --dpi 300 --threads 20` - """ ) parserRequired = parser.add_argument_group('Required arguments') parserRequired.add_argument('--interactionFile', '-if', help='path to the interaction files which should be used for plotting', - required=True, - nargs='+') + required=True) parserRequired.add_argument('--range', help='Defines the region upstream and downstream of a reference point which should be included. ' @@ -56,38 +54,21 @@ def parse_arguments(args=None): parserOpt.add_argument('--backgroundModelFile', '-bmf', help='path to the background file which should be used for plotting', required=False) - parserOpt.add_argument('--interactionFileFolder', '-iff', - help='Folder where the interaction files are stored. Applies only for batch mode' - ' (Default: %(default)s).', - required=False, - default='.') parserOpt.add_argument('--differentialTestResult', '-dif', help='Path to the H0 rejected files to highlight the regions in the plot.', - required=False, - nargs='+') - parserOpt.add_argument('--significantInteractionFileFolder', '-siff', - help='Folder where the files with detected significant interactions are stored. Applies only for batch mode' - ' (Default: %(default)s).', - required=False, - default='.') - parserOpt.add_argument('--differentialTestResultsFolder', '-diff', - help='Folder where the H0 rejected files are stored. Applies only for batch mode' - ' (Default: %(default)s).', - required=False, - default='.') + required=False) parserOpt.add_argument('--significantInteractions', '-si', help='Path to the files with detected significant interactions to highlight the regions in the plot.', - required=False, - nargs='+') + required=False) parserOpt.add_argument('--plotSignificantInteractions', '-psi', help='Highlights the significant interactions in the plot itself. If not set, only the p-values are updated', required=False, action='store_true') - parserOpt.add_argument('--outputFolder', '-of', - help='Output folder of the files' + parserOpt.add_argument('--outFileName', '-o', + help='Output tar.gz of the files' ' (Default: %(default)s).', required=False, - default='.') + default='plots.tar.gz') parserOpt.add_argument('--outputFormat', '-format', help='Output format of the plot' ' (Default: %(default)s).', @@ -100,12 +81,23 @@ def parse_arguments(args=None): type=int, default=300, required=False) - parserOpt.add_argument('--binResolution', '-r', - help='Resolution of the bin in genomic units. Values are set as number of bases, e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution' + parserOpt.add_argument('--combinationMode', + '-cm', + help='This option defines how the interaction data should be computed and combined: ' + 'dual: Combines as follows: [[matrix1_gene1, matrix2_gene1], [matrix2_gene1, matrix3_gene1],[matrix1_gene2, matrix2_gene2], ...]' + 'single: Combines as follows: [matrix1_gene1, matrix1_gene2, matrix2_gene1, ...], ' + 'allGenes: Combines as follows: [[matrix1_gene1, matrix2_gene1, matrix2_gene1], [matrix1_gene2, matrix2_gene2, matrix3_gene2], ...]' + 'oneGene: Computes all data of one gene, please specify \'--\'. If a gene is not unique, each viewpoint is treated independently.' ' (Default: %(default)s).', - type=int, - default=1000, - required=False) + default='dual', + choices=['dual', 'single', 'allGenes', 'oneGene'] + ) + + parserOpt.add_argument('--combinationName', '-cn', + help='Gene name or file name for modes \'oneGene\' or \'file\' of parameter \'--combinationMode\'' + ' (Default: %(default)s).', + required=False, + default=None) parserOpt.add_argument('--colorMapPvalue', help='Color map to use for the p-value. Available ' @@ -141,18 +133,6 @@ def parse_arguments(args=None): help='Sets all p-values which are equal to zero to one.', required=False, action='store_true') - parserOpt.add_argument('--outFileName', '-o', - help='File name to save the image. Not used in batch mode.') - parserOpt.add_argument('--batchMode', '-bm', - help='The given file for --interactionFile and or --targetFile contain a list of the to be processed files.', - required=False, - action='store_true') - parserOpt.add_argument('--plotSampleNumber', '-psn', - help='Number of samples per plot. Applies only in batch mode' - ' (Default: %(default)s).', - required=False, - default=2, - type=int) parserOpt.add_argument('--colorList', '-cl', help='Colorlist for the viewpoint lines (Default g b c m y k).', required=False, @@ -173,13 +153,16 @@ def parse_arguments(args=None): return parser -def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBackgroundData, pArgs, pViewpointObj, pSignificantRegionsFileList, pQueue=None): +def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBackgroundData, pArgs, pViewpointObj, pSignificantRegionsFileList, pResolution, pQueue=None): + images_array = [] + file_name_list = [] try: + for j, interactionFile in enumerate(pInteractionFileList): number_of_rows_plot = len(interactionFile) matplotlib.rcParams.update({'font.size': 9}) - fig = plt.figure(figsize=(9.4, 4.8)) - + fig = plt.figure(figsize=(9.4, 4.8), dpi=pArgs.dpi) + FigureCanvas(fig) z_score_heights = [0.07] * number_of_rows_plot viewpoint_height_ratio = 0.95 - (0.07 * number_of_rows_plot) if viewpoint_height_ratio < 0.4: @@ -197,50 +180,39 @@ def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBa colors = pArgs.colorList background_plot = True data_plot_label = None - gene = '' - for i, interactionFile_ in enumerate(interactionFile): - if pArgs.interactionFileFolder != '.': - absolute_path_interactionFile_ = pArgs.interactionFileFolder + '/' + interactionFile_ - else: - absolute_path_interactionFile_ = interactionFile_ - header, data, background_data_plot, p_values, viewpoint_index_start, viewpoint_index_end = pViewpointObj.getDataForPlotting(absolute_path_interactionFile_, pArgs.range, pBackgroundData, pArgs.binResolution) - # log.debug('data {}'.format(data)) + file_name = [] + for i, interactionFile_ in enumerate(interactionFile): + file_name.append(interactionFile_[0]) + data, background_data_plot, p_values, viewpoint_index_start, viewpoint_index_end, viewpoint = pViewpointObj.getDataForPlotting(pArgs.interactionFile, interactionFile_, pArgs.range, pBackgroundData, pResolution) if len(data) <= 1 or len(p_values) <= 1: log.warning('Only one data point in given range, no plot is created! Interaction file {} Range {}'.format(interactionFile_, pArgs.range)) continue - matrix_name, viewpoint, upstream_range, downstream_range, gene, _ = header.strip().split('\t') - log.debug('Matrix_name {}'.format(matrix_name)) - matrix_name = os.path.basename(matrix_name) - - matrix_name = matrix_name.split('.')[0] - log.debug('matrix_name {}'.format(matrix_name)) - # number_of_data_points = len(data) highlight_differential_regions = None significant_p_values = None significant_regions = None if pArgs.differentialTestResult: - if pArgs.differentialTestResultsFolder != '.': - differentialFilePath = pArgs.differentialTestResultsFolder + '/' + pHighlightDifferentialRegionsFileList[j] - else: - differentialFilePath = pHighlightDifferentialRegionsFileList[j] - - highlight_differential_regions = pViewpointObj.readRejectedFile(differentialFilePath, viewpoint_index_start, viewpoint_index_end, pArgs.binResolution, pArgs.range, viewpoint) + highlight_differential_regions = pViewpointObj.readRejectedFile(pArgs.differentialTestResult, pHighlightDifferentialRegionsFileList[j], viewpoint_index_start, viewpoint_index_end, pResolution, pArgs.range, viewpoint) if pArgs.significantInteractions: - if pArgs.significantInteractionFileFolder != '.': - significantInteractionsFilePath = pArgs.significantInteractionFileFolder + '/' + pSignificantRegionsFileList[j][i] - else: - significantInteractionsFilePath = pSignificantRegionsFileList[j][i] - significant_regions, significant_p_values = pViewpointObj.readSignificantRegionsFile(significantInteractionsFilePath, viewpoint_index_start, viewpoint_index_end, pArgs.binResolution, pArgs.range, viewpoint) + significant_regions = None + significant_p_values = None + try: + if i < len(pSignificantRegionsFileList[j]): + # if len(pSignificantRegionsFileList[j][i]) > 0: + significant_regions, significant_p_values = pViewpointObj.readSignificantRegionsFile(pArgs.significantInteractions, pSignificantRegionsFileList[j][i], viewpoint_index_start, viewpoint_index_end, pResolution, pArgs.range, viewpoint) + except Exception: + log.debug('len(pSignificantRegionsFileList) {}'.format(len(pSignificantRegionsFileList))) + log.debug('len(pSignificantRegionsFileList[j]) {}'.format(len(pSignificantRegionsFileList[j]))) + log.debug('i {}'.format(i)) + if not pArgs.plotSignificantInteractions: significant_regions = None if data_plot_label: - data_plot_label += pViewpointObj.plotViewpoint(pAxis=ax1, pData=data, pColor=colors[i % len(colors)], pLabelName=gene + ': ' + matrix_name, pHighlightRegion=highlight_differential_regions, pHighlightSignificantRegion=significant_regions) + data_plot_label += pViewpointObj.plotViewpoint(pAxis=ax1, pData=data, pColor=colors[i % len(colors)], pLabelName=':'.join(interactionFile_), pHighlightRegion=highlight_differential_regions, pHighlightSignificantRegion=significant_regions) else: - data_plot_label = pViewpointObj.plotViewpoint(pAxis=ax1, pData=data, pColor=colors[i % len(colors)], pLabelName=gene + ': ' + matrix_name, pHighlightRegion=highlight_differential_regions, pHighlightSignificantRegion=significant_regions) + data_plot_label = pViewpointObj.plotViewpoint(pAxis=ax1, pData=data, pColor=colors[i % len(colors)], pLabelName=':'.join(interactionFile_), pHighlightRegion=highlight_differential_regions, pHighlightSignificantRegion=significant_regions) if background_plot: - # log.debug('background_data_plot {}'.format(len(background_data_plot))) if background_data_plot is not None: data_plot_label += pViewpointObj.plotBackgroundModel(pAxis=ax1, pBackgroundData=background_data_plot, pXFold=pArgs.xFold) background_plot = False @@ -248,7 +220,7 @@ def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBa p_values = np.array(p_values, dtype=np.float32) mask = p_values == 0.0 p_values[mask] = 1.0 - if pArgs.minPValue is not None or pArgs.maxPValue is not None: + if pArgs.pValue and (pArgs.minPValue is not None or pArgs.maxPValue is not None): p_values = np.array(p_values, dtype=np.float32) if significant_p_values: @@ -260,7 +232,7 @@ def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBa if pArgs.pValue: pViewpointObj.plotPValue(pAxis=plt.subplot(gs[1 + i, 0]), pAxisLabel=plt.subplot(gs[1 + i, 1]), pPValueData=p_values, - pLabelText=gene + ': ' + matrix_name, pCmap=pArgs.colorMapPvalue, + pLabelText=':'.join(interactionFile_), pCmap=pArgs.colorMapPvalue, pFigure=fig, pValueSignificanceLevels=pArgs.pValueSignificanceLevels) if data_plot_label is not None: @@ -280,7 +252,6 @@ def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBa mod_legend = 5e4 elif pArgs.range[0] + pArgs.range[1] <= 5e5: mod_legend = 1e5 - log.debug('divisor_legend {}'.format(divisor_legend)) unit = 'kb' elif pArgs.range[0] + pArgs.range[1] > 2e6: @@ -291,17 +262,16 @@ def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBa for k, j in zip(range((pArgs.range[0])), range(pArgs.range[0], 1, -1)): if j % mod_legend == 0: x_labels.append(str(-int(j) // int(divisor_legend)) + unit) - ticks.append(k // pArgs.binResolution) + ticks.append(k // pResolution) x_labels.append('RP') - ticks.append(pArgs.range[0] // pArgs.binResolution) + ticks.append(pArgs.range[0] // pResolution) referencepoint_index = ticks[-1] for k, j in zip(range(pArgs.range[1]), range(1, pArgs.range[1] + 1, 1)): if j % mod_legend == 0: x_labels.append(str(int(j) // int(divisor_legend)) + unit) - ticks.append(referencepoint_index + (k // pArgs.binResolution)) + ticks.append(referencepoint_index + (k // pResolution)) - # log.debug('labels: {}'.format(x_labels)) ax1.set_ylabel('Number of interactions') ax1.set_xticks(ticks) ax1.set_xticklabels(x_labels) @@ -310,47 +280,28 @@ def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBa data_legend = [label.get_label() for label in data_plot_label] ax1.legend(data_plot_label, data_legend, loc=0) - sample_prefix = "" - if pArgs.outFileName: - if pArgs.outputFolder != '.': - outFileName = pArgs.outputFolder + '/' + pArgs.outFileName - else: - outFileName = pArgs.outFileName - - else: - for interactionFile_ in interactionFile: - sample_prefix += interactionFile_.split('/')[-1].split('_')[0] + '_' - if sample_prefix.endswith('_'): - sample_prefix = sample_prefix[:-1] - region_prefix = '_'.join(interactionFile[0].split('/')[-1].split('_')[1:4]) - outFileName = gene + '_' + sample_prefix + '_' + region_prefix - if pArgs.outputFolder != '.': - outFileName = pArgs.outputFolder + '/' + outFileName - - if pArgs.outputFormat != outFileName.split('.')[-1]: - outFileName = outFileName + '.' + pArgs.outputFormat - plt.savefig(outFileName, dpi=pArgs.dpi) + bufferObject = io.BytesIO() + plt.savefig(bufferObject, format=pArgs.outputFormat, dpi=300) + images_array.append(bufferObject) plt.close(fig) + file_name.append(interactionFile[0][2]) + file_name_list.append('_'.join(file_name)) except Exception as exp: - pQueue.put('Fail: ' + str(exp)) + pQueue.put('Fail: ' + str(exp) + traceback.format_exc()) return if pQueue is None: return - pQueue.put('done') + pQueue.put([images_array, file_name_list]) return def main(args=None): args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 + viewpointObj = Viewpoint() background_data = None - if not os.path.exists(args.outputFolder): - try: - os.makedirs(args.outputFolder) - except OSError as exc: # Guard against race condition - if exc.errno != errno.EEXIST: - raise if args.pValueSignificanceLevels: old = -100 for element in args.pValueSignificanceLevels: @@ -367,103 +318,207 @@ def main(args=None): highlightDifferentialRegionsFileList = [] highlightSignificantRegionsFileList = [] - if args.batchMode: - with open(args.interactionFile[0], 'r') as interactionFile: - - file_ = True - while file_: - lines = [] - for i in range(0, args.plotSampleNumber): - file_ = interactionFile.readline().strip() - if file_ != '': - lines.append(file_) - interactionFileList.append(lines) - if args.differentialTestResult: - - if args.differentialTestResult and args.plotSampleNumber != 2: - log.warning('Cannot use differential data, only possible for two samples in one plot.') - args.differentialTestResult = None - else: - with open(args.differentialTestResult[0], 'r') as differentialTestFile: - - file_ = True - while file_: - file_ = differentialTestFile.readline().strip() - if file_ != '': - highlightDifferentialRegionsFileList.append(file_) - if args.significantInteractions: - with open(args.significantInteractions[0], 'r') as significantRegionsFile: - - file_ = True - while file_: - lines = [] - for i in range(0, args.plotSampleNumber): - file_ = significantRegionsFile.readline().strip() - if file_ != '': - lines.append(file_) - if len(lines) > 0: - highlightSignificantRegionsFileList.append(lines) - interactionFilesPerThread = len(interactionFileList) // args.threads - highlightSignificantRegionsFileListThread = len(highlightSignificantRegionsFileList) // args.threads - - all_data_collected = False - queue = [None] * args.threads - process = [None] * args.threads - thread_done = [False] * args.threads - fail_flag = False - fail_message = '' + # read hdf file + interactionFileHDF5Object = h5py.File(args.interactionFile, 'r') + if interactionFileHDF5Object.attrs['type'] != 'interactions': + log.error('Please provide a file created by chicViewpoint for the parameter --interactionFile.') + exit(1) + keys_interactionFile = list(interactionFileHDF5Object.keys()) + resolution = interactionFileHDF5Object.attrs['resolution'][()] + + if args.differentialTestResult and args.combinationMode != 'dual': + log.warning('Cannot use differential data, only possible for two samples in one plot.') + exit(1) + + if args.combinationMode == 'dual': + if len(keys_interactionFile) > 1: + for i, sample in enumerate(keys_interactionFile): + for sample2 in keys_interactionFile[i + 1:]: + + matrix_obj1 = interactionFileHDF5Object[sample] + matrix_obj2 = interactionFileHDF5Object[sample] + + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList2 = sorted(list(matrix_obj2.keys())) + chromosomeList1.remove('genes') + chromosomeList2.remove('genes') + for chromosome1, chromosome2 in zip(chromosomeList1, chromosomeList2): + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + geneList2 = sorted(list(matrix_obj2[chromosome2].keys())) + + for gene1, gene2 in zip(geneList1, geneList2): + interactionFileList.append([[sample, chromosome1, gene1], [sample2, chromosome2, gene2]]) + + if args.differentialTestResult: + + differentialFileHDF5Object = h5py.File(args.differentialTestResult, 'r') + if differentialFileHDF5Object.attrs['type'] != 'differential': + log.error('Please provide a file created by chicDifferentialTest for the parameter --differentialTestResult.') + exit(1) + keys_significantFile = list(differentialFileHDF5Object.keys()) + for plotGroup in interactionFileList: + differential_group = [] + if plotGroup[0][0] in keys_significantFile: + matrix_object = differentialFileHDF5Object[plotGroup[0][0]] + if plotGroup[1][0] in matrix_object: + + matrix1_object = matrix_object[plotGroup[1][0]] + if plotGroup[1][1] in matrix1_object: + chromosome_object = matrix1_object[plotGroup[1][1]] + + if plotGroup[1][2] in chromosome_object: + differential_group = [plotGroup[0][0], plotGroup[1][0], plotGroup[1][1], plotGroup[1][2], 'rejected'] + # else: + + highlightDifferentialRegionsFileList.append(differential_group) + + else: + log.error('Dual mode selected but only one matrix is stored') + elif args.combinationMode == 'allGenes': + if len(keys_interactionFile) > 0: + matrix_obj1 = interactionFileHDF5Object[keys_interactionFile[0]] + gene_list = matrix_obj1['genes'].keys() + + for gene in gene_list: + gene_list = [] + for matrix in keys_interactionFile: + gene_list.append([matrix, 'genes', gene]) + interactionFileList.append(gene_list) + + elif args.combinationMode == 'single': + for i, sample in enumerate(keys_interactionFile): + + matrix_obj1 = interactionFileHDF5Object[sample] + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList1.remove('genes') + for chromosome1 in chromosomeList1: + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + for gene1 in geneList1: + interactionFileList.append([[sample, chromosome1, gene1]]) + elif args.combinationMode == 'oneGene': + if len(keys_interactionFile) > 0: + matrix_obj1 = interactionFileHDF5Object[keys_interactionFile[0]] + all_detected = False + counter = 0 + gene_list = [] + while not all_detected: + if counter == 0: + check_gene_name = args.combinationName + else: + check_gene_name = args.combinationName + '_' + str(counter) - for i in range(args.threads): + if check_gene_name in matrix_obj1['genes']: + gene_list.append(check_gene_name) + else: + all_detected = True - if i < args.threads - 1: - interactionFileListThread = interactionFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] - highlightDifferentialRegionsFileListThread = highlightDifferentialRegionsFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] - highlightSignificantRegionsFileListThread = highlightSignificantRegionsFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] - else: - interactionFileListThread = interactionFileList[i * interactionFilesPerThread:] - highlightDifferentialRegionsFileListThread = highlightDifferentialRegionsFileList[i * interactionFilesPerThread:] - highlightSignificantRegionsFileListThread = highlightSignificantRegionsFileList[i * interactionFilesPerThread:] - queue[i] = Queue() - process[i] = Process(target=plot_images, kwargs=dict( - pInteractionFileList=interactionFileListThread, - pHighlightDifferentialRegionsFileList=highlightDifferentialRegionsFileListThread, - pBackgroundData=background_data, - pArgs=args, - pViewpointObj=viewpointObj, - pSignificantRegionsFileList=highlightSignificantRegionsFileListThread, - pQueue=queue[i] - ) - ) - - process[i].start() - - while not all_data_collected: - for i in range(args.threads): - if queue[i] is not None and not queue[i].empty(): - return_content = queue[i].get() - if 'Fail:' in return_content: - fail_flag = True - fail_message = return_content[6:] - queue[i] = None - process[i].join() - process[i].terminate() - process[i] = None - thread_done[i] = True - all_data_collected = True - for thread in thread_done: - if not thread: - all_data_collected = False - time.sleep(1) - if fail_flag: - log.error(fail_message) + counter += 1 + + for gene in gene_list: + gene_list = [] + for matrix in keys_interactionFile: + gene_list.append([matrix, 'genes', gene]) + interactionFileList.append([[matrix, 'genes', gene]]) + interactionFileList.append(gene_list) + + if args.significantInteractions: + significantFileHDF5Object = h5py.File(args.significantInteractions, 'r') + if significantFileHDF5Object.attrs['type'] != 'significant': + log.error('Please provide a file created by chicSignificantInteractions for the parameter --significantInteractions. File type is {}'.format(significantFileHDF5Object.attrs['type'])) exit(1) - else: - interactionFileList = [args.interactionFile] - highlightDifferentialRegionsFileList = args.differentialTestResult - highlightSignificantRegionsFileList = [args.significantInteractions] - plot_images(pInteractionFileList=interactionFileList, - pHighlightDifferentialRegionsFileList=highlightDifferentialRegionsFileList, - pBackgroundData=background_data, - pArgs=args, - pViewpointObj=viewpointObj, - pSignificantRegionsFileList=highlightSignificantRegionsFileList) + keys_significantFile = list(significantFileHDF5Object.keys()) + for plotGroup in interactionFileList: + significant_group = [] + for item in plotGroup: + if item[0] in keys_significantFile: + matrix_object = significantFileHDF5Object[item[0]] + if item[1] in matrix_object: + chromosome_object = matrix_object[item[1]] + + if item[2] in chromosome_object: + significant_group.append(item) + else: + log.debug('Requested gene {} to plot significant areas is not available in the given data {}.'.format(item[2], args.significantInteractions)) + else: + log.debug('Requested chromosome {} to plot significant areas is not available in the given data {}.'.format(item[1], args.significantInteractions)) + + else: + log.debug('Requested matrix {} to plot significant areas is not available in the given data {}.'.format(item[0], args.significantInteractions)) + highlightSignificantRegionsFileList.append(significant_group) + + log.debug('len(interactionFileList) {}'.format(len(interactionFileList))) + log.debug('len(highlightSignificantRegionsFileListThread) {}'.format(len(highlightSignificantRegionsFileList))) + log.debug('len(highlightDifferentialRegionsFileListThread) {}'.format(len(highlightDifferentialRegionsFileList))) + + interactionFilesPerThread = len(interactionFileList) // args.threads + # highlightSignificantRegionsFileListThread = len(highlightSignificantRegionsFileList) // args.threads + + all_data_collected = False + images_array = [None] * args.threads + file_name_list = [None] * args.threads + queue = [None] * args.threads + process = [None] * args.threads + thread_done = [False] * args.threads + fail_flag = False + fail_message = '' + + for i in range(args.threads): + + if i < args.threads - 1: + interactionFileListThread = interactionFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] + highlightDifferentialRegionsFileListThread = highlightDifferentialRegionsFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] + highlightSignificantRegionsFileListThread = highlightSignificantRegionsFileList[i * interactionFilesPerThread:(i + 1) * interactionFilesPerThread] + else: + interactionFileListThread = interactionFileList[i * interactionFilesPerThread:] + highlightDifferentialRegionsFileListThread = highlightDifferentialRegionsFileList[i * interactionFilesPerThread:] + highlightSignificantRegionsFileListThread = highlightSignificantRegionsFileList[i * interactionFilesPerThread:] + queue[i] = Queue() + + process[i] = Process(target=plot_images, kwargs=dict( + pInteractionFileList=interactionFileListThread, + pHighlightDifferentialRegionsFileList=highlightDifferentialRegionsFileListThread, + pBackgroundData=background_data, + pArgs=args, + pViewpointObj=viewpointObj, + pSignificantRegionsFileList=highlightSignificantRegionsFileListThread, + pResolution=resolution, + pQueue=queue[i] + ) + ) + + process[i].start() + + while not all_data_collected: + for i in range(args.threads): + if queue[i] is not None and not queue[i].empty(): + return_content = queue[i].get() + if 'Fail:' in return_content: + fail_flag = True + fail_message = return_content[6:] + else: + images_array[i], file_name_list[i] = return_content + queue[i] = None + process[i].join() + process[i].terminate() + process[i] = None + thread_done[i] = True + all_data_collected = True + for thread in thread_done: + if not thread: + all_data_collected = False + time.sleep(1) + if fail_flag: + log.error(fail_message) + exit(1) + + images_array = [item for sublist in images_array for item in sublist] + file_name_list = [item for sublist in file_name_list for item in sublist] + + with tarfile.open(args.outFileName, "w:gz") as tar: + for i, bufferObject in enumerate(images_array): + with closing(bufferObject) as fobj: + tar_info = tarfile.TarInfo(name=file_name_list[i] + '.' + args.outputFormat) + tar_info.mtime = time.time() + tar_info.size = len(fobj.getvalue()) + fobj.seek(0) + tar.addfile(tarinfo=tar_info, fileobj=fobj) diff --git a/hicexplorer/chicQualityControl.py b/hicexplorer/chicQualityControl.py index 378647da..a01fedad 100644 --- a/hicexplorer/chicQualityControl.py +++ b/hicexplorer/chicQualityControl.py @@ -29,7 +29,7 @@ def parse_arguments(args=None): An example usage is: -$ chicQualityControl -m matrix1.h5 matrix2.h5 -rp referencePointsFile.bed --range 20000 40000 --sparsity 0.01 -o referencePointFile_QC_passed.bed +$ chicQualityControl -m matrix1.cool matrix2.cool -rp referencePointsFile.bed --range 20000 40000 --sparsity 0.01 -o referencePointFile_QC_passed.bed """ ) @@ -125,7 +125,7 @@ def compute_sparsity(pReferencePoints, pViewpointObj, pArgs, pQueue): def main(args=None): args = parse_arguments().parse_args(args) - + matplotlib.rcParams['pdf.fonttype'] = 42 viewpointObj = Viewpoint() referencePoints, _ = viewpointObj.readReferencePointFile( args.referencePoints) @@ -199,9 +199,6 @@ def main(args=None): sparsity_local = [item for sublist in sparsity_local for item in sublist] sparsity.append(sparsity_local) - # sparsity = np.array(sparsity) - # mask = sparsity == -1.0 - # change sparsity to sparsity values per viewpoint per matrix: viewpoint = [matrix1, ..., matrix_n] sparsity = np.array(sparsity).T count_accepted = 0 @@ -297,14 +294,11 @@ def main(args=None): plt.legend(loc='center', bbox_to_anchor=(1.4, 0.5)) plt.savefig(args.outFileNameSparsity, dpi=args.dpi) - # plt.xlabel("Length of list (number)") - # plt.ylabel("Time taken (seconds)") plt.close() for i in range(len(args.matrices)): plt.hist(x[i], bins=100, alpha=0.5, label=args.matrices[i].split('/')[-1]) plt.xlabel("Sparsity level") plt.ylabel("Number of counts") - # plt.legend(loc='upper right') ax = plt.gca() box = ax.get_position() diff --git a/hicexplorer/chicSignificantInteractions.py b/hicexplorer/chicSignificantInteractions.py index 9f6137f6..2749c6d2 100644 --- a/hicexplorer/chicSignificantInteractions.py +++ b/hicexplorer/chicSignificantInteractions.py @@ -16,6 +16,8 @@ from hicexplorer._version import __version__ from .lib import Viewpoint from hicexplorer.lib import cnb +import h5py +import traceback def parse_arguments(args=None): @@ -29,45 +31,30 @@ def parse_arguments(args=None): chicSignificantInteractions supports two modes to detect significant interactions, either by an x-fold over the average background or a loose p-value. In both cases neighboring significant peaks are merged together and an additional p-value is computed based on the sum of interactions for this neighborhood. Only interactions with a higher p-value (as specified by the threshold `--pValue`) are accepted as a significant interaction. -An example usage is for single mode is: - -`$ chicSignificantInteractions --interactionFile interactionFilesFolder/Sox17_FL-E13-5_chr1_1000_2000.bed --referencePoints referencePointsFile.bed --range 20000 40000 --backgroundModelFile background_model.bed --loosePValue 0.5 --pValue 0.01` - -An example usage is for batch mode is: - -`$ chicViewpointBackgroundModel --matrices matrix1.cool matrix2.cool matrix3.cool --referencePoints referencePointsFile.bed --range 20000 40000 --outFileName background_model.bed` - -The main difference between single mode and batch mode is that in single mode the parameter `--interactionFile` is interpreted as a list of viewpoint files created with `chicViewpoint`, whereas in batch mode only one file is allowed, containing the file names of viewpoint files (one per line). -This file is created by `chicViewpoint` and the parameter `--writeFileNamesToFile`. In batch mode, please remember to specify the folder (via `--interactionFileFolder`) where `chicViewpoint` wrote the files. """) parserRequired = parser.add_argument_group('Required arguments') parserRequired.add_argument('--interactionFile', '-if', - help='path to the interaction files which should be used for aggregation of the statistics.', - required=True, - nargs='+') + help='path to the interaction file (HDF5) which should be used for aggregation of the statistics.', + required=True) parserRequired.add_argument('--pValue', '-p', help='p-value threshold to filter target regions for inclusion in differential analysis.', - # type=float, required=True) parserMutuallyExclusiveGroupFilter = parser.add_mutually_exclusive_group( required=False) parserMutuallyExclusiveGroupFilter.add_argument('--xFoldBackground', '-xf', help='Filter x-fold over background. Used to merge neighboring bins with a broader peak but ' 'less significant interactions to a single peak with high significance. Used only for pValue option.' - # type=float - ) parserMutuallyExclusiveGroupFilter.add_argument('--loosePValue', '-lp', help='loose p-value threshold to filter target regions in a first round. ' 'Used to merge neighboring bins with a broader peak but less significant interactions to a single peak with high significance.' ' Used only for pValue option.' - # type=float ) parserRequired.add_argument('--backgroundModelFile', '-bmf', - help='path to the background file which is necessary to compute the rbz-score', + help='path to the background file.', required=True) parserRequired.add_argument('--range', help='Defines the region upstream and downstream of a reference point which should be included. ' @@ -78,38 +65,24 @@ def parse_arguments(args=None): parserOpt = parser.add_argument_group('Optional arguments') - parserOpt.add_argument('--outFileNameSuffix', '-suffix', + parserOpt.add_argument('--outFileNameSignificant', '-os', help='File name suffix to save the results; prefix is the input file name' ' (Default: %(default)s).', required=False, - default='_significant_interactions.txt') - - parserOpt.add_argument('--interactionFileFolder', '-iff', - help='Folder where the interaction files are stored. Applies only for batch mode' - ' (Default: %(default)s).', - required=False, - default='.') - parserOpt.add_argument('--targetFolder', '-tf', - help='Folder where the target files are stored' + default='significantInteractions.hdf5') + parserOpt.add_argument('--outFileNameTarget', '-ot', + help='The file to store the target data' ' (Default: %(default)s).', - required=False, - default='targetFolder') - parserOpt.add_argument('--outputFolder', '-o', - help='Output folder of the significant interaction files' + default='targetFile.hdf5') + parserOpt.add_argument('--combinationMode', + '-cm', + help='This option defines how the interaction data should be computed and combined: ' + 'dual: Combines as follows: [[matrix1_gene1, matrix2_gene1], [matrix2_gene1, matrix3_gene1],[matrix1_gene2, matrix2_gene2], ...]' + 'single: Combines as follows: [matrix1_gene1, matrix1_gene2, matrix2_gene1, ...], ' ' (Default: %(default)s).', - required=False, - default='significantFiles') - parserOpt.add_argument('--writeFileNamesToFile', '-w', - help='(Default: %(default)s).', - default='significantFilesBatch.txt') - parserOpt.add_argument('--targetFileList', '-tl', - help='The file to store the target file names' - ' (Default: %(default)s).', - default='targetList.txt') - parserOpt.add_argument('--batchMode', '-bm', - help='Turn on batch mode. The given file for --interactionFile and or --targetFile contain a list of the to be processed files.', - required=False, - action='store_true') + default='dual', + choices=['dual', 'single'] + ) parserOpt.add_argument('--threads', '-t', help='Number of threads (uses the python multiprocessing module)' ' (Default: %(default)s).', @@ -133,31 +106,6 @@ def parse_arguments(args=None): default=5, help='The minimum number of interactions a detected peak needs to have to be considered' ' (Default: %(default)s).') - - parserOpt.add_argument('--resolution', '-r', - help='Resolution of the bin in genomic units. Values are set as number of bases, e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.' - 'This value is used to merge neighboring bins' - ' (Default: %(default)s).', - type=int, - default=1000, - required=False) - - parserOpt.add_argument('--computeSampleNumber', '-csn', - help='Number of samples to compute together. Applies only in batch mode' - ' (Default: %(default)s).', - required=False, - default=2, - type=int) - parserOpt.add_argument('--multipleTesting', '-mt', - help='Multiple testing correction per relative distance with Bonferroni or FDR' - ' (Default: %(default)s).', - type=str, - default="None", - choices=['fdr', 'bonferroni', 'None'], - ) - parserOpt.add_argument('--thresholdMultipleTesting', '-tmt', - help='Threshold for Bonferroni / FDR. Either a float value for all or a file with one threshold per relative distance.' - ) parserOpt.add_argument("--help", "-h", action="help", help="show this help message and exit") @@ -166,95 +114,116 @@ def parse_arguments(args=None): return parser -def compute_interaction_file(pInteractionFilesList, pArgs, pViewpointObj, pBackground, pQueue=None): - outfile_names = [] +def compute_interaction_file(pInteractionFilesList, pArgs, pViewpointObj, pBackground, pFilePath, pResolution, pQueue=None): target_outfile_names = [] + significant_data_list = [] + significant_key_list = [] + + target_data_list = [] + target_key_list = [] + + reference_points_list_target = [] + reference_points_list_significant = [] + try: for interactionFile in pInteractionFilesList: target_list = [] - sample_prefix = '' + sample_prefix = [] + for sample in interactionFile: - # header, - # interaction_data:rel interaction, p-value, raw, x-fold::{-1000:[0.1, 0.01, 2.3, 5]}, - if pArgs.interactionFileFolder != '.': - absolute_sample_path = pArgs.interactionFileFolder + '/' + sample - else: - absolute_sample_path = sample - data = pViewpointObj.readInteractionFileForAggregateStatistics(absolute_sample_path) - sample_prefix += sample.split('/')[-1].split('_')[0] - sample_prefix += '_' - # filter by x-fold over background value or loose p-value - # and merge neighbors. Use center position to compute new p-value. + data = pViewpointObj.readInteractionFile(pFilePath, sample) + sample_prefix.append(sample[0]) + compute_new_p_values_bool = False if pArgs.xFoldBackground is not None: accepted_scores, merged_lines_dict = merge_neighbors_x_fold( - pArgs.xFoldBackground, data, pViewpointObj, pResolution=pArgs.resolution) - else: + pArgs.xFoldBackground, data, pViewpointObj, pResolution=pResolution) + compute_new_p_values_bool = True + elif pArgs.loosePValue is not None: accepted_scores, merged_lines_dict = merge_neighbors_loose_p_value( - pArgs.loosePValue, data, pViewpointObj, pResolution=pArgs.resolution, pTruncateZeroPvalues=pArgs.truncateZeroPvalues) + pArgs.loosePValue, data, pViewpointObj, pResolution=pResolution, pTruncateZeroPvalues=pArgs.truncateZeroPvalues) + compute_new_p_values_bool = True # compute new p-values and filter by them - accepted_scores, target_lines = compute_new_p_values( - accepted_scores, pBackground, pArgs.pValue, merged_lines_dict, pArgs.peakInteractionsThreshold, pViewpointObj) + if compute_new_p_values_bool: + accepted_scores, target_lines = compute_new_p_values( + accepted_scores, pBackground, pArgs.pValue, merged_lines_dict, pArgs.peakInteractionsThreshold) + else: + accepted_scores, target_lines = filter_by_pvalue( + data[0], pArgs.pValue, data[1], pArgs.peakInteractionsThreshold) # filter by new p-value if len(accepted_scores) == 0: - if pArgs.batchMode: - with open('errorLog.txt', 'a+') as errorlog: - errorlog.write('Failed for: {} and {}.\n'.format( - interactionFile[0], interactionFile[1])) - else: - log.info('No target regions found') - outFileName = '.'.join(sample.split( - '/')[-1].split('.')[:-1]) + '_' + pArgs.outFileNameSuffix - if pArgs.batchMode: - outfile_names.append(outFileName) - outFileName = pArgs.outputFolder + '/' + outFileName - # write only significant lines to file - write(outFileName, data[0], accepted_scores) + with open('errorLog.txt', 'a+') as errorlog: + errorlog.write('Failed for: {}.\n'.format( + interactionFile)) + target_list.append(target_lines) + significant_data_list.append(accepted_scores) + significant_key_list.append(sample) + reference_points_list_significant.append(data[2]) target_list = [item for sublist in target_list for item in sublist] - log.debug('interactionFile {}'.format(interactionFile)) - sample_name = '_'.join(interactionFile[0].split('/')[-1].split('.')[0].split('_')[1:]) - target_name = sample_prefix + sample_name + '_target.txt' - target_outfile_names.append(target_name) - target_name = pArgs.targetFolder + '/' + target_name - writeTargetList(target_list, target_name, pArgs) + sample_prefix.append('::') + sample_prefix.append(interactionFile[0][1]) + sample_prefix.append(interactionFile[0][2]) + target_data_list.append(target_list) + target_key_list.append(sample_prefix) + reference_points_list_target.append(data[2]) + if pQueue is None: return target_outfile_names except Exception as exp: if pQueue is None: - return 'Fail: ' + str(exp) - pQueue.put('Fail: ' + str(exp)) + return 'Fail: ' + str(exp) + traceback.format_exc() + pQueue.put('Fail: ' + str(exp) + traceback.format_exc()) return - pQueue.put([outfile_names, target_outfile_names]) + pQueue.put([significant_data_list, significant_key_list, target_data_list, target_key_list, reference_points_list_target, reference_points_list_significant]) return -def compute_new_p_values(pData, pBackgroundModel, pPValue, pMergedLinesDict, pPeakInteractionsThreshold, pViewpointObj): +def filter_by_pvalue(pData, pPValue, pMergedLinesDict, pPeakInteractionsThreshold): + accepted = {} + accepted_lines = [] + if isinstance(pPValue, float): + for key in pData: + if pData[key][-3] <= pPValue: + if float(pData[key][-1]) >= pPeakInteractionsThreshold: + accepted[key] = pMergedLinesDict[key] + target_content = pMergedLinesDict[key][:3] + accepted_lines.append(target_content) + elif isinstance(pPValue, dict): + for key in pData: + + if pData[key][-3] <= pPValue[key]: + if float(pData[key][-1]) >= pPeakInteractionsThreshold: + accepted[key] = pMergedLinesDict[key] + target_content = pMergedLinesDict[key][:3] + accepted_lines.append(target_content) + + return accepted, accepted_lines + + +def compute_new_p_values(pData, pBackgroundModel, pPValue, pMergedLinesDict, pPeakInteractionsThreshold): accepted = {} accepted_lines = [] if isinstance(pPValue, float): for key in pData: if key in pBackgroundModel: - log.debug('Recompute p-values. Old: {}'.format(pData[key][-3])) + pData[key][-3] = 1 - cnb.cdf(float(pData[key][-1]), float(pBackgroundModel[key][0]), float(pBackgroundModel[key][1])) - log.debug('new {}\n\n'.format(pData[key][-3])) if pData[key][-3] <= pPValue: if float(pData[key][-1]) >= pPeakInteractionsThreshold: accepted[key] = pData[key] target_content = pMergedLinesDict[key][0][:3] + target_content[2] = pMergedLinesDict[key][-1][2] accepted_lines.append(target_content) else: - log.debug('key not in background') + log.debug('key not in background {}'.format(key)) elif isinstance(pPValue, dict): for key in pData: if key in pBackgroundModel: - log.debug('Recompute p-values. Old: {}'.format(pData[key][-3])) - pData[key][-3] = 1 - cnb.cdf(float(pData[key][-1]), float(pBackgroundModel[key][0]), float(pBackgroundModel[key][1])) - log.debug('new {}\n\n'.format(pData[key][-3])) if pData[key][-3] <= pPValue[key]: if float(pData[key][-1]) >= pPeakInteractionsThreshold: @@ -263,7 +232,7 @@ def compute_new_p_values(pData, pBackgroundModel, pPValue, pMergedLinesDict, pPe target_content[2] = pMergedLinesDict[key][-1][2] accepted_lines.append(target_content) else: - log.debug('key not in background') + log.debug('key not in background {}'.format(key)) return accepted, accepted_lines @@ -271,18 +240,18 @@ def merge_neighbors_x_fold(pXfold, pData, pViewpointObj, pResolution): accepted = {} accepted_line = {} if isinstance(pXfold, float): - for key in pData[1]: + for key in pData[0]: - if pData[1][key][-1] < pXfold: + if pData[0][key][-1] < pXfold: continue - accepted[key] = pData[1][key] - accepted_line[key] = pData[2][key] + accepted[key] = pData[0][key] + accepted_line[key] = pData[1][key] elif isinstance(pXfold, dict): - for key in pData[1]: - if pData[1][key][-1] < pXfold[key]: + for key in pData[0]: + if pData[0][key][-1] < pXfold[key]: continue - accepted[key] = pData[1][key] - accepted_line[key] = pData[2][key] + accepted[key] = pData[0][key] + accepted_line[key] = pData[1][key] if accepted_line: return pViewpointObj.merge_neighbors(accepted_line, pMergeThreshold=pResolution) return accepted_line, None @@ -292,50 +261,39 @@ def merge_neighbors_loose_p_value(pLoosePValue, pData, pViewpointObj, pResolutio accepted = {} accepted_line = {} if isinstance(pLoosePValue, float): - for key in pData[1]: + for key in pData[0]: if pTruncateZeroPvalues: - if pData[1][key][1] == 0 or pData[1][key][1] > pLoosePValue: + if pData[0][key][1] == 0 or pData[0][key][1] > pLoosePValue: continue else: - if pData[1][key][1] > pLoosePValue: + if pData[0][key][1] > pLoosePValue: continue - accepted[key] = pData[1][key] - accepted_line[key] = pData[2][key] + accepted[key] = pData[0][key] + accepted_line[key] = pData[1][key] elif isinstance(pLoosePValue, dict): - for key in pData[1]: + for key in pData[0]: if pTruncateZeroPvalues: - if pData[1][key][1] == 0 or pData[1][key][1] > pLoosePValue[key]: + if pData[0][key][1] == 0 or pData[0][key][1] > pLoosePValue[key]: continue else: - if pData[1][key][1] > pLoosePValue[key]: + if pData[0][key][1] > pLoosePValue[key]: continue - accepted[key] = pData[1][key] - accepted_line[key] = pData[2][key] + accepted[key] = pData[0][key] + accepted_line[key] = pData[1][key] if accepted_line: return pViewpointObj.merge_neighbors(accepted_line, pMergeThreshold=pResolution) return accepted_line, None -def write(pOutFileName, pHeader, pInteractionLines): +def call_multi_core(pInteractionFilesList, pArgs, pViewpointObj, pBackground, pFilePath, pResolution): + significant_data_list = [None] * pArgs.threads + significant_key_list = [None] * pArgs.threads - # sum_of_interactions = float(pHeader.split('\t')[-1].split(' ')[-1]) - with open(pOutFileName, 'w') as file: - file.write(pHeader) - file.write( - '#Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative interactions\tp-value\tx-fold\tRaw target') - file.write('\n') + target_data_list = [None] * pArgs.threads + target_key_list = [None] * pArgs.threads + reference_points_list_target = [None] * pArgs.threads + reference_points_list_significant = [None] * pArgs.threads - for data in pInteractionLines: - new_line = '\t'.join(pInteractionLines[data][:6]) - new_line += '\t' + '\t'.join(format(float(x), "0.20f") - for x in pInteractionLines[data][6:]) - new_line += '\n' - file.write(new_line) - - -def call_multi_core(pInteractionFilesList, pArgs, pViewpointObj, pBackground): - outfile_names = [None] * pArgs.threads - target_list_name = [None] * pArgs.threads interactionFilesPerThread = len(pInteractionFilesList) // pArgs.threads all_data_collected = False queue = [None] * pArgs.threads @@ -358,6 +316,8 @@ def call_multi_core(pInteractionFilesList, pArgs, pViewpointObj, pBackground): pArgs=pArgs, pViewpointObj=pViewpointObj, pBackground=pBackground, + pFilePath=pFilePath, + pResolution=pResolution, pQueue=queue[i] ) ) @@ -372,7 +332,7 @@ def call_multi_core(pInteractionFilesList, pArgs, pViewpointObj, pBackground): fail_flag = True fail_message = background_data_thread[6:] else: - outfile_names[i], target_list_name[i] = background_data_thread + significant_data_list[i], significant_key_list[i], target_data_list[i], target_key_list[i], reference_points_list_target[i], reference_points_list_significant[i] = background_data_thread queue[i] = None process[i].join() process[i].terminate() @@ -387,44 +347,22 @@ def call_multi_core(pInteractionFilesList, pArgs, pViewpointObj, pBackground): log.error(fail_message) exit(1) - outfile_names = [item for sublist in outfile_names for item in sublist] - target_list_name = [ - item for sublist in target_list_name for item in sublist] - - return outfile_names, target_list_name + significant_data_list = [item for sublist in significant_data_list for item in sublist] + significant_key_list = np.array([item for sublist in significant_key_list for item in sublist]) + reference_points_list_target = np.array([item for sublist in reference_points_list_target for item in sublist]) + reference_points_list_significant = np.array([item for sublist in reference_points_list_significant for item in sublist]) + significant_key_list, indices = np.unique(significant_key_list, axis=0, return_index=True) -def writeTargetList(pTargetList, pOutFileName, pArgs): - # remove duplicates - target_list_ = [] - for line in pTargetList: - target_list_.append('\t'.join(line)) - target_set = set(target_list_) - pTargetList = sorted(list(target_set)) + significant_data_list_new = [] + for x in indices: + significant_data_list_new.append(significant_data_list[x]) + significant_data_list = significant_data_list_new - a = pybedtools.BedTool(pTargetList) + target_data_list = [item for sublist in target_data_list for item in sublist] + target_key_list = [item for sublist in target_key_list for item in sublist] - header = '# Significant interactions result file of HiCExplorer\'s chicSignificantInteractions version ' - header += str(__version__) - header += '\n' - header += '# {}\n'.format(pOutFileName) - - if pArgs.xFoldBackground: - header += '# Mode: x-fold background with ' - header += str(pArgs.xFoldBackground) - header += '\n' - else: - header += '# Mode: loose p-value with ' - header += str(pArgs.loosePValue) - header += '\n' - header += '# Used p-value: ' - header += str(pArgs.pValue) - header += '\n#\n' - if len(pTargetList) == 0: - with open(pOutFileName, 'w') as file: - file.write(header) - else: - a.sort().merge(d=pArgs.resolution).saveas(pOutFileName, trackline=header) + return significant_data_list, significant_key_list, target_data_list, target_key_list, reference_points_list_target, reference_points_list_significant def read_threshold_file(pFile): @@ -442,24 +380,203 @@ def read_threshold_file(pFile): return distance_value_dict -def main(args=None): +def writeSignificantHDF(pOutFileName, pSignificantDataList, pSignificantKeyList, pViewpointObj, pReferencePointsList, pArgs): + + significantFileH5Object = h5py.File(pOutFileName, 'w') + significantFileH5Object.attrs['type'] = "significant" + significantFileH5Object.attrs['version'] = __version__ + + significantFileH5Object.attrs['pvalue'] = pArgs.pValue + + if pArgs.xFoldBackground is not None: + significantFileH5Object.attrs['mode_preselection'] = "xfold" + significantFileH5Object.attrs['mode_preselection_value'] = pArgs.xFoldBackground + + elif pArgs.loosePValue is not None: + significantFileH5Object.attrs['mode_preselection'] = "loosePValue" + significantFileH5Object.attrs['mode_preselection_value'] = pArgs.loosePValue + else: + significantFileH5Object.attrs['mode_preselection'] = "None" + significantFileH5Object.attrs['mode_preselection_value'] = "None" + + significantFileH5Object.attrs['range'] = pArgs.range + significantFileH5Object.attrs['combinationMode'] = pArgs.combinationMode + + significantFileH5Object.attrs['truncateZeroPvalues'] = pArgs.truncateZeroPvalues + significantFileH5Object.attrs['fixateRange'] = pArgs.fixateRange + significantFileH5Object.attrs['peakInteractionsThreshold'] = pArgs.peakInteractionsThreshold + + keys_seen = {} + + for i, (key, data) in enumerate(zip(pSignificantKeyList, pSignificantDataList)): + if len(data) == 0: + continue + chromosome = None + start_list = [] + end_list = [] + gene_name = None + sum_of_interactions = None + relative_distance_list = [] + relative_interactions_list = [] + pvalue_list = [] + xfold_list = [] + raw_target_list = [] + + for datum in data.values(): + chromosome = datum[0] + start_list.append(datum[1]) + end_list.append(datum[2]) + gene_name = datum[3] + sum_of_interactions = datum[4] + relative_distance_list.append(datum[5]) + relative_interactions_list.append(datum[6]) + pvalue_list.append(datum[7]) + xfold_list.append(datum[8]) + raw_target_list.append(datum[9]) + + if key[0] not in significantFileH5Object: + matrixGroup = significantFileH5Object.create_group(key[0]) + keys_seen[key[0]] = set() + else: + matrixGroup = significantFileH5Object[key[0]] + + if chromosome not in matrixGroup: + chromosomeObject = matrixGroup.create_group(chromosome) + else: + chromosomeObject = matrixGroup[chromosome] + + if 'genes' not in matrixGroup: + geneGroup = matrixGroup.create_group('genes') + else: + geneGroup = matrixGroup['genes'] + + success = False + counter = 0 + while not success: + + if counter != 0: + gene_name_key = key[2] + '_' + str(counter) + else: + gene_name_key = key[2] + if gene_name_key in keys_seen[key[0]]: + success = False + else: + keys_seen[key[0]].add(gene_name_key) + success = True + counter += 1 + + group_name = pViewpointObj.writeInteractionFileHDF5( + chromosomeObject, gene_name_key, [chromosome, start_list, end_list, gene_name, sum_of_interactions, relative_distance_list, + relative_interactions_list, pvalue_list, xfold_list, raw_target_list], pReferencePointsList[i]) - args = parse_arguments().parse_args(args) - # args.p_value_dict = None - # args.p_loose_value_dict = None - # args.x_fold_dict = None - if not os.path.exists(args.outputFolder): try: - os.makedirs(args.outputFolder) - except OSError as exc: # Guard against race condition - if exc.errno != errno.EEXIST: - raise - if not os.path.exists(args.targetFolder): + geneGroup[group_name] = chromosomeObject[group_name] + except Exception as exp: + log.debug('exception {}'.format(str(exp))) + log.debug('Gene group given: {}'.format(key[2])) + log.debug('Gene group return: {}'.format(group_name)) + + significantFileH5Object.close() + + +def writeTargetHDF(pOutFileName, pTargetDataList, pTargetKeyList, pViewpointObj, pResolution, pReferencePointsList, pArgs): + + targetFileH5Object = h5py.File(pOutFileName, 'w') + targetFileH5Object.attrs['type'] = "target" + targetFileH5Object.attrs['version'] = __version__ + + targetFileH5Object.attrs['pvalue'] = pArgs.pValue + + if pArgs.xFoldBackground is not None: + targetFileH5Object.attrs['mode_preselection'] = "xfold" + targetFileH5Object.attrs['mode_preselection_value'] = pArgs.xFoldBackground + + elif pArgs.loosePValue is not None: + targetFileH5Object.attrs['mode_preselection'] = "loosePValue" + targetFileH5Object.attrs['mode_preselection_value'] = pArgs.loosePValue + else: + targetFileH5Object.attrs['mode_preselection'] = "None" + targetFileH5Object.attrs['mode_preselection_calue'] = "None" + + targetFileH5Object.attrs['range'] = pArgs.range + targetFileH5Object.attrs['combinationMode'] = pArgs.combinationMode + + targetFileH5Object.attrs['truncateZeroPvalues'] = pArgs.truncateZeroPvalues + targetFileH5Object.attrs['fixateRange'] = pArgs.fixateRange + targetFileH5Object.attrs['peakInteractionsThreshold'] = pArgs.peakInteractionsThreshold + keys_seen = {} + for i, (key, data) in enumerate(zip(pTargetKeyList, pTargetDataList)): + if len(data) == 0: + continue + + chromosome = None + start_list = [] + end_list = [] + a = pybedtools.BedTool(data) + data_sorted_merged = a.sort().merge(d=pResolution) + for datum in data_sorted_merged: + chromosome = datum[0] + start_list.append(datum[1]) + end_list.append(datum[2]) + + if key[0] not in targetFileH5Object: + matrixGroup = targetFileH5Object.create_group(key[0]) + keys_seen[key[0]] = set() + else: + matrixGroup = targetFileH5Object[key[0]] + + for matrix_name in key[1:]: + if matrix_name == '::': + break + if matrix_name not in matrixGroup: + matrixGroup = matrixGroup.create_group(matrix_name) + keys_seen[matrix_name] = set() + else: + matrixGroup = matrixGroup[matrix_name] + + if 'genes' not in matrixGroup: + geneGroup = matrixGroup.create_group('genes') + else: + geneGroup = matrixGroup['genes'] + if chromosome not in matrixGroup: + chromosomeObject = matrixGroup.create_group(chromosome) + else: + chromosomeObject = matrixGroup[chromosome] + + success = False + counter = 0 + while not success: + + if counter != 0: + gene_name_key = key[-1] + '_' + str(counter) + else: + gene_name_key = key[-1] + if gene_name_key in keys_seen[key[0]]: + success = False + else: + keys_seen[key[0]].add(gene_name_key) + success = True + counter += 1 + + groupObject, groupName = pViewpointObj.createUniqueHDFGroup(chromosomeObject, gene_name_key) + + groupObject["chromosome"] = chromosome + groupObject.create_dataset("start_list", data=start_list) + groupObject.create_dataset("end_list", data=end_list) + groupObject.create_dataset("reference_point_start", data=int(pReferencePointsList[i][0])) + groupObject.create_dataset("reference_point_end", data=int(pReferencePointsList[i][1])) try: - os.makedirs(args.targetFolder) - except OSError as exc: # Guard against race condition - if exc.errno != errno.EEXIST: - raise + geneGroup[groupName] = chromosomeObject[groupName] + except Exception as exp: + log.debug('exception {}'.format(str(exp))) + log.debug('Gene group: {}'.format(key[-1])) + log.debug('Adjusted name {}'.format(groupName)) + targetFileH5Object.close() + + +def main(args=None): + + args = parse_arguments().parse_args(args) if args.pValue: try: @@ -478,45 +595,56 @@ def main(args=None): args.xFoldBackground = read_threshold_file(args.xFoldBackground) viewpointObj = Viewpoint() - outfile_names = [] - - interactionFileList = [] background_model = viewpointObj.readBackgroundDataFile( args.backgroundModelFile, args.range, args.fixateRange) - if args.batchMode: - with open(args.interactionFile[0], 'r') as interactionFile: - file_ = True - while file_: - lines = [] - for i in range(0, args.computeSampleNumber): - file_ = interactionFile.readline().strip() - if file_ != '': - lines.append(file_) - if len(lines) > 0: - interactionFileList.append(lines) - log.debug('interactionFileList {}'.format(interactionFileList)) - outfile_names, target_list_name = call_multi_core( - interactionFileList, args, viewpointObj, background_model) - else: - i = 0 - while i < len(args.interactionFile): - lines = [] - for j in range(0, args.computeSampleNumber): - if i < len(args.interactionFile): - lines.append(args.interactionFile[i]) - i += 1 - interactionFileList.append(lines) - - target_list_name = compute_interaction_file( - interactionFileList, args, viewpointObj, background_model) - if 'Fail: ' in target_list_name: - log.error(target_list_name[6:]) - - if args.batchMode: - with open(args.writeFileNamesToFile, 'w') as nameListFile: - nameListFile.write('\n'.join(outfile_names)) - - with open(args.targetFileList, 'w') as targetNamesFile: - targetNamesFile.write('\n'.join(target_list_name)) + # read hdf file + interactionFileHDF5Object = h5py.File(args.interactionFile, 'r') + keys_interactionFile = list(interactionFileHDF5Object.keys()) + + if interactionFileHDF5Object.attrs['type'] != 'interactions': + log.error('Please provide a file created by chicViewpoint for the parameter --interactionFile.') + exit(1) + + interactionList = [] + if args.combinationMode == 'dual': + if len(keys_interactionFile) > 1: + for i, sample in enumerate(keys_interactionFile): + for sample2 in keys_interactionFile[i + 1:]: + + matrix_obj1 = interactionFileHDF5Object[sample] + matrix_obj2 = interactionFileHDF5Object[sample] + + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList2 = sorted(list(matrix_obj2.keys())) + chromosomeList1.remove('genes') + chromosomeList2.remove('genes') + for chromosome1, chromosome2 in zip(chromosomeList1, chromosomeList2): + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + geneList2 = sorted(list(matrix_obj2[chromosome2].keys())) + + for gene1, gene2 in zip(geneList1, geneList2): + interactionList.append([[sample, chromosome1, gene1], [sample2, chromosome2, gene2]]) + + else: + log.error('Dual mode selected but only one matrix is stored') + elif args.combinationMode == 'single': + for i, sample in enumerate(keys_interactionFile): + + matrix_obj1 = interactionFileHDF5Object[sample] + chromosomeList1 = sorted(list(matrix_obj1.keys())) + chromosomeList1.remove('genes') + for chromosome1 in chromosomeList1: + geneList1 = sorted(list(matrix_obj1[chromosome1].keys())) + for gene1 in geneList1: + interactionList.append([[sample, chromosome1, gene1]]) + + resolution = interactionFileHDF5Object.attrs['resolution'][()] + interactionFileHDF5Object.close() + + significant_data_list, significant_key_list, target_data_list, target_key_list, reference_points_list_target, reference_points_list_significant = call_multi_core( + interactionList, args, viewpointObj, background_model, args.interactionFile, resolution) + + writeSignificantHDF(args.outFileNameSignificant, significant_data_list, significant_key_list, viewpointObj, reference_points_list_significant, args) + writeTargetHDF(args.outFileNameTarget, target_data_list, target_key_list, viewpointObj, resolution, reference_points_list_target, args) diff --git a/hicexplorer/chicViewpoint.py b/hicexplorer/chicViewpoint.py index 940c5ba9..bc032f57 100644 --- a/hicexplorer/chicViewpoint.py +++ b/hicexplorer/chicViewpoint.py @@ -8,6 +8,7 @@ import logging log = logging.getLogger(__name__) +import h5py import numpy as np import hicmatrix.HiCMatrix as hm @@ -20,20 +21,7 @@ def parse_arguments(args=None): parser = argparse.ArgumentParser(add_help=False, formatter_class=argparse.RawDescriptionHelpFormatter, description=""" -Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, and the files -are named by the name of the reference point, the sample name and the location of the reference point: - -gene_matrix_name_chr_start_end.txt - -If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. All the file names will be written to this file; in the case of multiple samples two consecutive lines are considered as treatment vs. control for the differential analysis. - -An example usage is: - -$ chicViewpoint --matrices matrix1.cool matrix2.cool matrix3.cool --referencePoints referencePointsFile.txt --range 20000 40000 --outputFolder interactionFilesFolder - -An example usage for batch mode is: - -$ chicViewpoint --matrices matrix1.cool matrix2.cool matrix3.cool --referencePoints referencePointsFile.txt --range 20000 40000 --outputFolder interactionFilesFolder --writeFileNamesToFile interactionFile.txt +Computes per input matrix all viewpoints which are defined in the reference points file. """) @@ -58,6 +46,10 @@ def parse_arguments(args=None): parserRequired.add_argument('--backgroundModelFile', '-bmf', help='path to the background file computed by chicViewpointBackgroundModel', required=True) + parserRequired.add_argument('--outFileName', '-o', + help='This hdf5 file contains all created viewpoint files.', + required=False, + default='chic_files.hdf5') parserOpt = parser.add_argument_group('Optional arguments') parserOpt.add_argument('--threads', '-t', help='Number of threads (uses the python multiprocessing module)' @@ -70,13 +62,6 @@ def parse_arguments(args=None): ' (Default: %(default)s).', type=int, default=5) - parserOpt.add_argument('--decimalPlaces', - help='Decimal places for all output floating numbers in the viewpoint files' - ' (Default: %(default)s).', - type=int, - default=12) - parserOpt.add_argument('--writeFileNamesToFile', '-w', - help='Set this parameter to have a file with all file names of the viewpoint files (useful only in batch processing mode).') parserOpt.add_argument('--fixateRange', '-fs', help='Fixate range of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin' @@ -85,15 +70,7 @@ def parse_arguments(args=None): default=500000, type=int ) - parserOpt.add_argument('--allViewpointsList', '-avl', - help='Writes a file where all viewpoints all samples are sorted by the viewpoints.', - required=False, - action='store_true') - parserOpt.add_argument('--outputFolder', '-o', - help='This folder contains all created viewpoint files' - ' (Default: %(default)s).', - required=False, - default='interactionFiles') + parserOpt.add_argument("--help", "-h", action="help", help="show this help message and exit") @@ -134,8 +111,8 @@ def compute_x_fold(pDataList, pBackgroundList): return pDataList / pBackgroundList -def compute_viewpoint(pViewpointObj, pArgs, pQueue, pReferencePoints, pGeneList, pMatrix, pBackgroundModel, pBackgroundModelRelativeInteractions, pOutputFolder): - file_list = [] +def compute_viewpoint(pViewpointObj, pArgs, pQueue, pReferencePoints, pGeneList, pMatrix, pBackgroundModel, pBackgroundModelRelativeInteractions): + interaction_data_list = [] try: for i, referencePoint in enumerate(pReferencePoints): @@ -183,9 +160,9 @@ def compute_viewpoint(pViewpointObj, pArgs, pQueue, pReferencePoints, pGeneList, region_start_range, region_end_range, _ = pViewpointObj.calculateViewpointRange( referencePoint, (pArgs.range[0], pArgs.range[1])) - interaction_data = pViewpointObj.createInteractionFileData(referencePoint, referencePoint[0], - region_start_range, region_end_range, data_list, data_list_raw, - pGeneList[i], denominator_relative_interactions) + interaction_data = pViewpointObj.createInteractionFileDataHDF5(referencePoint, referencePoint[0], + region_start_range, region_end_range, data_list, data_list_raw, + pGeneList[i], denominator_relative_interactions, p_value_list, x_fold_list) referencePointString = '_'.join(str(j) for j in referencePoint) @@ -202,21 +179,14 @@ def compute_viewpoint(pViewpointObj, pArgs, pQueue, pReferencePoints, pGeneList, matrix_name = '.'.join(pMatrix.split('/')[-1].split('.')[:-1]) matrix_name = '_'.join( [matrix_name, referencePointString, pGeneList[i]]) - file_list.append(matrix_name + '.txt') - - matrix_name = pOutputFolder + '/' + matrix_name - log.debug('type(p_value_list) {}'.format(type(p_value_list))) - log.debug('type(x_fold_list) {}'.format(type(x_fold_list))) - log.debug('p_value_list {}'.format(p_value_list)) - log.debug('x_fold_list {}'.format(x_fold_list)) - - pViewpointObj.writeInteractionFile( - matrix_name, interaction_data, header_information, p_value_list, x_fold_list, pArgs.decimalPlaces) + referencePointGenename = '_'.join([referencePointString, pGeneList[i]]) + referencePointGenename = str(referencePointGenename) + interaction_data_list.append([matrix_name, interaction_data, header_information, referencePointGenename]) except Exception as exp: log.debug('Error! {}'.format(str(exp))) pQueue.put('Fail: ' + str(exp)) return - pQueue.put(file_list) + pQueue.put(interaction_data_list) return @@ -227,37 +197,47 @@ def main(args=None): referencePoints, gene_list = viewpointObj.readReferencePointFile( args.referencePoints) + referencePointsPerThread = len(referencePoints) // args.threads + queue = [None] * args.threads process = [None] * args.threads - file_list = [] background_model = viewpointObj.readBackgroundDataFile( args.backgroundModelFile, args.range, args.fixateRange) background_model_mean_values = viewpointObj.readBackgroundDataFile( args.backgroundModelFile, args.range, args.fixateRange, pMean=True) - # background_sum_of_densities_dict = viewpointObj.computeSumOfDensities( - # background_model, args, pXfoldMaxValue=args.xFoldMaxValueNB) - - if not os.path.exists(args.outputFolder): - try: - os.makedirs(args.outputFolder) - except OSError as exc: # Guard against race condition - if exc.errno != errno.EEXIST: - raise + + # create hdf5 output file + interactionFileH5Object = h5py.File(args.outFileName, 'w') + interactionFileH5Object.attrs['type'] = 'interactions' + interactionFileH5Object.attrs['version'] = __version__ + + interactionFileH5Object.attrs['range'] = args.range + interactionFileH5Object.attrs['averageContactBin'] = args.averageContactBin + interactionFileH5Object.attrs['fixateRange'] = args.fixateRange + fail_flag = False fail_message = '' - + matrix_collection = {} + resolution = 0 for matrix in args.matrices: hic_ma = hm.hiCMatrix(matrix) viewpointObj.hicMatrix = hic_ma file_list_sample = [None] * args.threads + interaction_data_list_sample = [None] * args.threads + all_data_collected = False + if resolution == 0: + resolution = hic_ma.getBinSize() + interactionFileH5Object.attrs['resolution'] = resolution + for i in range(args.threads): if i < args.threads - 1: referencePointsThread = referencePoints[i * referencePointsPerThread:(i + 1) * referencePointsPerThread] geneListThread = gene_list[i * referencePointsPerThread:(i + 1) * referencePointsPerThread] + else: referencePointsThread = referencePoints[i * referencePointsPerThread:] geneListThread = gene_list[i * referencePointsPerThread:] @@ -276,8 +256,7 @@ def main(args=None): pGeneList=geneListThread, pMatrix=matrix, pBackgroundModel=background_model, - pBackgroundModelRelativeInteractions=background_model_mean_values, - pOutputFolder=args.outputFolder + pBackgroundModelRelativeInteractions=background_model_mean_values ) ) @@ -290,7 +269,7 @@ def main(args=None): if 'Fail:' in file_list_: fail_flag = True fail_message = file_list_[6:] - file_list_sample[i] = file_list_ + interaction_data_list_sample[i] = file_list_ process[i].join() process[i].terminate() process[i] = None @@ -306,30 +285,28 @@ def main(args=None): log.error(fail_message) exit(1) - file_list_sample = [item for sublist in file_list_sample for item in sublist] - file_list.append(file_list_sample) - - log.debug('file_list {}'.format(file_list)) - if args.writeFileNamesToFile: - with open(args.writeFileNamesToFile, 'w') as file: - log.debug('len(file_list) {}'.format(len(file_list))) - if len(file_list) > 1: - for i, sample in enumerate(file_list): - for sample2 in file_list[i + 1:]: - for viewpoint, viewpoint2 in zip(sample, sample2): - file.write(viewpoint + '\n') - file.write(viewpoint2 + '\n') - else: - for viewpoint in file_list[0]: - file.write(viewpoint + '\n') - if args.allViewpointsList: - - with open(args.writeFileNamesToFile + 'all', 'w') as file: - if len(file_list) > 1: - for i, sample in enumerate(file_list[0]): - file.write(sample + '\n') - for j in range(1, len(file_list)): - file.write(file_list[j][i] + '\n') - else: - for viewpoint in file_list[0]: - file.write(viewpoint + '\n') + interaction_data_list = [] + for sublist in interaction_data_list_sample: + if sublist is not None: + for item in sublist: + interaction_data_list.append(item) + matrix_collection[matrix] = interaction_data_list + + for matrix in matrix_collection: + + matrixGroup = interactionFileH5Object.create_group(os.path.basename(matrix).split('.')[0]) + geneGroup = matrixGroup.create_group('genes') + + for i, interaction_data in enumerate(matrix_collection[matrix]): + if interaction_data[1][0] not in matrixGroup: + chromosomeObject = matrixGroup.create_group(interaction_data[1][0]) + + group_name = viewpointObj.writeInteractionFileHDF5( + chromosomeObject, interaction_data[1][3], interaction_data[1], referencePoints[i][1:]) + + try: + geneGroup[group_name] = chromosomeObject[group_name] + except Exception as e: + log.debug(str(e)) + log.debug('group_name {}'.format(group_name)) + log.debug('gene name {}'.format(interaction_data[1][3])) diff --git a/hicexplorer/hicAdjustMatrix.py b/hicexplorer/hicAdjustMatrix.py index 0ef80482..0f4eb6fe 100644 --- a/hicexplorer/hicAdjustMatrix.py +++ b/hicexplorer/hicAdjustMatrix.py @@ -49,7 +49,13 @@ def parse_arguments(args=None): default='keep', choices=['keep', 'remove', 'mask'] ) - + parserOpt.add_argument('--interIntraHandling', + '-iih', + help='Remove the inter- or intra-chromosomal contacts of the given chromosomes.' + ' (Default: %(default)s).', + default=None, + choices=[None, 'inter', 'intra'] + ) parserOpt.add_argument('--help', '-h', action='help', help='show this help message and exit') parserOpt.add_argument('--version', action='version', version='%(prog)s {}'.format(__version__)) @@ -76,23 +82,33 @@ def adjustMatrix(pArgs): chromosomes_list = list(hic_matrix.chrBinBoundaries) chromosomes_list_to_operate_on = [] + log.debug('pArgs.chromosomes {}'.format(pArgs.chromosomes)) for chromosome in pArgs.chromosomes: if chromosome in chromosomes_list: chromosomes_list_to_operate_on.append(chromosome) else: log.warning('Chromosome not available in matrix: {} {}'.format(pArgs.matrix, chromosome)) + log.debug('85: chromosomes_list_to_operate_on {}'.format(chromosomes_list_to_operate_on)) if len(chromosomes_list_to_operate_on) == 0: log.error('No valid chromosome given: {}. Available: {}'.format(pArgs.chromosomes, chromosomes_list)) exit(1) if pArgs.action == 'keep': hic_matrix.reorderChromosomes(chromosomes_list_to_operate_on) elif pArgs.action == 'remove': - for chromosome in chromosomes_list: - if chromosome in chromosomes_list_to_operate_on: + log.debug('chromosomes_list {}'.format(chromosomes_list)) + + for chromosome in chromosomes_list_to_operate_on: + if chromosome in chromosomes_list: chromosomes_list.remove(chromosome) + # for chromosome in chromosomes_list: + # if chromosome in chromosomes_list_to_operate_on: + # chromosomes_list.remove(chromosome) + log.debug('chromosome {}'.format(chromosome)) + log.debug('chromosomes_list {}'.format(chromosomes_list)) hic_matrix.reorderChromosomes(chromosomes_list) elif pArgs.action == 'mask': hic_matrix.maskChromosomes(chromosomes_list_to_operate_on) + elif pArgs.regions: hic_matrix = hm.hiCMatrix(pArgs.matrix) chromosomes_list = list(hic_matrix.chrBinBoundaries) @@ -150,6 +166,27 @@ def adjustMatrix(pArgs): else: log.info('No data to adjust given. Please specify either --chromosomes or --region parameter.') + if pArgs.interIntraHandling is not None: + if pArgs.interIntraHandling == 'inter': + # iterate over all given chromosomes + chromosomes_list = list(hic_matrix.chrBinBoundaries) + for chromosome in chromosomes_list: + # get start and end bins of that chromosome + start, end = hic_matrix.getChrBinRange(chromosome) + # remove inter region + hic_matrix.matrix[start:end, end:] = 0 + + elif pArgs.interIntraHandling == 'intra': + # iterate over all given chromosomes + chromosomes_list = list(hic_matrix.chrBinBoundaries) + for chromosome in chromosomes_list: + # get start and end bins of that chromosome + start, end = hic_matrix.getChrBinRange(chromosome) + # remove intra region + hic_matrix.matrix[start:end, start:end] = 0 + else: + log.warning('Option not valid: {}'.format(pArgs.interIntraHandling)) + return hic_matrix diff --git a/hicexplorer/hicAggregateContacts.py b/hicexplorer/hicAggregateContacts.py index 051a62d8..4d5739fa 100755 --- a/hicexplorer/hicAggregateContacts.py +++ b/hicexplorer/hicAggregateContacts.py @@ -3,13 +3,14 @@ warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) import argparse import numpy as np - +from itertools import compress import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec import matplotlib.cm as cm from mpl_toolkits.mplot3d import Axes3D + # from scipy.cluster.vq import vq, kmeans # from scipy.cluster.hierarchy import fcluster, linkage import sklearn.cluster as skclust @@ -106,7 +107,7 @@ def parse_arguments(args=None): parserOpt.add_argument('--largeRegionsOperation', help='If a given coordinate in the bed file is larger than ' 'a bin of the input matrix, by default only the first bin ' - 'is taken into account. However there are more posibilities ' + 'is taken into account. However there are more possibilities ' 'to handel such a case. Users can ask for the last bin or ' 'for center of the region. As an example if a region falls into bins [4,5,6] ' 'and `--numberOfBins = 2` then if first, bins [3,4,5] are kept. ' @@ -179,6 +180,15 @@ def parse_arguments(args=None): ' (Default: %(default)s).', choices=['full', 'center', 'diagonal'], default='full') + parserClust.add_argument('--keep_outlier', + help="keep outliers before clustering. They will be removed by default. " + "Note that removing outliers is also applied to the case where the number of " + "clusters is one (e.g. no clustering is required) unless keep_outlier is set.", + action='store_true') + parserClust.add_argument('--max_deviation', + help="max deviation from mean to be determined as outlier.", + type=int, + default=2) parserPlot = parser.add_argument_group('Plotting options') @@ -244,10 +254,11 @@ def read_bed_per_chrom(fh, chrom_list): return interval -def aggregate_contacts(bed1, bed2, agg_info, ma, M_half, largeRegionsOperation, range=None, transform=None, mode='', perChr=False): +def aggregate_contacts(bed1, bed2, agg_info, ma, M_half, largeRegionsOperation, range=None, transform=None, mode=''): """ To aggregate the contacts of desired sumatrices. """ + seen_chrs = [] for k1, v1 in bed1.items(): for k2, v2 in bed2.items(): if (mode == 'inter-chr') & (k1 == k2): @@ -262,25 +273,27 @@ def aggregate_contacts(bed1, bed2, agg_info, ma, M_half, largeRegionsOperation, if (k1 == k2) and (coord1 == coord2): continue interval = [(k1, coord1[0], coord1[1]), (k2, coord2[0], coord2[1])] - count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, range, transform, perChr) - # over_1_5 = 0 - # - - # if len(chrom_matrix[chrom]) == 0: - # log.warn("No valid submatrices were found for chrom: {}".format(chrom)) - # chrom_matrix.pop(chrom) - # else: - # log.info("Number of matrices with ratio over 1.5 at center {}, fraction w.r.t. non empty submatrices: ({:.2f})". - # format(over_1_5, float(over_1_5) / len(chrom_matrix[chrom]))) - # - # log.info("Number of discarded empty submatrices {} ({:.2f})". - # format(empty_mat, float(empty_mat) / counter)) + count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, seen_chrs, range, transform) + to_del = [] + for k1, v1 in agg_info["agg_matrix"].items(): + if v1 == {}: + log.info("no matrix on {}".format(k1)) + to_del.append(k1) + else: + new_v1 = {k: v for k, v in v1.items() if v != []} + if new_v1 != {}: + agg_info["agg_matrix"][k1] = new_v1 + else: + to_del.append(k1) + agg_info["agg_matrix"] = {key: val for key, val in agg_info["agg_matrix"].items() if key not in to_del} + agg_info["agg_contact_position"] = {key: val for key, val in agg_info["agg_contact_position"].items() if key not in to_del} def aggregate_contacts_per_row(bed1, bed2, agg_info, ma, chrom_list, M_half, largeRegionsOperation, range=None, transform=None, mode='', perChr=False): """ To aggregate the contacts of the desired submatrices , if row-wise. """ + seen_chrs = [] for line1, line2 in zip(bed1, bed2): line1 = line1.strip().split() line2 = line2.strip().split() @@ -298,17 +311,28 @@ def aggregate_contacts_per_row(bed1, bed2, agg_info, ma, chrom_list, M_half, lar elif mode == 'intra-chr': # skip the lines with different chrom if line1[0] != line2[0]: continue - interval = (line1[0:3], line2[0:3]) - count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, range, transform, perChr) - - -def count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, range=None, transform=None, perChr=False): + interval = [(line1[0], line1[1], line1[2]), (line2[0], line2[1], line2[2])] + count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, seen_chrs, range, transform) + to_del = [] + for k1, v1 in agg_info["agg_matrix"].items(): + if v1 == {}: + log.info("no matrix on {}".format(k1)) + to_del.append(k1) + elif (mode == 'intra-chr') and (v1[k1] == []): + log.info("no matrix between {} and {}".format(k1, k1)) + to_del.append(k1) + agg_info["agg_matrix"] = {key: val for key, val in agg_info["agg_matrix"].items() if key not in to_del} + agg_info["agg_contact_position"] = {key: val for key, val in agg_info["agg_contact_position"].items() if key not in to_del} + + +def count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, seen_chrs, range=None, transform=None): """ To count the number of contacts for a given pair of intervals """ chrom1, start1, end1 = interval[0] chrom2, start2, end2 = interval[1] + if chrom1 not in agg_info["chrom_coord"]: return if chrom2 not in agg_info["chrom_coord"]: @@ -320,7 +344,7 @@ def count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, bin_id1 = ma.getRegionBinRange(toString(chrom1), start1, end1) bin_id2 = ma.getRegionBinRange(toString(chrom2), start2, end2) - if bin_id1 == bin_id2: + if bin_id1 == bin_id2: # does not count the contact between a bin and itslef return if (bin_id1 is None) or (bin_id2 is None): return @@ -338,9 +362,9 @@ def count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, if chrom1 == chrom2: bin_id1, bin_id2 = sorted([bin_id1, bin_id2]) else: - chr1, str1, en1, bin1 = chrom1, start1, end1, bin_id1 + tmp_chrom, tmp_start, tmp_end, tmp_bin = chrom1, start1, end1, bin_id1 # intermediate variables chrom1, start1, end1, bin_id1 = chrom2, start2, end2, bin_id2 - chrom2, start2, end2, bin_id2 = chr1, str1, en1, bin1 + chrom2, start2, end2, bin_id2 = tmp_chrom, tmp_start, tmp_end, tmp_bin agg_info["counter"] += 1 if agg_info["counter"] % 50000 == 0: log.info("Number of contacts considered: {:,}".format(agg_info["counter"])) @@ -349,14 +373,15 @@ def count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, chrom1_bin_range = ma.getChrBinRange(toString(chrom1)) chrom2_bin_range = ma.getChrBinRange(toString(chrom2)) - if chrom1 == chrom2: # chrom1 == chrom2 can happen in intra or all - if (chrom1 not in agg_info["agg_total"]) and (mode == "intra-chr") and (perChr == True): - agg_info["agg_total"][chrom1] = 0 - agg_info["agg_matrix"][chrom1] = [] - agg_info["agg_diagonals"][chrom1] = [] - agg_info["agg_contact_position"][chrom1] = [] - agg_info["agg_center_values"][chrom1] = [] + if [chrom1, chrom2] not in seen_chrs: # we only want to count one side of the diagonal + agg_info["agg_total"][chrom1][chrom2] = 0 + agg_info["agg_matrix"][chrom1][chrom2] = [] + agg_info["agg_diagonals"][chrom1][chrom2] = [] + agg_info["agg_contact_position"][chrom1][chrom2] = [] + agg_info["agg_center_values"][chrom1][chrom2] = [] + seen_chrs.append([chrom1, chrom2]) + if mode == "intra-chr": min_dist, max_dist = range.split(":") min_dist_in_bins = int(min_dist) // bin_size max_dist_in_bins = int(max_dist) // bin_size @@ -390,28 +415,11 @@ def count_contacts(interval, ma, M_half, mode, agg_info, largeRegionsOperation, # total submatrix sum. if transform == 'total-counts' and mat_to_append.sum() > 0: mat_to_append = mat_to_append / mat_to_append.sum() - - if (mode == "intra-chr") and (perChr == True): # chrom1 == chrom2 - agg_info["agg_total"][chrom1] += 1 - agg_info["agg_matrix"][chrom1].append(mat_to_append) - agg_info["agg_diagonals"][chrom1].append(mat_to_append.diagonal()) - agg_info["agg_center_values"][chrom1].append(ma.matrix[bin_id1, bin_id2]) - agg_info["agg_contact_position"][chrom1].append((start1, end1, start2, end2)) - - else: - - if 'genome' not in agg_info["agg_total"]: - agg_info["agg_total"]["genome"] = 0 - agg_info["agg_matrix"]["genome"] = [] - agg_info["agg_diagonals"]["genome"] = [] - agg_info["agg_contact_position"]["genome"] = [] - agg_info["agg_center_values"]["genome"] = [] - - agg_info["agg_total"]["genome"] += 1 - agg_info["agg_matrix"]["genome"].append(mat_to_append) - agg_info["agg_diagonals"]["genome"].append(mat_to_append.diagonal()) - agg_info["agg_center_values"]["genome"].append(ma.matrix[bin_id1, bin_id2]) - agg_info["agg_contact_position"]["genome"].append((start1, end1, start2, end2)) + agg_info["agg_total"][chrom1][chrom2] += 1 + agg_info["agg_matrix"][chrom1][chrom2].append(mat_to_append) + agg_info["agg_diagonals"][chrom1][chrom2].append(mat_to_append.diagonal()) + agg_info["agg_center_values"][chrom1][chrom2].append(ma.matrix[bin_id1, bin_id2]) + agg_info["agg_contact_position"][chrom1][chrom2].append((start1, end1, start2, end2)) def get_outlier_indices(data, max_deviation=200): @@ -439,22 +447,98 @@ def get_outlier_indices(data, max_deviation=200): if mad == 0: return None deviation = abs(data - median) / mad + # any is used to get, per row, if any of the values is True. # as a row will be considered as an outlier if any of the elements # is an outlier + outliers = (deviation > max_deviation).any(axis=1) return outliers -def cluster_matrices(submatrices_dict, k, method='kmeans', how='full'): - """ - clusters the submatrices per chromosome +def compute_clusters(updated_info, k, method="kmeans", how='full', max_deviation=2, keep_outlier=False): + submat_vectors = [] + shape = updated_info["submatrices"][0].shape + center_bin = (shape[0] + 1) // 2 + for submatrix in updated_info["submatrices"]: + if how == 'diagonal': + # take from each matrix the diagonal + submat_vectors.append(submatrix.diagonal()) + elif how == 'center': + # take the mean of a smaller submatrix of 3 x 3 centered on the submatrix + submat_vectors.append(submatrix[center_bin - 2:center_bin + 1, + center_bin - 2:center_bin + 1].reshape((1, 9)).mean()) + else: + # Transform list of submatrices in an array of shape: + # shape = (num_submatrices, submatrix.shape[0] * submatrix.shape[1] + # In other words, each submatrix is converted into a row of the matrix + submat_vectors.append(submatrix.reshape((1, shape[0] * shape[1]))) + matrix = np.vstack(submat_vectors) + if how == 'diagonal': + assert matrix.shape == (len(updated_info["submatrices"]), shape[0]) + elif how == 'center': + assert matrix.shape == (len(updated_info["submatrices"]), 1) + else: + assert matrix.shape == (len(updated_info["submatrices"]), shape[0] * shape[1]) + + # remove outliers + updated_coords = updated_info["coords"] + updated_centers = updated_info["centers"] + updated_submatrices = updated_info["submatrices"] + updated_diags = updated_info["diagonal"] + if not keep_outlier: + out_ind = get_outlier_indices(matrix, max_deviation=max_deviation) + if out_ind is not None and len(np.flatnonzero(out_ind)) > 0: + if len(np.flatnonzero(out_ind)) == matrix.shape[0]: + exit("ERROR: all submatrices have been detected as outliers. You can consider changing the threshold") + log.info("Outliers detected. Number of outliers: {}".format(len(np.flatnonzero(out_ind)))) + # keep in matrix all indices that are not outliers + matrix = matrix[np.logical_not(out_ind), :] + + updated_coords = list(compress(updated_info["coords"], np.logical_not(out_ind))) + updated_centers = list(compress(updated_info["centers"], np.logical_not(out_ind))) + updated_submatrices = list(compress(updated_info["submatrices"], np.logical_not(out_ind))) + updated_diags = list(compress(updated_info["diagonal"], np.logical_not(out_ind))) + + if np.any(np.isnan(matrix)): + # replace nans for 0 otherwise kmeans produces a weird behaviour + log.warning("For clustering nan values have to be replaced by zeros.") + matrix[np.isnan(matrix)] = 0 + + if (k == 1) and (method == 'no_clust'): # no clustering + cluster_labels = np.asarray([0] * matrix.shape[0]) + if method == 'kmeans': + clustering = skclust.KMeans(n_clusters=k, random_state=0).fit(matrix) + cluster_labels = clustering.labels_ + if method == 'hierarchical': + clustering = skclust.AgglomerativeClustering(n_clusters=k, distance_threshold=None).fit(matrix) + cluster_labels = clustering.labels_ + if method == 'spectral': + clustering = skclust.SpectralClustering(n_clusters=k, assign_labels="discretize", random_state=0).fit(matrix) + cluster_labels = clustering.labels_ + + # sort clusters + clustered_dict = [] + for cluster in range(k): + cluster_ids = np.flatnonzero(cluster_labels == cluster) + clustered_dict.append(cluster_ids) + + # matrix = np.array(matrix).reshape((matrix.shape[0], int(np.sqrt(matrix.shape[1])), int(np.sqrt(matrix.shape[1])))) + updated_info = {'coords': updated_coords, 'centers': updated_centers, + 'submatrices': updated_submatrices, 'clustered_dict': clustered_dict, + 'diagonal': updated_diags} + return updated_info + + +def cluster_matrices(agg_info, k, method='kmeans', how='full', perChr=False, max_deviation=2, keep_outlier=False): + """ + clusters the submatrices . Parameters ---------- - submatrices_dict key: chrom name, values, a list of submatrices + agg_info["agg_matrix"] key: chrom name, values, a list of submatrices k number of clusters method either kmeans, hierarchical or spectral how how to cluster. Options are 'full', 'center' and 'diagonal'. More info in the argparse options @@ -465,137 +549,101 @@ def cluster_matrices(submatrices_dict, k, method='kmeans', how='full'): indices dict key: chrom_name, value: list of list, with one list per cluster with the ids of the submatrices that belong to that list """ - clustered_dict = {} - for chrom in submatrices_dict: - log.info("Length of entry: {}".format(len(submatrices_dict[chrom]))) - if len(submatrices_dict[chrom]) < k: - log.info("number of the submatrices on chromosome {} is less than {}. Clustering is skipped.".format(chrom, k)) - k = 1 - submat_vectors = [] - shape = submatrices_dict[chrom][0].shape - center_bin = (shape[0] + 1) // 2 - for submatrix in submatrices_dict[chrom]: - if how == 'diagonal': - # take from each matrix the diagonal - submat_vectors.append(submatrix.diagonal()) - elif how == 'center': - # take the mean of a smaller submatrix of 3 x 3 centered on the submatrix - submat_vectors.append( - submatrix[center_bin - 2:center_bin + 1, center_bin - 2:center_bin + 1].reshape((1, 9)).mean()) + updated_info = dict() + if not perChr: + updated_info["genome"] = {"coords": [], "centers": [], "submatrices": [], + "clustered_dict": [], "diagonal": []} + for chrom1 in agg_info["agg_matrix"].keys(): + for chrom2, matrices in agg_info["agg_matrix"][chrom1].items(): + if perChr: + full_coords = [(chrom1, i[0], i[1], chrom2, i[2], i[3]) for i in agg_info["agg_contact_position"][chrom1][chrom2]] + updated_info[chrom1] = {"coords": full_coords, "centers": agg_info["agg_center_values"][chrom1][chrom2], + "submatrices": agg_info["agg_matrix"][chrom1][chrom2], + "clustered_dict": [], "diagonal": agg_info["agg_diagonals"][chrom1][chrom2]} + assert(chrom1 == chrom2) + log.info("Length of entry on chr {}: {}".format(chrom1, len(agg_info["agg_matrix"][chrom1][chrom2]))) + if len(agg_info["agg_matrix"][chrom1][chrom2]) < k: + log.info("number of the submatrices on chromosome {} is less than {}. Clustering is skipped.".format(chrom1, k)) + k = 1 + updated_info[chrom1] = compute_clusters(updated_info[chrom1], k, method, how, max_deviation, keep_outlier) else: - # Transform list of submatrices in an array of shape: - # shape = (num_submatrices, submatrix.shape[0] * submatrix.shape[1] - # In other words, each submatrix is converted into a row of the matrix - submat_vectors.append(submatrix.reshape((1, shape[0] * shape[1]))) - - matrix = np.vstack(submat_vectors) - if how == 'diagonal': - assert matrix.shape == (len(submatrices_dict[chrom]), shape[0]) - elif how == 'center': - assert matrix.shape == (len(submatrices_dict[chrom]), 1) - else: - assert matrix.shape == (len(submatrices_dict[chrom]), shape[0] * shape[1]) - - # remove outliers - out_ind = get_outlier_indices(matrix, max_deviation=2) - if out_ind is not None and len(np.flatnonzero(out_ind)) > 0: - log.info("Outliers detected in chrom: {}. Number of outliers: {}". - format(chrom, len(np.flatnonzero(out_ind)))) - - # keep in matrix all indices that are not outliers - matrix = matrix[np.logical_not(out_ind), :] - - if np.any(np.isnan(matrix)): - # replace nans for 0 otherwise kmeans produces a weird behaviour - log.warning("For clustering nan values have to be replaced by zeros.") - matrix[np.isnan(matrix)] = 0 - - if method == 'kmeans': - clustering = skclust.KMeans(n_clusters=k, random_state=0).fit(matrix) - cluster_labels = clustering.labels_ - if method == 'hierarchical': - clustering = skclust.AgglomerativeClustering(n_clusters=k).fit(matrix) - cluster_labels = clustering.labels_ - if method == 'spectral': - clustering = skclust.SpectralClustering(n_clusters=k, assign_labels="discretize", random_state=0).fit(matrix) - cluster_labels = clustering.labels_ - - # sort clusters - clustered_dict[chrom] = [] - for cluster in range(k): - cluster_ids = np.flatnonzero(cluster_labels == cluster) - clustered_dict[chrom].append(cluster_ids) - - return clustered_dict + updated_info['genome']["submatrices"] += agg_info["agg_matrix"][chrom1][chrom2] + # Add all corrdinates in a new container + for idx, matrix in enumerate(matrices): + start1, end1, start2, end2 = agg_info["agg_contact_position"][chrom1][chrom2][idx] + updated_info['genome']["coords"].append((chrom1, start1, end1, chrom2, start2, end2)) + updated_info['genome']["centers"].append(agg_info["agg_center_values"][chrom1][chrom2][idx]) + updated_info['genome']["diagonal"].append(agg_info["agg_diagonals"][chrom1][chrom2][idx]) + + if not perChr: + this_sum = [] + for i in range(len(updated_info['genome']["submatrices"])): + this_sum.append(updated_info['genome']["submatrices"][i].sum()) + updated_info["genome"] = compute_clusters(updated_info["genome"], k, method, how, max_deviation, keep_outlier) + # TODO Do I need to update submatrices and positions here too? + + return updated_info + + +def compute_avg(submatrices, operationType): + if operationType == 'median': + _median = np.median(submatrices, axis=0) + if _median.sum() == 0 or np.isnan(_median.sum()): + # test if the mean matrix is not zero + if np.mean(submatrices, axis=0).sum() != 0: + log.info("The median of the matrices is zero. Consider using " + "the mean instead.") + else: + log.info("Apparently no matrices could be computed. All of them " + "are zeros or nans.") + return _median + elif operationType == 'mean': + return np.mean(submatrices, axis=0) + else: + return np.sum(submatrices, axis=0) + return -def plot_aggregated_contacts(chrom_matrix, chrom_contact_position, cluster_ids, num_clusters, M_half, args): +def plot_aggregated_contacts(clustered_info, num_clusters, M_half, args): - num_chromosomes = len(chrom_matrix) + num_figs = len(clustered_info.keys()) - fig = plt.figure(figsize=(5.5 * num_chromosomes, 5.5 * num_clusters + 0.5)) - gs = gridspec.GridSpec(num_clusters + 1, num_chromosomes, - width_ratios=[10] * len(chrom_matrix), + fig = plt.figure(figsize=(5.5 * num_figs, 5.5 * num_clusters + 0.5)) + gs = gridspec.GridSpec(num_clusters + 1, num_figs, + width_ratios=[10] * num_figs, height_ratios=[10] * num_clusters + [0.6]) gs.update(wspace=0.01, hspace=0.2) - chrom_avg = {} - chrom_cluster_len = {} - for idx, chrom in enumerate(chrom_matrix): - chrom_avg[chrom] = [] - chrom_cluster_len[chrom] = [] - for cluster_number, cluster_indices in enumerate(cluster_ids[chrom]): - # compute median values - if num_clusters == 1: - # this means no clustering - submatrices = np.array(chrom_matrix[chrom]) - else: - submatrices = np.array([chrom_matrix[chrom][x] for x in cluster_indices]) - - chrom_cluster_len[chrom].append(len(cluster_ids)) - - if args.operationType == 'median': - _median = np.median(submatrices, axis=0) - if _median.sum() == 0 or np.isnan(_median.sum()): - # test if the mean matrix is not zero - if np.mean(submatrices, axis=0).sum() != 0: - log.info("The median of the matrices is zero. Consider using " - "the mean instead.") - else: - log.info("Apparently no matrices could be computed. All are " - "zeros or nans.") - chrom_avg[chrom].append(_median) - elif args.operationType == 'mean': - chrom_avg[chrom].append(np.mean(submatrices, axis=0)) - else: - chrom_avg[chrom].append(np.sum(submatrices, axis=0)) - - log.info("Mean aggregate matrix values: {}".format(chrom_avg[chrom][cluster_number].mean())) - vmin, vmax = (args.vMin, args.vMax) cmap = cm.get_cmap(args.colorMap) log.debug("vmax: {}, vmin: {}".format(vmax, vmin)) - for idx, chrom in enumerate(chrom_matrix): - for cluster_number, cluster_indices in enumerate(cluster_ids[chrom]): - log.info("total pairs considered for {}, cluster_{}: {}".format(chrom, cluster_number + 1, - len(cluster_indices))) - try: - chrom_avg[chrom][cluster_number].shape[0] - except IndexError: - continue - if chrom_avg[chrom][cluster_number].shape[0] == 0: - log.debug("matrix for chrom {} is empty".format(chrom)) + chrom_avg = OrderedDict() + for idx, (chrom1, v1) in enumerate(clustered_info.items()): + assert(v1 != {}) + if chrom1 not in chrom_avg.keys(): + chrom_avg[chrom1] = [] + + for cluster_number, cluster_indices in enumerate(clustered_info[chrom1]["clustered_dict"]): + # compute median values + submatrices = np.array([clustered_info[chrom1]["submatrices"][x] for x in cluster_indices]) + + chrom_avg[chrom1].append(compute_avg(submatrices, args.operationType)) + log.info("Mean aggregate matrix values: {}".format(chrom_avg[chrom1][cluster_number].mean())) + log.info("total pairs considered on cluster_{}: " + "{}".format(cluster_number + 1, len(cluster_indices))) + + if chrom_avg[chrom1][cluster_number].shape[0] == 0: + log.debug("matrix for contacts on cluster_{} is empty".format(cluster_number + 1)) continue - if num_clusters == 1: - title = chrom - else: - title = "{} cluster_{}".format(chrom, cluster_number + 1) + title = "cluster_{}".format(cluster_number + 1) if args.plotType == '2d': ax = plt.subplot(gs[cluster_number, idx]) - - ax.set_title(title) - img = ax.imshow(chrom_avg[chrom][cluster_number], aspect='equal', + if num_clusters != 1: + ax.set_title(title) + if (cluster_number + 1) == num_clusters: + ax.set_xlabel("{}".format(chrom1)) + img = ax.imshow(chrom_avg[chrom1][cluster_number], aspect='equal', interpolation='nearest', vmax=vmax, vmin=vmin, cmap=cmap, extent=[-M_half, M_half + 1, -M_half, M_half + 1]) @@ -609,8 +657,7 @@ def plot_aggregated_contacts(chrom_matrix, chrom_contact_position, cluster_ids, ax.margins(0) X, Y = np.meshgrid(range(-M_half, M_half + 1), range(-M_half, M_half + 1)) - Z = chrom_avg[chrom][cluster_number].copy() - + Z = chrom_avg[chrom1][cluster_number].copy() img = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, linewidth=0, cmap=cmap, vmax=vmax, vmin=vmin, edgecolor='none') @@ -621,11 +668,25 @@ def plot_aggregated_contacts(chrom_matrix, chrom_contact_position, cluster_ids, if args.outFilePrefixMatrix: # save aggregate matrix values if num_clusters == 1: - output_matrix_name = "{file}_{chrom}.tab".format(file=args.outFilePrefixMatrix, chrom=chrom) + output_matrix_name = "{file}_{chrom}.tab".format(file=args.outFilePrefixMatrix, chrom=chrom1) else: output_matrix_name = "{file}_{chrom}_cluster_{id}.tab".format(file=args.outFilePrefixMatrix, - chrom=chrom, id=cluster_number + 1) - np.savetxt(output_matrix_name, chrom_avg[chrom][cluster_number], '%0.5f', delimiter='\t') + chrom=chrom1, id=cluster_number + 1) + np.savetxt(output_matrix_name, chrom_avg[chrom1][cluster_number], '%0.5f', delimiter='\t') + + if args.outFileContactPairs: + center_values_to_order = np.array(clustered_info[chrom1]["centers"])[cluster_indices] + center_values_order = np.argsort(center_values_to_order)[::-1] + if num_clusters == 1: + output_name = "{file}_{chrom}.tab".format(file=args.outFileContactPairs, chrom=chrom1) + else: + output_name = "{file}_{chrom}_cluster_{id}.tab".format(file=args.outFileContactPairs, + chrom=chrom1, id=cluster_number + 1) + with open(output_name, 'w') as fh: + for cl_idx in center_values_order: + value = center_values_to_order[cl_idx] + chrom, start, end, chrom2, start2, end2 = clustered_info[chrom1]["coords"][cl_idx] + fh.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(chrom, start, end, chrom2, start2, end2, value)) cbar_x = plt.subplot(gs[-1, idx]) fig.colorbar(img, cax=cbar_x, orientation='horizontal') @@ -637,10 +698,91 @@ def plot_aggregated_contacts(chrom_matrix, chrom_contact_position, cluster_ids, plt.close() - -def plot_diagnostic_heatmaps(chrom_diagonals, cluster_ids, M_half, args): - - num_chromosomes = len(chrom_diagonals) +# def plot_aggregated_contacts(clustered_info, num_clusters, M_half, args): +# +# fig = plt.figure(figsize=(5.5 , 5.5 * num_clusters + 0.5)) +# gs = gridspec.GridSpec(num_clusters+1, 1, +# width_ratios=[10], +# height_ratios=[10] * num_clusters + [0.6]) +# +# gs.update(wspace=0.01, hspace=0.2) +# vmin, vmax = (args.vMin, args.vMax) +# cmap = cm.get_cmap(args.colorMap) +# log.debug("vmax: {}, vmin: {}".format(vmax, vmin)) +# chrom_avg = [] +# for cluster_number, cluster_indices in enumerate(clustered_info["clustered_dict"]): +# # compute median values +# submatrices = np.array([clustered_info["submatrices"][x] for x in cluster_indices]) +# chrom_avg.append(compute_avg(submatrices, args.operationType)) +# log.info("Mean aggregate matrix values: {}".format(chrom_avg[cluster_number].mean())) +# log.info("total pairs considered on cluster_{}: " +# "{}".format(cluster_number + 1, len(cluster_indices))) +# +# if chrom_avg[cluster_number].shape[0] == 0: +# log.debug("matrix for contacts on cluster_{} is empty".format(cluster_number + 1)) +# continue +# title = "cluster_{}".format(cluster_number + 1) +# if args.plotType == '2d': +# ax = plt.subplot(gs[cluster_number, 0]) +# ax.set_title(title) +# img = ax.imshow(chrom_avg[cluster_number], aspect='equal', +# interpolation='nearest', vmax=vmax, vmin=vmin, +# cmap=cmap, +# extent=[-M_half, M_half + 1, -M_half, M_half + 1]) +# +# else: +# # Axes3D is required for projection='3d' to work +# # but since is imported but not used, flake8 will complain +# # thus I add this dummy variable to avoid the error +# Axes3D(fig) +# ax = plt.subplot(gs[cluster_number, 1], projection='3d') +# # ax.set_aspect('equal') +# ax.margins(0) +# X, Y = np.meshgrid(range(-M_half, M_half + 1), +# range(-M_half, M_half + 1)) +# Z = chrom_avg[chrom][cluster_number].copy() +# img = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, linewidth=0, cmap=cmap, +# vmax=vmax, vmin=vmin, edgecolor='none') +# +# ax.set_zticklabels([]) +# if vmax is not None and vmax is not None: +# ax.set_zlim(vmin, vmax) +# +# if args.outFilePrefixMatrix: +# # save aggregate matrix values +# if num_clusters == 1: +# output_matrix_name = "{file}_genome.tab".format(file=args.outFilePrefixMatrix) +# else: +# output_matrix_name = "{file}_genome_cluster_{id}.tab".format(file=args.outFilePrefixMatrix, +# id=cluster_number + 1) +# np.savetxt(output_matrix_name, chrom_avg[cluster_number], '%0.5f', delimiter='\t') +# +# if args.outFileContactPairs: +# center_values_to_order = np.array(clustered_info["centers"])[cluster_indices] +# center_values_order = np.argsort(center_values_to_order)[::-1] +# +# output_name = "{file}_cluster_{id}.tab".format(file=args.outFileContactPairs, +# id=cluster_number + 1) +# with open(output_name, 'w') as fh: +# for cl_idx in center_values_order: +# value = center_values_to_order[cl_idx] +# chrom1, start1, end1, chrom2, start2, end2 = clustered_info["coords"][cl_idx] +# fh.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(chrom1, start1, end1, chrom2, start2, end2, value)) +# +# +# cbar_x = plt.subplot(gs[-1, 0]) +# fig.colorbar(img, cax=cbar_x, orientation='horizontal') +# +# if args.disable_bbox_tight: +# plt.savefig(args.outFileName.name, dpi=args.dpi) +# else: +# plt.savefig(args.outFileName.name, dpi=args.dpi, bbox_inches='tight') +# +# plt.close() + + +def plot_diagnostic_heatmaps(clustered_info, M_half, args): + num_chromosomes = len(clustered_info.keys()) vmax_heat = args.vMax if vmax_heat is not None: vmax_heat *= 5 @@ -651,22 +793,22 @@ def plot_diagnostic_heatmaps(chrom_diagonals, cluster_ids, M_half, args): else: vmin_heat = 0 - num_plots = len(chrom_diagonals) + num_plots = len(clustered_info.keys()) fig = plt.figure(figsize=(num_plots * 4, 20)) gs0 = gridspec.GridSpec(2, num_plots + 1, width_ratios=[10] * num_plots + [0.5], height_ratios=[1, 5], wspace=0.1, hspace=0.1) gs_list = [] - for idx, (chrom_name, values) in enumerate(chrom_diagonals.items()): + for idx, (chrom_name, values) in enumerate(clustered_info.items()): # One more for loop should be added as it is or this container needs to be updated too. I would go for the latter try: - heatmap = np.asarray(np.vstack(values)) + heatmap = np.asarray(np.vstack(clustered_info[chrom_name]['diagonal'])) except ValueError: log.error("Error computing diagnostic heatmap for chrom: {}".format(chrom_name)) continue # get size of each cluster for the given chrom - clust_len = [(len(v)) for v in cluster_ids[chrom_name]] + clust_len = [(len(v)) for v in clustered_info[chrom_name]["clustered_dict"]] # prepare layout gs_list.append(gridspec.GridSpecFromSubplotSpec(len(clust_len), 1, @@ -676,7 +818,7 @@ def plot_diagnostic_heatmaps(chrom_diagonals, cluster_ids, M_half, args): summary_plot_ax = plt.subplot(gs0[0, idx]) summary_plot_ax.set_title(chrom_name) - for cluster_number, cluster_indices in enumerate(cluster_ids[chrom_name]): + for cluster_number, cluster_indices in enumerate(clustered_info[chrom_name]["clustered_dict"]): # sort by the value at the center of the rows heatmap_to_plot = heatmap[cluster_indices, :] @@ -716,6 +858,7 @@ def plot_diagnostic_heatmaps(chrom_diagonals, cluster_ids, M_half, args): def main(args=None): args = parse_arguments().parse_args(args) + matplotlib.rcParams['pdf.fonttype'] = 42 ma = hm.hiCMatrix(args.matrix) ma.maskBins(ma.nan_bins) @@ -729,13 +872,17 @@ def main(args=None): ma.keepOnlyTheseChr(args.chromosomes) default_range = '1000000:20000000' + if args.range is not None: + if (args.mode == "inter-chr") or (args.mode == "all"): + log.info("--range is ineffective for inter-chr and all mode.") if args.range is None: if args.mode == "intra-chr": log.warning("You have not set any range. This is by default set to {} for intra-chr.".format(default_range)) args.range = default_range min_dist, max_dist = args.range.split(":") - log.info("checking range {}-{}".format(min_dist, max_dist)) - assert int(min_dist) < int(max_dist), "Error lower range is larger than upper range!" + if args.mode == "intra-chr": + log.info("checking range {}-{}".format(min_dist, max_dist)) + assert int(min_dist) < int(max_dist), "Error lower range is larger than upper range!" if args.transform == "z-score": # use zscore matrix log.info("Computing z-score matrix. This may take a while.\n") if args.mode == 'intra-chr': @@ -772,18 +919,22 @@ def main(args=None): chrom_coord[chrom] = (first[1], last[2]) agg_info = dict() - agg_info["chrom_coord"] = chrom_coord - agg_info["seen"] = [] - agg_info["agg_matrix"] = OrderedDict() - agg_info["agg_total"] = {} - agg_info["agg_diagonals"] = OrderedDict() - agg_info["agg_contact_position"] = {} - agg_info["agg_center_values"] = {} + agg_info["chrom_coord"] = chrom_coord # coordinates of each chrom + agg_info["seen"] = [] # seen bins + agg_info["agg_matrix"] = {chrom: {} for chrom in chrom_list} # important + agg_info["agg_total"] = {chrom: {} for chrom in chrom_list} + agg_info["agg_diagonals"] = {chrom: {} for chrom in chrom_list} + agg_info["agg_contact_position"] = {chrom: {} for chrom in chrom_list} # important + agg_info["agg_center_values"] = {chrom: {} for chrom in chrom_list} # important agg_info["counter"] = 0 agg_info["used_counter"] = 0 agg_info["empty_mat"] = 0 if (args.mode == 'inter-chr') and (len(agg_info["chrom_coord"]) == 1): exit("Error: 'inter-chr' mode can not be applied on matrices of only one chromosme.") + if (args.mode == 'inter-chr') and (args.perChr): + exit("Error: 'inter-chr' mode can not be used along with --perChr.") + if (args.mode == 'all') and (args.perChr): + exit("Error: 'all' mode can not be used along with --perChr.") if args.row_wise: # read bed files bed_intervals = args.BED.readlines() @@ -792,8 +943,13 @@ def main(args=None): else: log.error("Error computing row-wise contacts requires two bed files!") exit("Error computing row-wise contacts requires two bed files!") + if len(bed_intervals) != len(bed_intervals2): + log.error("row_wise only works if both bed files have the same length.") + exit("Error row_wise only works if both bed files have the same length.") # agg_matrix could be either per chromosome or genome wide - aggregate_contacts_per_row(bed_intervals, bed_intervals2, agg_info, ma, chrom_list, M_half, args.largeRegionsOperation, args.range, args.transform, mode=args.mode, perChr=args.perChr) + aggregate_contacts_per_row(bed_intervals, bed_intervals2, agg_info, ma, chrom_list, + M_half, args.largeRegionsOperation, args.range, + args.transform, mode=args.mode, perChr=args.perChr) else: # not row-wise # read and sort bed files. bed_intervals = read_bed_per_chrom(args.BED, chrom_list) @@ -802,44 +958,59 @@ def main(args=None): else: bed_intervals2 = bed_intervals # agg_matrix could be either per chromosome or genome wide - aggregate_contacts(bed_intervals, bed_intervals2, agg_info, ma, M_half, args.largeRegionsOperation, args.range, args.transform, mode=args.mode, perChr=args.perChr) + aggregate_contacts(bed_intervals, bed_intervals2, agg_info, ma, M_half, + args.largeRegionsOperation, args.range, args.transform, + mode=args.mode) + if len(agg_info["agg_matrix"]) == 0: + exit("No susbmatrix found to be aggregated.") if args.kmeans is not None: - cluster_ids = cluster_matrices(agg_info["agg_matrix"], args.kmeans, method='kmeans', how=args.howToCluster) + assert(args.kmeans > 1) + if args.perChr == True: + clustered_info = cluster_matrices(agg_info, + k=args.kmeans, method='kmeans', how=args.howToCluster, + perChr=args.perChr, max_deviation=args.max_deviation, + keep_outlier=args.keep_outlier) + else: + clustered_info = cluster_matrices(agg_info, + k=args.kmeans, method='kmeans', how=args.howToCluster, + perChr=False, max_deviation=args.max_deviation, + keep_outlier=args.keep_outlier) num_clusters = args.kmeans elif args.hclust is not None: + assert(args.hclust > 1) log.info("Performing hierarchical clustering." "Please note that it might be very slow for large datasets.\n") - cluster_ids = cluster_matrices(agg_info["agg_matrix"], args.hclust, method='hierarchical', - how=args.howToCluster) + if args.perChr == True: + clustered_info = cluster_matrices(agg_info, + k=args.hclust, method='hierarchical', + how=args.howToCluster, + perChr=args.perChr, max_deviation=args.max_deviation, + keep_outlier=args.keep_outlier) + else: + clustered_info = cluster_matrices(agg_info, + k=args.hclust, method='hierarchical', + how=args.howToCluster, + perChr=False, max_deviation=args.max_deviation, + keep_outlier=args.keep_outlier) num_clusters = args.hclust else: # make a 'fake' clustering to generalize the plotting of the submatrices - cluster_ids = {} - num_clusters = 1 - for k in agg_info["agg_matrix"].keys(): - cluster_ids[k] = [range(len(agg_info["agg_matrix"][k]))] - if len(agg_info["agg_matrix"]) == 0: - exit("No susbmatrix found to be aggregated.") - plot_aggregated_contacts(agg_info["agg_matrix"], agg_info["agg_contact_position"], cluster_ids, num_clusters, M_half, args) + k = 1 + if args.perChr == True: + clustered_info = cluster_matrices(agg_info, k=k, method='no_clust', + how='full', perChr=args.perChr, max_deviation=args.max_deviation, + keep_outlier=args.keep_outlier) - if args.outFileContactPairs: - for idx, chrom in enumerate(agg_info["agg_matrix"]): - if chrom not in bed_intervals or chrom not in bed_intervals2: - continue - for cluster_number, cluster_indices in enumerate(cluster_ids[chrom]): - center_values_to_order = np.array(agg_info["agg_center_values"][chrom])[cluster_indices] - center_values_order = np.argsort(center_values_to_order)[::-1] + else: + clustered_info = cluster_matrices(agg_info, k=k, method='no_clust', + how='full', perChr=False, max_deviation=args.max_deviation, + keep_outlier=args.keep_outlier) + num_clusters = k - output_name = "{file}_{chrom}_cluster_{id}.tab".format(file=args.outFileContactPairs, - chrom=chrom, id=cluster_number + 1) - with open(output_name, 'w') as fh: - for cl_idx in center_values_order: - value = center_values_to_order[cl_idx] - start, end, start2, end2 = agg_info["agg_contact_position"][chrom][cl_idx] - fh.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(chrom, start, end, chrom, start2, end2, value)) + plot_aggregated_contacts(clustered_info, num_clusters, M_half, args) # plot the diagonals # the diagonals plot is useful to see individual cases and if they had a contact in the center if args.diagnosticHeatmapFile: - plot_diagnostic_heatmaps(agg_info["agg_diagonals"], cluster_ids, M_half, args) + plot_diagnostic_heatmaps(clustered_info, M_half, args) diff --git a/hicexplorer/hicBuildMatrix.py b/hicexplorer/hicBuildMatrix.py index 6cf74ec6..409ce14c 100644 --- a/hicexplorer/hicBuildMatrix.py +++ b/hicexplorer/hicBuildMatrix.py @@ -21,7 +21,6 @@ from intervaltree import IntervalTree, Interval from Bio.Seq import Seq -from Bio.Alphabet import generic_dna # own tools from hicmatrix import HiCMatrix as hm @@ -215,15 +214,14 @@ def parse_arguments(args=None): required=False, type=genomicRegion ) - # currently not implemented - parserOpt.add_argument('--removeSelfLigation', + parserOpt.add_argument('--keepSelfLigation', help='If set, inward facing reads less than 1000 bp apart and having a restriction' 'site in between are removed. Although this reads do not contribute to ' 'any distant contact, they are useful to account for bias in the data' ' (for the moment is always True).', # help=argparse.SUPPRESS, - default=True - # action='store_true' + # default=True + action='store_true' ) parserOpt.add_argument('--keepSelfCircles', @@ -368,7 +366,7 @@ def get_bins(bin_size, chrom_size, region=None): return bin_intvals -def bed2interval_list(bed_file_handler): +def bed2interval_list(bed_file_handler, pChromosomeSize, pRegion): r""" reads a BED file and returns a list of tuples containing @@ -383,10 +381,15 @@ def bed2interval_list(bed_file_handler): >>> foo = file_tmp.write('chr1\t10\t20\tH1\t0\n') >>> foo = file_tmp.write("chr1\t60\t70\tH2\t0\n") >>> file_tmp.close() - >>> bed2interval_list(open(_file.name, 'r')) + >>> bed2interval_list(open(_file.name, 'r'), None, None) [('chr1', 10, 20), ('chr1', 60, 70)] >>> os.remove(_file.name) """ + + if pRegion is not None: + chrom_size, start_region, end_region, _ = \ + getUserRegion(pChromosomeSize, pRegion) + count = 0 interval_list = [] for line in bed_file_handler: @@ -394,10 +397,16 @@ def bed2interval_list(bed_file_handler): fields = line.strip().split() try: chrom, start, end = fields[0], int(fields[1]), int(fields[2]) + except IndexError: log.error("error reading BED file at line {}".format(count)) - interval_list.append((chrom, start, end)) + if pRegion is not None: + if chrom == chrom_size[0] and start_region <= start and end_region <= end: + interval_list.append((chrom, start, end)) + else: + interval_list.append((chrom, start, end)) + return interval_list @@ -774,7 +783,7 @@ def readBamFiles(pFileOneIterator, pFileTwoIterator, pNumberOfItemsPerBuffer, pS def process_data(pMateBuffer1, pMateBuffer2, pMinMappingQuality, - pKeepSelfCircles, pRestrictionSequence, pRemoveSelfLigation, pMatrixSize, + pKeepSelfCircles, pRestrictionSequence, pKeepSelfLigation, pMatrixSize, pRfPositions, pRefId2name, pDanglingSequences, pBinsize, pResultIndex, pQueueOut, pTemplate, pOutputBamSet, pCounter, @@ -793,7 +802,7 @@ def process_data(pMateBuffer1, pMateBuffer2, pMinMappingQuality, pMinMappingQuality : integer, minimum mapping quality of a read pKeepSelfCircles : boolean, if self circles should be kept pRestrictionSequence : List of String, the restriction sequence - pRemoveSelfLigation : If self ligations should be removed + pKeepSelfLigation : If self ligations should be removed pMatrixSize : integer, the size of the interaction matrix pRfPositions : intervalTree, only used if a restriction cut file and not a bin size was defined. pRefId2name : Tuple, Maps a reference id to a name @@ -1022,7 +1031,7 @@ def process_data(pMateBuffer1, pMateBuffer2, pMinMappingQuality, self_ligation += 1 - if pRemoveSelfLigation: + if not pKeepSelfLigation: # skip self ligations continue @@ -1153,7 +1162,7 @@ def main(args=None): rf_interval = [] for restrictionCutFile in args.restrictionCutFile: - rf_interval.extend(bed2interval_list(restrictionCutFile)) + rf_interval.extend(bed2interval_list(restrictionCutFile, chrom_sizes, args.region)) rf_positions = intervalListToIntervalTree(rf_interval) log.debug('rf_positions {}'.format(rf_positions.keys())) @@ -1193,7 +1202,7 @@ def main(args=None): dangling_sequences[args.restrictionSequence[i]] = {} dangling_sequences[args.restrictionSequence[i]]['pat_forw'] = args.danglingSequence[i] dangling_sequences[args.restrictionSequence[i]]['pat_rev'] = str( - Seq(args.danglingSequence[i], generic_dna).reverse_complement()) + Seq(args.danglingSequence[i]).reverse_complement()) log.info("dangling sequences to check " "are {}\n".format(dangling_sequences)) @@ -1310,7 +1319,7 @@ def main(args=None): pMinMappingQuality=args.minMappingQuality, pKeepSelfCircles=args.keepSelfCircles, pRestrictionSequence=args.restrictionSequence, - pRemoveSelfLigation=args.removeSelfLigation, + pKeepSelfLigation=args.keepSelfLigation, pMatrixSize=matrix_size, pRfPositions=rf_positions, pRefId2name=ref_id2name, @@ -1475,7 +1484,7 @@ def main(args=None): hic_matrix.maskBins(get_poor_bins(bin_max)) hic_matrix.save(args.outFileName.name) """ - if args.removeSelfLigation: + if not args.keepSelfLigation: msg = " (removed)" else: msg = " (not removed)" @@ -1522,8 +1531,8 @@ def main(args=None): for key in dangling_end: # dangling_sequences[args.restrictionSequence[i]]['pat_forw'] - intermediate_qc_log.write("dangling end {}\t{}\t({:.2f})\n". - format(dangling_sequences[key]['pat_forw'], dangling_end[key], 100 * float(dangling_end[key]) / mappable_unique_high_quality_pairs)) + intermediate_qc_log.write("dangling end {} (restriction sequence {})\t{}\t({:.2f})\n". + format(dangling_sequences[key]['pat_forw'], key, dangling_end[key], 100 * float(dangling_end[key]) / mappable_unique_high_quality_pairs)) else: intermediate_qc_log.write("dangling end\t{}\t({:.2f})\n". format(0, 100 * float(0) / mappable_unique_high_quality_pairs)) @@ -1570,6 +1579,9 @@ def main(args=None): log_file = open(log_file_name, 'w') log_file.write(intermediate_qc_log.getvalue()) log_file.close() + log.debug('log_file_name {}'.format(log_file_name)) + log.debug('args.QCfolder {}'.format(args.QCfolder)) + QC.main("-l {} -o {}".format(log_file_name, args.QCfolder).split()) args.outFileName.close() diff --git a/hicexplorer/hicCompareMatrices.py b/hicexplorer/hicCompareMatrices.py index 1a7b9850..4bdbbe73 100644 --- a/hicexplorer/hicCompareMatrices.py +++ b/hicexplorer/hicCompareMatrices.py @@ -39,6 +39,12 @@ def parse_arguments(args=None): choices=['diff', 'ratio', 'log2ratio'], default='log2ratio') + parserOpt.add_argument('--noNorm', + help='Do not apply normalisation before' + ' computing the operation (Default: False).', + required=False, + action='store_true') + parserOpt.add_argument("--help", "-h", action="help", help="show this help message and exit") parserOpt.add_argument('--version', action='version', @@ -66,9 +72,10 @@ def main(args=None): "{}: {}".format(args.matrices[0], hic1.chrBinBoundaries.keys(), args.matrices[1], hic2.chrBinBoundaries.keys())) - # normalize by total matrix sum - hic1.matrix.data = hic1.matrix.data.astype(float) / hic1.matrix.data.sum() - hic2.matrix.data = hic2.matrix.data.astype(float) / hic2.matrix.data.sum() + if not args.noNorm: + # normalize by total matrix sum + hic1.matrix.data = hic1.matrix.data.astype(float) / hic1.matrix.data.sum() + hic2.matrix.data = hic2.matrix.data.astype(float) / hic2.matrix.data.sum() nan_bins = set(hic1.nan_bins) nan_bins = nan_bins.union(hic2.nan_bins) diff --git a/hicexplorer/hicCompartmentalization.py b/hicexplorer/hicCompartmentalization.py index 89b506b0..c3a3c148 100644 --- a/hicexplorer/hicCompartmentalization.py +++ b/hicexplorer/hicCompartmentalization.py @@ -3,6 +3,7 @@ import pandas as pd import matplotlib import matplotlib.pyplot as plt + import logging from hicmatrix import HiCMatrix as hm from hicexplorer._version import __version__ @@ -83,6 +84,12 @@ def parse_arguments(): return parser +def get_indices(obs_exp, row): + indices = np.arange(obs_exp.getRegionBinRange(row['chr'], row['start'], row['end'] - 1)[0], + obs_exp.getRegionBinRange(row['chr'], row['start'], row['end'] - 1)[1] + 1) # end is inclusive + return indices + + def count_interactions(obs_exp, pc1, quantiles_number, offset): "Counts the total interaction on obs_exp matrix per quantile and " "normalizes it by the number of bins per quantile." @@ -90,30 +97,28 @@ def count_interactions(obs_exp, pc1, quantiles_number, offset): interaction_sum = np.zeros((quantiles_number, quantiles_number)) number_of_bins = np.zeros((quantiles_number, quantiles_number)) - - for chrom in chromosomes: - pc1_chr = pc1.loc[pc1["chr"] == chrom].reset_index(drop=True) - chr_range = obs_exp.getChrBinRange(chrom) - - chr_submatrix = obs_exp.matrix[chr_range[0]:chr_range[1], - chr_range[0]:chr_range[1]] - - if offset: - for dist in offset: - assert(dist >= 0) - indices = np.arange(0, chr_submatrix.shape[0] - dist) - chr_submatrix[indices, indices + dist] = np.nan - chr_submatrix[indices + dist, indices] = np.nan - + if offset: + for dist in offset: + assert(dist >= 0) + indices = np.arange(0, obs_exp.matrix.shape[0] - dist) + obs_exp.matrix[indices, indices + dist] = np.nan + obs_exp.matrix[indices + dist, indices] = np.nan + for chrom in chromosomes: # It is only handeling cis contacts + # pc1_chr = pc1.loc[pc1["chr"] == chrom].reset_index(drop=True) + # chr_range = obs_exp.getChrBinRange(chrom) + # chr_submatrix = obs_exp.matrix[chr_range[0]:chr_range[1], + # chr_range[0]:chr_range[1]] for qi in range(0, quantiles_number): - row_indices = pc1_chr.loc[pc1_chr["quantile"] == qi].index + row_indices = pc1.loc[pc1["quantile"] == qi]["bin_id"] if row_indices.empty: continue + row_indices = [i for list in row_indices for i in list] for qj in range(0, quantiles_number): - col_indices = pc1_chr.loc[pc1_chr["quantile"] == qj].index + col_indices = pc1.loc[pc1["quantile"] == qj]["bin_id"] if col_indices.empty: continue - submatrix = chr_submatrix[np.ix_(row_indices, col_indices)] + col_indices = [i for list in col_indices for i in list] + submatrix = obs_exp.matrix[np.ix_(row_indices, col_indices)] submatrix = submatrix.todense() submatrix = submatrix[~np.isnan(submatrix)] # remove nans submatrix = submatrix[~np.isinf(submatrix)] @@ -121,7 +126,6 @@ def count_interactions(obs_exp, pc1, quantiles_number, offset): interaction_sum[qj, qi] += np.sum(submatrix) number_of_bins[qi, qj] += submatrix.shape[1] number_of_bins[qj, qi] += submatrix.shape[1] - return interaction_sum / number_of_bins @@ -172,6 +176,7 @@ def main(args=None): Main function to generate the polarization plot. """ args = parse_arguments().parse_args(args) + matplotlib.rcParams['pdf.fonttype'] = 42 pc1 = pd.read_table(args.pca, header=None, sep="\t", dtype={0: "object", 1: "Int64", 2: "Int64", 3: "float32"}) @@ -192,11 +197,13 @@ def main(args=None): pc1['pc1'].values.astype(float), side="right") pc1.loc[pc1["pc1"] == np.nan]["quantile"] = args.quantile + 1 + polarization_ratio = [] output_matrices = [] labels = [] for matrix in args.obsexp_matrices: obs_exp = hm.hiCMatrix(matrix) + pc1["bin_id"] = pc1.apply(lambda row: get_indices(obs_exp, row), axis=1) name = ".".join(matrix.split("/")[-1].split(".")[0:-1]) labels.append(name) normalised_sum_per_quantile = count_interactions(obs_exp, pc1, diff --git a/hicexplorer/hicConvertFormat.py b/hicexplorer/hicConvertFormat.py index 809ba5cf..fb3e1f87 100644 --- a/hicexplorer/hicConvertFormat.py +++ b/hicexplorer/hicConvertFormat.py @@ -15,6 +15,8 @@ from hicmatrix import HiCMatrix from copy import deepcopy +from collections import OrderedDict +from scipy.sparse import csr_matrix, coo_matrix, lil_matrix def parse_arguments(args=None): @@ -49,19 +51,19 @@ def parse_arguments(args=None): help='File format of the input matrix file. \n' 'The following options are available: `h5` (native HiCExplorer ' 'format based on hdf5 storage format), ' - ' `cool`, `hic`, `homer`, `hicpro`.', + ' `cool`, `hic`, `homer`, `hicpro`, `2D-text`.', choices=['h5', 'cool', 'hic', - 'homer', 'hicpro'], + 'homer', 'hicpro', '2D-text'], required=True) parserRequired.add_argument('--outputFormat', help='Output format. The following options are available: `h5` (native HiCExplorer ' 'format based on hdf5 storage format). ' - ' `cool`, `ginteractions`, `homer` and `mcool`' + ' `cool`, `ginteractions`, `homer`, `mcool` and `hicpro`' ' (Default: %(default)s).', default='cool', choices=['cool', 'h5', 'homer', - 'ginteractions', 'mcool'], + 'ginteractions', 'mcool', 'hicpro'], required=True) parserOpt = parser.add_argument_group('Optional arguments') @@ -92,7 +94,14 @@ def parse_arguments(args=None): parserOpt.add_argument("--help", "-h", action="help", help="show this help message and exit." ) - + parserOpt.add_argument('--chromosomeSizes', '-cs', + help=('This option is for the input format `2D-text` only and will be ignored else.' + 'File with the chromosome sizes for your genome. A tab-delimited two column layout \"chr_name size\" is expected' + 'Please consider that this option causes that only reads are considered which are on the listed chromosomes.' + 'Use this option to guarantee fixed sizes. An example file is available via UCSC: ' + 'http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes'), + type=argparse.FileType('r'), + metavar='txt file') parserOpt.add_argument('--version', action='version', version='%(prog)s {}'.format(__version__)) parserOpt.add_argument('--bedFileHicpro', '-bf', @@ -110,8 +119,11 @@ def main(args=None): if args.inputFormat != 'hic' and args.outputFormat != 'mcool': if len(args.matrices) != len(args.outFileName): log.error( - 'Number of input matrices does not match number output matrices!') + 'Number of input matrices does not match number output matrices!: Input matrices {}; output matrices {}'.format(len(args.matrices), len(args.outFileName))) exit(1) + if args.inputFormat == 'hic' and args.outputFormat != 'cool': + log.error('The export of a hic file is only possible to a cool file.') + exit(1) if args.inputFormat == 'hic' and args.outputFormat == 'cool': log.info('Converting with hic2cool.') for i, matrix in enumerate(args.matrices): @@ -125,7 +137,7 @@ def main(args=None): out_name = '.'.join(out_name) hic2cool_convert(matrix, out_name, resolution) return - elif args.inputFormat in ['hicpro', 'homer', 'h5', 'cool']: + elif args.inputFormat in ['hicpro', 'homer', 'h5', 'cool', '2D-text']: format_was_h5 = False if args.inputFormat == 'h5': format_was_h5 = True @@ -140,10 +152,76 @@ def main(args=None): len(args.matrices), len(args.bedFileHicpro))) sys.exit(1) + if args.inputFormat == '2D-text': + if args.resolutions is None: + log.error('The resolution must be defined via --resolutions') + sys.exit(1) + if args.chromosomeSizes is None: + log.error('The sizes of the chromosomes must be defined via --chromosomeSizes.') + sys.exit(1) + for i, matrix in enumerate(args.matrices): if args.inputFormat == 'hicpro': matrixFileHandlerInput = MatrixFileHandler(pFileType=args.inputFormat, pMatrixFile=matrix, pBedFileHicPro=args.bedFileHicpro[i]) + _matrix, cut_intervals, nan_bins, \ + distance_counts, correction_factors = matrixFileHandlerInput.load() + elif args.inputFormat == '2D-text': + chrom_sizes = OrderedDict() + size_genome = 0 + with open(args.chromosomeSizes.name, 'r') as file: + file_ = True + while file_: + file_ = file.readline().strip() + if file_ != '': + line_split = file_.split('\t') + chrom_sizes[line_split[0]] = int(line_split[1]) + size_genome += int(line_split[1]) + chrom_sizes = list(chrom_sizes.items()) + + # log.debug('chrom_sizes: {}'.format(chrom_sizes)) + args.resolutions = [int(x) for x in args.resolutions] + # internal_matrix_size = size_genome // args.resolutions[0] + + cut_intervals = [] + for chromosome in chrom_sizes: + for interval in range(0, chromosome[1], args.resolutions[0]): + cut_intervals.append(tuple([chromosome[0], interval, + min(chromosome[1], interval + args.resolutions[0]), 1.0])) + + hic_matrix_csr = lil_matrix((len(cut_intervals), len(cut_intervals))) + log.debug('cut_intervals {}'.format(cut_intervals[:20])) + + hic_matrix = HiCMatrix.hiCMatrix() + hic_matrix.setMatrix(hic_matrix_csr, cut_intervals) + # tmp_matrix = coo_matrix(()) + with open(matrix, 'r') as file: + for j, line in enumerate(file): + line_split = line.split('\t') + chromosome_1 = str(line_split[0]) + start_1 = int(line_split[1]) + end_1 = int(line_split[2]) + + chromosome_2 = str(line_split[3]) + start_2 = int(line_split[4]) + end_2 = int(line_split[5]) + + value = float(line_split[6]) + bin_id_1 = hic_matrix.getRegionBinRange(chromosome_1, start_1, end_1) + bin_id_2 = hic_matrix.getRegionBinRange(chromosome_2, start_2, end_2) + try: + hic_matrix.matrix[bin_id_1, bin_id_2] = value + except Exception as exp: + log.debug(str(exp)) + if j % 1000 == 0: + log.debug('{} lines computed'.format(j)) + log.debug('csr with values filled!') + hic_matrix.matrix = hic_matrix.matrix.tocsr() + + _matrix, cut_intervals, nan_bins, \ + distance_counts, correction_factors = hic_matrix.matrix, hic_matrix.cut_intervals, hic_matrix.nan_bins, \ + hic_matrix.distance_counts, hic_matrix.correction_factors + else: correction_operator = None @@ -163,26 +241,50 @@ def main(args=None): pEnforceInteger=args.enforce_integer, pApplyCorrectionCoolerLoad=applyCorrectionCoolerLoad) - _matrix, cut_intervals, nan_bins, \ - distance_counts, correction_factors = matrixFileHandlerInput.load() + _matrix, cut_intervals, nan_bins, \ + distance_counts, correction_factors = matrixFileHandlerInput.load() + + log.debug('cut_intervals {}'.format(cut_intervals[:20])) log.debug('Setting done') if args.outputFormat in ['cool', 'h5', 'homer', 'ginteractions']: + log.debug('cool h5 homer ginteractions hicpro branch') + if args.outputFormat in ['homer', 'ginteractions']: + log.debug('homer ginteractions branch') + # make it a upper triangular matrix in case it is not already _matrix = triu(_matrix) # make it a full symmetrical matrix _matrix = _matrix.maximum(_matrix.T) hic2CoolVersion = None + cool_metadata = None if args.inputFormat == 'cool': hic2CoolVersion = matrixFileHandlerInput.matrixFile.hic2cool_version - matrixFileHandlerOutput = MatrixFileHandler(pFileType=args.outputFormat, pEnforceInteger=args.enforce_integer, pFileWasH5=format_was_h5, pHic2CoolVersion=hic2CoolVersion) + cool_metadata = matrixFileHandlerInput.matrixFile.hic_metadata + + log.debug('cool_metadata {}'.format(cool_metadata)) + matrixFileHandlerOutput = MatrixFileHandler(pFileType=args.outputFormat, pEnforceInteger=args.enforce_integer, pFileWasH5=format_was_h5, pHic2CoolVersion=hic2CoolVersion, pHiCInfo=cool_metadata) matrixFileHandlerOutput.set_matrix_variables(_matrix, cut_intervals, nan_bins, correction_factors, distance_counts) + log.debug('len(args.outFileName) {}, i {}'.format(len(args.outFileName), i)) matrixFileHandlerOutput.save( args.outFileName[i], pSymmetric=True, pApplyCorrection=applyCorrection) + + if args.outputFormat == 'hicpro': + log.debug('hicpro branch') + if len(args.matrices) == len(args.outFileName) and len(args.outFileName) == len(args.bedFileHicpro): + log.debug('args.bedFileHicpro[i] {}'.format(args.bedFileHicpro[i])) + matrixFileHandlerOutput = MatrixFileHandler(pFileType=args.outputFormat, pBedFileHicPro=args.bedFileHicpro[i]) + + matrixFileHandlerOutput.set_matrix_variables(_matrix, cut_intervals, nan_bins, + correction_factors, distance_counts) + matrixFileHandlerOutput.save(args.outFileName[i], pSymmetric=True, pApplyCorrection=applyCorrection) + else: + log.error('The number of input matrices, output files and bed files does not match: Input: {}; Output: {}; Bed: {}'.format(len(args.matrix), len(args.outFileName), len(args.bedFileHicpro))) + exit(1) elif args.outputFormat in ['mcool']: log.debug('outformat is mcool') @@ -196,7 +298,11 @@ def main(args=None): hic_matrix.setMatrix(_matrix, cut_intervals) bin_size = hic_matrix.getBinSize() - + hic2CoolVersion = None + cool_metadata = None + if args.inputFormat == 'cool': + hic2CoolVersion = matrixFileHandlerInput.matrixFile.hic2cool_version + cool_metadata = matrixFileHandlerInput.matrixFile.hic_metadata for j, resolution in enumerate(args.resolutions): hic_matrix_res = deepcopy(hic_matrix) @@ -212,7 +318,7 @@ def main(args=None): append = False if j > 0: append = True - matrixFileHandlerOutput = MatrixFileHandler(pFileType='cool', pEnforceInteger=args.enforce_integer, pAppend=append, pFileWasH5=format_was_h5) + matrixFileHandlerOutput = MatrixFileHandler(pFileType='cool', pEnforceInteger=args.enforce_integer, pAppend=append, pFileWasH5=format_was_h5, pHic2CoolVersion=hic2CoolVersion, pHiCInfo=cool_metadata) matrixFileHandlerOutput.set_matrix_variables(merged_matrix.matrix, merged_matrix.cut_intervals, diff --git a/hicexplorer/hicCorrectMatrix.py b/hicexplorer/hicCorrectMatrix.py index 6ff59e01..9037faee 100644 --- a/hicexplorer/hicCorrectMatrix.py +++ b/hicexplorer/hicCorrectMatrix.py @@ -21,7 +21,7 @@ import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec from matplotlib.ticker import MultipleLocator, FormatStrFormatter - +import matplotlib import numpy as np debug = 0 @@ -590,6 +590,8 @@ def filter_by_zscore(hic_ma, lower_threshold, upper_threshold, perchr=False): def main(args=None): args = parse_arguments().parse_args(args) + matplotlib.rcParams['pdf.fonttype'] = 42 + if args.verbose: log.setLevel(logging.INFO) @@ -739,7 +741,7 @@ def main(args=None): # set it to False since the vector is already normalised # with the previous True # correction_factors = np.true_divide(1, kr.get_normalisation_vector(False).todense()) - correction_factors = kr.get_normalisation_vector(False).todense() + correction_factors = kr.get_normalisation_vector(True).todense() if args.outFileName.endswith('.h5'): corrected_matrix = kr.get_normalised_matrix(True) diff --git a/hicexplorer/hicCorrelate.py b/hicexplorer/hicCorrelate.py index bf240256..510fa096 100644 --- a/hicexplorer/hicCorrelate.py +++ b/hicexplorer/hicCorrelate.py @@ -15,12 +15,14 @@ from hicexplorer.utilities import check_cooler # for plotting from matplotlib import use as mplt_use +import matplotlib as mpl + mplt_use('Agg') import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec from matplotlib.ticker import FixedLocator - +import matplotlib.colors as pltcolors import logging log = logging.getLogger(__name__) @@ -73,14 +75,6 @@ def parse_arguments(args=None): 'http://matplotlib.org/examples/color/colormaps_reference.html' ' (Default: %(default)s).') - parserHeatmap.add_argument('--plotFileFormat', - metavar='FILETYPE', - help='Image format type. If given, this option ' - 'overrides the image format based on the plotFile ' - 'ending. The available options are: png, emf, ' - 'eps, pdf and svg.', - choices=['png', 'pdf', 'svg', 'eps', 'emf']) - parserHeatmap.add_argument('--plotNumbers', help='If set, then the correlation number is plotted ' 'on top of the heatmap.', @@ -118,11 +112,13 @@ def parse_arguments(args=None): 'domains in the genome you are working with.') parserOpt.add_argument('--outFileNameHeatmap', '-oh', - help='File name to save the resulting heatmap plot.', + help='File name to save the resulting heatmap plot. Supported file formats are given by matplotlib, usually these are: png, pdf, ps, eps and svg. ', + default='heatmap.png', required=True) parserOpt.add_argument('--outFileNameScatter', '-os', - help='File name to save the resulting scatter plot.', + help='File name to save the resulting scatter plot. Supported file formats are given by matplotlib, usually these are: png, pdf, ps, eps and svg. ', + default='scatter.png', required=True) parserOpt.add_argument('--chromosomes', @@ -150,7 +146,7 @@ def parse_arguments(args=None): def plot_correlation(corr_matrix, labels, plot_filename, vmax=None, - vmin=None, colormap='Reds', image_format=None): + vmin=None, colormap='Reds', pPlotNumbers=None): import scipy.cluster.hierarchy as sch num_rows = corr_matrix.shape[0] @@ -177,7 +173,10 @@ def plot_correlation(corr_matrix, labels, plot_filename, vmax=None, # are too dark at the end of the range that do not offer # a good contrast between the correlation numbers that are # plotted on black. - cmap = cmap.from_list(colormap + "clipped", cmap([0.0, 0.8])) + # cmap = cmap.from_list(colormap + "clipped", cmap([0.0, 0.8])) + if pPlotNumbers: + cmap = pltcolors.LinearSegmentedColormap.from_list(colormap + "clipped", + cmap(np.linspace(0, 0.9, 10))) # Plot distance matrix. axmatrix = fig.add_axes([0.13, 0.1, 0.6, 0.7]) index = z_var['leaves'] @@ -201,13 +200,15 @@ def plot_correlation(corr_matrix, labels, plot_filename, vmax=None, # Plot colorbar. axcolor = fig.add_axes([0.13, 0.065, 0.6, 0.02]) plt.colorbar(img_mat, cax=axcolor, orientation='horizontal') - for row in range(num_rows): - for col in range(num_rows): - axmatrix.text(row + 0.5, col + 0.5, - "{:.2f}".format(corr_matrix[row, col]), - ha='center', va='center') - fig.savefig(plot_filename, format=image_format) + if pPlotNumbers: + for row in range(num_rows): + for col in range(num_rows): + axmatrix.text(row + 0.5, col + 0.5, + "{:.2f}".format(corr_matrix[row, col]), + ha='center', va='center') + + fig.savefig(plot_filename) def get_vectors(mat1, mat2): @@ -246,7 +247,7 @@ def get_vectors(mat1, mat2): def main(args=None): args = parse_arguments().parse_args(args) - + mpl.rcParams['pdf.fonttype'] = 42 if args.labels and len(args.matrices) != len(args.labels): log.error("The number of labels does not match the number of matrices.") exit(0) @@ -445,5 +446,4 @@ def main(args=None): args.zMax, args.zMin, args.colorMap, - image_format=args.plotFileFormat) -# plot_numbers=args.plotNumbers) + pPlotNumbers=args.plotNumbers) diff --git a/hicexplorer/hicDifferentialTAD.py b/hicexplorer/hicDifferentialTAD.py index 91989140..0e850855 100644 --- a/hicexplorer/hicDifferentialTAD.py +++ b/hicexplorer/hicDifferentialTAD.py @@ -5,6 +5,7 @@ from multiprocessing import Process, Queue import time import traceback +from copy import deepcopy import logging log = logging.getLogger(__name__) from hicmatrix import HiCMatrix as hm @@ -36,7 +37,9 @@ def parse_arguments(args=None): required=False) parserRequired.add_argument('--outFileNamePrefix', '-o', help='Outfile name prefix to store the accepted / rejected H0 TADs.', - required=False) + required=False, + default='output_differential_tad' + ) parserOpt = parser.add_argument_group('Optional arguments') parserOpt.add_argument('--pValue', '-p', type=float, @@ -79,207 +82,202 @@ def computeDifferentialTADs(pMatrixTarget, pMatrixControl, pDomainList, pCoolOrH accepted_inter_right = [] accepted_intra = [] p_values_list = [] + stats_list = [] rows = [] - old_chromosome = None + chromosome_list = pDomainList + for i, row in enumerate(chromosome_list): + + if pThreadId is None: + log.debug('first thread') + if i == len(chromosome_list) - 1: + continue + elif pThreadId == True: + log.debug('middle thread') + + if i == 0 or i == len(chromosome_list) - 1: + log.debug('i: {}'.format(i)) + log.debug('len(chromosome_list): {}'.format(len(chromosome_list))) + + continue + elif pThreadId == False: + log.debug('last thread') + + if i == 0: + continue + + if i - 1 >= 0: + chromosom = chromosome_list[i - 1][0] + start = chromosome_list[i - 1][1] + else: + chromosom = chromosome_list[i][0] + start = chromosome_list[i][1] + if i + 1 < len(chromosome_list): + end = chromosome_list[i + 1][2] + else: + end = chromosome_list[i][2] + # midpos = row[1] + ((row[2] - row[1]) / 2) + + if pCoolOrH5: + + # # get intra-TAD data + hic_matrix_target = hm.hiCMatrix( + pMatrixFile=pMatrixTarget, pChrnameList=[str(row[0]) + ':' + str(row[1]) + '-' + str(row[2])]) + hic_matrix_control = hm.hiCMatrix( + pMatrixFile=pMatrixControl, pChrnameList=[str(row[0]) + ':' + str(row[1]) + '-' + str(row[2])]) + matrix_target = hic_matrix_target.matrix.toarray() + matrix_control = hic_matrix_control.matrix.toarray() - tads_per_chromosome = [] + hic_matrix_target_inter_tad = hm.hiCMatrix( + pMatrixFile=pMatrixTarget, pChrnameList=[str(chromosom) + ':' + str(start) + '-' + str(end)]) + hic_matrix_control_inter_tad = hm.hiCMatrix( + pMatrixFile=pMatrixControl, pChrnameList=[str(chromosom) + ':' + str(start) + '-' + str(end)]) - for j in range(len(pDomainList)): - if old_chromosome is None: - old_chromosome = pDomainList[j][0] - per_chromosome = [] - per_chromosome.append(pDomainList[j]) + matrix_target_inter_tad = hic_matrix_target_inter_tad.matrix + matrix_control_inter_tad = hic_matrix_control_inter_tad.matrix + + else: + # in case of h5 pMatrixTarget is already a HiCMatrix object + hic_matrix_target = pMatrixTarget + hic_matrix_control = pMatrixControl + hic_matrix_target_inter_tad = pMatrixTarget + hic_matrix_control_inter_tad = pMatrixControl + indices_target = hic_matrix_target.getRegionBinRange(str(row[0]), row[1], row[2]) + indices_control = hic_matrix_control.getRegionBinRange(str(row[0]), row[1], row[2]) + + matrix_target = hic_matrix_target.matrix[indices_target[0]:indices_target[1], indices_target[0]:indices_target[1]].toarray() + matrix_control = hic_matrix_control.matrix[indices_control[0]:indices_control[1], indices_control[0]:indices_control[1]].toarray() + matrix_target_inter_tad = pMatrixTarget.matrix + matrix_control_inter_tad = pMatrixControl.matrix + + matrix_target = matrix_target.flatten() + matrix_control = matrix_control.flatten() + # tad_midpoint = hic_matrix_target_inter_tad.getRegionBinRange(str(row[0]), midpos, midpos)[0] + + # if i - 1 >= 0: + # get index position left tad with tad + left_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), row[1], row[1])[0] + left_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), row[1], row[1])[0] + if pCoolOrH5: + outer_left_boundary_index_target = 0 + outer_left_boundary_index_control = 0 + + outer_right_boundary_index_control = -1 + outer_right_boundary_index_target = -1 - elif old_chromosome == pDomainList[j][0]: - per_chromosome.append(pDomainList[j]) - continue else: - tads_per_chromosome.append(per_chromosome) - per_chromosome = [] - old_chromosome = pDomainList[j][0] - tads_per_chromosome.append(per_chromosome) - log.debug('tads_per_chromosome {}'.format(len(tads_per_chromosome))) - for chromosome_list in tads_per_chromosome: - - for i, row in enumerate(chromosome_list): - - if pThreadId is None: - log.debug('first thread') - if i == len(chromosome_list) - 1: - continue - elif pThreadId == True: - log.debug('middle thread') - - if i == 0 or i == len(chromosome_list) - 1: - continue - elif pThreadId == False: - log.debug('last thread') - - if i == 0: - continue - - if i - 1 >= 0: - chromosom = chromosome_list[i - 1][0] - start = chromosome_list[i - 1][1] - else: - chromosom = chromosome_list[i][0] - start = chromosome_list[i][1] - if i + 1 < len(chromosome_list): - end = chromosome_list[i + 1][2] - else: - end = chromosome_list[i][2] - # midpos = row[1] + ((row[2] - row[1]) / 2) - - if pCoolOrH5: - - # # get intra-TAD data - hic_matrix_target = hm.hiCMatrix( - pMatrixFile=pMatrixTarget, pChrnameList=[str(row[0]) + ':' + str(row[1]) + '-' + str(row[2])]) - hic_matrix_control = hm.hiCMatrix( - pMatrixFile=pMatrixControl, pChrnameList=[str(row[0]) + ':' + str(row[1]) + '-' + str(row[2])]) - matrix_target = hic_matrix_target.matrix.toarray() - matrix_control = hic_matrix_control.matrix.toarray() - - hic_matrix_target_inter_tad = hm.hiCMatrix( - pMatrixFile=pMatrixTarget, pChrnameList=[str(chromosom) + ':' + str(start) + '-' + str(end)]) - hic_matrix_control_inter_tad = hm.hiCMatrix( - pMatrixFile=pMatrixControl, pChrnameList=[str(chromosom) + ':' + str(start) + '-' + str(end)]) - - matrix_target_inter_tad = hic_matrix_target_inter_tad.matrix - matrix_control_inter_tad = hic_matrix_control_inter_tad.matrix - - else: - # in case of h5 pMatrixTarget is already a HiCMatrix object - hic_matrix_target = pMatrixTarget - hic_matrix_control = pMatrixControl - hic_matrix_target_inter_tad = pMatrixTarget - hic_matrix_control_inter_tad = pMatrixControl - indices_target = hic_matrix_target.getRegionBinRange(str(row[0]), row[1], row[2]) - indices_control = hic_matrix_control.getRegionBinRange(str(row[0]), row[1], row[2]) - - matrix_target = hic_matrix_target.matrix[indices_target[0]:indices_target[1], indices_target[0]:indices_target[1]].toarray() - matrix_control = hic_matrix_control.matrix[indices_control[0]:indices_control[1], indices_control[0]:indices_control[1]].toarray() - matrix_target_inter_tad = pMatrixTarget.matrix - matrix_control_inter_tad = pMatrixControl.matrix - - matrix_target = matrix_target.flatten() - matrix_control = matrix_control.flatten() - # tad_midpoint = hic_matrix_target_inter_tad.getRegionBinRange(str(row[0]), midpos, midpos)[0] - - # if i - 1 >= 0: - # get index position left tad with tad - left_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), row[1], row[1])[0] - left_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), row[1], row[1])[0] - if pCoolOrH5: - outer_left_boundary_index_target = 0 - outer_left_boundary_index_control = 0 - - outer_right_boundary_index_control = -1 - outer_right_boundary_index_target = -1 - - else: - outer_left_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), start, end)[0] - outer_left_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), start, end)[0] - - outer_right_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), start, end)[1] - outer_right_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), start, end)[1] - - if i + 1 < len(chromosome_list) and not pCoolOrH5: - # get index position left tad with tad - right_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] - right_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] - elif i + 1 < len(chromosome_list) - 1: - right_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] - right_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] - - if i - 1 >= 0 and i + 1 < len(chromosome_list): - intertad_left_target = matrix_target_inter_tad[outer_left_boundary_index_target:left_boundary_index_target, left_boundary_index_target:right_boundary_index_target].toarray() - intertad_right_target = matrix_target_inter_tad[left_boundary_index_target:right_boundary_index_target, right_boundary_index_target:outer_right_boundary_index_target].toarray() - intertad_left_control = matrix_control_inter_tad[outer_left_boundary_index_control:left_boundary_index_control, left_boundary_index_control:right_boundary_index_control].toarray() - intertad_right_control = matrix_control_inter_tad[left_boundary_index_control:right_boundary_index_control, right_boundary_index_control:outer_right_boundary_index_control].toarray() - - elif i - 1 < 0 and i + 1 < len(chromosome_list): - intertad_right_target = matrix_target_inter_tad[left_boundary_index_target:right_boundary_index_target, right_boundary_index_target:outer_right_boundary_index_target].toarray() - intertad_right_control = matrix_control_inter_tad[left_boundary_index_control:right_boundary_index_control, right_boundary_index_control:outer_right_boundary_index_control].toarray() - - elif i - 1 > 0 and i + 1 >= len(chromosome_list): - intertad_left_target = matrix_target_inter_tad[outer_left_boundary_index_target:left_boundary_index_target, left_boundary_index_target:right_boundary_index_target].toarray() - intertad_left_control = matrix_control_inter_tad[outer_left_boundary_index_control:left_boundary_index_control, left_boundary_index_control:right_boundary_index_control].toarray() - - significance_level_left = None - significance_level_right = None - statistic_left = None - statistic_right = None - - if i - 1 >= 0 and i + 1 < len(chromosome_list): - intertad_left_target = intertad_left_target.flatten() - intertad_left_control = intertad_left_control.flatten() - intertad_right_target = intertad_right_target.flatten() - intertad_right_control = intertad_right_control.flatten() - - statistic_left, significance_level_left = ranksums(intertad_left_target, intertad_left_control) - statistic_right, significance_level_right = ranksums(intertad_right_target, intertad_right_control) - elif i - 1 < 0 and i + 1 < len(chromosome_list): - intertad_right_target = intertad_right_target.flatten() - intertad_right_control = intertad_right_control.flatten() - statistic_right, significance_level_right = ranksums(intertad_right_target, intertad_right_control) - elif i - 1 > 0 and i + 1 >= len(chromosome_list): - intertad_left_target = intertad_left_target.flatten() - intertad_left_control = intertad_left_control.flatten() - log.debug('intertad_left_target {}'.format(intertad_left_target)) - log.debug('intertad_left_control {}'.format(intertad_left_control)) - - statistic_left, significance_level_left = ranksums(intertad_left_target, intertad_left_control) - - # log.debug('matrix_target {}'.format(matrix_target)) - # log.debug('matrix_control {}'.format(matrix_control)) - - statistic, significance_level = ranksums(matrix_target, matrix_control) - log.debug('statistic {}, significance_level {}'.format(statistic, significance_level)) - log.debug('right statistic {}, significance_level {}'.format(statistic_right, significance_level_right)) - log.debug('left statistic {}, significance_level {}'.format(statistic_left, significance_level_left)) - - p_values = [] - if significance_level_left is None or np.isnan(significance_level_left): - accepted_inter_left.append(0) - p_values.append(np.nan) - elif significance_level_left <= pPValue: - accepted_inter_left.append(1) - p_values.append(significance_level_left) - else: - accepted_inter_left.append(0) - p_values.append(significance_level_left) - - if significance_level_right is None or np.isnan(significance_level_right): - accepted_inter_right.append(0) - p_values.append(np.nan) - elif significance_level_right <= pPValue: - accepted_inter_right.append(1) - p_values.append(significance_level_right) - else: - accepted_inter_right.append(0) - p_values.append(significance_level_right) - - if significance_level is None or np.isnan(significance_level): - accepted_intra.append(0) - p_values.append(np.nan) - elif significance_level <= pPValue: - accepted_intra.append(1) - p_values.append(significance_level) - else: - accepted_intra.append(0) - p_values.append(significance_level) - - p_values_list.append(p_values) - - rows.append(row) + outer_left_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), start, end)[0] + outer_left_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), start, end)[0] + + outer_right_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), start, end)[1] + outer_right_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), start, end)[1] + + if i + 1 < len(chromosome_list) and not pCoolOrH5: + # get index position right tad with tad + right_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] + right_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] + elif i + 1 < len(chromosome_list): + right_boundary_index_target = hic_matrix_target_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] + right_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] + + if i - 1 >= 0 and i + 1 < len(chromosome_list): + intertad_left_target = matrix_target_inter_tad[outer_left_boundary_index_target:left_boundary_index_target, left_boundary_index_target:right_boundary_index_target].toarray() + intertad_right_target = matrix_target_inter_tad[left_boundary_index_target:right_boundary_index_target, right_boundary_index_target:outer_right_boundary_index_target].toarray() + intertad_left_control = matrix_control_inter_tad[outer_left_boundary_index_control:left_boundary_index_control, left_boundary_index_control:right_boundary_index_control].toarray() + intertad_right_control = matrix_control_inter_tad[left_boundary_index_control:right_boundary_index_control, right_boundary_index_control:outer_right_boundary_index_control].toarray() + + elif i - 1 < 0 and i + 1 < len(chromosome_list): + intertad_right_target = matrix_target_inter_tad[left_boundary_index_target:right_boundary_index_target, right_boundary_index_target:outer_right_boundary_index_target].toarray() + intertad_right_control = matrix_control_inter_tad[left_boundary_index_control:right_boundary_index_control, right_boundary_index_control:outer_right_boundary_index_control].toarray() + + elif i - 1 > 0 and i + 1 >= len(chromosome_list): + intertad_left_target = matrix_target_inter_tad[outer_left_boundary_index_target:left_boundary_index_target, left_boundary_index_target:right_boundary_index_target].toarray() + intertad_left_control = matrix_control_inter_tad[outer_left_boundary_index_control:left_boundary_index_control, left_boundary_index_control:right_boundary_index_control].toarray() + + significance_level_left = None + significance_level_right = None + statistic_left = None + statistic_right = None + + if i - 1 >= 0 and i + 1 < len(chromosome_list): + intertad_left_target = intertad_left_target.flatten() + intertad_left_control = intertad_left_control.flatten() + intertad_right_target = intertad_right_target.flatten() + intertad_right_control = intertad_right_control.flatten() + + statistic_left, significance_level_left = ranksums(intertad_left_target, intertad_left_control) + statistic_right, significance_level_right = ranksums(intertad_right_target, intertad_right_control) + elif i - 1 < 0 and i + 1 < len(chromosome_list): + intertad_right_target = intertad_right_target.flatten() + intertad_right_control = intertad_right_control.flatten() + statistic_right, significance_level_right = ranksums(intertad_right_target, intertad_right_control) + elif i - 1 > 0 and i + 1 >= len(chromosome_list): + intertad_left_target = intertad_left_target.flatten() + intertad_left_control = intertad_left_control.flatten() + # log.debug('intertad_left_target {}'.format(intertad_left_target)) + # log.debug('intertad_left_control {}'.format(intertad_left_control)) + + statistic_left, significance_level_left = ranksums(intertad_left_target, intertad_left_control) + + # log.debug('matrix_target {}'.format(matrix_target)) + # log.debug('matrix_control {}'.format(matrix_control)) + + statistic, significance_level = ranksums(matrix_target, matrix_control) + # log.debug('statistic {}, significance_level {}'.format(statistic, significance_level)) + # log.debug('right statistic {}, significance_level {}'.format(statistic_right, significance_level_right)) + # log.debug('left statistic {}, significance_level {}'.format(statistic_left, significance_level_left)) + + p_values = [] + stats = [] + if significance_level_left is None or np.isnan(significance_level_left): + accepted_inter_left.append(0) + p_values.append(np.nan) + stats.append(np.nan) + elif significance_level_left <= pPValue: + accepted_inter_left.append(1) + p_values.append(significance_level_left) + stats.append(statistic_left) + else: + accepted_inter_left.append(0) + p_values.append(significance_level_left) + stats.append(statistic_left) + + if significance_level_right is None or np.isnan(significance_level_right): + accepted_inter_right.append(0) + p_values.append(np.nan) + stats.append(np.nan) + elif significance_level_right <= pPValue: + accepted_inter_right.append(1) + p_values.append(significance_level_right) + stats.append(statistic_right) + else: + accepted_inter_right.append(0) + p_values.append(significance_level_right) + stats.append(statistic_right) + + if significance_level is None or np.isnan(significance_level): + accepted_intra.append(0) + p_values.append(np.nan) + stats.append(np.nan) + elif significance_level <= pPValue: + accepted_intra.append(1) + p_values.append(significance_level) + stats.append(statistic) + else: + accepted_intra.append(0) + p_values.append(significance_level) + stats.append(statistic) + + p_values_list.append(p_values) + stats_list.append(stats) + + rows.append(row) except Exception as exp: pQueue.put('Fail: ' + str(exp) + traceback.format_exc()) return # hic_matrix_target_inter_tad.save('manipulated_target.cool') # hic_matrix_control_inter_tad.save('manipulated_control.cool') - pQueue.put([p_values_list, accepted_inter_left, accepted_inter_right, accepted_intra, rows]) + pQueue.put([stats_list, p_values_list, accepted_inter_left, accepted_inter_right, accepted_intra, rows]) def main(args=None): @@ -287,6 +285,29 @@ def main(args=None): # read domains file domains_df = readDomainBoundaries(args.tadDomains) + log.debug('len(domains_df) {}'.format(len(domains_df))) + domains = domains_df.values.tolist() + old_chromosome = None + + tads_per_chromosome = [] + + for j in range(len(domains)): + if old_chromosome is None: + old_chromosome = domains[j][0] + per_chromosome = [] + per_chromosome.append(domains[j]) + + elif old_chromosome == domains[j][0]: + per_chromosome.append(domains[j]) + continue + else: + tads_per_chromosome.append(per_chromosome) + per_chromosome = [] + per_chromosome.append(domains[j]) + old_chromosome = domains[j][0] + tads_per_chromosome.append(per_chromosome) + # log.debug('len(tads_per_chromosome) {}'.format(len(tads_per_chromosome[0]) + len(tads_per_chromosome[1]))) + # read full h5 or only region if cooler is_cooler_target = check_cooler(args.targetMatrix) is_cooler_control = check_cooler(args.controlMatrix) @@ -303,91 +324,125 @@ def main(args=None): # accepted_H0 = [] # rejected_H0 = [] # log.debug('domains_df {}'.format(domains_df)) - domains = domains_df.values.tolist() - p_values_threads = [None] * args.threads - accepted_left_inter_threads = [None] * args.threads - accepted_right_inter_threads = [None] * args.threads - accepted_intra_threads = [None] * args.threads - rows_threads = [None] * args.threads - - domainsPerThread = len(domains) // args.threads - all_data_collected = False - queue = [None] * args.threads - process = [None] * args.threads - thread_done = [False] * args.threads - - # None --> first thread, process first element in list, ignore last one - # True --> middle thread: ignore first and last element in tad processing - # False --> last thread: ignore first element, process last one - thread_id = None - for i in range(args.threads): - - if i == 0: - domainListThread = domains[i * domainsPerThread:((i + 1) * domainsPerThread) + 1] - thread_id = None - elif i < args.threads - 1: - domainListThread = domains[(i * domainsPerThread) - 1:((i + 1) * domainsPerThread) + 1] - thread_id = True - - else: - domainListThread = domains[(i * domainsPerThread) - 1:] - thread_id = False - - if args.threads == 1: - thread_id = '' - queue[i] = Queue() - process[i] = Process(target=computeDifferentialTADs, kwargs=dict( - pMatrixTarget=hic_matrix_target, - pMatrixControl=hic_matrix_control, - pDomainList=domainListThread, - pCoolOrH5=is_cooler_control, - pPValue=args.pValue, - pThreadId=thread_id, - pQueue=queue[i] - ) - ) - - process[i].start() - fail_flag = False - fail_message = '' - while not all_data_collected: + stats_chromosomes = [] + p_values_chromosomes = [] + accepted_inter_left_chromosomes = [] + accepted_inter_right_chromosomes = [] + accepted_intra_chromosomes = [] + rows_chromosomes = [] + + stats_threads = [[]] * args.threads + p_values_threads = [[]] * args.threads + accepted_left_inter_threads = [[]] * args.threads + accepted_right_inter_threads = [[]] * args.threads + accepted_intra_threads = [[]] * args.threads + rows_threads = [[]] * args.threads + + threads_save = deepcopy(args.threads) + for chromosome in tads_per_chromosome: + log.debug('tads_per_chromosome {}'.format(chromosome)) + domainsPerThread = len(chromosome) // args.threads + if domainsPerThread == 0 and len(chromosome) > 0: + domainsPerThread = 1 + args.threads = 1 + elif domainsPerThread > 0: + args.threads = threads_save + + all_data_collected = False + queue = [None] * args.threads + process = [None] * args.threads + thread_done = [False] * args.threads + # None --> first thread, process first element in list, ignore last one + # True --> middle thread: ignore first and last element in tad processing + # False --> last thread: ignore first element, process last one + thread_id = None for i in range(args.threads): - if queue[i] is not None and not queue[i].empty(): - queue_data = queue[i].get() - if 'Fail:' in queue_data: - fail_flag = True - fail_message = queue_data - else: - p_values_threads[i], accepted_left_inter_threads[i], \ - accepted_right_inter_threads[i], \ - accepted_intra_threads[i], rows_threads[i] = queue_data - - queue[i] = None - process[i].join() - process[i].terminate() - process[i] = None - thread_done[i] = True - all_data_collected = True - for thread in thread_done: - if not thread: - all_data_collected = False - time.sleep(1) - - # outfile_names = [item for sublist in outfile_names for item in sublist] - # target_list_name = [ - # item for sublist in target_list_name for item in sublist] - if fail_flag: - log.error(fail_message[6:]) - exit(1) + if args.threads == 1: + domainListThread = chromosome - p_values_list = [item for sublist in p_values_threads for item in sublist] - accepted_inter_left = [item for sublist in accepted_left_inter_threads for item in sublist] - accepted_inter_right = [item for sublist in accepted_right_inter_threads for item in sublist] - accepted_intra = [item for sublist in accepted_intra_threads for item in sublist] - rows = [item for sublist in rows_threads for item in sublist] + elif i == 0: + domainListThread = chromosome[i * domainsPerThread:((i + 1) * domainsPerThread) + 1] + thread_id = None + elif i < args.threads - 1: + domainListThread = chromosome[(i * domainsPerThread) - 1:((i + 1) * domainsPerThread) + 1] + thread_id = True + else: + domainListThread = chromosome[(i * domainsPerThread) - 1:] + thread_id = False + + if args.threads == 1: + thread_id = '' + + log.debug('len(domainListThread) {}'.format(len(domainListThread))) + log.debug('len(thread_id) {}'.format(thread_id)) + + queue[i] = Queue() + process[i] = Process(target=computeDifferentialTADs, kwargs=dict( + pMatrixTarget=hic_matrix_target, + pMatrixControl=hic_matrix_control, + pDomainList=domainListThread, + pCoolOrH5=is_cooler_control, + pPValue=args.pValue, + pThreadId=thread_id, + pQueue=queue[i] + ) + ) + + process[i].start() + fail_flag = False + fail_message = '' + while not all_data_collected: + for i in range(args.threads): + + if queue[i] is not None and not queue[i].empty(): + queue_data = queue[i].get() + if 'Fail:' in queue_data: + fail_flag = True + fail_message = queue_data + else: + stats_threads[i], p_values_threads[i], accepted_left_inter_threads[i], \ + accepted_right_inter_threads[i], \ + accepted_intra_threads[i], rows_threads[i] = queue_data + + queue[i] = None + process[i].join() + process[i].terminate() + process[i] = None + thread_done[i] = True + # elif queue[i] is None and + + all_data_collected = True + for thread in thread_done: + if not thread: + all_data_collected = False + time.sleep(1) + + # outfile_names = [item for sublist in outfile_names for item in sublist] + # target_list_name = [ + # item for sublist in target_list_name for item in sublist] + if fail_flag: + log.error(fail_message[6:]) + exit(1) + stats_chromosomes.append([item for sublist in stats_threads for item in sublist]) + p_values_chromosomes.append([item for sublist in p_values_threads for item in sublist]) + accepted_inter_left_chromosomes.append([item for sublist in accepted_left_inter_threads for item in sublist]) + accepted_inter_right_chromosomes.append([item for sublist in accepted_right_inter_threads for item in sublist]) + accepted_intra_chromosomes.append([item for sublist in accepted_intra_threads for item in sublist]) + rows_chromosomes.append([item for sublist in rows_threads for item in sublist]) + + log.debug('rows_threads {}'.format(rows_threads)) + + stats_list = [item for sublist in stats_chromosomes for item in sublist] + p_values_list = [item for sublist in p_values_chromosomes for item in sublist] + accepted_inter_left = [item for sublist in accepted_inter_left_chromosomes for item in sublist] + accepted_inter_right = [item for sublist in accepted_inter_right_chromosomes for item in sublist] + accepted_intra = [item for sublist in accepted_intra_chromosomes for item in sublist] + rows = [item for sublist in rows_chromosomes for item in sublist] + + stats_list = np.array(stats_list) p_values_list = np.array(p_values_list) accepted_inter_left = np.array(accepted_inter_left) accepted_inter_right = np.array(accepted_inter_right) @@ -395,7 +450,7 @@ def main(args=None): rows = np.array(rows) if args.mode == 'intra-TAD': - mask = accepted_intra + mask = np.array(accepted_intra, dtype=bool) elif args.mode == 'left-inter-TAD': if args.modeReject == 'all': mask = np.logical_and(accepted_inter_left, accepted_intra) @@ -416,15 +471,21 @@ def main(args=None): mask = np.logical_or(accepted_inter_left, accepted_inter_right) mask = np.logical_or(mask, accepted_intra) + log.debug('len(mask) {}'.format(len(mask))) + log.debug('mask.sum() {}'.format(mask.sum())) + log.debug('mask[:10] {}'.format(mask[:10])) + accepted_H0 = p_values_list[~mask] + accepted_H0_s = stats_list[~mask] rejected_H0 = p_values_list[mask] + rejected_H0_s = stats_list[mask] accepted_rows = rows[~mask] rejected_rows = rows[mask] with open(args.outFileNamePrefix + '_accepted.diff_tad', 'w') as file: header = '# Created with HiCExplorer\'s hicDifferentialTAD version ' + __version__ + '\n' header += '# H0 \'regions are equal\' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential.\n' header += '# Accepted regions with Wilcoxon rank-sum test to p-value: {} with used mode: {} and modeReject: {} \n'.format(args.pValue, args.mode, args.modeReject) - header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n' + header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\tW left-inter-TAD\tW right-inter-TAD\tW intra-TAD\n' file.write(header) for i, row in enumerate(accepted_rows): row_list = list(map(str, row)) @@ -432,13 +493,16 @@ def main(args=None): file.write('\t') pvalue_list = list(map(str, accepted_H0[i])) file.write('\t'.join(pvalue_list)) + file.write('\t') + stats_list = list(map(str, accepted_H0_s[i])) + file.write('\t'.join(stats_list)) file.write('\n') with open(args.outFileNamePrefix + '_rejected.diff_tad', 'w') as file: header = '# Created with HiCExplorer\'s hicDifferentialTAD version ' + __version__ + '\n' header += '# H0 \'regions are equal\' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.\n' header += '# Rejected regions with Wilcoxon rank-sum test to p-value: {} with used mode: {} and modeReject: {} \n'.format(args.pValue, args.mode, args.modeReject) - header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n' + header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\tW left-inter-TAD\tW right-inter-TAD\tW intra-TAD\n' file.write(header) @@ -448,4 +512,7 @@ def main(args=None): file.write('\t') pvalue_list = list(map(str, rejected_H0[i])) file.write('\t'.join(pvalue_list)) + file.write('\t') + stats_list = list(map(str, rejected_H0_s[i])) + file.write('\t'.join(stats_list)) file.write('\n') diff --git a/hicexplorer/hicFindRestSite.py b/hicexplorer/hicFindRestSite.py index 90ac31a1..a09603b3 100644 --- a/hicexplorer/hicFindRestSite.py +++ b/hicexplorer/hicFindRestSite.py @@ -11,7 +11,6 @@ from functools import partial from Bio import SeqIO from Bio.Seq import Seq -from Bio.Alphabet import generic_dna from hicexplorer._version import __version__ import logging @@ -39,7 +38,8 @@ def parse_arguments(args=None): 'is a regexp and can contain regexp specif syntax ' '(see https://docs.python.org/2/library/re.html). For example the pattern' 'CG..GC will find all occurrence of CG followed by any two bases and then GC.', - required=True) + required=True, + nargs='+') parserRequired.add_argument('--outFile', '-o', help='Name for the resulting bed file.', @@ -54,7 +54,7 @@ def parse_arguments(args=None): return parser -def find_pattern(pattern, fasta_file, out_file): +def find_pattern(pPattern, fasta_file, out_file): r""" Finds the occurrences of the match in the fasta file and saves a bed file. @@ -85,43 +85,43 @@ def find_pattern(pattern, fasta_file, out_file): >>> fa = open("/tmp/test.fa", 'w') >>> foo = fa.write(">chr1\nCTACGGTACGAACGTACGGTACGcgtaCGNAGTCATG\n") >>> fa.close() - >>> find_pattern("GTAC", "/tmp/test.fa", open("/tmp/test.bed", 'w')) + >>> find_pattern(["GTAC"], "/tmp/test.fa", open("/tmp/test.bed", 'w')) >>> open("/tmp/test.bed", 'r').readlines() ['chr1\t5\t9\t.\t0\t+\n', 'chr1\t13\t17\t.\t0\t+\n', 'chr1\t18\t22\t.\t0\t+\n', 'chr1\t24\t28\t.\t0\t+\n'] Test with non palindromic sequence with regexp - >>> find_pattern("CG.AG", "/tmp/test.fa", open("/tmp/test.bed", 'w')) + >>> find_pattern(["CG.AG"], "/tmp/test.fa", open("/tmp/test.bed", 'w')) >>> open("/tmp/test.bed", 'r').readlines() ['chr1\t0\t5\t.\t0\t-\n', 'chr1\t27\t32\t.\t0\t+\n'] """ - # get the reverse complement of the pattern - rev_compl = str(Seq(pattern, generic_dna).reverse_complement()) - temp = NamedTemporaryFile(suffix=".bed", delete=False, mode='wt') - try: - fasta_file_name = fasta_file.name - except AttributeError: - fasta_file_name = fasta_file - - encoding = guess_type(fasta_file_name)[1] # uses file extension - _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open - - with _open(fasta_file_name) as f: - for record in SeqIO.parse(f, 'fasta', generic_dna): - # find all the occurrences of pattern - for match in re.finditer(pattern, str(record.seq), re.IGNORECASE): - _ = temp.write('{}\t{}\t{}\t.\t0\t+\n'.format(record.name, - match.start(), - match.end())) - if rev_compl != pattern: - # search for the reverse complement only if the pattern is not palindromic - for match in re.finditer(rev_compl, str(record.seq), re.IGNORECASE): - _ = temp.write('{}\t{}\t{}\t.\t0\t-\n'.format(record.name, + + for pattern in pPattern: + rev_compl = str(Seq(pattern).reverse_complement()) + try: + fasta_file_name = fasta_file.name + except AttributeError: + fasta_file_name = fasta_file + + encoding = guess_type(fasta_file_name)[1] # uses file extension + _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open + + with _open(fasta_file_name) as f: + for record in SeqIO.parse(f, 'fasta'): + # find all the occurrences of pattern + for match in re.finditer(pattern, str(record.seq), re.IGNORECASE): + _ = temp.write('{}\t{}\t{}\t.\t0\t+\n'.format(record.name, match.start(), match.end())) - log.info("Sorting file ...") + if rev_compl != pattern: + # search for the reverse complement only if the pattern is not palindromic + for match in re.finditer(rev_compl, str(record.seq), re.IGNORECASE): + _ = temp.write('{}\t{}\t{}\t.\t0\t-\n'.format(record.name, match.start(), + match.end())) + + log.info("Sorting file ...") tmpfile_name = temp.name temp.close() subprocess.check_output(["cat", tmpfile_name]) diff --git a/hicexplorer/hicFindTADs.py b/hicexplorer/hicFindTADs.py index f2d5b946..f1648a1f 100644 --- a/hicexplorer/hicFindTADs.py +++ b/hicexplorer/hicFindTADs.py @@ -38,16 +38,12 @@ def parse_arguments(args=None): positions having a local TAD-separation score minimum. The TAD-separation score is measured using the z-score of the Hi-C matrix and is defined as the mean zscore of all the matrix contacts between the left and right regions (diamond). - To find the TADs, the program needs to compute first the TAD scores at different window sizes. Then, the results of that computation are used to call the TADs. This is convenient to test different filtering criteria quickly as the demanding step is the computation of TAD-separation scores. - A simple example usage is: - $ hicFindTads -m hic_matrix.h5 --outPrefix TADs --correctForMultipleTesting fdr - The bedgraph file produced by this tool can be used to plot the so-called insulation score along the genome or at specific regions. This score is much more reliable across samples than the number of TADs or the TADs width that can vary depending on the sequencing depth because of the lack @@ -181,7 +177,6 @@ def get_cut_weight_by_bin_id(matrix, cut, depth, return_mean=False): """ like get_cut_weight which is the 'diamond' representing the counts from a region -dept to +depth from the given bin position (cut): - """ if cut < 0 or cut > matrix.shape[0]: return None @@ -209,7 +204,6 @@ def get_idx_of_bins_at_given_distance(hic_matrix, idx, window_len): ---------- idx reference index window_len distance in bp - Returns ------- tuple, with left and right bin indices @@ -242,7 +236,6 @@ def get_cut_weight(hic_matrix, cut, window_len, return_mean=False): """ 'diamond' (when matrix is rotated 45 degrees) representing the counts from a region -window_len to +window_len from the given bin position (cut): - """ if cut < 0 or cut > hic_matrix.matrix.shape[0]: return None @@ -268,7 +261,6 @@ def get_triangle(hic_matrix, cut, window_len, return_mean=False): """ like get_cut_weight which is the 'diamond' representing the counts from a region -window_len to +window_len from the given bin position (cut): - """ if cut < 0 or cut > hic_matrix.matrix.shape[0]: return None @@ -291,7 +283,6 @@ def remove_lower_triangle(matrix): def get_incremental_step_size(min_win_size, max_win_size, start_step_len): """ generates a list of incremental windows sizes (measured in bins) - :param min_win_size: starting window size :param max_win_size: end window size :param start_step_len: start length @@ -313,7 +304,6 @@ def get_incremental_step_size(min_win_size, max_win_size, start_step_len): def compute_matrix(bins_list, min_win_size=8, max_win_size=50, step_len=2): """ Receives a number of bins for which the tad-score should be computed. - Parameters ---------- hic_ma Hi-C matrix object @@ -321,10 +311,8 @@ def compute_matrix(bins_list, min_win_size=8, max_win_size=50, step_len=2): min_win_size max_win_size step_len - Returns ------- - """ """ @@ -366,7 +354,6 @@ def __init__(self, matrix, num_processors=1, max_depth=None, min_depth=None, ste min_boundary_distance=None, use_zscore=True, p_correct_for_multiple_testing="fdr", p_threshold_comparisons=0.01, pChromosomes=None): """ - Parameters ---------- matrix Either a filename or a Hi-C Matrix object @@ -433,7 +420,6 @@ def set_variables(self): """ Checks the value of the max_depth, min_depth and step variables, setting default parameters if neccesary. - Returns ------- None @@ -482,11 +468,9 @@ def peakdetect(y_axis, x_axis=None, lookahead=3, delta=0, chrom=None): """ Based on the MATLAB script at: http://billauer.co.il/peakdet.html - function for detecting local maximum and minimum in a signal. Discovers peaks by searching for values which are surrounded by lower or larger values for maximum and minimum respectively - keyword arguments: :param: y_axis -- A list containing the signal over which to find peaks :param: x_axis -- (optional) A x-axis whose values correspond to the y_axis list @@ -498,8 +482,6 @@ def peakdetect(y_axis, x_axis=None, lookahead=3, delta=0, chrom=None): the following points, before a peak may be considered a peak. Useful to hinder the function from picking up false peaks towards to end of the signal. To work well delta should be set to delta >= RMSnoise * 5. - - :return: -- two lists [max_peaks, min_peaks] containing the positive and negative peaks respectively. Each cell of the lists contains a tuple of: (position, peak_value) @@ -596,18 +578,15 @@ def delta_wrt_window(min_idx_list, matrix_avg, chrom, window_len=10): delta is defined as the difference between the TAD-separation score at the minimum with respect to each of the TAD-separation scores of the `window_len` to the left, plus the `window_len` to the right of each minimum. The minimum itself is excluded. - Parameters ---------- matrix TAD score matrix for different window sizes chrom list of chrom names for each matrix row window_len the length of the window to look for the local TAD-score average - Returns ------- A dict of each minima delta to the mean of the TAD-separation score surrounding the minima. The keys are the min_idx - """ # compute the start and end points of the chromosomes @@ -666,13 +645,9 @@ def hierarchical_clustering(self, boundary_list, clusters_cutoff=[]): (chrom, start, value) :param clusters_cutoff: List of values to separate clusters. The clusters found at those value thresholds are returned. - - :return: z_value, clusters - For z_value, the format used is similar as the scipy.cluster.hierarchy.linkage() function which is described as follows: - A 4 by :math:`(n-1)` matrix ``z_value`` is returned. At the :math:`i`-th iteration, clusters with indices ``z_value[i, 0]`` and ``z_value[i, 1]`` are combined to form cluster :math:`n + i`. A @@ -681,11 +656,9 @@ def hierarchical_clustering(self, boundary_list, clusters_cutoff=[]): clusters ``z_value[i, 0]`` and ``z_value[i, 1]`` is given by ``z_value[i, 2]``. The fourth value ``z_value[i, 3]`` represents the number of original observations in the newly formed cluster. - The difference is that instead of a 4 times n-1 array, a 6 times n-1 array is returned. Where positions 4, and 5 correspond to the genomic coordinates of ``z_value[i, 0]`` and ``z_value[i, 1]`` - """ # run the hierarchical clustering per chromosome if clusters_cutoff: @@ -737,11 +710,8 @@ def cluster_to_regions(clusters_, chrom_name): :param clusters_: cluster ids :param chrom_name: chromosome name :return: list of tuples with (chrom_name, start, end) - Example: - clusters = [set(1,2,3), set(4,5,10)] - """ start_list = [] end_list = [] @@ -826,7 +796,6 @@ def cluster_to_regions(clusters_, chrom_name): def save_linkage(Z, file_name): """ - :param Z: Z has a format similar to the scipy.cluster.linkage matrix (see function hierarchical_clustering). :param file_name: File name to save the results @@ -881,7 +850,6 @@ def save_bedgraph_matrix(self, outfile): """ Save matrix as chrom, start, end ,row, values separated by tab I call this a bedgraph matrix and the ending is .bm - Returns ------- None @@ -906,7 +874,6 @@ def save_bedgraph_matrix(self, outfile): def save_clusters(clusters, file_prefix): """ - :param clusters: is a dictionary whose key is the cut of used to create it. the value is a list of tuples, each representing a genomec interval as ('chr', start, end). @@ -1050,11 +1017,9 @@ def save_domains_and_boundaries(self, prefix): def compute_spectra_matrix(self, perchr=True): """ Uses multiple processors to compute the TAD-score - Returns ------- bed matrix (chrom start end value1 value2 ... value_n) - """ # remove self counts @@ -1204,15 +1169,12 @@ def min_pvalue(self, min_idx): """ For each putative local minima, find the -window_len diammond and the +window_len diamond and compare with the local minima using wilcoxon rank sum. - Parameters ---------- min_idx list of local minima - Returns ------- list of p-values per each local minima - """ log.info("Computing p-values for window length: {}\n".format(self.min_depth)) @@ -1338,10 +1300,8 @@ def print_args(args): Parameters ---------- args - Returns ------- - """ for key, value in args._get_kwargs(): log.info("{}:\t{}\n".format(key, value)) diff --git a/hicexplorer/hicHyperoptDetectLoops.py b/hicexplorer/hicHyperoptDetectLoops.py index 74e15cd0..1a97b3f5 100644 --- a/hicexplorer/hicHyperoptDetectLoops.py +++ b/hicexplorer/hicHyperoptDetectLoops.py @@ -49,6 +49,11 @@ def parse_arguments(args=None): default=10000, help='Resolution of matrix' ' (Default: %(default)s).') + parserOpt.add_argument('--chrPrefixLoops', '-cl', + help='Adding / removing / do nothing a \'chr\'-prefix to chromosome name of the loops.', + choices=[None, 'add', 'remove'], + default=None + ) parserOpt.add_argument('--threads', '-t', help='Number of threads (uses the python multiprocessing module)' ' (Default: %(default)s).', @@ -70,14 +75,13 @@ def parse_arguments(args=None): return parser -def compute_score(pLoopFile, pProteinFile, pMaximumNumberOfLoops, pResolution): +def compute_score(pLoopFile, pProteinFile, pMaximumNumberOfLoops, pResolution, pChrPrefixLoops): with open(pLoopFile, 'r') as file: lines = file.readlines() if len(lines) == 0: return 1 outfile_statistics = NamedTemporaryFile() - args = "--data {} --protein {} -cl --resolution {} --outFileName {}".format(pLoopFile, pProteinFile, pResolution, outfile_statistics.name).split() - print(args) + args = "--data {} --protein {} -cl {} --resolution {} --outFileName {}".format(pLoopFile, pProteinFile, pChrPrefixLoops, pResolution, outfile_statistics.name).split() hicValidateLocations.main(args) data_dict = {} @@ -108,7 +112,7 @@ def objective(pArgs): pArgs['maxLoopDistance'], pArgs['threads'], pArgs['threads']).split() hicDetectLoops.main(args) - error_score = compute_score(outfile_loop.name, pArgs['proteinFile'], pArgs['maximumNumberOfLoops'], pArgs['resolution']) + error_score = compute_score(outfile_loop.name, pArgs['proteinFile'], pArgs['maximumNumberOfLoops'], pArgs['resolution'], pArgs['chrPrefixLoops']) print('Error score: {}'.format(error_score)) return error_score @@ -116,7 +120,6 @@ def objective(pArgs): def main(args=None): args = parse_arguments().parse_args(args) - space = { 'pit': hp.uniform('pit', 0, 100), @@ -130,7 +133,8 @@ def main(args=None): 'proteinFile': args.proteinFile, 'maximumNumberOfLoops': args.maximumNumberOfLoops, 'resolution': args.resolution, - 'threads': args.threads + 'threads': args.threads, + 'chrPrefixLoops': args.chrPrefixLoops } diff --git a/hicexplorer/hicHyperoptDetectLoopsHiCCUPS.py b/hicexplorer/hicHyperoptDetectLoopsHiCCUPS.py index 823213f4..11b9b4b7 100755 --- a/hicexplorer/hicHyperoptDetectLoopsHiCCUPS.py +++ b/hicexplorer/hicHyperoptDetectLoopsHiCCUPS.py @@ -49,6 +49,11 @@ def parse_arguments(args=None): default=10000, help='Resolution of matrix' ' (Default: %(default)s).') + parserOpt.add_argument('--chrPrefixLoops', '-cl', + help='Adding / removing / do nothing a \'chr\'-prefix to chromosome name of the loops.', + choices=[None, 'add', 'remove'], + default=None + ) parserOpt.add_argument('--runs', type=int, default=100, @@ -80,13 +85,13 @@ def parse_arguments(args=None): return parser -def compute_score(pLoopFile, pProteinFile, pMaximumNumberOfLoops, pResolution): +def compute_score(pLoopFile, pProteinFile, pMaximumNumberOfLoops, pResolution, pChrPrefixLoops): with open(pLoopFile, 'r') as file: lines = file.readlines() if len(lines) == 0: return 1 outfile_statistics = NamedTemporaryFile() - args = "--data {} --protein {} -cl --resolution {} --outFileName {}".format(pLoopFile, pProteinFile, pResolution, outfile_statistics.name).split() + args = "--data {} --protein {} -cl {} --resolution {} --outFileName {}".format(pLoopFile, pProteinFile, pChrPrefixLoops, pResolution, outfile_statistics.name).split() hicValidateLocations.main(args) data_dict = {} @@ -116,7 +121,7 @@ def objective(pArgs): subprocess.check_output(['bash', '-c', bashCommand]) bashCommand = 'bedtools sort -i {}/merged_loops.bedpe > {}/merged_sorted.bedpe'.format(output_folder, output_folder) subprocess.check_output(['bash', '-c', bashCommand]) - error_score = compute_score(output_folder + '/merged_sorted.bedpe', pArgs['proteinFile'], pArgs['maximumNumberOfLoops'], pArgs['resolution']) + error_score = compute_score(output_folder + '/merged_sorted.bedpe', pArgs['proteinFile'], pArgs['maximumNumberOfLoops'], pArgs['resolution'], pArgs['chrPrefixLoops']) print('Error score: {}'.format(error_score)) return error_score @@ -135,7 +140,8 @@ def main(args=None): 'juicer': args.juicerPath, 'restricted': '--restricted' if args.restricted else '', 'cpu': '--cpu' if args.cpu else '', - 'threads': args.threads + 'threads': args.threads, + 'chrPrefixLoops': args.chrPrefixLoops } diff --git a/hicexplorer/hicInterIntraTAD.py b/hicexplorer/hicInterIntraTAD.py new file mode 100644 index 00000000..cd06cff5 --- /dev/null +++ b/hicexplorer/hicInterIntraTAD.py @@ -0,0 +1,514 @@ +import pandas as pd +import argparse +from multiprocessing import Process, Queue +import time +import traceback +from copy import deepcopy +import matplotlib.pyplot as plt +import matplotlib as mpl +import logging +log = logging.getLogger(__name__) +from hicmatrix import HiCMatrix as hm + +from hicexplorer.utilities import check_cooler +from hicexplorer._version import __version__ + + +def parse_arguments(args=None): + + parser = argparse.ArgumentParser( + formatter_class=argparse.RawDescriptionHelpFormatter, + add_help=False, + description=""" +Extracts and computes different inter and intra TAD values and ratios.""") + + parserRequired = parser.add_argument_group('Required arguments') + + parserRequired.add_argument('--matrix', '-m', + help='The matrix which was used to compute the TADs', + required=False) + parserRequired.add_argument('--tadDomains', '-td', + help='The TADs domain file computed by hicFindTADs.', + required=False) + parserRequired.add_argument('--outFileName', '-o', + help='Outfile name', + required=False, + default='output_interintra_tad.tzt' + ) + parserOpt = parser.add_argument_group('Optional arguments') + parserOpt.add_argument('--outFileNameRatioPlot', '-op', + help='Outfile name for the inter-left/intra vs inter-right/intra ratio plot', + required=False, + default='ratio.png' + ) + parserOpt.add_argument('--fontsize', + help='Fontsize in the plot for x and y axis.', + type=float, + default=15) + parserOpt.add_argument('--dpi', + help='The dpi of the scatter plot.', + required=False, + default=300, + type=int) + parserOpt.add_argument('--threads', '-t', + help='Number of threads to use, the parallelization is implemented per chromosome' + ' (Default: %(default)s).', + required=False, + default=4, + type=int + ) + parserOpt.add_argument('--help', '-h', action='help', help='show this help message and exit') + + parserOpt.add_argument('--version', action='version', + version='%(prog)s {}'.format(__version__)) + return parser + + +def readDomainBoundaries(pFile): + domains_df = pd.read_csv(pFile, sep='\t', header=None)[[0, 1, 2, 3, 4, 5]] + + return domains_df + + +def computeInterIntraTADs(pMatrix, pDomainList, pCoolOrH5, pThreadId, pQueue): + try: + + inter_left_sum_list = [] + inter_right_sum_list = [] + inter_left_densit_list = [] + inter_right_density_list = [] + inter_left_number_of_contacts_list = [] + inter_right_number_of_contacts_list = [] + inter_left_number_of_contacts_nnz_list = [] + inter_right_number_of_contacts_nzz_list = [] + + intra_sum_list = [] + intra_number_of_contacts_list = [] + intra_number_of_contacts_nnz_list = [] + intra_density_list = [] + inter_left_intra_ratio_list = [] + inter_right_intra_ratio_list = [] + inter_left_inter_right_intra_ratio_list = [] + + rows = [] + + chromosome_list = pDomainList + for i, row in enumerate(chromosome_list): + + if pThreadId is None: + log.debug('first thread') + if i == len(chromosome_list) - 1: + continue + elif pThreadId == True: + log.debug('middle thread') + + if i == 0 or i == len(chromosome_list) - 1: + log.debug('i: {}'.format(i)) + log.debug('len(chromosome_list): {}'.format(len(chromosome_list))) + + continue + elif pThreadId == False: + log.debug('last thread') + + if i == 0: + continue + + if i - 1 >= 0: + chromosom = chromosome_list[i - 1][0] + start = chromosome_list[i - 1][1] + else: + chromosom = chromosome_list[i][0] + start = chromosome_list[i][1] + if i + 1 < len(chromosome_list): + end = chromosome_list[i + 1][2] + else: + end = chromosome_list[i][2] + # midpos = row[1] + ((row[2] - row[1]) / 2) + + if pCoolOrH5: + + # # get intra-TAD data + hic_matrix = hm.hiCMatrix( + pMatrixFile=pMatrix, pChrnameList=[str(row[0]) + ':' + str(row[1]) + '-' + str(row[2])]) + matrix = hic_matrix.matrix + + hic_matrix_inter_tad = hm.hiCMatrix( + pMatrixFile=pMatrix, pChrnameList=[str(chromosom) + ':' + str(start) + '-' + str(end)]) + + matrix_inter_tad = hic_matrix_inter_tad.matrix + + else: + # in case of h5 pMatrixTarget is already a HiCMatrix object + hic_matrix = pMatrix + hic_matrix_inter_tad = pMatrix + indices = hic_matrix.getRegionBinRange(str(row[0]), row[1], row[2]) + + matrix = hic_matrix.matrix[indices[0]:indices[1], indices[0]:indices[1]] + matrix_inter_tad = pMatrix.matrix + + # matrix = matrix.flatten() + + # get index position left tad with tad + left_boundary_index = hic_matrix_inter_tad.getRegionBinRange(str(chromosom), row[1], row[1])[0] + if pCoolOrH5: + outer_left_boundary_index = 0 + + outer_right_boundary_index = -1 + + else: + outer_left_boundary_index = hic_matrix_inter_tad.getRegionBinRange(str(chromosom), start, end)[0] + + outer_right_boundary_index = hic_matrix_inter_tad.getRegionBinRange(str(chromosom), start, end)[1] + + if i + 1 < len(chromosome_list) and not pCoolOrH5: + # get index position right tad with tad + right_boundary_index = hic_matrix_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] + elif i + 1 < len(chromosome_list): + right_boundary_index = hic_matrix_inter_tad.getRegionBinRange(str(chromosom), row[2], row[2])[0] + + if i - 1 >= 0 and i + 1 < len(chromosome_list): + intertad_left = matrix_inter_tad[outer_left_boundary_index:left_boundary_index, left_boundary_index:right_boundary_index] + intertad_right = matrix_inter_tad[left_boundary_index:right_boundary_index, right_boundary_index:outer_right_boundary_index] + + elif i - 1 < 0 and i + 1 < len(chromosome_list): + intertad_right = matrix_inter_tad[left_boundary_index:right_boundary_index, right_boundary_index:outer_right_boundary_index] + + elif i - 1 > 0 and i + 1 >= len(chromosome_list): + intertad_left = matrix_inter_tad[outer_left_boundary_index:left_boundary_index, left_boundary_index:right_boundary_index] + + inter_left_sum = 0 + inter_right_sum = 0 + inter_left_density = 0 + inter_right_density = 0 + inter_left_number_of_contacts = 0 + inter_right_number_of_contacts = 0 + inter_left_number_of_contacts_nnz = 0 + inter_right_number_of_contacts_nzz = 0 + + intra_sum = matrix.sum() + intra_number_of_contacts = matrix.shape[0] * matrix.shape[1] + intra_number_of_contacts_nnz = matrix.nnz + intra_density = intra_number_of_contacts_nnz / intra_number_of_contacts + # both inter, left and right is available + if i - 1 >= 0 and i + 1 < len(chromosome_list): + # intertad_left = intertad_left.flatten() + # intertad_right = intertad_right.flatten() + inter_left_sum = intertad_left.sum() + inter_right_sum = intertad_right.sum() + + inter_left_number_of_contacts = intertad_left.shape[0] * intertad_left.shape[1] + inter_right_number_of_contacts = intertad_right.shape[0] * intertad_right.shape[1] + inter_left_number_of_contacts_nnz = intertad_left.nnz + inter_right_number_of_contacts_nzz = intertad_right.nnz + + inter_left_density = inter_left_number_of_contacts_nnz / inter_left_number_of_contacts + inter_right_density = inter_right_number_of_contacts_nzz / inter_right_number_of_contacts + # statistic_left, significance_level_left = ranksums(intertad_left, intertad_left_control) + # statistic_right, significance_level_right = ranksums(intertad_right, intertad_right_control) + elif i - 1 < 0 and i + 1 < len(chromosome_list): + # inter right is available + # intertad_right = intertad_right.flatten() + inter_right_sum = intertad_right.sum() + inter_right_number_of_contacts = intertad_right.shape[0] * intertad_right.shape[1] + inter_right_number_of_contacts_nzz = intertad_right.nnz + inter_right_density = inter_right_number_of_contacts_nzz / inter_right_number_of_contacts + + # statistic_right, significance_level_right = ranksums(intertad_right, intertad_right_control) + elif i - 1 > 0 and i + 1 >= len(chromosome_list): + # inter left is available + + # intertad_left = intertad_left.flatten() + inter_left_sum = intertad_left.sum() + inter_left_number_of_contacts = intertad_left.shape[0] * intertad_left.shape[1] + inter_left_number_of_contacts_nnz = intertad_left.nnz + inter_left_density = inter_left_number_of_contacts_nnz / inter_left_number_of_contacts + + # statistic_left, significance_level_left = ranksums(intertad_left, intertad_left_control) + + inter_left_intra_ratio = inter_left_sum / intra_sum + inter_right_intra_ratio = inter_right_sum / intra_sum + inter_left_inter_right_intra_ratio = (inter_left_sum + inter_right_sum) / intra_sum + + inter_left_sum_list.append(inter_left_sum) + inter_right_sum_list.append(inter_right_sum) + inter_left_densit_list.append(inter_left_density) + inter_right_density_list.append(inter_right_density) + inter_left_number_of_contacts_list.append(inter_left_number_of_contacts) + inter_right_number_of_contacts_list.append(inter_right_number_of_contacts) + inter_left_number_of_contacts_nnz_list.append(inter_left_number_of_contacts_nnz) + inter_right_number_of_contacts_nzz_list.append(inter_right_number_of_contacts_nzz) + + intra_sum_list.append(intra_sum) + intra_number_of_contacts_list.append(intra_number_of_contacts) + intra_number_of_contacts_nnz_list.append(intra_number_of_contacts_nnz) + intra_density_list.append(intra_density) + inter_left_intra_ratio_list.append(inter_left_intra_ratio) + inter_right_intra_ratio_list.append(inter_right_intra_ratio) + inter_left_inter_right_intra_ratio_list.append(inter_left_inter_right_intra_ratio) + + rows.append(row) + except Exception as exp: + pQueue.put('Fail: ' + str(exp) + traceback.format_exc()) + return + pQueue.put([inter_left_sum_list, + inter_right_sum_list, + inter_left_densit_list, + inter_right_density_list, + inter_left_number_of_contacts_list, + inter_right_number_of_contacts_list, + inter_left_number_of_contacts_nnz_list, + inter_right_number_of_contacts_nzz_list, + intra_sum_list, + intra_number_of_contacts_list, + intra_number_of_contacts_nnz_list, + intra_density_list, + inter_left_intra_ratio_list, + inter_right_intra_ratio_list, + inter_left_inter_right_intra_ratio_list, + rows]) + + +def main(args=None): + args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 + + # read domains file + domains_df = readDomainBoundaries(args.tadDomains) + # log.debug('len(domains_df) {}'.format(len(domains_df))) + domains = domains_df.values.tolist() + old_chromosome = None + + tads_per_chromosome = [] + + for j in range(len(domains)): + if old_chromosome is None: + old_chromosome = domains[j][0] + per_chromosome = [] + per_chromosome.append(domains[j]) + + elif old_chromosome == domains[j][0]: + per_chromosome.append(domains[j]) + continue + else: + tads_per_chromosome.append(per_chromosome) + per_chromosome = [] + per_chromosome.append(domains[j]) + old_chromosome = domains[j][0] + tads_per_chromosome.append(per_chromosome) + + # read full h5 or only region if cooler + is_cooler = check_cooler(args.matrix) + + if not is_cooler: + hic_matrix = hm.hiCMatrix(args.matrix) + else: + hic_matrix = args.matrix + + inter_left_sum_list_chromosomes = [] + inter_right_sum_list_chromosomes = [] + inter_left_density_list_chromosomes = [] + inter_right_density_list_chromosomes = [] + inter_left_number_of_contacts_list_chromosomes = [] + inter_right_number_of_contacts_list_chromosomes = [] + inter_left_number_of_contacts_nnz_list_chromosomes = [] + inter_right_number_of_contacts_nzz_list_chromosomes = [] + + intra_sum_list_chromosomes = [] + intra_number_of_contacts_list_chromosomes = [] + intra_number_of_contacts_nnz_list_chromosomes = [] + intra_density_list_chromosomes = [] + inter_left_intra_ratio_list_chromosomes = [] + inter_right_intra_ratio_list_chromosomes = [] + inter_left_inter_right_intra_ratio_list_chromosomes = [] + + rows_chromosomes = [] + + inter_left_sum_list_threads = [[]] * args.threads + inter_right_sum_list_threads = [[]] * args.threads + inter_left_density_list_threads = [[]] * args.threads + inter_right_density_list_threads = [[]] * args.threads + inter_left_number_of_contacts_list_threads = [[]] * args.threads + inter_right_number_of_contacts_list_threads = [[]] * args.threads + inter_left_number_of_contacts_nnz_list_threads = [[]] * args.threads + inter_right_number_of_contacts_nzz_list_threads = [[]] * args.threads + + intra_sum_list_threads = [[]] * args.threads + intra_number_of_contacts_list_threads = [[]] * args.threads + intra_number_of_contacts_nnz_list_threads = [[]] * args.threads + intra_density_list_threads = [[]] * args.threads + inter_left_intra_ratio_list_threads = [[]] * args.threads + inter_right_intra_ratio_list_threads = [[]] * args.threads + inter_left_inter_right_intra_ratio_list_threads = [[]] * args.threads + + rows_threads = [[]] * args.threads + + threads_save = deepcopy(args.threads) + for chromosome in tads_per_chromosome: + # log.debug('tads_per_chromosome {}'.format(chromosome)) + domainsPerThread = len(chromosome) // args.threads + if domainsPerThread == 0 and len(chromosome) > 0: + domainsPerThread = 1 + args.threads = 1 + elif domainsPerThread > 0: + args.threads = threads_save + + all_data_collected = False + queue = [None] * args.threads + process = [None] * args.threads + thread_done = [False] * args.threads + # None --> first thread, process first element in list, ignore last one + # True --> middle thread: ignore first and last element in tad processing + # False --> last thread: ignore first element, process last one + thread_id = None + for i in range(args.threads): + + if args.threads == 1: + domainListThread = chromosome + + elif i == 0: + domainListThread = chromosome[i * domainsPerThread:((i + 1) * domainsPerThread) + 1] + thread_id = None + elif i < args.threads - 1: + domainListThread = chromosome[(i * domainsPerThread) - 1:((i + 1) * domainsPerThread) + 1] + thread_id = True + + else: + domainListThread = chromosome[(i * domainsPerThread) - 1:] + thread_id = False + + if args.threads == 1: + thread_id = '' + + # log.debug('len(domainListThread) {}'.format(len(domainListThread))) + # log.debug('len(thread_id) {}'.format(thread_id)) + + queue[i] = Queue() + process[i] = Process(target=computeInterIntraTADs, kwargs=dict( + pMatrix=hic_matrix, + # pMatrixControl=hic_matrix_control, + pDomainList=domainListThread, + pCoolOrH5=is_cooler, + # pPValue=args.pValue, + pThreadId=thread_id, + pQueue=queue[i] + ) + ) + + process[i].start() + fail_flag = False + fail_message = '' + while not all_data_collected: + for i in range(args.threads): + + if queue[i] is not None and not queue[i].empty(): + queue_data = queue[i].get() + if 'Fail:' in queue_data: + fail_flag = True + fail_message = queue_data + else: + inter_left_sum_list_threads[i], \ + inter_right_sum_list_threads[i], \ + inter_left_density_list_threads[i], \ + inter_right_density_list_threads[i], \ + inter_left_number_of_contacts_list_threads[i], \ + inter_right_number_of_contacts_list_threads[i], \ + inter_left_number_of_contacts_nnz_list_threads[i], \ + inter_right_number_of_contacts_nzz_list_threads[i], \ + intra_sum_list_threads[i], \ + intra_number_of_contacts_list_threads[i], \ + intra_number_of_contacts_nnz_list_threads[i], \ + intra_density_list_threads[i], \ + inter_left_intra_ratio_list_threads[i], \ + inter_right_intra_ratio_list_threads[i], \ + inter_left_inter_right_intra_ratio_list_threads[i], \ + rows_threads[i] = queue_data + + queue[i] = None + process[i].join() + process[i].terminate() + process[i] = None + thread_done[i] = True + # elif queue[i] is None and + + all_data_collected = True + for thread in thread_done: + if not thread: + all_data_collected = False + time.sleep(1) + + if fail_flag: + log.error(fail_message[6:]) + exit(1) + + inter_left_sum_list_chromosomes.append([item for sublist in inter_left_sum_list_threads for item in sublist]) + inter_right_sum_list_chromosomes.append([item for sublist in inter_right_sum_list_threads for item in sublist]) + inter_left_density_list_chromosomes.append([item for sublist in inter_left_density_list_threads for item in sublist]) + inter_right_density_list_chromosomes.append([item for sublist in inter_right_density_list_threads for item in sublist]) + inter_left_number_of_contacts_list_chromosomes.append([item for sublist in inter_left_number_of_contacts_list_threads for item in sublist]) + inter_right_number_of_contacts_list_chromosomes.append([item for sublist in inter_right_number_of_contacts_list_threads for item in sublist]) + inter_left_number_of_contacts_nnz_list_chromosomes.append([item for sublist in inter_left_number_of_contacts_nnz_list_threads for item in sublist]) + inter_right_number_of_contacts_nzz_list_chromosomes.append([item for sublist in inter_right_number_of_contacts_nzz_list_threads for item in sublist]) + + intra_sum_list_chromosomes.append([item for sublist in intra_sum_list_threads for item in sublist]) + intra_number_of_contacts_list_chromosomes.append([item for sublist in intra_number_of_contacts_list_threads for item in sublist]) + intra_number_of_contacts_nnz_list_chromosomes.append([item for sublist in intra_number_of_contacts_nnz_list_threads for item in sublist]) + intra_density_list_chromosomes.append([item for sublist in intra_density_list_threads for item in sublist]) + inter_left_intra_ratio_list_chromosomes.append([item for sublist in inter_left_intra_ratio_list_threads for item in sublist]) + inter_right_intra_ratio_list_chromosomes.append([item for sublist in inter_right_intra_ratio_list_threads for item in sublist]) + inter_left_inter_right_intra_ratio_list_chromosomes.append([item for sublist in inter_left_inter_right_intra_ratio_list_threads for item in sublist]) + + rows_chromosomes.append([item for sublist in rows_threads for item in sublist]) + + inter_left_sum_list = [item for sublist in inter_left_sum_list_chromosomes for item in sublist] + inter_right_sum_list = [item for sublist in inter_right_sum_list_chromosomes for item in sublist] + inter_left_density_list = [item for sublist in inter_left_density_list_chromosomes for item in sublist] + inter_right_density_list = [item for sublist in inter_right_density_list_chromosomes for item in sublist] + inter_left_number_of_contacts_list = [item for sublist in inter_left_number_of_contacts_list_chromosomes for item in sublist] + inter_right_number_of_contacts_list = [item for sublist in inter_right_number_of_contacts_list_chromosomes for item in sublist] + inter_left_number_of_contacts_nnz_list = [item for sublist in inter_left_number_of_contacts_nnz_list_chromosomes for item in sublist] + inter_right_number_of_contacts_nzz_list = [item for sublist in inter_right_number_of_contacts_nzz_list_chromosomes for item in sublist] + + intra_sum_list = [item for sublist in intra_sum_list_chromosomes for item in sublist] + intra_number_of_contacts_list = [item for sublist in intra_number_of_contacts_list_chromosomes for item in sublist] + intra_number_of_contacts_nnz_list = [item for sublist in intra_number_of_contacts_nnz_list_chromosomes for item in sublist] + intra_density_list = [item for sublist in intra_density_list_chromosomes for item in sublist] + inter_left_intra_ratio_list = [item for sublist in inter_left_intra_ratio_list_chromosomes for item in sublist] + inter_right_intra_ratio_list = [item for sublist in inter_right_intra_ratio_list_chromosomes for item in sublist] + inter_left_inter_right_intra_ratio_list = [item for sublist in inter_left_inter_right_intra_ratio_list_chromosomes for item in sublist] + + rows = [item for sublist in rows_chromosomes for item in sublist] + + with open(args.outFileName, 'w') as file: + header = '# Created with HiCExplorer\'s hicInterIntraTAD version ' + __version__ + '\n' + header += '# Chromosome\tstart\tend\tname\tscore\tstrand\tinter_left_sum\tinter_right_sum\tinter_left_density\tinter_right_density\tinter_left_number_of_contacts\tinter_right_number_of_contacts\t' \ + 'inter_left_number_of_contacts_nnz\tinter_right_number_of_contacts_nnz\tintra_sum\tintra_number_of_contacts\tintra_number_of_contacts_nnz\tintra_density\tinter_left_intra_ratio\tinter_right_intra_ratio\tinter_left_inter_right_intra_ratio\n' + file.write(header) + for i, row in enumerate(rows): + row_list = list(map(str, row)) + + file.write('\t'.join(row_list)) + + file.write('\t{}'.format(inter_left_sum_list[i])) + file.write('\t{}'.format(inter_right_sum_list[i])) + file.write('\t{}'.format(inter_left_density_list[i])) + file.write('\t{}'.format(inter_right_density_list[i])) + file.write('\t{}'.format(inter_left_number_of_contacts_list[i])) + file.write('\t{}'.format(inter_right_number_of_contacts_list[i])) + file.write('\t{}'.format(inter_left_number_of_contacts_nnz_list[i])) + file.write('\t{}'.format(inter_right_number_of_contacts_nzz_list[i])) + file.write('\t{}'.format(intra_sum_list[i])) + file.write('\t{}'.format(intra_number_of_contacts_list[i])) + file.write('\t{}'.format(intra_number_of_contacts_nnz_list[i])) + file.write('\t{}'.format(intra_density_list[i])) + file.write('\t{}'.format(inter_left_intra_ratio_list[i])) + file.write('\t{}'.format(inter_right_intra_ratio_list[i])) + file.write('\t{}'.format(inter_left_inter_right_intra_ratio_list[i])) + + file.write('\n') + + plt.scatter(inter_left_intra_ratio_list, inter_right_intra_ratio_list, s=20, alpha=0.7) + plt.xlabel('Inter-left/intra TAD contact ratio', fontsize=args.fontsize) + plt.ylabel('Inter-right/intra TAD contact ratio', fontsize=args.fontsize) + plt.tight_layout() + plt.savefig(args.outFileNameRatioPlot, dpi=args.dpi) + plt.close() diff --git a/hicexplorer/hicPCA.py b/hicexplorer/hicPCA.py index dc163d9b..5eb1ddf9 100644 --- a/hicexplorer/hicPCA.py +++ b/hicexplorer/hicPCA.py @@ -53,12 +53,12 @@ def parse_arguments(): parserOpt = parser.add_argument_group('Optional arguments') - parserOpt.add_argument('--numberOfEigenvectors', '-noe', - help='The number of eigenvectors that the PCA ' - 'should compute' + parserOpt.add_argument('--whichEigenvectors', '-we', + help='The list of eigenvectors that the PCA ' + 'should compute e.g. 1 2 5 will return the first, second and fifth eigenvector.' ' (Default: %(default)s).', - default=2, - type=int, + default='1 2', + nargs='+', required=False) parserOpt.add_argument('--format', '-f', @@ -92,10 +92,11 @@ def parse_arguments(): action='store_true') parserOpt.add_argument('--extraTrack', - help='Either a gene track or a histon mark coverage' + help='Either a gene track or a histone mark coverage' ' file (preferably a broad mark) is needed to decide' ' if the values of the eigenvector need a sign flip' - ' or not.', + ' or not. Please consider: bed files are interpreted as' + ' gene tracks and bigwig files as histone marks.', default=None) parserOpt.add_argument('--histonMarkType', @@ -140,7 +141,7 @@ def correlateEigenvectorWithGeneTrack(pMatrix, pEigenvector, pGeneTrack): density. If the correlation is negative, the eigenvector values are multiplied with -1. ''' - + log.debug('correlate eigenvector!') file_h = opener(pGeneTrack) bed = ReadBed(file_h) @@ -153,10 +154,21 @@ def correlateEigenvectorWithGeneTrack(pMatrix, pEigenvector, pGeneTrack): chromosome_name = interval.chromosome if chromosome_name not in chromosome_list: continue + if interval.start > pMatrix.get_chromosome_sizes()[chromosome_name]: + log.warning('Your chromosome sizes do not match the chromosome sizes of the extraTrack data!') + log.warning('Your chromosome {}; Size {}. ExtraTrack data {} {} {}'.format(chromosome_name, pMatrix.get_chromosome_sizes()[chromosome_name], interval.chromosome, + interval.start, interval.end)) + log.warning('Please create your interaction matrix with a chromosome size file! However, if the sizes are intended and it is accepted that certain regions are not part of the correlation, you can ignore this message.') + continue # in which bin of the Hi-C matrix is the given gene? bin_id = pMatrix.getRegionBinRange(interval.chromosome, interval.start, interval.end) - + if bin_id is None: + log.warning('Your chromosome sizes do not match the chromosome sizes of the extraTrack data!') + log.warning('Your chromosome {}; Size {}. ExtraTrack data {} {} {}'.format(chromosome_name, pMatrix.get_chromosome_sizes()[chromosome_name], interval.chromosome, + interval.start, interval.end)) + log.warning('Please create your interaction matrix with a chromosome size file! However, if the sizes are intended and it is accepted that certain regions are not part of the correlation, you can ignore this message.') + continue # add +1 for one gene occurrence in this bin gene_occurrence[bin_id[1]] += 1 @@ -175,11 +187,11 @@ def correlateEigenvectorWithGeneTrack(pMatrix, pEigenvector, pGeneTrack): for chromosome in chromosome_list: bin_id = pMatrix.getChrBinRange(chromosome) for i, eigenvector in enumerate(pEigenvector): - _correlation = pearsonr(eigenvector[bin_id[0]:bin_id[1]].real, + _correlation = pearsonr(np.array(eigenvector[bin_id[0]:bin_id[1]]).real, gene_occurrence_per_chr[chromosome]) if _correlation[0] < 0: eigenvector[bin_id[0]:bin_id[1]] = np.negative(eigenvector[bin_id[0]:bin_id[1]]) - + # log.debug('correlated to {}!'.format(_correlation[0])) return np.array(pEigenvector).transpose() @@ -227,19 +239,19 @@ def correlateEigenvectorWithHistonMarkTrack(pEigenvector, bwTrack, chromosome, def main(args=None): args = parse_arguments().parse_args(args) - if int(args.numberOfEigenvectors) != len(args.outputFileName): + if len(args.whichEigenvectors) != len(args.outputFileName): log.error("Number of output file names and number of eigenvectors" - " does not match. Please" + " does not match. Please " "provide the name of each file.\nFiles: {}\nNumber of " "eigenvectors: {}".format(args.outputFileName, - args.numberOfEigenvectors)) + len(args.whichEigenvectors))) exit(1) ma = hm.hiCMatrix(args.matrix) - ma.maskBins(ma.nan_bins) + # ma.maskBins(ma.nan_bins) if args.ignoreMaskedBins: - # ma.maskBins(ma.nan_bins) + ma.maskBins(ma.nan_bins) new_intervals = enlarge_bins(ma.cut_intervals) ma.setCutIntervals(new_intervals) @@ -255,7 +267,7 @@ def main(args=None): chromosome_count = len(ma.getChrNames()) if args.pearsonMatrix: transf_matrix_pearson = lil_matrix(ma.matrix.shape) - + log.debug('ma.matrix.shape {}'.format(ma.matrix.shape)) if args.obsexpMatrix: transf_matrix_obsexp = lil_matrix(ma.matrix.shape) @@ -291,21 +303,27 @@ def main(args=None): corrmatrix = convertNansToZeros(csr_matrix(corrmatrix)).todense() corrmatrix = convertInfsToZeros(csr_matrix(corrmatrix)).todense() evals, eigs = linalg.eig(corrmatrix) - k = args.numberOfEigenvectors + # k = len(rgs.numberOfEigenvectors chrom, start, end, _ = zip(*ma.cut_intervals[chr_range[0]:chr_range[1]]) chrom_list += chrom start_list += start end_list += end + eigenvectors_correlate = None + for id in args.whichEigenvectors: + if eigenvectors_correlate is None: + eigenvectors_correlate = eigs[:, int(id) - 1:int(id)] + else: + eigenvectors_correlate = np.hstack((eigenvectors_correlate, eigs[:, int(id) - 1:int(id)])) + if args.extraTrack and (args.extraTrack.endswith('.bw') or args.extraTrack.endswith('.bigwig')): assert(len(end) == len(start)) - correlateEigenvectorWithHistonMarkTrack(eigs[:, :k].transpose(), + correlateEigenvectorWithHistonMarkTrack(eigenvectors_correlate.transpose(), bwTrack, chrname, start, end, args.extraTrack, args.histonMarkType) - - vecs_list += eigs[:, :k].tolist() + vecs_list += eigenvectors_correlate.tolist() if args.pearsonMatrix: file_type = 'cool' @@ -338,11 +356,12 @@ def main(args=None): if args.format == 'bedgraph': for idx, outfile in enumerate(args.outputFileName): + assert(len(vecs_list) == len(chrom_list)) with open(outfile, 'w') as fh: for i, value in enumerate(vecs_list): - if len(value) == args.numberOfEigenvectors: + if len(value) == len(args.whichEigenvectors): if isinstance(value[idx], np.complex): value[idx] = value[idx].real fh.write("{}\t{}\t{}\t{:.12f}\n".format(toString(chrom_list[i]), start_list[i], end_list[i], value[idx])) @@ -376,7 +395,7 @@ def main(args=None): # create entry lists for i, value in enumerate(vecs_list): # it can happen that some 'value' is having less dimensions than it should - if len(value) == args.numberOfEigenvectors: + if len(value) == len(args.whichEigenvectors): if isinstance(value[idx], np.complex): value[idx] = value[idx].real values.append(value[idx]) diff --git a/hicexplorer/hicPlotAverageRegions.py b/hicexplorer/hicPlotAverageRegions.py index 3dc69241..2a99ebfc 100644 --- a/hicexplorer/hicPlotAverageRegions.py +++ b/hicexplorer/hicPlotAverageRegions.py @@ -8,6 +8,7 @@ from scipy.sparse import load_npz import matplotlib matplotlib.use('Agg') +import matplotlib as mpl from matplotlib.colors import LogNorm import matplotlib.pyplot as plt import numpy as np @@ -74,6 +75,7 @@ def parse_arguments(args=None): def main(args=None): args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 matrix = load_npz(args.matrix) diff --git a/hicexplorer/hicPlotDistVsCounts.py b/hicexplorer/hicPlotDistVsCounts.py index 23cc245f..b147bd93 100644 --- a/hicexplorer/hicPlotDistVsCounts.py +++ b/hicexplorer/hicPlotDistVsCounts.py @@ -12,12 +12,14 @@ import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt +import matplotlib as mpl from collections import OrderedDict from past.builtins import zip from scipy.sparse import triu +from .utilities import change_chrom_names import logging log = logging.getLogger(__name__) @@ -77,6 +79,13 @@ def parse_arguments(args=None): 'the Y chromosome. The names of the chromosomes should be separated by space.', nargs='+') + parserOpt.add_argument('--domains', + help='Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts,' + ' compute it for intra-domains.', + default=None, + type=argparse.FileType('r') + ) + parserOpt.add_argument('--outFileData', help='If given, the data underlying the plots is saved on this file.', type=argparse.FileType('w'), @@ -97,18 +106,17 @@ def parse_arguments(args=None): return parser -def compute_distance_mean(hicmat, maxdepth=None, perchr=False): +def compute_distance_mean(hicmat, maxdepth=None, perchr=False, custom_cut_intervals=None): """ - Converts a corrected counts matrix into a - obs / expected matrix or z-scores fast. + Compute average of values for each distance (only intra-chr or intra-unit defined in custom_cut_intervals) - The caveat is that the obs/exp or z-score are only + The caveat is that the average are only computed for non-zero values, although zero values that are not part of the sparse matrix are considered. - For each diagonal the mean (and std when computing z-scores) are - calculated and then each non-zero value of the sparse matrix is - replaced by the obs/exp or z-score. + For each diagonal the mean are calculated + + All unit whose names begin with _ignore_ are ignored Parameters ---------- @@ -116,51 +124,55 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): maxdepth: maximum distance from the diagonal to consider. All contacts beyond this distance will not be considered. perchr: bool to indicate if computations should be perform per chromosome + custom_cut_intervals: by default the distance mean is computed for intra-chr + but another unit can be defined for example TADs. + then custom_cut_intervals should contains a list of tuple + with the same length as hic.cut_intervals for example: + if cut_intervals are [('a', 0, 10, 1), ('a', 10, 20, 1), ('a', 20, 30, 1), ('a', 30, 40, 1), ('b', 40, 50, 1)] + custom could be [('tad1', 0, 10, 1), ('tad1', 10, 20, 1), ('tad2', 0, 10, 1), ('tad2', 10, 20, 1), ('tad3', 0, 10, 1)] Returns ------- - observed / expected sparse matrix + dictionary where keys are either 'all' or the chromosome names when perchr is set to True + and values are ordered dictionary where keys are distances and values are a + 2-tuple with the mean and the number of bins considered. - >>> from scipy.sparse import csr_matrix, dia_matrix - >>> row, col = np.triu_indices(5) + >>> from scipy.sparse import csr_matrix >>> cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), - ... ('a', 20, 30, 1), ('a', 30, 40, 1), ('b', 40, 50, 1)] + ... ('a', 20, 30, 1), ('a', 30, 40, 1), + ... ('b', 20, 30, 1), ('b', 30, 40, 1), ('b', 40, 50, 1)] >>> hic = HiCMatrix.hiCMatrix() >>> hic.nan_bins = [] >>> matrix = np.array([ - ... [ 1, 8, 5, 3, 0], - ... [ 0, 4, 15, 5, 1], - ... [ 0, 0, 0, 7, 2], - ... [ 0, 0, 0, 0, 1], - ... [ 0, 0, 0, 0, 0]]) + ... [ 1, 8, 5, 3, 0, 0, 0], + ... [ 0, 4, 15, 5, 1, 0, 0], + ... [ 0, 0, 0, 7, 2, 0, 1], + ... [ 0, 0, 0, 0, 1, 0, 2], + ... [ 0, 0, 0, 0, 10, 0, 20], + ... [ 0, 0, 0, 0, 0, 0, 0], + ... [ 0, 0, 0, 0, 0, 0, 6]]) >>> hic.matrix = csr_matrix(matrix) >>> hic.setMatrix(hic.matrix, cut_intervals) - >>> hic.convert_to_obs_exp_matrix().todense() - matrix([[1. , 0.8, 1. , 1. , 0. ], - [0. , 4. , 1.5, 1. , 1. ], - [0. , 0. , 0. , 0.7, 2. ], - [0. , 0. , 0. , 0. , 1. ], - [0. , 0. , 0. , 0. , 0. ]]) - - >>> hic.matrix = csr_matrix(matrix) - >>> hic.convert_to_obs_exp_matrix(maxdepth=20).todense() - matrix([[1. , 0.8, 1. , 0. , 0. ], - [0. , 4. , 1.5, 1. , 0. ], - [0. , 0. , 0. , 0.7, nan], - [0. , 0. , 0. , 0. , nan], - [0. , 0. , 0. , 0. , 0. ]]) - - >>> hic.matrix = csr_matrix(matrix) - >>> hic.convert_to_obs_exp_matrix(zscore=True).todense() - matrix([[ 0. , -0.56195149, nan, nan, -1.41421356], - [ 0. , 1.93649167, 1.40487872, nan, 0. ], - [ 0. , 0. , -0.64549722, -0.84292723, 1.41421356], - [ 0. , 0. , 0. , -0.64549722, 0. ], - [ 0. , 0. , 0. , 0. , -0.64549722]]) - - nans occur where the standard deviation is zero + >>> compute_distance_mean(hic) + {'all': OrderedDict([(0, (3.0, 7)), (10, (6.0, 5)), (20, (10.0, 3)), (30, (3.0, 1))])} + >>> compute_distance_mean(hic, perchr=True) + {'a': OrderedDict([(0, (1.25, 4)), (10, (10.0, 3)), (20, (5.0, 2)), (30, (3.0, 1))]), 'b': OrderedDict([(0, (5.333333333333333, 3)), (10, (0.0, 2)), (20, (20.0, 1))])} + >>> custom_cut = [('tad1', 0, 10, 1), ('tad1', 10, 20, 1), ('tad2', 0, 10, 1), + ... ('tad2', 10, 20, 1), ('tad3', 0, 10, 1), ('tad3', 10, 20, 1), ('tad3', 20, 30, 1)] + >>> compute_distance_mean(hic, custom_cut_intervals=custom_cut) + {'all': OrderedDict([(0, (3.0, 7)), (10, (3.75, 4)), (20, (20.0, 1))])} + >>> compute_distance_mean(hic, perchr=True, custom_cut_intervals=custom_cut) + {'a': OrderedDict([(0, (1.25, 4)), (10, (7.5, 2))]), 'b': OrderedDict([(0, (5.333333333333333, 3)), (10, (0.0, 2)), (20, (20.0, 1))])} + >>> custom_cut = [('_ignore_0', 0, 10, 1), ('0', 0, 10, 1), + ... ('0', 10, 20, 1), ('_ignore_3', 0, 10, 1), + ... ('1', 0, 10, 1), ('1', 10, 20, 1), ('1', 20, 30, 1)] + >>> compute_distance_mean(hic, custom_cut_intervals=custom_cut) + {'all': OrderedDict([(0, (4.0, 5)), (10, (5.0, 3)), (20, (20.0, 1))])} + + # >>> compute_distance_mean(hic, custom_cut_intervals=custom_cut, perchr=True) + # {'a': OrderedDict([(0, (2.0, 2)), (10, (15.0, 1))]), 'b': OrderedDict([(0, (5.333333333333333, 3)), (10, (0.0, 2)), (20, (20.0, 1))])} """ binsize = hicmat.getBinSize() @@ -172,7 +184,7 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): max_depth_in_bins = int(float(maxdepth * 1.5) / binsize) # work only with the upper matrix # and remove all pixels that are beyond - # max_depth_in_bis + # max_depth_in_bins # (this is done by subtracting a second sparse matrix # that contains only the upper matrix that wants to be removed. hicmat.matrix = triu(hicmat.matrix, k=0, format='csr') - \ @@ -184,20 +196,32 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): chr_submatrix = OrderedDict() cut_intervals = OrderedDict() - chrom_sizes = OrderedDict() + unit_sizes = OrderedDict() chrom_range = OrderedDict() + + if custom_cut_intervals is None: + cut_intervals_genome_wide = hicmat.cut_intervals + else: + assert len(custom_cut_intervals) == len(hicmat.cut_intervals), \ + "The custom_cut_intervals should have the same size as hicmat.cut_intervals" + cut_intervals_genome_wide = custom_cut_intervals + if perchr: for chrname in hicmat.getChrNames(): chr_range = hicmat.getChrBinRange(chrname) chr_submatrix[chrname] = hicmat.matrix[chr_range[0]:chr_range[1], chr_range[0]:chr_range[1]].tocoo() - cut_intervals[chrname] = [hicmat.cut_intervals[x] for x in range(chr_range[0], chr_range[1])] - chrom_sizes[chrname] = [chr_submatrix[chrname].shape[0]] + cut_intervals[chrname] = [cut_intervals_genome_wide[x] for x in range(chr_range[0], chr_range[1])] + unit_sizes[chrname] = np.array([v[1] - v[0] + for k, v in hicmat.intervalListToIntervalTree(cut_intervals[chrname])[1].items() + if not k.startswith('_ignore_')]) chrom_range[chrname] = (chr_range[0], chr_range[1]) else: chr_submatrix['all'] = hicmat.matrix.tocoo() - cut_intervals['all'] = hicmat.cut_intervals - chrom_sizes['all'] = np.array([v[1] - v[0] for k, v in hicmat.chrBinBoundaries.items()]) + cut_intervals['all'] = cut_intervals_genome_wide + unit_sizes['all'] = np.array([v[1] - v[0] + for k, v in hicmat.intervalListToIntervalTree(cut_intervals_genome_wide)[1].items() + if not k.startswith('_ignore_')]) chrom_range['all'] = (0, hicmat.matrix.shape[0]) mean_dict = {} @@ -206,6 +230,8 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): log.info("processing chromosome {}\n".format(chrname)) dist_list, chrom_list = hicmat.getDistList(submatrix.row, submatrix.col, HiCMatrix.hiCMatrix.fit_cut_intervals(cut_intervals[chrname])) + # We filter out the interactions where the chrom starts with _ignore_ + dist_list = dist_list[[not chrom.startswith('_ignore_') for chrom in chrom_list]] # to get the sum of all values at a given distance I use np.bincount which # is quite fast. However, the input of bincount is positive integers. Moreover @@ -221,23 +247,26 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): dist_list = (np.array(dist_list).astype(float) / binsize).astype(int) + 1 # for each distance, return the sum of all values - sum_counts = np.bincount(dist_list, weights=submatrix.data) + sum_counts = np.bincount(dist_list, weights=submatrix.data[[not chrom.startswith('_ignore_') for chrom in chrom_list]]) distance_len = np.bincount(dist_list) # compute the average for each distance mat_size = submatrix.shape[0] # compute mean value for each distance mu = {} + # also store the number of bins used to do the average + nb = {} zero_value_bins = [] for bin_dist_plus_one, sum_value in enumerate(sum_counts): - if maxdepth and bin_dist_plus_one == 0: # this is for intra chromosomal counts + if maxdepth and bin_dist_plus_one == 0: # this is for inter chromosomal counts # when max depth is set, the computation - # of the total_intra is not accurate and is safer to + # of the total_inter is not accurate and is safer to # output np.nan mu[bin_dist_plus_one] = np.nan + nb[bin_dist_plus_one] = np.nan continue if bin_dist_plus_one == 0: - total_intra = mat_size ** 2 - sum([size ** 2 for size in chrom_sizes[chrname]]) + total_intra = mat_size ** 2 - sum([size ** 2 for size in unit_sizes[chrname]]) diagonal_length = total_intra / 2 else: # to compute the average counts per distance we take the sum_counts and divide @@ -257,7 +286,7 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): # idx - 1 because earlier the values where # shifted. - diagonal_length = sum([size - (bin_dist_plus_one - 1) for size in chrom_sizes[chrname] + diagonal_length = sum([size - (bin_dist_plus_one - 1) for size in unit_sizes[chrname] if size > (bin_dist_plus_one - 1)]) # the diagonal length should contain the number of values at a certain distance. @@ -269,8 +298,10 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): if diagonal_length == 0: mu[bin_dist_plus_one] = np.nan + nb[bin_dist_plus_one] = 0 else: mu[bin_dist_plus_one] = np.float64(sum_value) / diagonal_length + nb[bin_dist_plus_one] = diagonal_length if sum_value == 0: zero_value_bins.append(bin_dist_plus_one) log.info("zero value for {}, diagonal len: {}\n".format(bin_dist_plus_one, diagonal_length)) @@ -286,13 +317,86 @@ def compute_distance_mean(hicmat, maxdepth=None, perchr=False): if maxdepth is None: maxdepth = np.inf - mean_dict[chrname] = OrderedDict([((k - 1) * binsize, v) for k, v in mu.items() if k > 0 and + mean_dict[chrname] = OrderedDict([((k - 1) * binsize, (v, nb[k])) for k, v in mu.items() if k > 0 and (k - 1) * binsize <= maxdepth]) # mean_dict[chrname]['intra_chr'] = mu[0] return mean_dict +def from_bed_to_cut_interval(hicmat, fh): + """ + Generate cut_interval (list of 4-uple) compatible with a HiCMatrix + where 'chrom' are units from the bed file + + Parameters + ---------- + hicmat: HiCMatrix object + bedfile: bed file with non-overlapping intervals and not more than 2 features should overlap a bin (for example domains.bed) + + Returns + ------- + list of tuple like hicmat.cut_intervals + + >>> from scipy.sparse import csr_matrix + >>> row, col = np.triu_indices(5) + >>> cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1), + ... ('a', 20, 30, 1), ('a', 30, 40, 1), + ... ('b', 20, 30, 1), ('b', 40, 50, 1)] + >>> hic = HiCMatrix.hiCMatrix() + >>> hic.nan_bins = [] + >>> matrix = np.array([ + ... [ 1, 8, 5, 3, 0, 0], + ... [ 0, 4, 15, 5, 1, 0], + ... [ 0, 0, 0, 7, 2, 1], + ... [ 0, 0, 0, 0, 1, 2], + ... [ 0, 0, 0, 0, 10, 20], + ... [ 0, 0, 0, 0, 0, 5]]) + + >>> hic.matrix = csr_matrix(matrix) + >>> hic.setMatrix(hic.matrix, cut_intervals) + >>> tad_line='a\\t0\\t30\\nb\\t20\\t50' + >>> with open('/tmp/test.bed', 'w') as fh: + ... fh.write(tad_line) + 14 + >>> fh = open('/tmp/test.bed', 'r') + >>> from_bed_to_cut_interval(hic, fh) + [('0', 0, 10, 1), ('0', 10, 20, 1), ('0', 20, 30, 1), ('_ignore_3', 0, 10, 1), ('1', 0, 10, 1), ('1', 20, 30, 1)] + """ + original_cut_intervals = hicmat.cut_intervals + new_cut_intervals = [()] * len(original_cut_intervals) + chrom_list = hicmat.getChrNames() + id = 0 + for line in fh: + if line[0] == "#": + continue + fields = line.strip().split() + if fields[0] not in chrom_list: + if change_chrom_names(fields[0]) in chrom_list: + fields[0] = change_chrom_names(fields[0]) + else: + continue + chrom, start, end = fields[:3] + overlapping_bins = [i for s, e, i in hicmat.interval_trees[chrom].overlap(int(start), int(end))] + original_start_bin_pos = original_cut_intervals[min(overlapping_bins)][1] + for i in overlapping_bins: + # Check it does not overlap another region + if len(new_cut_intervals[i]) != 0: + raise Exception("2 features must not overlap the same bin." + "{} is overlapped twice".format(original_cut_intervals[i])) + # Fill the new_cut_interval + new_cut_intervals[i] = (str(id), original_cut_intervals[i][1] - original_start_bin_pos, + original_cut_intervals[i][2] - original_start_bin_pos, + original_cut_intervals[i][3]) + id += 1 + assert id > 0, \ + "No region overlapped with bins." + # Fill all intervals which are not in the fh with a 'chromosome' which starts with '_ignore_' + for i in [i for i, interval in enumerate(new_cut_intervals) if len(interval) == 0]: + new_cut_intervals[i] = ('_ignore_{}'.format(i), 0, original_cut_intervals[i][2] - original_cut_intervals[i][1], original_cut_intervals[i][3]) + return new_cut_intervals + + def main(args=None): """ for each distance, compare the @@ -301,6 +405,8 @@ def main(args=None): """ args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 + mean_dict = OrderedDict() matrix_sum = {} if args.labels is None: @@ -318,7 +424,11 @@ def main(args=None): chrtokeep = [x for x in list(hic_ma.interval_trees) if x not in args.chromosomeExclude] hic_ma.keepOnlyTheseChr(chrtokeep) - mean_dict[matrix_file] = compute_distance_mean(hic_ma, maxdepth=args.maxdepth, perchr=args.perchr) + if args.domains: + custom_cut_interval = from_bed_to_cut_interval(hic_ma, args.domains) + else: + custom_cut_interval = None + mean_dict[matrix_file] = compute_distance_mean(hic_ma, maxdepth=args.maxdepth, perchr=args.perchr, custom_cut_intervals=custom_cut_interval) chroms = chroms.union([k for k in list(mean_dict[matrix_file]) if len(mean_dict[matrix_file][k]) > 1]) # compute scale factors such that values are comparable @@ -349,7 +459,7 @@ def main(args=None): if len(mean_values) <= 1: log.debug("No values found for: {}, chromosome: {}\n".format(matrix_file, chrom)) continue - x, y = zip(*[(k, v) for k, v in mean_values.items() if v > 0]) + x, y, z = zip(*[(k, v, nb) for k, (v, nb) in mean_values.items() if v > 0]) if len(x) <= 1: log.debug("No values found for: {}, chromosome: {}\n".format(matrix_file, chrom)) continue @@ -385,10 +495,13 @@ def main(args=None): if args.outFileData is not None: x_vals = np.stack(x).T y_vals = np.stack(y).T + z_vals = np.stack(z).T table_to_export = pd.DataFrame({'Matrix': labels[matrix_file], 'Chromosome': chrom, 'Distance': x_vals, - 'Contacts': y_vals}) + 'Contacts': y_vals, + 'Number_bins': z_vals, + 'Scale_factor': scale_factor[matrix_file]}) table_to_export.to_csv(args.outFileData, sep='\t') for ax in axs.reshape(-1): diff --git a/hicexplorer/hicPlotMatrix.py b/hicexplorer/hicPlotMatrix.py index 1b1611ff..36218f3d 100644 --- a/hicexplorer/hicPlotMatrix.py +++ b/hicexplorer/hicPlotMatrix.py @@ -6,6 +6,7 @@ import matplotlib.pyplot as plt from matplotlib.colors import LogNorm import matplotlib +import matplotlib as mpl import argparse from past.builtins import zip import pyBigWig @@ -174,6 +175,18 @@ def parse_arguments(args=None): 'from hicDetectLoops.', type=str, default=None) + parserOpt.add_argument('--loopLargeRegionsOperation', + help='If a given coordinate in the bed file is larger than ' + 'a bin of the input matrix, by default only the first bin ' + 'is taken into account. However there are more possibilities ' + 'to handel such a case. Users can ask for the last bin or ' + 'for center of the region.', + choices=['first', 'last', 'center'], + default='first') + parserOpt.add_argument('--tads', + help='Bedgraph file to plot detected tads', + type=str, + default=None) parserOpt.add_argument('--help', '-h', action='help', help='show this help message and exit') @@ -204,69 +217,9 @@ def relabel_ticks(pXTicks): return labels -# def getRegion(args, ma): -# chrom = region_start = region_end = idx1 = start_pos1 = chrom2 = region_start2 = region_end2 = idx2 = start_pos2 = None -# chrom, region_start, region_end = translate_region(args.region) - -# chrom = check_chrom_str_bytes(ma.interval_trees, chrom) -# # if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]: -# # chrom = toBytes(chrom) - -# if chrom not in list(ma.interval_trees): - -# chrom = change_chrom_names(chrom) - -# chrom = check_chrom_str_bytes(ma.interval_trees, chrom) - -# # if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]: -# # chrom = toBytes(chrom) - -# if chrom not in list(ma.interval_trees): -# exit("Chromosome name {} in --region not in matrix".format(change_chrom_names(chrom))) - -# args.region = [chrom, region_start, region_end] -# is_cooler = check_cooler(args.matrix) -# if is_cooler: -# idx1, start_pos1 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom and # noqa: W504 -# ((x[1] >= region_start and x[2] < region_end) or # noqa: W504 -# (x[1] < region_end and x[2] < region_end and x[2] > region_start) or # noqa: W504 -# (x[1] > region_start and x[1] < region_end))]) -# else: -# idx1, start_pos1 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom and # noqa: W504 -# x[1] >= region_start and x[2] < region_end]) -# if hasattr(args, 'region2') and args.region2: -# chrom2, region_start2, region_end2 = translate_region(args.region2) -# chrom2 = check_chrom_str_bytes(ma.interval_trees, chrom2) - -# # if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]: -# # chrom2 = toBytes(chrom) -# if chrom2 not in list(ma.interval_trees): -# chrom2 = change_chrom_names(chrom2) -# chrom2 = check_chrom_str_bytes(ma.interval_trees, chrom2) - -# # if type(next(iter(ma.interval_trees))) in [np.bytes_, bytes]: -# # chrom2 = toBytes(chrom) -# if chrom2 not in list(ma.interval_trees): -# exit("Chromosome name {} in --region2 not in matrix".format(change_chrom_names(chrom2))) -# if is_cooler: -# idx2, start_pos2 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom2 and # noqa: W504 -# ((x[1] >= region_start2 and x[2] < region_end2) or # noqa: W504 -# (x[1] < region_end2 and x[2] < region_end2 and x[2] > region_start2) or # noqa: W504 -# (x[1] > region_start2 and x[1] < region_end2))]) -# else: -# idx2, start_pos2 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom2 and # noqa: W504 -# x[1] >= region_start2 and x[2] < region_end2]) -# else: -# idx2 = idx1 -# chrom2 = chrom -# start_pos2 = start_pos1 - -# return chrom, region_start, region_end, idx1, start_pos1, chrom2, region_start2, region_end2, idx2, start_pos2 - - def plotHeatmap(ma, chrBinBoundaries, fig, position, args, cmap, xlabel=None, ylabel=None, start_pos=None, start_pos2=None, pNorm=None, pAxis=None, pBigwig=None, - pLoops=None, pHiCMatrix=None, pChromsomeStartEndDict=None, pResolution=None): + pLoops=None, pLoopLargeRegionsOperation=None, pHiCMatrix=None, pChromsomeStartEndDict=None, pResolution=None, pTads=None): log.debug("plotting heatmap") if ma.shape[0] < 5: # This happens when a tiny matrix wants to be plotted, or by using per chromosome and @@ -365,10 +318,13 @@ def plotHeatmap(ma, chrBinBoundaries, fig, position, args, cmap, xlabel=None, if pLoops: log.debug('pLoops called') - plotLongRangeContacts(axHeat2, pLoops, pHiCMatrix, + plotLongRangeContacts(axHeat2, pLoops, pLoopLargeRegionsOperation, args.region, args.chromosomeOrder) # pLongRangeContacts=None, pHiCMatrix=None # plotLongRangeContacts(pAxis, pNameOfLongRangeContactsFile, pHiCMatrix) + if pTads: + plotTADs(axHeat2, pTads, pHiCMatrix, + args.region, args.chromosomeOrder) axHeat2.invert_yaxis() if pBigwig: @@ -680,6 +636,8 @@ def bigwig_axes_config(pArgs, pBigWigInfo): def main(args=None): args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 + if args.title: args.title = remove_non_ascii(args.title) @@ -862,7 +820,7 @@ def main(args=None): plotHeatmap(matrix, ma.get_chromosome_sizes(), fig, position, args, cmap, xlabel=chrom, ylabel=chrom2, start_pos=start_pos1, start_pos2=start_pos2, pNorm=norm, pAxis=ax1, pBigwig=bigwig_info, - pLoops=args.loops, pHiCMatrix=ma, pChromsomeStartEndDict=chromosome_start_end(ma), pResolution=resolution) + pLoops=args.loops, pLoopLargeRegionsOperation=args.loopLargeRegionsOperation, pHiCMatrix=ma, pChromsomeStartEndDict=chromosome_start_end(ma), pResolution=resolution, pTads=args.tads) if not args.disable_tight_layout: if args.perChromosome or args.bigwig: @@ -1071,7 +1029,7 @@ def plotBigwig(pAxis, pNameOfBigwigList, pChromosomeSizes=None, pRegion=None, pX x_values, 0, bigwig_scores, edgecolor='none') -def plotLongRangeContacts(pAxis, pNameOfLongRangeContactsFile, pHiCMatrix, pRegion, pChromosomeOrder): +def plotLongRangeContacts(pAxis, pNameOfLongRangeContactsFile, pLoopLargeRegionsOperation, pRegion, pChromosomeOrder): x_list = [] y_list = [] @@ -1089,8 +1047,16 @@ def plotLongRangeContacts(pAxis, pNameOfLongRangeContactsFile, pHiCMatrix, pRegi elif pChromosomeOrder is not None and (chrom_X not in pChromosomeOrder or chrom_Y not in pChromosomeOrder): continue - x = int(start_X) - y = int(start_Y) + if pLoopLargeRegionsOperation == 'first': + x = int(start_X) + y = int(start_Y) + elif pLoopLargeRegionsOperation == 'last': + x = int(end_X) + y = int(end_Y) + elif pLoopLargeRegionsOperation == 'center': + x = (int(start_X) + int(end_X)) // 2 + y = (int(start_Y) + int(end_Y)) // 2 + log.debug('x {} y {}'.format(x, y)) if x >= int(pRegion[1]) and x <= int(pRegion[2]): if y >= int(pRegion[1]) and y <= int(pRegion[2]): @@ -1105,3 +1071,36 @@ def plotLongRangeContacts(pAxis, pNameOfLongRangeContactsFile, pHiCMatrix, pRegi pAxis.plot(x_list, y_list, 's', lw=2, markerfacecolor='none', markeredgecolor='red') + + +def plotTADs(pAxis, pNameOfLongRangeContactsFile, pHiCMatrix, pRegion, pChromosomeOrder): + x_list = [] + y_list = [] + with open(pNameOfLongRangeContactsFile, 'rb') as file: + for line in file.readlines(): + line = toString(line) + fields = line.strip().split('\t') + try: + chrom_X, start_X, end_X = fields[0:3] + + if pRegion is not None and chrom_X != pRegion[0]: + continue + elif pChromosomeOrder is not None and chrom_X not in pChromosomeOrder: + continue + + x = int(start_X) + y = int(end_X) + if x >= int(pRegion[1]) and x <= int(pRegion[2]): + if y >= int(pRegion[1]) and y <= int(pRegion[2]): + x_list.append(x) + y_list.append(y) + except Exception as exp: + log.debug('Exception! {}'.format(str(exp))) + + if pRegion is not None and (int(pRegion[1]) != 0 and int(pRegion[2]) != 1e15): + pAxis.set_xlim(int(pRegion[1]), int(pRegion[2])) + pAxis.set_ylim(int(pRegion[1]), int(pRegion[2])) + + for x_id, y_id in zip(x_list, y_list): + pAxis.plot([x_id, x_id], [y_id, x_id], 'k') + pAxis.plot([x_id, y_id], [y_id, y_id], 'k') diff --git a/hicexplorer/hicPlotSVL.py b/hicexplorer/hicPlotSVL.py index 0ae90888..e9e6b683 100644 --- a/hicexplorer/hicPlotSVL.py +++ b/hicexplorer/hicPlotSVL.py @@ -11,6 +11,7 @@ matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.patches as mpatches +import matplotlib as mpl from scipy.stats import ranksums from hicmatrix import HiCMatrix as hm @@ -130,6 +131,8 @@ def compute_relation_short_long_range(pHiCMatrix, pChromosomes, pDistance, pIsCo def main(args=None): args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 + short_v_long_range = [] sum_smaller = [] sum_greater = [] diff --git a/hicexplorer/hicPlotViewpoint.py b/hicexplorer/hicPlotViewpoint.py index 3e1ed5dc..d3c38937 100644 --- a/hicexplorer/hicPlotViewpoint.py +++ b/hicexplorer/hicPlotViewpoint.py @@ -9,6 +9,7 @@ import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt +import matplotlib as mpl import os from hicexplorer._version import __version__ @@ -104,6 +105,8 @@ def getViewpointValues(pMatrix, pReferencePoint, pChromViewpoint, pRegion_start, def main(args=None): args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 + log.warning('This tool is deprecated. Please use chicViewpoint, chicViewpointBackgroundModel and chicPlotViewpoint.') if args.region: diff --git a/hicexplorer/hicPrepareQCreport.py b/hicexplorer/hicPrepareQCreport.py index 26c57e6f..51bbc9eb 100644 --- a/hicexplorer/hicPrepareQCreport.py +++ b/hicexplorer/hicPrepareQCreport.py @@ -9,6 +9,7 @@ import pandas as pd matplotlib.use('Agg') import matplotlib.pyplot as plt +import matplotlib as mpl from hicexplorer._version import __version__ import logging @@ -259,6 +260,8 @@ def main(args=None): """ args = parse_arguments().parse_args(args) + mpl.rcParams['pdf.fonttype'] = 42 + params = dict() make_sure_path_exists(args.outputFolder) for fh in args.logfiles: @@ -281,6 +284,7 @@ def main(args=None): except ValueError: params[fields[0]].append(fields[1]) + log.debug('params {}'.format(params)) table = pd.DataFrame(params) if args.labels and len(args.labels) == len(args.logfiles): try: diff --git a/hicexplorer/hicTADClassifier.py b/hicexplorer/hicTADClassifier.py new file mode 100644 index 00000000..ab121665 --- /dev/null +++ b/hicexplorer/hicTADClassifier.py @@ -0,0 +1,86 @@ +import argparse +import logging +from .lib import TADClassifier + +# taken and altered from hicFindTads +log = logging.getLogger(__name__) +from hicexplorer._version import __version__ + + +def parse_arguments(args=None): + """ + get command line arguments + """ + parser = argparse.ArgumentParser( + formatter_class=argparse.RawDescriptionHelpFormatter, + conflict_handler='resolve', + description=""" +Uses Supervised Learning to call TAD boundaries. One or multiple HiC-Matrices can be passed, from which a BED file will be produced containing the predicted boundary positions. By default, a EasyEnsembleClassifier as described in Liu et al.: “Exploratory Undersampling for Class-Imbalance Learning” will be used to call TADs. Internally this classifier relies on Resampling, Boosting and Bagging. Passed matrices will be range normalized by default. Alternatively, obs/exp normalization can be used. Currently, only classifiers for 10kb resolution are implemented. For building own classifiers or tune existing ones, hicTrainClassifier can be used and passed with the saved_classifer argument. A simple usage example can be seen here: + +$ hicTADClassifier -m my_matrix.cool -o predictions -n range + """) + + parserRequired = parser.add_argument_group('Required arguments') + + parserRequired.add_argument('--matrices', '-m', + help='HiC-Matrix file or list of files for input. Only COOLER files are supported!', + required=True, + nargs='+') + + parserRequired.add_argument('--out_file', '-o', + help='output file path for predictions', + required=True, + nargs='+') + + parserOpt = parser.add_argument_group('Optional arguments') + + parserOpt.add_argument('--normalization_method', '-n', + help='set the normalization mode, with which the passed matrices will be normalized. If not set, matrices will be range normalized', + type=str, + choices=[ + 'obs_exp', + 'range' + ], + default='range') + + parserOpt.add_argument('--saved_classifier', + help='Default classifier are available for 10kb, 25kb, 50kb and 100kb resolution. Do not set this parameter to use the default models. ' + 'Pass a self-trained classifier (from hicTrainTADClassifier) to load a non-default model.', + type=str, + default=None) + + parserOpt.add_argument('--unselect_border_cases', + help='set whether genes at the border of the matrices will not be predicted', + required=False, + action='store_true') + + parserOpt.add_argument('--threads', '-t', + help='number of threads used', + default=4, + type=int) + + parserOpt.add_argument('--chromosomes', + help='Chromosomes to include in the analysis. If not set, all chromosomes are included.', + nargs='+') + parserOpt.add_argument("--help", "-h", action="help", + help="show this help message and exit") + + parserOpt.add_argument('--version', action='version', + version='%(prog)s {}'.format(__version__)) + + return parser + + +def main(args=None): + + args = parse_arguments().parse_args(args) + program = TADClassifier('predict', + args.out_file, + saved_classifier=args.saved_classifier, + normalization_method=args.normalization_method, + unselect_border_cases=args.unselect_border_cases, + threads=args.threads, + pAddRemoveChrPrexix=None + ) + + program.run_hicTADClassifier(args.matrices, args.chromosomes) diff --git a/hicexplorer/hicTrainTADClassifier.py b/hicexplorer/hicTrainTADClassifier.py new file mode 100644 index 00000000..892a2053 --- /dev/null +++ b/hicexplorer/hicTrainTADClassifier.py @@ -0,0 +1,218 @@ +from .lib import TADClassifier +import argparse +import logging + +from hicexplorer._version import __version__ + +# taken and altered from hicFindTads +log = logging.getLogger(__name__) + + +def parse_arguments(args=None): + """ + get command line arguments + """ + parser = argparse.ArgumentParser( + formatter_class=argparse.RawDescriptionHelpFormatter, + conflict_handler='resolve', + description=""" +Check out hicTADClassifier for calling TADs using our default classifiers or your trained classifier. + +This program can be used to train and test new and existing classifiers for hicTADClassifier. These classifiers can later be run to call boundaries for TADs. There are four modes available: train_new, train_existing, train_test and predict_test. By default, an EasyEnsembleClassifier as described in Liu et al.: “Exploratory Undersampling for Class-Imbalance Learning” will be trained, but you can pass any sklearn classifier that allows for a warm start. You may also vary the resampling method and a range of hyperparameters to fine tune the model. Do mind to set the correct normalization method and resolution for the classifier. The program will check and raise warnings, when resolutions and normalization methods are mixed up. Also, a protein track file in the narrowPeak format with a threshold value may be passed to filter out low quality boundaries. + + +train_test mode: this is a convenience function, where a single matrix/domains set can be passed to quickly assert the performance of a new classifier. Nothing will be saved from this mode, instead, the classifier will be trained on 80% of the data and tested on the remaining 20%. The output will be a performance report. A quick usage example can be seen here: + +$ hicTrainTADClassifier -m 'train_test' -f 'my_test_matrix.cool' -d 'domains.bed' -o 'report.txt' -n 'range' -r 10000 + +train_new mode: this mode allows the training of a new classifier. Note that range of optional arguments, that can be used to fine tune. The resulting classifier will be pickled at the specified out_file. A quick example can be seen here, where we varied the feature distance: + +$ hicTrainTADClassifier -m 'train_new' -f 'my_test_matrix.cool' -d 'domains.bed' -o 'new_classifier.data' -n 'range' -r 10000 --distance 18 + +train_existing mode: train the classifier specified in saved_classifier on new data. When not setting the saved_classifier, the preset classifiers will be used as preset. The output will be the classifier trained with additional data and more internal estimators. + +$ hicTrainTADClassifier -m 'train_existing' -f 'my_test_matrix.cool' -d 'domains.bed' -o 'updated_classifier.data' -n 'range' -r 10000 + +predict_test mode: predict using an existing classifier and produce a classification report. The difference in using this over hicTADClassifier is, that this version will predict on a balanced test set. Normally, HiC-Matrices contain a lot more non-boundaries than boundaries, which skews the classification report to the point, where it does not contain usefull information anymore. By passing a domain file produced by another TAD Caller, hicTrainClassifier will build a test set using the boundaries of this domain file and will pick at random as many non-boundaries from the passed matrix. Use this over hicTADClassifier to produce a meaningful output, but not for TAD calling. + +$ hicTrainTADClassifier -m 'predict_test' -f 'my_test_matrix.cool' -d 'domains.bed' -o 'report.txt' -n 'range' -r 10000 + """) + + def check_leniency(le): + li = int(le) + if li < 0: + raise argparse.ArgumentTypeError( + "leniency %s is not within valid range 0 -" % le) + return li + + parserRequired = parser.add_argument_group('Required arguments') + + parserRequired.add_argument('--mode', '-mo', + choices=[ + 'train_new', + 'train_existing', + 'train_test', + 'predict_test'], + help='choice of program', + required=True, + type=str) + + parserRequired.add_argument('--matrices', '-m', + help='HiC-Matrix file or list of files for input. Only COOLER files are supported!', + required=True, + nargs='+') + + parserRequired.add_argument('--domain_file', '-d', + help='domain file or list of files containing tad boundaries', + required=True, + nargs='+') + + parserRequired.add_argument('--out_file', '-o', + help='output file for either the classification report or the saved classifier', + required=True, + type=str) + + parserRequired.add_argument('--normalization_method', '-n', + help='set the normalization mode, with which the passed matrices will be normalized', + type=str, + choices=[ + 'obs_exp', + 'range' + ]) + + parserRequired.add_argument('--resolution', '-r', + help='resolution in bases of the classifier', + type=int) + + parserOpt = parser.add_argument_group('Optional arguments') + + parserOpt.add_argument('--threshold', + help='threshold for protein quality check', + type=float, + default=None) + + parserOpt.add_argument('--leniency', + help='leniency for protein quality check. Widens peaks of protein file by leniency*resolution', + type=check_leniency, + default=0) + + parserOpt.add_argument('--saved_classifier', + help='pickled classifier to be trained or used for prediction', + type=str, + default=None) + + parserOpt.add_argument('--unselect_border_cases', + help='set whether genes at the border of the matrix up to set distance will not be used for training and testing', + action='store_false') + + parserOpt.add_argument('--protein_file', + help='provide a bed file for TAD quality control', + nargs='+', + default=None) + + parserOpt.add_argument('--threads', '-t', + help='number of threads used', + default=4, + type=int) + parserOpt.add_argument('--chromosomes', + help='Chromosomes to include in the analysis. If not set, all chromosomes are included.', + nargs='+') + parserOpt.add_argument('--concatenate_before_resample', + help='whether features build from matrix list are concatenated and resampled together or resampled separatly per matrix. Not important for random undersampling, but alter for other resampling methods and check if performance increases.', + default=False, + action='store_true') + + parserOpt.add_argument('--estimators_per_step', + help='how many estimators are added in each training step for the classifier (new classifier)', + # choices=range(5, 1001), + metavar="[5-1000]", + default=20, + type=int) + + parserOpt.add_argument('--resampling_method', + help='the method used to resample the training set(new classifier)', + type=str, + choices=[ + 'undersample_cluster_centroids', + 'undersample_random', + 'passed_method' + ], + default='undersample_random') + + parserOpt.add_argument('--alternative_resampling_method', + help='pass alternative resampling method from imblearn library (new classifier)', + default=None) + + parserOpt.add_argument('--distance', + help='max distance between TADs to be used in calculation (new classifier)', + # choices=range(5, 31), + metavar="[5-30]", + default=15, + type=int) + + parserOpt.add_argument('--impute_value', + help='non-numerical float values in matrix will be replaced by this value (new classifier)', + type=float, + default=-1.0) + + parserOpt.add_argument('--alternative_classifier', + help='pass custom classifier, needs to implement warm_start (new classifier)', + default=None) + + parserOpt.add_argument('--use_cleanlab', + help='use Confident Learning with the cleanlab library (new classifier)', + action='store_true') + # parserOpt.add_argument('--chrPrefixProtein', '-cp', + # help='Adding / removing / do nothing a \'chr\'-prefix to chromosome name of the protein.', + # choices=[None, 'add', 'remove'], + # default=None + # ) + parserOpt.add_argument("--help", "-h", action="help", + help="show this help message and exit") + + parserOpt.add_argument('--version', action='version', + version='%(prog)s {}'.format(__version__)) + + return parser +# def print_args(args): +# """ +# Print to stderr the parameters used +# Parameters +# ---------- +# args + +# Returns +# ------- + +# """ +# for key, value in args._get_kwargs(): +# log.info("{}:\t{}\n".format(key, value)) + + +def main(args=None): + + args = parse_arguments().parse_args(args) + program = TADClassifier(args.mode, + args.out_file, + saved_classifier=args.saved_classifier, + normalization_method=args.normalization_method, + unselect_border_cases=args.unselect_border_cases, + threshold=args.threshold, + leniency=args.leniency, + resolution=args.resolution, + threads=args.threads, + concatenate_before_resample=args.concatenate_before_resample, + distance=args.distance, + impute_value=args.impute_value, + resampling_method=args.resampling_method, + alternative_resampling_method=args.alternative_resampling_method, + alternative_classifier=args.alternative_classifier, + use_cleanlab=args.use_cleanlab, + estimators_per_step=args.estimators_per_step, + pAddRemoveChrPrexix=None + ) + program.run_hicTrainClassifier( + args.matrices, + args.domain_file, + args.protein_file, + args.chromosomes) diff --git a/hicexplorer/hicValidateLocations.py b/hicexplorer/hicValidateLocations.py index a46b62d3..287274d4 100644 --- a/hicexplorer/hicValidateLocations.py +++ b/hicexplorer/hicValidateLocations.py @@ -12,6 +12,7 @@ import pandas as pd from pybedtools import BedTool import numpy as np +import cooler def parse_arguments(args=None): @@ -32,23 +33,25 @@ def parse_arguments(args=None): The value of the protein is not considered, only match or non-match. """) - # TAD or Loop data track - # protein data, compute correlation parserRequired = parser.add_argument_group('Required arguments') parserRequired.add_argument('--data', '-d', help='The loop file from hicDetectLoops. To use files from other sources, ' 'please follow \'chr start end chr start end\' format.', required=True) - parserRequired.add_argument('--protein', '-p', - help='The protein peak file. Can be narrowPeak or broadPeak', + parserRequired.add_argument('--validationData', '-vd', + help='The data file to validate the given locations. Can be narrowPeak, broadPeak, cool, or 2D text.', required=True) - parserRequired.add_argument('--method', '-m', # loop or domain + parserRequired.add_argument('--validationType', '-vt', + help='The type of the validation data. Can be bed, or cool format', + choices=['bed', 'cool'], + default='bed') + parserRequired.add_argument('--method', '-m', help='The method used (for the moment only loop is possible)' ' (Default: %(default)s).', - choices=['loops'], + choices=['loops', 'tad'], default='loops') - parserRequired.add_argument('--resolution', '-r', # loop or domain + parserRequired.add_argument('--resolution', '-r', help='The used resolution of the Hi-C interaction matrix.', required=True, type=int) @@ -57,14 +60,17 @@ def parse_arguments(args=None): help='The prefix name of the output files. Two file are written: output_matched_locations and output_statistics.' 'First file contains all loop locations with protein location matches, second file contains statistics about this matching.' ) - parserOpt.add_argument('--addChrPrefixLoops', '-cl', - help='Adding a \'chr\'-prefix to chromosome name of the loops.', - action='store_true' + parserOpt.add_argument('--chrPrefixLoops', '-cl', + help='Adding / removing / do nothing a \'chr\'-prefix to chromosome name of the loops.', + choices=[None, 'add', 'remove'], + default=None ) - parserOpt.add_argument('--addChrPrefixProtein', '-cp', - help='Adding a \'chr\'-prefix to chromosome name of the protein.', - action='store_true' + parserOpt.add_argument('--chrPrefixProtein', '-cp', + help='Adding / removing / do nothing a \'chr\'-prefix to chromosome name of the protein.', + choices=[None, 'add', 'remove'], + default=None ) + parserOpt.add_argument('--help', '-h', action='help', help='show this help message and exit') @@ -74,18 +80,24 @@ def parse_arguments(args=None): return parser -def readProtein(pFile, pAddChr): +def readThreeColumn(pFile, pChrPrefixProtein): protein_df = pd.read_csv(pFile, sep='\t', header=None)[[0, 1, 2]] - if pAddChr: + if pChrPrefixProtein == 'add': protein_df[0] = 'chr' + protein_df[0].astype(str) + elif pChrPrefixProtein == 'remove': + protein_df[0] = protein_df[0].str.lstrip('chr') return protein_df -def readLoopFile(pInputFile, pAddChr): +def readLoopFile(pInputFile, pChrPrefixLoops): full_loop = pd.read_csv(pInputFile, sep='\t', header=None) - if pAddChr: + if pChrPrefixLoops == 'add': full_loop[0] = 'chr' + full_loop[0].astype(str) full_loop[3] = 'chr' + full_loop[3].astype(str) + elif pChrPrefixLoops == 'remove': + full_loop[0] = full_loop[0].str.lstrip('chr') + full_loop[3] = full_loop[3].str.lstrip('chr') + return full_loop @@ -104,20 +116,53 @@ def overlapLoop(pDataFrameLoop, pDataFrameProtein): return selection -# def overlapTAD(pDataFrameTAD, pDataFrameProtein): -# loop_bedtool_x = BedTool.from_dataframe(pDataFrameTAD[[0,1,2]]) -# # loop_bedtool_y = BedTool.from_dataframe(pDataFrameLoop[[3,4,5]]) -# protein_bedtool = BedTool.from_dataframe(pDataFrameProtein) -# x = loop_bedtool_x.intersect(protein_bedtool, c=True).to_dataframe() -# # y = loop_bedtool_y.intersect(protein_bedtool, c=True).to_dataframe() +def overlapTAD(pDataFrameTAD, pDataFrameProtein): + loop_bedtool_x = BedTool.from_dataframe(pDataFrameTAD) + # loop_bedtool_y = BedTool.from_dataframe(pDataFrameLoop[[3,4,5]]) + + protein_bedtool = BedTool.from_dataframe(pDataFrameProtein) + x = loop_bedtool_x.intersect(protein_bedtool, c=True).to_dataframe() + # y = loop_bedtool_y.intersect(protein_bedtool, c=True).to_dataframe() + + mask_x = x['name'] >= 1 + # mask_y = y['name'] >= 1 + + # selection = (mask_x) & (mask_y) + return mask_x + + +def correlateCool(pCoolFile, pDataFrameLoop): + cool_obj = cooler.Cooler(pCoolFile) + number_of_peaks = cool_obj.info['nnz'] + match_list = [] + for line in pDataFrameLoop.itertuples(): + try: + matrix_data = cool_obj.matrix(balance=False, sparse=True).fetch(str(line[1]) + ':' + str(line[2]) + '-' + str(line[3]), str(line[4]) + ':' + str(line[5]) + '-' + str(line[6])) + + if matrix_data.nnz > 0: + match_list.append(True) + else: + match_list.append(False) + except Exception: + match_list.append(False) -# mask_x = x['name'] >= 1 -# # mask_y = y['name'] >= 1 + selection = pd.Series(match_list) + log.debug(selection) -# # selection = (mask_x) & (mask_y) + return number_of_peaks, selection -# return mask_x + +def correlate2DText(pDataFrameProtein, pDataFrameLoop): + loop_bedtool_x = BedTool.from_dataframe(pDataFrameLoop[[0, 1, 2, 3, 4, 5]]) + + protein_bedtool = BedTool.from_dataframe(pDataFrameProtein) + x = loop_bedtool_x.intersect(protein_bedtool, c=True).to_dataframe() + + mask_x = x['name'] >= 1 + + log.debug(mask_x) + return mask_x def applyBinning(pDataFrame, pBinSize): @@ -140,27 +185,34 @@ def main(args=None): args = parse_arguments().parse_args(args) if args.method == 'loops': - loop_df = readLoopFile(args.data, args.addChrPrefixLoops) + + loop_df = readLoopFile(args.data, args.chrPrefixLoops) if loop_df is None: log.error('Empty loop file') return loop_df_bedtool = BedTool.from_dataframe(loop_df) loop_df = loop_df_bedtool.sort().to_dataframe( disable_auto_names=True, header=None) + if args.validationType == 'bed': + protein_df = readThreeColumn(args.validationData, args.chrPrefixProtein) + if protein_df is None: + log.error('Empty protein file') + return + protein_df_bedtool = BedTool.from_dataframe(protein_df) + protein_df = protein_df_bedtool.sort().to_dataframe( + disable_auto_names=True, header=None) + + protein_df_resolution = applyBinning(protein_df, args.resolution) + + overlap_mask_df = overlapLoop(loop_df, protein_df_resolution) + loop_df_ = loop_df[overlap_mask_df] - protein_df = readProtein(args.protein, args.addChrPrefixProtein) - if protein_df is None: - log.error('Empty protein file') - return - protein_df_bedtool = BedTool.from_dataframe(protein_df) - protein_df = protein_df_bedtool.sort().to_dataframe( - disable_auto_names=True, header=None) - - protein_df_resolution = applyBinning(protein_df, args.resolution) + number_of_proteins = len(protein_df_resolution) + elif args.validationType == 'cool': + number_of_proteins, overlap_mask_df = correlateCool(args.validationData, loop_df) + loop_df_ = loop_df[overlap_mask_df] - overlap_mask_df = overlapLoop(loop_df, protein_df_resolution) - loop_df_ = loop_df[overlap_mask_df] - print('Protein peaks: {}'.format(len(protein_df_resolution))) + print('Protein peaks: {}'.format(number_of_proteins)) print('Matched Loops: {}'.format(len(loop_df_))) print('Total Loops: {}'.format(len(loop_df))) @@ -174,10 +226,38 @@ def main(args=None): file.write( '# HiCExplorer hicValidateLocations {}\n'.format(__version__)) file.write('# Overlap of loop file {} with protein file {}\n#\n'.format( - args.data, args.protein)) + args.data, args.validationData)) file.write('Protein peaks: {}\n'.format( - len(protein_df_resolution))) + number_of_proteins)) file.write('Matched Loops: {}\n'.format(len(loop_df_))) file.write('Total Loops: {}\n'.format(len(loop_df))) file.write('Loops match protein: {}\n'.format( len(loop_df_) / len(loop_df))) + elif args.method == 'tad': + tad_df = readThreeColumn(args.data, args.addChrPrefixLoops) + protein_df = readThreeColumn(args.protein, args.addChrPrefixProtein) + + # log.debug('') + tad_df_bedtool = BedTool.from_dataframe(tad_df) + tad_df = tad_df_bedtool.sort().to_dataframe( + disable_auto_names=True, header=None) + + protein_df_bedtool = BedTool.from_dataframe(protein_df) + protein_df = protein_df_bedtool.sort().to_dataframe( + disable_auto_names=True, header=None) + + tad_df_resolution = applyBinning(tad_df, args.resolution) + protein_df_resolution = applyBinning(protein_df, args.resolution) + + overlap_mask_df = overlapTAD(tad_df_resolution, protein_df_resolution).to_frame() + + log.debug('{}'.format(tad_df_resolution)) + log.debug('{}'.format(protein_df_resolution)) + log.debug('{}'.format(overlap_mask_df)) + + tad_df_ = tad_df[overlap_mask_df] + print('Protein peaks: {}'.format(len(protein_df_resolution))) + print('Matched TADs: {}'.format(len(tad_df_))) + print('Total TADs: {}'.format(len(tad_df))) + + print('TADs match protein: {}'.format(len(tad_df_) / len(tad_df))) diff --git a/hicexplorer/lib/__init__.py b/hicexplorer/lib/__init__.py index f4a4d061..4ec3eb5f 100644 --- a/hicexplorer/lib/__init__.py +++ b/hicexplorer/lib/__init__.py @@ -1 +1,2 @@ from .viewpoint import Viewpoint +from .tadClassifier import TADClassifier diff --git a/hicexplorer/lib/tadClassifier.py b/hicexplorer/lib/tadClassifier.py new file mode 100644 index 00000000..ef916ed2 --- /dev/null +++ b/hicexplorer/lib/tadClassifier.py @@ -0,0 +1,1296 @@ +# import statements + +# classic python libraries +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt +from numpy.random import Generator +from os import EX_CANTCREAT, walk +from os import listdir +import os +import re +import math +import argparse +import warnings +import logging +import scipy.stats as statsw +from scipy.sparse import csr_matrix, lil_matrix +import pickle +import site +# hicexplorer and pybedtools +from hicexplorer import hicFindTADs +from hicexplorer import hicTransform +from hicmatrix import HiCMatrix as hm +from pybedtools import BedTool +import cooler +from hicexplorer.utilities import obs_exp_matrix +from hicexplorer.utilities import convertNansToZeros, convertInfsToZeros + +# machine learning libraries +# https://imbalanced-learn.readthedocs.io/en/stable/ +from sklearn.model_selection import train_test_split +from sklearn.preprocessing import StandardScaler +from sklearn.ensemble import BaggingClassifier +from sklearn import metrics +from sklearn.metrics import classification_report, confusion_matrix, accuracy_score +from sklearn.impute import SimpleImputer +from sklearn.ensemble import AdaBoostClassifier +from sklearn.metrics import roc_auc_score +from sklearn.metrics import roc_curve, auc + +from cleanlab.classification import LearningWithNoisyLabels +from imblearn.under_sampling import * + +# PCA +# from sklearn import decomposition + + +log = logging.getLogger(__name__) + + +class TADClassifier: + '''wrapper class for hicTADClassifier program''' + + pretrained_classifier_10000_obsexp = 'pretrained_classifier_10000_obsexp.BIN' + pretrained_classifier_10000_range = 'pretrained_classifier_10000_range.BIN' + + class MP_Domain_Data: + '''represents domain and protein information and implements helper functions for their preparation''' + + def __init__(self, domain_file, protein_file=None, + threshold=None, leniency=0, resolution=10000, pAddRemoveChrPrexix=None): + '''read the necessary files and check domains against proteins''' + + # read domain file + self.domain_df = TADClassifier.MP_Domain_Data.read_domain_file( + domain_file) + + # read protein file and intersect if necessary + if(protein_file is not None): + # if pAddRemoveChrPrexix: + + self.protein_df = TADClassifier.MP_Domain_Data.readProtein( + protein_file, pAddRemoveChrPrexix) + TADClassifier.MP_Domain_Data.apply_binning_and_leniency( + self.protein_df, pBinSize=resolution, leniency=leniency) + self.domain_df = TADClassifier.MP_Domain_Data.check_domains_against_protein( + self.domain_df, self.protein_df, resolution=resolution, threshold=threshold) + + # build dictionary for tads from domain file + self.chromosomes = self.domain_df['Chrom'].unique().tolist() + self.domain_dict = TADClassifier.MP_Domain_Data.build_tad_dictionary( + self.domain_df, chromosomes=self.chromosomes) + + def readProtein(pFile, pAddChr): + '''read in a bed protein file (add pAddChr, if chr are in single digit form)''' + + # read + protein_df = pd.read_csv(pFile, sep='\t', header=None)[ + [0, 1, 2, 6, 7, 8]] + if pAddChr is None: + pass + elif pAddChr: + protein_df[0] = 'chr' + protein_df[0].astype(str) + elif not pAddChr: + # protein_df[0] = 'chr' + protein_df[0].astype(str) + protein_df[0] = protein_df[0].str.lstrip('chr') + log.debug('protein_df {}'.format(protein_df)) + if(protein_df.size < 1): + raise ValueError('empty protein file passed') + + # use bedtools sorting and apply proper column names + protein_df_bedtool = BedTool.from_dataframe(protein_df) + protein_df = protein_df_bedtool.sort().to_dataframe( + disable_auto_names=True, header=None) + protein_df.columns = TADClassifier.MP_Domain_Data.get_protein_col_names() + return protein_df + + def read_domain_file(tad_file): + '''read in the domain.bed output file of hicFindTads''' + + # read and sort + domains_by_hicfindtads = pd.read_csv( + tad_file, sep="\t", header=None) + domains_by_hicfindtads.columns = TADClassifier.MP_Domain_Data.get_domain_col_names() + domains_by_hicfindtads = domains_by_hicfindtads.sort_values( + by=["Chrom", "Start"]) + + if(domains_by_hicfindtads.size < 1): + raise ValueError('empty domain file passed') + + return domains_by_hicfindtads + + def check_domains_against_protein( + domain_df, protein_df, resolution, threshold=None): + '''check the given tads in the domain df against the protein peaks in the protein file with a threshold''' + + # build bedtools from dfs + domain_df['Name'] = domain_df['End'] + domain_df['End'] = domain_df['Start'] + resolution + + tad_bedtool = BedTool.from_dataframe( + domain_df[["Chrom", "Start", "End", "Name"]]) + protein_bedtool = BedTool.from_dataframe(protein_df) + + # intersect domains and proteins + domain_protein = tad_bedtool.intersect( + protein_bedtool, wa=True, wb=True).to_dataframe() + domain_protein.columns = TADClassifier.MP_Domain_Data.get_domain_protein_col_names() + + # aggregate multiple peaks at one domain + domain_protein = domain_protein.groupby(['Chrom', 'Start', 'End', 'Name']).agg( + signal_value=pd.NamedAgg(column='signalValue', aggfunc=max), + p_value=pd.NamedAgg(column='pValue', aggfunc=max), + q_value=pd.NamedAgg(column='qValue', aggfunc=max) + ) + + # select only domains with certain threshold if given + if threshold is not None: + mask = domain_protein['signal_value'] >= threshold + domain_protein = domain_protein[mask] + + # build output + domain_protein.reset_index(inplace=True) + domain_protein['End'] = domain_protein['Name'] + + # debug information; TODO: move + log.debug('protein peaks: {}'.format(len(protein_df))) + log.debug('TADs: {}'.format(len(domain_df))) + log.debug('Matched TADs: {}'.format(len(domain_protein))) + + return domain_protein + + def apply_binning_and_leniency(pDataFrame, pBinSize=10000, leniency=0): + """bin the given protein file and make peaks wider if necessary""" + + pDataFrame_out = pDataFrame.copy() + pDataFrame_out['Start'] = ( + pDataFrame['Start'] / pBinSize).astype(int) * pBinSize + pDataFrame_out['End'] = ( + (pDataFrame['End'] / pBinSize).astype(int) + 1) * pBinSize + + if (leniency > 0): + pDataFrame_out['Start'] = np.maximum( + 0, pDataFrame_out['Start'] - int(pBinSize * leniency)) + pDataFrame_out['End'] = pDataFrame_out['End'] + \ + int(pBinSize * leniency) + + pDataFrame_out.drop_duplicates() + bedtools_data = BedTool.from_dataframe(pDataFrame_out) + bedtools_data = bedtools_data.merge() + bedtools_data = bedtools_data.sort() + + return bedtools_data.to_dataframe() + + def get_protein_col_names(): + '''get column names''' + + return ['Chrom', 'Start', 'End', 'signalValue', 'pValue', 'qValue'] + + def get_domain_col_names(): + '''get column names''' + + return ["Chrom", "Start", "End", "Name", "Score", + "Strand", "ThickStart", "ThickEnd", "ItemRGB"] + + def get_domain_protein_col_names(): + '''get column names''' + + return ["Chrom", "Start", "End", "Name", "Chrom_p", + "Start_p", "End_p", 'signalValue', 'pValue', 'qValue'] + + def build_tad_dictionary(domains, chromosomes): + '''get a dictionary based on domain file for multiple chromosomes''' + + # for given chromosome names, build dictionary from dataframe + # this is done for performance reasons only + domain_dicts = {} + for chromosome in chromosomes: + + # add current chromosomes, then add all positions + chr_domains = domains[domains['Chrom'] == chromosome] + b = chr_domains["Start"] + chr_dict = dict((int(position), True) for position in b) + domain_dicts[str(chromosome)] = chr_dict + + return domain_dicts + + class MP_Matrix: + '''acts as a wrapper class for a HiCMatrix Object and implements helper functions for matrix data preparation''' + # currently supports matrices of one chromosome + + def __init__(self, matrix_file, method=None, range_max=None, pChromosome=None, pThreads=None): + + # use input directly, if already normalized + if method == 'obs_exp': + hic_ma, hic_ma_np = TADClassifier.MP_Matrix.read_matrix_file( + matrix_file, pChromosome) + hic_ma = TADClassifier.MP_Matrix.obs_exp_normalization(hic_ma, pThreads=pThreads) + # hic_ma_np = np.array(hic_ma.getMatrix()) + # hic_ma_np = hic_ma.matrix + + # perform range normalization, with given max value or infer from + # matrix + elif method == 'range': + hic_ma, hic_ma_np = TADClassifier.MP_Matrix.read_matrix_file( + matrix_file, pChromosome) + range_min = 0.0 + o_min = 0.0 + o_max = 1.0 + + if range_max is None: + # range_max = np.nanmax(hic_ma_np) + range_max = hic_ma_np.max() + + # elif (range_max < np.nanmax(hic_ma_np)): + elif (range_max < hic_ma_np.max()): + + raise ValueError('range maximum too low for input matrix') + + hic_ma_np = TADClassifier.MP_Matrix.range_normalization( + hic_ma_np, range_min, range_max, o_min, o_max) + + else: + raise NotImplementedError + + self.numpy_matrix = hic_ma_np + self.hic_matrix = hic_ma + self.positions = self.get_positions() + self.range_max = range_max + self.resolution = None + + def get_positions(self): + '''get positions for matrix''' + + # get start and end position for every bin in the matrix + indices = np.arange(0, self.numpy_matrix.shape[0]) + # print('indices {}'.format(indices)) + # print('self.hic_matrix.cut_intervals {}'.format(self.hic_matrix.cut_intervals)) + vec_bin_pos = np.vectorize(self.hic_matrix.getBinPos) + pos = vec_bin_pos(indices) + + # return it as an ordered array + return np.transpose(np.array(pos)[0:3, :], (1, 0)) + + def get_resolution(self): + """resolution of matrix""" + + if(self.resolution is None): + self.resolution = self.hic_matrix.getBinSize() + + return self.resolution + + def get_boundary_positions(self, domain_dicts): + '''return a list of booleans, denoting if a boundary exists at the current index''' + + # build necessary function and df to check if there is a boundary + # at position + + is_boundary = np.full(self.positions.shape[0], False, dtype=bool) + # log.debug(domain_dicts) + # check for all indices + for k in range(self.positions.shape[0]): + try: + is_boundary[k] = int(self.positions[k, 1]) in domain_dicts[self.positions[k, 0]] + except KeyError: + is_boundary[k] = False + return is_boundary + + def get_features(self, distance, use_gradient=False): + '''build features for self''' + + # run build features for self + features = TADClassifier.MP_Matrix.build_features( + self.numpy_matrix, distance) + if features is None: + return None + # experimental: use gradient matrix too + if(use_gradient): + x_gradient, y_gradient = self.build_gradient_features(distance) + features = np.concatenate( + (features, x_gradient, y_gradient), axis=1) + + return features + + def build_features(numpy_matrix, distance): + '''select features from input matrix''' + + # build necessary structures + m_indices = np.arange( + distance, numpy_matrix.shape[0] - distance, 1) + m_list = [] + + # get triangle at position index + def get_triangle(index): + start = index - distance + end = index + distance + 1 + + # log.debug('triu submatrix: {}'.format(numpy_matrix[start:end, start:end])) + # log.debug('start {} end {}'.format(start, end)) + triangle = np.triu(numpy_matrix[start:end, start:end].todense(), k=0) + triangle = triangle.astype(float) + triangle[np.tril_indices(triangle.shape[0], -1)] = np.NINF + mask = triangle != float('-inf') + flattened_triangle = np.ndarray.flatten(triangle[mask]) + return flattened_triangle + + # run for all positions + # can refactor for vectorization, but resampling and fitting takes + # way longer anyway + for i in m_indices: + m_list.append(get_triangle(i)) + + # build output + # at boundaries: use filler, those will be unselected later anyways + if len(m_list) == 0: + return None + features = np.stack(m_list, axis=1) + sentinel1 = np.full((features.shape[0], distance), np.nan) + sentinel2 = np.full((features.shape[0], distance), np.nan) + features = np.concatenate([sentinel1, features, sentinel2], axis=1) + + return np.transpose(features, (1, 0)) + + def unselect_border_cases(X, distance): + '''unselect cases at border of matrix''' + + return X[(distance - 1):(X.shape[0] - distance), :] + + def unselect_border_cases_list(y, distance): + '''unselect cases at border of matrix''' + + return y[(distance - 1):y.shape[0] - distance] + + def write_input_to_file(positions, X, y, out_file): + '''save positions,features and is_boundary to file''' + + output = np.concatenate((positions, X, y[:, np.newaxis]), axis=1) + np.savetxt(out_file, output, delimiter=";") + + def read_matrix_file(matrix_file, pChromosome): + ''''reads a given cool file and returns its hiCMatrix and numpy representation''' + # log.debug('matrix_file {}'.format(matrix_file)) + # log.debug('pChromosome {}'.format(pChromosome)) + # check if instance of string or file and load appropriate + if isinstance(matrix_file, str): + if pChromosome is not None: + hic_ma = hm.hiCMatrix(matrix_file, pChrnameList=[pChromosome]) + else: + hic_ma = hm.hiCMatrix(matrix_file) + + # log.debug('hic_ma: {}'.format(hic_ma.matrix)) + + else: + hic_ma = matrix_file + + # hic_ma_np = np.array(hic_ma.getMatrix()) + hic_ma_np = hic_ma.matrix + + return (hic_ma, hic_ma_np) + + def range_normalization(n, n_min, n_max, o_min, o_max): + '''apply range normalization''' + + return o_min + (n - n_min) * (o_max - o_min) / (n_max - n_min) + + def obs_exp_normalization(hic_ma, pThreads=None): + '''apply obs_exp normalization''' + log.debug('obs/exp matrix computation...') + + trasf_matrix = lil_matrix(hic_ma.matrix.shape) + + # from hicTransformTADs + def _obs_exp(pSubmatrix, pThreads=None): + obs_exp_matrix_ = obs_exp_matrix(pSubmatrix, pThreads=pThreads, pDistance=100) + obs_exp_matrix_ = convertNansToZeros( + csr_matrix(obs_exp_matrix_)) + obs_exp_matrix_ = convertInfsToZeros( + csr_matrix(obs_exp_matrix_)) + # if len(obs_exp_matrix_.data) == 0: + # return np.array([[]]) + return obs_exp_matrix_ # .todense() + + for chrname in hic_ma.getChrNames(): + chr_range = hic_ma.getChrBinRange(chrname) + submatrix = hic_ma.matrix[chr_range[0]:chr_range[1], chr_range[0]:chr_range[1]] + submatrix.astype(float) + obs_exp = _obs_exp(submatrix, pThreads) + if obs_exp.nnz != 0: + trasf_matrix[chr_range[0]:chr_range[1], chr_range[0]:chr_range[1]] = lil_matrix(obs_exp) + + hic_ma.setMatrix( + trasf_matrix.tocsr(), + cut_intervals=hic_ma.cut_intervals) + log.debug('obs/exp matrix computation... DONE') + + return hic_ma + + class MP_Classifier: + '''acts as a wrapper for a classifier''' + + def __init__(self, resolution=10000, + normalization_method='range', + resampling_method='undersample_random', + alternative_resampling_method=None, + alternative_classifier=None, + impute_value=-1.0, + estimators_per_step=10, + use_cleanlab=False, + threads=4, + use_gradient=False, + distance=15): + + # set some attribute + self.resolution = resolution + self.normalization_method = normalization_method + self.resampling_method = resampling_method + self.alternative_resampling_method = alternative_resampling_method + self.impute_value = impute_value + self.estimators_per_step = estimators_per_step + self.use_cleanlab = use_cleanlab + self.threads = threads + self.use_gradient = use_gradient + self.distance = distance + self.is_default_classifier = alternative_classifier is None + + if(alternative_classifier is None): + self.classifier = BaggingClassifier( + base_estimator=AdaBoostClassifier(), + n_estimators=0, + warm_start=True, + n_jobs=threads) + + else: + self.classifier = alternative_classifier + + if (use_cleanlab): + estimators = self.classifier.get_params( + )['n_estimators'] + self.estimators_per_step + self.classifier.set_params(n_estimators=estimators) + self.classifier = LearningWithNoisyLabels( + clf=self.classifier, n_jobs=self.threads) + + def single_run(self, positions, X, y, test_size_n=0.2): + '''train and test the classifier on the given dataset''' + + # impute missing values + X = TADClassifier.MP_Classifier.impute(X, self.impute_value) + + # division into training set and test set + pos_train, pos_test, X_train, X_test, y_train, y_test = train_test_split( + positions, X, y, test_size=test_size_n, random_state=0) + + # enact imbalance strategy + X_train, y_train = TADClassifier.MP_Classifier.resample( + X_train, y_train, self.resampling_method, self.alternative_resampling_method, threads=self.threads) + + # set estimators to real wanted value + estimators = self.classifier.get_params( + )['n_estimators'] + self.estimators_per_step + self.classifier.set_params(n_estimators=estimators) + + # train model + # if input contains only one class, an exception is thrown + log.debug('fitting') + if(np.unique(y).shape[0] >= 2): + self.classifier.fit(X, y) + + else: + warnings.warn( + 'input does not contain boundaries or no non-boundaries, fitting aborted') + + # test model + pos_test, X_test, y_test = TADClassifier.MP_Classifier.resample_test( + pos_test, X_test, y_test, threads=self.threads) + y_pred = self.classifier.predict(X_test) + + return (y_test, y_pred) + + def incremental_fit(self, X, y, resample=True): + '''train existing model incrementally on a new dataset, by adding estimators''' + + # impute missing values + X = TADClassifier.MP_Classifier.impute(X, self.impute_value) + + # enact oversample imbalance strategy + if(resample): + X, y = TADClassifier.MP_Classifier.resample( + X, y, self.resampling_method, self.alternative_resampling_method, threads=self.threads) + + # introduce additional estimators to accomodate for new dataset + if(self.use_cleanlab): + estimators = self.classifier.clf.get_params( + )['n_estimators'] + self.estimators_per_step + self.classifier.clf.set_params(n_estimators=estimators) + + else: + estimators = self.classifier.get_params( + )['n_estimators'] + self.estimators_per_step + self.classifier.set_params(n_estimators=estimators) + + # train model + # if input contains only one class, an exception is thrown + log.debug('fitting') + self.classifier.fit(X, y) + + def predict(self, positions, X): + '''predict with existing model''' + + if X is None or len(X) == 0: + return None, None + # impute missing values + X = TADClassifier.MP_Classifier.impute(X, self.impute_value) + + # test model + log.debug('predicting') + y_pred = self.classifier.predict(X) + return positions, y_pred + + def predict_test(self, positions, X, y_test): + + # impute missing values + X = TADClassifier.MP_Classifier.impute(X, self.impute_value) + + # enact resampling test strategy + positions, X, y_test = TADClassifier.MP_Classifier.resample_test( + positions, X, y_test, threads=self.threads) + + # test model + log.debug('predicting') + if(not y_test[y_test == False].shape[0] <= 0 and not y_test[y_test == True].shape[0] <= 0): + y_pred = self.classifier.predict(X) + return positions, X, y_test, y_pred + else: + raise ValueError( + 'input does not contain boundaries and non-boundaries') + + def impute(X, fill_value=-1.0): + '''impute missing nan values by setting them to fill_value''' + + # call Simple Imputer, which will fill all non real numbers with + # another value + log.debug('imputing with value: ' + str(fill_value)) + imp = SimpleImputer( + missing_values=np.nan, + strategy='constant', + fill_value=-1.0) + X = imp.fit_transform(X) + + return X + + def resample(X, y, method='undersample_random', + passed_method=None, threads=4): + '''enact resample method chosen with method''' + + # resample method: KMEANs + if(method == 'undersample_cluster_centroids'): + log.debug('resampling with: ' + method) + cc = ClusterCentroids(random_state=42, n_jobs=threads) + return cc.fit_resample(X, y) + + # resample method: random + elif(method == 'undersample_random'): + log.debug('resampling with: ' + method) + rus = RandomUnderSampler(random_state=42) + return rus.fit_resample(X, y) + + # use users method + elif(method == 'passed_method' and passed_method is not None): + log.debug('resampling with: ' + method) + return passed_method.fit_resample(X, y) + + # just return, if none is chosen + else: + return X, y + + def resample_test(positions, X, y, threads=4): + '''call imblearn random undersample for prediction''' + + # resample test set, for correct accuracy score + if (np.unique(y).shape[0] > 1): + pos_X = np.concatenate((positions, X), axis=1) + rus = RandomUnderSampler(random_state=42) + pos_X, y = rus.fit_resample(pos_X, y) + positions = pos_X[:, 0:3] + X = pos_X[:, 3:(pos_X.shape[1])] + + return positions, X, y + + def print_results(self, y_test, y_pred, out_file=None): + '''print accuracy, confusion matrix and classification report to logger''' + + # important: perform a balanced test predict using y_test!!! + acc = "accuracy score: " + \ + str(accuracy_score(y_test, y_pred)) + '\n\n' + classification = "classification report:\n" + \ + classification_report(y_test, y_pred) + '\n' + conf = "confusion matrix:\n" + \ + str(confusion_matrix(y_test, y_pred)) + + log.debug(acc) + log.debug(classification) + log.debug(conf) + + if(out_file): + + f = open(out_file, "w") + f.writelines(acc) + f.writelines(classification) + f.writelines(conf) + f.close() + + def get_feature_importance(self, out_file): + '''print feature importances''' + + if(self.is_default_classifier and not self.use_cleanlab): + # only use on Bagging Classifier + feature_importances = np.mean( + [est.feature_importances_ for est in self.classifier.estimators_], axis=0) + ind = np.arange(0, feature_importances.shape[0]) + + barlist = plt.bar(ind, feature_importances) + + d = self.distance * 2 + off = 0 + barlist[off].set_color('red') + + while(d > 0): + off = d + off + barlist[off].set_color('red') + d = d - 1 + + plt.savefig(out_file) + + def get_roc(self, X_test, y_test, out_file): + '''get receiver operating characteristic''' + + if(self.is_default_classifier and not self.use_cleanlab): + # from + # https://scikit-learn.org/stable/auto_examples/model_selection/plot_roc.html + fpr = dict() + tpr = dict() + roc_auc = dict() + + y_score = self.classifier.decision_function(X_test) + y_test = y_test.astype(int) + + # Compute micro-average ROC curve and ROC area + fpr["micro"], tpr["micro"], _ = roc_curve( + y_test.ravel(), y_score.ravel()) + roc_auc["micro"] = auc(fpr["micro"], tpr["micro"]) + + plt.figure() + lw = 2 + + plt.plot(fpr["micro"], tpr["micro"], color='aqua', + lw=lw, label='ROC curve (area = %0.2f)' % roc_auc["micro"]) + + plt.plot([0, 1], [0, 1], color='navy', lw=lw, linestyle='--') + plt.xlim([0.0, 1.0]) + plt.ylim([0.0, 1.05]) + plt.xlabel('False Positive Rate') + plt.ylabel('True Positive Rate') + plt.title('Receiver operating characteristic') + plt.legend(loc="lower right") + plt.savefig(out_file) + + # TAD classifier program + + def __init__(self, mode, + out_file, + normalization_method='range', + saved_classifier=None, + unselect_border_cases=True, + threads=4, + threshold=None, + leniency=0, + resolution=10000, + distance=15, + impute_value=-1.0, + resampling_method='undersample_random', + alternative_resampling_method=None, + alternative_classifier=None, + use_cleanlab=False, + estimators_per_step=50, + concatenate_before_resample=False, + pAddRemoveChrPrexix=None + ): + + self.mode = mode + self.out_file = out_file + self.threshold = threshold + self.leniency = leniency + self.unselect_border_cases = unselect_border_cases + self.concatenate_before_resample = concatenate_before_resample + self.addRemoveChrPrexix = pAddRemoveChrPrexix + + if(mode == 'predict' or mode == 'train_existing' or mode == 'predict_test'): + if(saved_classifier is not None): + try: + self.classifier = pickle.load(open(saved_classifier, 'rb')) + except Exception as exp: + log.error('Tried to load ML model but failed! {}'.format(str(exp))) + exit(1) + + else: + model_location = site.getsitepackages()[0] + '/hicexplorer/trained_models/' + + if(normalization_method == 'obs_exp'): + if resolution == 10000: + model_location += '10kb_model_cleanlab_proteins_obs_exp.BIN' + elif resolution == 25000: + model_location += '25kb_model_cleanlab_proteins_obs_exp.BIN' + elif resolution == 50000: + model_location += '50kb_model_cleanlab_proteins_obs_exp.BIN' + elif resolution == 100000: + model_location += '100kb_model_cleanlab_proteins_obs_exp.BIN' + else: + log.error('No trained model for this resolution! Please train a model on your own with hicTrainTADClassifier!') + exit(1) + + log.debug('using obs/exp default classifier') + else: + if resolution == 10000: + model_location += '10kb_model_cleanlab_proteins_range.BIN' + elif resolution == 25000: + model_location += '25kb_model_cleanlab_proteins_range.BIN' + elif resolution == 50000: + model_location += '50kb_model_cleanlab_proteins_range.BIN' + elif resolution == 100000: + model_location += '100kb_model_cleanlab_proteins_range.BIN' + else: + log.error('No trained model for this resolution! Please train a model on your own with hicTrainTADClassifier!') + exit(1) + + try: + self.classifier = pickle.load( + open(model_location, 'rb')) + except Exception as exp: + log.error('Tried to load ML model but failed! {}'.format(str(exp))) + exit(1) + if(mode == 'train_new' or mode == 'train_test'): + if(alternative_classifier is not None and not isinstance(alternative_classifier, sklearn.base.BaseEstimator)): + raise ValueError('the passed classifier is not valid') + + if(not resampling_method == 'passed_method' and alternative_resampling_method is not None): + warnings.warn( + 'default resampling method chosen, but custom method passed; using passed method') + resampling_method = 'passed_method' + + if(alternative_resampling_method is not None and not isinstance(alternative_resampling_method, imblearn.base.BaseCleaningSampler)): + raise ValueError('the passed resampling method is not valid') + + self.classifier = TADClassifier.MP_Classifier( + resolution=resolution, + normalization_method=normalization_method, + resampling_method=resampling_method, + alternative_resampling_method=alternative_resampling_method, + alternative_classifier=alternative_classifier, + impute_value=impute_value, + estimators_per_step=estimators_per_step, + use_cleanlab=use_cleanlab, + use_gradient=False, + distance=distance, + threads=threads) + + def prepare_train(self, matrix_file, domain_file, protein_file, pChromosome, ): + '''prepare matrix and its derivatives for the run''' + + log.debug('preparing domain data') + prep = TADClassifier.MP_Domain_Data( + domain_file, + protein_file, + resolution=self.classifier.resolution, + threshold=self.threshold, + leniency=self.leniency, + pAddRemoveChrPrexix=self.addRemoveChrPrexix) + domain_dict = prep.domain_dict + + log.debug('loading matrix') + # ingest matrix + matrix = TADClassifier.MP_Matrix(matrix_file, + method=self.classifier.normalization_method, pChromosome=pChromosome) + + # build inputs for classifier + log.debug('build features') + is_boundary = matrix.get_boundary_positions(domain_dict) + features = matrix.get_features( + self.classifier.distance, + self.classifier.use_gradient) + if features is None: + return matrix, None, features, is_boundary + positions = matrix.positions + + if(not self.classifier.resolution == matrix.get_resolution()): + warnings.warn( + 'training matrix with resolution {} on classifier with resolution {}'.format( + self.classifier.resolution, + matrix.get_resolution())) + + # get rid of cases at the border of matrix + if(self.unselect_border_cases): + features = TADClassifier.MP_Matrix.unselect_border_cases( + features, self.classifier.distance) + positions = TADClassifier.MP_Matrix.unselect_border_cases( + positions, self.classifier.distance) + is_boundary = TADClassifier.MP_Matrix.unselect_border_cases_list( + is_boundary, self.classifier.distance) + + return matrix, positions, features, is_boundary + + def prepare_predict(self, matrix_file, pChromosome): + '''prepare matrix and its derivatives for the run''' + + log.debug('loading matrix') + # ingest matrix + matrix = TADClassifier.MP_Matrix(matrix_file, + method=self.classifier.normalization_method, pChromosome=pChromosome) + + # build inputs for classifier + log.debug('build features') + features = matrix.get_features( + self.classifier.distance, + self.classifier.use_gradient) + positions = matrix.positions + + # get rid of cases at the border of matrix + if(self.unselect_border_cases): + features = TADClassifier.MP_Matrix.unselect_border_cases( + features, self.classifier.distance) + positions = TADClassifier.MP_Matrix.unselect_border_cases( + positions, self.classifier.distance) + + return matrix, positions, features + + def train_test(self, matrix_list, domain_list, protein_list, pChromosome): + '''perform train_test program mode''' + + # prepare + matrix, positions, features, is_boundary = self.prepare_train( + matrix_list[0], domain_list[0], protein_list[0], pChromosome=pChromosome[0][0]) + + out_file_s = self.out_file.split('.') + + if(out_file_s[-1] == 'txt'): + out_file = self.out_file + else: + out_file = self.out_file + '.txt' + + # run and print classifier output + try: + y_test, y_pred = self.classifier.single_run( + positions, features, is_boundary) + self.classifier.print_results( + y_test, y_pred, out_file=out_file) + except ValueError: + raise ValueError( + 'training or test set does not contain any boundaries') + + def multi_train(self, matrix_list, domain_list, + protein_list, nm_conc_features=1, pChromosome=None): + '''perform train and on multiple matrices in list, resample separatly, but train once''' + + # note, that the parameter nm_conc_features can be used to resample a + # few matrices together + nm_conc_features = nm_conc_features - 1 + i = 0 + conc_features = None + conc_is_boundary = None + resampled_X = None + resampled_y = None + + for j, data in enumerate(zip(matrix_list, domain_list, protein_list, pChromosome)): + for chromosome in pChromosome[j]: + matrix, positions, features, is_boundary = self.prepare_train( + data[0], data[1], data[2], pChromosome=chromosome) + + if features is None: + continue + matrix.numpy_matrix = None + matrix.hic_matrix = None + matrix = None + + if(conc_features is None): + conc_features = features + conc_is_boundary = is_boundary + + else: + conc_features = np.concatenate( + (conc_features, features), axis=0) + conc_is_boundary = np.concatenate( + (conc_is_boundary, is_boundary), axis=0) + + if(i == nm_conc_features): + resampled_X, resampled_y = self.incremental_resample( + resampled_X, resampled_y, conc_features, conc_is_boundary) + i = 0 + conc_features = None + conc_is_boundary = None + + else: + i = i + 1 + + features = None + is_boundary = None + + if (conc_features is not None): + resampled_X, resampled_y = self.incremental_resample( + resampled_X, resampled_y, conc_features, conc_is_boundary) + conc_features = None + conc_is_boundary = None + + try: + self.classifier.incremental_fit( + resampled_X, resampled_y, resample=False) + self.persist(self.out_file) + + except ValueError: + warnings.warn( + 'training matrix does not contain any boundaries, training skipped') + + def multi_train_concatenate_before_resample( + self, matrix_list, domain_list, protein_list, pChromosome, nm_conc_features=1000000): + '''perform train on multiple matrice, concatenate the features of each matrices and then resample and train''' + + # use nm_conc_features to reduce the number of matrices, that are + # concatenated + nm_conc_features = nm_conc_features - 1 + i = 0 + conc_features = None + conc_is_boundary = None + + for j, data in enumerate(zip(matrix_list, domain_list, protein_list)): + for chromosome in pChromosome[j]: + matrix, positions, features, is_boundary = self.prepare_train( + data[0], data[1], data[2], pChromosome=chromosome) + + matrix.numpy_matrix = None + matrix.hic_matrix = None + matrix = None + + if(conc_features is None): + conc_features = features + conc_is_boundary = is_boundary + + else: + conc_features = np.concatenate( + (conc_features, features), axis=0) + conc_is_boundary = np.concatenate( + (conc_is_boundary, is_boundary), axis=0) + + if(i == nm_conc_features): + try: + self.classifier.incremental_fit( + conc_features, conc_is_boundary, resample=True) + except ValueError: + warnings.warn( + 'training matrix does not contain any boundaries, training skipped') + + i = 0 + conc_features = None + conc_is_boundary = None + + else: + i = i + 1 + + features = None + is_boundary = None + + if (conc_features is not None): + try: + self.classifier.incremental_fit( + conc_features, conc_is_boundary, resample=True) + except ValueError: + warnings.warn( + 'training matrix does not contain any boundaries, training skipped') + + conc_features = None + conc_is_boundary = None + + self.persist(self.out_file) + + def multi_test_predict(self, matrix_list, domain_list, protein_list, pChromosome): + '''predict a balanced dataset for a meaningful classification report''' + + conc_test_boundary = None + conc_is_boundary = None + conc_positions = None + + # ROC + conc_features = None + + for i, data in enumerate(zip(matrix_list, domain_list, protein_list)): + + for chromosome in pChromosome[i]: + matrix, positions, features, is_boundary = self.prepare_train( + data[0], data[1], data[2], pChromosome=chromosome) + + matrix.numpy_matrix = None + matrix.hic_matrix = None + matrix = None + + try: + positions, features, y_test, y_pred = self.classifier.predict_test( + positions, features, y_test=is_boundary) + + if(conc_test_boundary is None): + conc_test_boundary = y_test + conc_is_boundary = y_pred + conc_positions = positions + + # ROC + conc_features = features + + else: + conc_test_boundary = np.concatenate( + (conc_test_boundary, y_test), axis=0) + conc_is_boundary = np.concatenate( + (conc_is_boundary, y_pred), axis=0) + conc_positions = np.concatenate( + (conc_positions, positions), axis=0) + + # ROC + conc_features = np.concatenate( + (conc_features, features), axis=0) + + except BaseException: + log.debug('one of the inputs did not contain boundaries') + + is_boundary = None + positions = None + features = None + + out_file_results = self.out_file + '_results.txt' + out_file_fi = self.out_file + '_feature_importance.png' + out_file_roc = self.out_file + '_roc.png' + + self.classifier.get_feature_importance(out_file_fi) + self.classifier.print_results( + conc_test_boundary, + conc_is_boundary, + out_file=out_file_results) + self.classifier.get_roc( + conc_features, + conc_test_boundary, + out_file_roc) + # TADClassifier.print_to_bed(TADClassifier.get_domains(conc_positions,conc_is_boundary),self.out_file) + + def incremental_resample(self, X, y, X_i, y_i): + '''resample without fitting''' + + try: + if(X is None): + X, y = TADClassifier.MP_Classifier.resample( + X_i, y_i, method=self.classifier.resampling_method, passed_method=self.classifier.alternative_resampling_method, threads=self.classifier.threads) + + else: + X_i, y_i = TADClassifier.MP_Classifier.resample( + X_i, y_i, method=self.classifier.resampling_method, passed_method=self.classifier.alternative_resampling_method, threads=self.classifier.threads) + X = np.concatenate((X, X_i), axis=0) + y = np.concatenate((y, y_i), axis=0) + + return X, y + + except ValueError: + warnings.warn( + 'training matrix does not contain boundaries, training skipped') + + return X, y + + def persist(self, out_file): + + out_file_s = out_file.split('.') + + if(not out_file_s[-1] == 'BIN'): + out_file = out_file + '.BIN' + + pickle.dump(self.classifier, open(out_file, 'wb')) + + def run_hicTrainClassifier(self, matrix_list, domain_list, protein_list, pChromosomes): + '''run hicTrainClassifier with specified mode on file''' + + if(isinstance(matrix_list, str)): + matrix_list = [matrix_list] + + if(isinstance(domain_list, str)): + domain_list = [domain_list] + + if(len(domain_list) == 1): + domain_list = domain_list * len(matrix_list) + + if(protein_list is None): + protein_list = [None] * len(matrix_list) + + elif(isinstance(protein_list, str)): + protein_list = [protein_list] + + if(len(protein_list) == 1): + protein_list = protein_list * len(matrix_list) + + if(not (len(matrix_list) == len(domain_list) and len(protein_list) == len(domain_list))): + raise ValueError( + 'please pass domain (,optional protein) and matrix lists of same length or pass a single domain (and optional protein) file') + + chromosome_list = [] + if pChromosomes is not None: + chromosome_list = pChromosomes + else: + for matrix in matrix_list: + cooler_obj = cooler.Cooler(matrix) + chromosome_list.append(cooler_obj.chromnames) + + if(self.mode == 'train_new' or self.mode == 'train_existing'): + + if(self.concatenate_before_resample): + self.multi_train_concatenate_before_resample( + matrix_list, domain_list, protein_list, pChromosome=chromosome_list) + + else: + self.multi_train(matrix_list, domain_list, protein_list, pChromosome=chromosome_list) + + elif(self.mode == 'train_test'): + self.train_test(matrix_list, domain_list, protein_list, pChromosome=chromosome_list) + + elif(self.mode == 'predict_test'): + self.multi_test_predict(matrix_list, domain_list, protein_list, pChromosome=chromosome_list) + + def run_hicTADClassifier(self, matrix_list, pChromosomes): + '''predict a dataset''' + + if(isinstance(matrix_list, str)): + matrix_list = [matrix_list] + + chromosome_list = [] + if pChromosomes is None: + for matrix in matrix_list: + cooler_obj = cooler.Cooler(matrix) + chromosome_list.append(cooler_obj.chromnames) + else: + chromosome_list = pChromosomes + # i = 0 + conc_is_boundary = None + conc_positions = None + for i, data in enumerate(matrix_list): + for chromosome in chromosome_list[i]: + matrix, positions, features = self.prepare_predict(data, pChromosome=chromosome) + + matrix.numpy_matrix = None + matrix.hic_matrix = None + matrix = None + + positions, is_boundary = self.classifier.predict( + positions, features) + if positions is None or len(positions) == 0: + continue + if conc_is_boundary is None: + conc_positions = positions + conc_is_boundary = is_boundary + else: + conc_positions = np.concatenate((conc_positions, positions), axis=0) + + conc_is_boundary = np.concatenate((conc_is_boundary, is_boundary), axis=0) + + features = None + is_boundary = None + positions = None + # i = i + 1 + + # matrix_name = ".".join(os.path.basename(matrix_list[i]).split(".")[:-1]) + out_file_i = self.out_file[i] + TADClassifier.print_to_bed(TADClassifier.get_domains( + conc_positions, conc_is_boundary), out_file_i) + + def print_to_bed(domain_df, path): + '''print domain file''' + + domain_df.to_csv(path, sep='\t', header=None, index=False) + + def filter_domains(domains): + '''filter out to small domains''' + + min_tad_size = 50000 - 1 + domain_df = pd.DataFrame({'Chrom': domains[:, + 0], + 'Start': domains[:, + 1], + 'End': domains[:, + 2]}) + + domain_df['Start'] = domain_df.Start.apply(np.int64) + domain_df['End'] = domain_df.End.apply(np.int64) + domain_df = domain_df.sort_values(by=["Chrom", "Start"]) + domain_df['Test'] = domain_df['Start'].shift(1, fill_value=0) + domain_df['Chrom_Test'] = domain_df['Chrom'].shift(1, fill_value=0) + domain_df['Chrom_Test_Bool'] = domain_df['Chrom'] != domain_df['Chrom_Test'] + domain_df['Test_Bool'] = domain_df['Test'] + min_tad_size <= domain_df['Start'] + domain_df['Test_Bool'] = np.logical_or(domain_df['Test_Bool'], domain_df['Chrom_Test_Bool']) + domain_df = domain_df[domain_df['Test_Bool']] + + return domain_df[['Chrom', 'Start', 'End']].to_numpy() + + def get_domains(positions, y): + '''return dataframe of predicted TADs''' + + pos_mask = y[:] == True + # print('pos_mask {}'.format(pos_mask)) + domains = positions[pos_mask] + # print('domains {}'.format(domains)) + + domains = TADClassifier.filter_domains(domains) + # print('domains {}'.format(domains)) + + name = np.arange(1, domains.shape[0] + 1) + score = np.full(domains.shape[0], -1) + strand = np.full(domains.shape[0], 0) + item_rgb = np.tile([0, 1], domains.shape[0]) + item_rgb = item_rgb[0:domains.shape[0]] + # print('Chrom {}'.format(domains[:, 0])) + + domain_df = pd.DataFrame({'Chrom': domains[:, + 0], + 'Start': domains[:, + 1], + 'End': domains[:, + 1], + 'Name': name, + 'Score': score, + 'Strand': strand, + 'ThickStart': domains[:, + 1], + 'ThickEnd': domains[:, + 1], + 'ItemRGB': item_rgb}) + # print('domain_df 1 {}'.format(domain_df)) + + def rgb_helper(i): + if(i == 0): + return '31,120,180' + else: + return '51,160,44' + + def name_helper(i): + return 'ID_0.03_' + str(i) + + def strand_helper(s): + return '.' + + domain_df["ItemRGB"] = domain_df["ItemRGB"].map(rgb_helper) + domain_df["Name"] = domain_df["Name"].map(name_helper) + domain_df["Strand"] = domain_df["Strand"].map(strand_helper) + + domain_df['Start'] = domain_df.Start.apply(np.int64) + domain_df['End'] = domain_df.End.apply(np.int64) + + domain_df = domain_df.sort_values(by=["Chrom", "Start"]) + + domain_df['Start'] = domain_df['Start'].shift(1, fill_value=0) + domain_df['ThickStart'] = domain_df['ThickStart'].shift( + 1, fill_value=0) + # print('domain_df 2{}'.format(domain_df)) + + # domain_df = domain_df[1:] + # print('domain_df 3{}'.format(domain_df)) + + domain_df = domain_df[domain_df['Start'] < domain_df['End']] + + return domain_df diff --git a/hicexplorer/lib/viewpoint.py b/hicexplorer/lib/viewpoint.py index c6ff57c2..9c470a9c 100644 --- a/hicexplorer/lib/viewpoint.py +++ b/hicexplorer/lib/viewpoint.py @@ -9,6 +9,7 @@ from scipy.stats import nbinom from scipy.special import gammaln from scipy import special +import h5py from hicexplorer.lib import cnb @@ -60,75 +61,184 @@ def readReferencePointFile(self, pBedFile, pGene=True): else: return viewpoints - def readInteractionFile(self, pBedFile): + # def readInteractionFile(self, pBedFile): + # ''' + # Reads an interaction file produced by chicViewpoint. Contains header information, these lines + # start with '#'. + # Interactions files contain: + # Chromosome Viewpoint, Start, End, Gene, Chromosome Interation, Start, End, Relative position (to viewpoint start / end), + # Relative number of interactions, p-score based on relative interactions. + + # This function returns: + # - header as a string + # - interaction data in relation to relative position as a dict e.g. {-1000:0.1, -1500:0.2} + # - p-score in relation to relative position as a dict (same format as interaction data) + # - interaction_file_data: the raw line in relation to the relative position. Needed for additional output file. + # ''' + # # use header info to store reference point, and based matrix + # interaction_data = {} + # p_score = {} + # interaction_file_data = {} + # genomic_coordinates = {} + # with open(pBedFile) as fh: + # fh.readline() + # header = fh.readline() + # for line in fh.readlines(): + # # Addition header information for end users + # if line.strip().startswith('#'): + # continue + + # _line = line.strip().split('\t') + # # relative postion and relative interactions + # interaction_data[int(_line[-5])] = float(_line[-4]) + # p_score[int(_line[-5])] = float(_line[-3]) + # interaction_file_data[int(_line[-5])] = _line + # genomic_coordinates[int(_line[-5])] = [_line[0], _line[1], _line[2]] + + # return header, interaction_data, p_score, interaction_file_data, genomic_coordinates + + def readInteractionFile(self, pFilePath, pInternalIdentifierTriplet): ''' Reads an interaction file produced by chicViewpoint. Contains header information, these lines start with '#'. Interactions files contain: Chromosome Viewpoint, Start, End, Gene, Chromosome Interation, Start, End, Relative position (to viewpoint start / end), - Relative number of interactions, p-score based on relative interactions. + Relative number of interactions, p-value based on negative binomial distribution for the relative position. This function returns: - header as a string - - interaction data in relation to relative position as a dict e.g. {-1000:0.1, -1500:0.2} - - p-score in relation to relative position as a dict (same format as interaction data) + - interaction data in relation to relative position as a dict together with p-value, raw and x-fold: e.g. {-1000:[0.1, 0.01, 2.3, 5]} - interaction_file_data: the raw line in relation to the relative position. Needed for additional output file. ''' - # use header info to store reference point, and based matrix - interaction_data = {} - p_score = {} - interaction_file_data = {} - genomic_coordinates = {} - with open(pBedFile) as fh: - fh.readline() - header = fh.readline() - for line in fh.readlines(): - # Addition header information for end users - if line.strip().startswith('#'): - continue - _line = line.strip().split('\t') - # relative postion and relative interactions - interaction_data[int(_line[-5])] = float(_line[-4]) - p_score[int(_line[-5])] = float(_line[-3]) - interaction_file_data[int(_line[-5])] = _line - genomic_coordinates[int(_line[-5])] = [_line[0], _line[1], _line[2]] + # interaction_data[int(_line[-5])] = np.array([float(_line[-4]), float(_line[-3]), float(_line[-1]), float(_line[-2])]) + # interaction_file_data[int(_line[-5])] = _line - return header, interaction_data, p_score, interaction_file_data, genomic_coordinates + interactionFileHDF5Object = h5py.File(pFilePath, 'r') + arrays_to_retrieve = ['relative_position_list', 'interaction_data_list', 'pvalue', 'raw', 'xfold'] + internal_path = '/'.join(pInternalIdentifierTriplet) + data = [] - def readInteractionFileForAggregateStatistics(self, pBedFile): - ''' - Reads an interaction file produced by chicViewpoint. Contains header information, these lines - start with '#'. - Interactions files contain: - Chromosome Viewpoint, Start, End, Gene, Chromosome Interation, Start, End, Relative position (to viewpoint start / end), - Relative number of interactions, p-value based on negative binomial distribution for the relative position. + if internal_path not in interactionFileHDF5Object: + log.debug('internal path not found: {}'.format(internal_path)) + return {}, {}, [] + if list(interactionFileHDF5Object[internal_path].keys()) == 0: + log.debug('interactionFileHDF5Object[internal_path] {}'.format(interactionFileHDF5Object[internal_path])) + return {}, {}, [] - This function returns: - - header as a string - - interaction data in relation to relative position as a dict together with p-value, raw and x-fold: e.g. {-1000:[0.1, 0.01, 2.3, 5]} - - interaction_file_data: the raw line in relation to the relative position. Needed for additional output file. - ''' - # use header info to store reference point, and based matrix + for array_name in arrays_to_retrieve: + try: + if internal_path + '/' + array_name in interactionFileHDF5Object: + data.append(np.array(interactionFileHDF5Object[internal_path + '/' + array_name][:])) + # log.debug('datatype of {} {} '.format(array_name, data[-1].dtype)) + # data.append(interactionFileHDF5Object.get( internal_path + '/' + array_name).value) + except Exception as exp: + log.debug(internal_path + '/' + array_name) + log.debug(str(exp)) + + for array_name in ['start_list', 'end_list']: + try: + if internal_path + '/' + array_name in interactionFileHDF5Object: + data.append(np.array(interactionFileHDF5Object[internal_path + '/' + array_name][:])) + # data.append(interactionFileHDF5Object.get( internal_path + '/' + array_name).value) + except Exception as exp: + log.debug(internal_path + '/' + array_name) + log.debug(str(exp)) + + if internal_path + '/' + 'chromosome' in interactionFileHDF5Object: + chromosome = interactionFileHDF5Object.get(internal_path + '/' + 'chromosome')[()].decode("utf-8") + else: + log.debug('internal path not found: {}'.format(internal_path + '/' + 'chromosome')) + + if internal_path + '/' + 'gene' in interactionFileHDF5Object: + gene = interactionFileHDF5Object.get(internal_path + '/' + 'gene')[()].decode("utf-8") + else: + log.debug('internal path not found: {}'.format(internal_path + '/' + 'gene')) + + if internal_path + '/' + 'sum_of_interactions' in interactionFileHDF5Object: + sum_of_interactions = interactionFileHDF5Object.get(internal_path + '/' + 'sum_of_interactions')[()] + else: + log.debug('internal path not found: {}'.format(internal_path + '/' + 'sum_of_interactions')) + + reference_point_start = None + reference_point_end = None + if 'reference_point_start' in interactionFileHDF5Object[internal_path]: + reference_point_start = interactionFileHDF5Object.get(internal_path + '/' + 'reference_point_start')[()] + if 'reference_point_end' in interactionFileHDF5Object[internal_path]: + reference_point_end = interactionFileHDF5Object.get(internal_path + '/' + 'reference_point_end')[()] + + interactionFileHDF5Object.close() + # log.debug('chromosomes: {}'.format(chromosome)) + + # log.debug(data) interaction_data = {} interaction_file_data = {} - with open(pBedFile) as fh: - fh.readline() - header = fh.readline() - fh.readline() - for line in fh.readlines(): - # Addition header information for end users - if line.strip().startswith('#'): - continue - if not line: - continue - _line = line.strip().split('\t') - # relative postion and relative interactions - interaction_data[int( - _line[-5])] = np.array([float(_line[-4]), float(_line[-3]), float(_line[-1]), float(_line[-2])]) - interaction_file_data[int(_line[-5])] = _line - return header, interaction_data, interaction_file_data + try: + for i in range(len(data[0])): + interaction_data[data[0][i]] = list([float(data[1][i]), float(data[2][i]), float(data[3][i]), float(data[4][i])]) + interaction_file_data[data[0][i]] = list([str(chromosome), int(float(data[5][i])), int(float(data[6][i])), str(gene), float(sum_of_interactions), int(float(data[0][i])), float(data[1][i]), float(data[2][i]), float(data[4][i]), float(data[3][i])]) + except Exception: + return {}, {}, [] + # log.debug('153') + # log.debug('interaction_data {}'.format(interaction_data[0])) + # log.debug('interaction_file_data {}'.format(interaction_file_data[0])) + + return interaction_data, interaction_file_data, [reference_point_start, reference_point_end] + + # -5: relative position relative_position_list + # -4: relative interaction: interaction_data_list + # -3: p-value: pvalue + # -1: raw: raw + # -2: x-fold: xfold + + # # use header info to store reference point, and based matrix + # interaction_data = {} + # interaction_file_data = {} + # with open(pBedFile) as fh: + # fh.readline() + # header = fh.readline() + # fh.readline() + + # for line in fh.readlines(): + # # Addition header information for end users + # if line.strip().startswith('#'): + # continue + # if not line: + # continue + # _line = line.strip().split('\t') + # # relative postion and relative interactions + + # interaction_data[int( + # _line[-5])] = np.array([float(_line[-4]), float(_line[-3]), float(_line[-1]), float(_line[-2])]) + # interaction_file_data[int(_line[-5])] = _line + # return header, interaction_data, interaction_file_data + + def interactionDataForPlot(self, pFilePath, pInternalIdentifierTriplet): + + # header, interaction_data, p_value_data, #_interaction_file_data_raw#, genomic_coordinates = self.readInteractionFile(pInteractionFile) + # matrix_name, viewpoint, upstream_range, downstream_range, gene, _ = header.split('\t') + interaction_data, interaction_file_data, reference_point = self.readInteractionFile(pFilePath, pInternalIdentifierTriplet) + + # _line = line.strip().split('\t') + # # relative postion and relative interactions + # interaction_data[int(_line[-5])] = float(_line[-4]) + # p_score[int(_line[-5])] = float(_line[-3]) + # interaction_file_data[int(_line[-5])] = _line + # genomic_coordinates[int(_line[-5])] = [_line[0], _line[1], _line[2]] + + # arrays_to_retrieve = ['relative_position_list', 'interaction_data_list', 'pvalue', 'raw', 'xfold'] + interaction_data = {} + p_score = {} + # interaction_file_data = {} + genomic_coordinates = {} + + for key, value in interaction_file_data.items(): + interaction_data[key] = value[6] + p_score[key] = value[7] + genomic_coordinates[key] = value[:3] + + return interaction_data, p_score, genomic_coordinates, reference_point def readBackgroundDataFile(self, pBedFile, pRange, pFixateRange, pMean=False): ''' @@ -188,6 +298,73 @@ def writeInteractionFile(self, pBedFile, pData, pHeader, pPValueData, pXfold, pD interaction[2], interaction[3], interaction[4], interaction[5], interaction[6], pPValueData[j], pXfold[j], interaction[7], decimal_places=pDecimalPlaces)) return + def writeInteractionFileHDF5(self, pInteractionFileGroupH5Object, pFileName, pData, pReferencePoint): + ''' + Writes an interaction file for one viewpoint and one sample as a tab delimited file with one interaction per line. + Header contains information about the interaction: + Chromosome Interation, Start, End, Relative position (to viewpoint start / end), + Relative number of interactions, p-values based on negative binomial distribution per relative distance, raw interaction data + ''' + + # chrom, start_list, end_list, gene, sum_of_interactions, relative_position_list, interaction_data_list, pPValueList, xFoldList, raw_data_list + # log.debug(pFileName) + + groupObject, file_name = self.createUniqueHDFGroup(pInteractionFileGroupH5Object, pFileName) + # if counter != 0: + # pass + # log.debug('Gene name {} occurred {} times! Stored as {}_{}'.format(pFileName, counter, pFileName, counter)) + # groupObject.create_dataset("header", data=pHeader) + # groupObject.create_dataset("chromosome", data=pData[0].decode("utf-8")) + groupObject["chromosome"] = str(pData[0]) + + groupObject.create_dataset("start_list", data=pData[1], compression="gzip", compression_opts=9) + groupObject.create_dataset("end_list", data=pData[2], compression="gzip", compression_opts=9) + groupObject.create_dataset("gene", data=pData[3]) + groupObject.create_dataset("sum_of_interactions", data=pData[4]) + groupObject.create_dataset("relative_position_list", data=pData[5], compression="gzip", compression_opts=9) + groupObject.create_dataset("interaction_data_list", data=pData[6], compression="gzip", compression_opts=9) + groupObject.create_dataset("pvalue", data=pData[7], compression="gzip", compression_opts=9) + groupObject.create_dataset("xfold", data=pData[8], compression="gzip", compression_opts=9) + groupObject.create_dataset("raw", data=pData[9], compression="gzip", compression_opts=9) + + # groupObject.create_dataset("start_list", data=pData[1]) + # groupObject.create_dataset("end_list", data=pData[2]) + # groupObject.create_dataset("gene", data=pData[3]) + # groupObject.create_dataset("sum_of_interactions", data=pData[4]) + # groupObject.create_dataset("relative_position_list", data=pData[5]) + # groupObject.create_dataset("interaction_data_list", data=pData[6]) + # groupObject.create_dataset("pvalue", data=pData[7]) + # groupObject.create_dataset("xfold", data=pData[8]) + # groupObject.create_dataset("raw", data=pData[9]) + + groupObject.create_dataset("reference_point_start", data=int(pReferencePoint[0])) + groupObject.create_dataset("reference_point_end", data=int(pReferencePoint[1])) + + # with open((pBedFile + '.txt').strip(), 'w') as fh: + # fh.write('{}\n'.format(pHeader)) + # for j, interaction in enumerate(pData): + # fh.write("{}\t{}\t{}\t{}\t{}\t{}\t{:.{decimal_places}f}\t{:.{decimal_places}f}\t{:.{decimal_places}f}\t{:.{decimal_places}f}\n". + # format(interaction[0], interaction[1], + # interaction[2], interaction[3], interaction[4], interaction[5], interaction[6], pPValueData[j], pXfold[j], interaction[7], decimal_places=pDecimalPlaces)) + return file_name + + def createUniqueHDFGroup(self, pGroupObject, pAdditionalGroupName): + + success = False + counter = 0 + while not success: + try: + if counter != 0: + pAdditionalGroupName = pAdditionalGroupName + '_' + str(counter) + else: + file_name = pAdditionalGroupName + groupObject = pGroupObject.create_group(file_name) + success = True + except ValueError: + counter += 1 + + return groupObject, file_name + def computeViewpoint(self, pReferencePoint, pChromViewpoint, pRegion_start, pRegion_end): ''' This function computes a viewpoint for a given sample and a given pReferencePoint within the @@ -274,6 +451,58 @@ def createInteractionFileData(self, pReferencePoint, pChromViewpoint, pRegion_st exit(1) return interactions_list + def createInteractionFileDataHDF5(self, pReferencePoint, pChromViewpoint, pRegion_start, pRegion_end, pInteractionData, pInteractionDataRaw, pGene, pSumOfInteractions, pPValueList, xFoldList): + ''' + Creates out of internal information a list of tuples which can be written to an interaction file. + Tuple contains: + Chromosome viewpoint, start, end, chromosome interaction, start, end, relative_position, interaction data + ''' + chrom = '' + start_list = [] + end_list = [] + gene = pGene + # sum_of_interactions_list = pSumOfInteractions + relative_position_list = [] + interaction_data_list = [] + raw_data_list = [] + + view_point_start, view_point_end = self.getReferencePointAsMatrixIndices( + pReferencePoint) + view_point_range = self.getViewpointRangeAsMatrixIndices( + pChromViewpoint, pRegion_start, pRegion_end) + view_point_range = list(view_point_range) + view_point_range[1] += 1 + + chrom, start, _, _ = self.hicMatrix.getBinPos(view_point_start) + _, _, end, _ = self.hicMatrix.getBinPos(view_point_end) + interaction_positions = list( + range(view_point_range[0], view_point_start, 1)) + interaction_positions.extend([view_point_start]) + interaction_positions.extend( + list(range(view_point_end + 1, view_point_range[1], 1))) + relative_position = -1 + for j, idx in zip(range(len(pInteractionData)), interaction_positions): + try: + + chrom_second, start_second, end_second, _ = self.hicMatrix.getBinPos( + idx) + if relative_position < 0: + relative_position = int(start_second) - int(start) + else: + relative_position = int(end_second) - int(end) + + chrom = chrom_second + start_list.append(start_second) + end_list.append(end_second) + relative_position_list.append(relative_position) + interaction_data_list.append(float(pInteractionData[j])) + raw_data_list.append(float(pInteractionDataRaw[j])) + + except Exception: + log.error('Failed to get bin position of index {}'.format(idx)) + exit(1) + return [chrom, start_list, end_list, gene, pSumOfInteractions, relative_position_list, interaction_data_list, pPValueList, xFoldList, raw_data_list] + def getViewpointRangeAsMatrixIndices(self, pChromViewpoint, pRegion_start, pRegion_end): ''' Returns the matrix indices of a chromosome and a specific position. @@ -292,14 +521,14 @@ def getReferencePointAsMatrixIndices(self, pReferencePoint): view_point_start, view_point_end = self.hicMatrix.getRegionBinRange( pReferencePoint[0], int(pReferencePoint[1]), int(pReferencePoint[1])) elif len(pReferencePoint) == 3: - log.debug('pReferencePoint: {}'.format(pReferencePoint)) + # log.debug('pReferencePoint: {}'.format(pReferencePoint)) view_point_start, view_point_end = self.hicMatrix.getRegionBinRange( pReferencePoint[0], int(pReferencePoint[1]), int(pReferencePoint[2])) else: log.error("No valid reference point given. {}".format( pReferencePoint)) exit(1) - log.debug('view_point_start: {} view_point_end {}'.format(view_point_start, view_point_end)) + # log.debug('view_point_start: {} view_point_end {}'.format(view_point_start, view_point_end)) return view_point_start, view_point_end @@ -372,9 +601,12 @@ def calculateViewpointRange(self, pViewpoint, pRange): _range[1] = (max_length - int(pViewpoint[2])) + bin_size return region_start, region_end, _range - def getDataForPlotting(self, pInteractionFile, pRange, pBackgroundModel, pResolution): - header, interaction_data, p_value_data, _interaction_file_data_raw, genomic_coordinates = self.readInteractionFile(pInteractionFile) - matrix_name, viewpoint, upstream_range, downstream_range, gene, _ = header.split('\t') + def getDataForPlotting(self, pFilePath, pInteractionFile, pRange, pBackgroundModel, pResolution): + # header, interaction_data, p_value_data, _interaction_file_data_raw, genomic_coordinates = self.readInteractionFile(pInteractionFile) + # matrix_name, viewpoint, upstream_range, downstream_range, gene, _ = header.split('\t') + + # data = pViewpointObj.readInteractionFile(pFilePath, sample) + interaction_data, p_value_data, genomic_coordinates, viewpoint = self.interactionDataForPlot(pFilePath, pInteractionFile) data = [] p_value = [] @@ -493,7 +725,7 @@ def getDataForPlotting(self, pInteractionFile, pRange, pBackgroundModel, pResolu viewpoint_index_end = viewpoint_index_start else: viewpoint_index_end += viewpoint_index_start - return header, data, data_background, p_value, viewpoint_index_start, viewpoint_index_end + return data, data_background, p_value, viewpoint_index_start, viewpoint_index_end, viewpoint def plotViewpoint(self, pAxis, pData, pColor, pLabelName, pHighlightRegion=None, pHighlightSignificantRegion=None): data_plot_label = pAxis.plot( @@ -594,48 +826,57 @@ def rbz_score(self, pRelativeInteractions, pBackgroundModel, pBackgroundModelSEM _rbz_score[mask] = -1 return _rbz_score - def readRejectedFile(self, pDifferentialHighlightFiles, pViewpointIndexStart, pViewpointIndexEnd, pResolution, pRange, pViewpoint): + def readRejectedFile(self, pFilePath, pDifferentialHighlightTriplet, pViewpointIndexStart, pViewpointIndexEnd, pResolution, pRange, pViewpoint): # list of start and end point of regions to highlight - # [[start, end], [start, end]] - highlight_areas_list = [] - # for bed_file in pDifferentialHighlightFiles: - _, reference_point_start, reference_point_end = pViewpoint.split('_') - with open(pDifferentialHighlightFiles) as fh: - # skip header - for line in fh.readlines(): - if line.startswith('#'): - continue - _line = line.split('\t') + if pDifferentialHighlightTriplet is None or len(pDifferentialHighlightTriplet) == 0: + return None - start = int(_line[1]) - end = int(_line[2]) + differentialFileHDF5Object = h5py.File(pFilePath, 'r') - if int(_line[4]) >= -pRange[0] and int(_line[4]) <= pRange[1]: + # arrays_to_retrieve = ['relative_position_list', 'interaction_data_list', 'pvalue', 'raw', 'xfold'] + internal_path = '/'.join(pDifferentialHighlightTriplet) - width = (end - start) / pResolution - if int(_line[4]) < 0: - # reference_point_position = reference_point_start - relative_position_genomic_coordinates = start - int(reference_point_start) - viewpointIndex = pViewpointIndexStart - else: - relative_position_genomic_coordinates = start - int(reference_point_end) - viewpointIndex = pViewpointIndexEnd + if internal_path not in differentialFileHDF5Object: + log.debug('internal path not found: {}'.format(internal_path)) + return None + if list(differentialFileHDF5Object[internal_path].keys()) == 0: + log.debug('differentialFileHDF5Object[internal_path] {}'.format(differentialFileHDF5Object[internal_path])) + return None - log.debug('_line[4] {}'.format(_line[4])) - log.debug('relative_position_genomic_coordinates {}'.format(relative_position_genomic_coordinates)) - log.debug('start {} end {}'.format(start, end)) - log.debug('reference_point_start {} reference_point_end {}'.format(reference_point_start, reference_point_end)) + try: + start_list = np.array(differentialFileHDF5Object[internal_path + '/' + 'start_list'][:]) + end_list = np.array(differentialFileHDF5Object[internal_path + '/' + 'end_list'][:]) + relative_distance_list = np.array(differentialFileHDF5Object[internal_path + '/' + 'relative_distance_list'][:]) + except Exception: + return None + if len(start_list) == 0: + return None + + highlight_areas_list = [] + # for bed_file in pDifferentialHighlightFiles: + reference_point_start, reference_point_end = pViewpoint - # start + for start, end, relative_distance in zip(start_list, end_list, relative_distance_list): - # relative_position_genomic_coordinates = reference_point_position - relative_position = viewpointIndex + \ - (relative_position_genomic_coordinates / pResolution) - highlight_areas_list.append( - [relative_position, relative_position + width]) + if int(relative_distance) >= -pRange[0] and int(relative_distance) <= pRange[1]: + + width = (end - start) / pResolution + if int(relative_distance) < 0: + relative_position_genomic_coordinates = start - int(reference_point_start) + viewpointIndex = pViewpointIndexStart + else: + relative_position_genomic_coordinates = start - int(reference_point_end) + viewpointIndex = pViewpointIndexEnd + + # relative_position_genomic_coordinates = reference_point_position + relative_position = viewpointIndex + \ + (relative_position_genomic_coordinates / pResolution) + highlight_areas_list.append( + [relative_position, relative_position + width]) if len(highlight_areas_list) == 0: return None + log.debug('highlight_areas_list {}'.format(highlight_areas_list)) return highlight_areas_list def pvalues(self, pBackgroundModel, pDataList, pIndexReferencePoint): @@ -669,73 +910,6 @@ def pvalues(self, pBackgroundModel, pDataList, pIndexReferencePoint): p_value_list[mask] = 1.0 return p_value_list - # def computeSumOfDensities(self, pBackgroundModel, pArgs, pXfoldMaxValue=None): - # background_nbinom = {} - # background_sum_of_densities_dict = {} - # max_value = 0 - - # fixateRange = int(pArgs.fixateRange) - # for distance in pBackgroundModel: - # max_value_distance = int(pBackgroundModel[distance][2]) - # if max_value < int(pBackgroundModel[distance][2]): - # max_value = int(pBackgroundModel[distance][2]) - - # if pXfoldMaxValue is not None: - # if max_value_distance == 0: - # max_value_distance = 1 - # if pXfoldMaxValue == 0: - # pXfoldMaxValue = 1 - # max_value_distance *= pXfoldMaxValue - - # if -int(pArgs.fixateRange) < distance and int(pArgs.fixateRange) > distance: - # # background_nbinom[distance] = nbinom(pBackgroundModel[distance][0], pBackgroundModel[distance][1]) - # background_nbinom[distance] = (pBackgroundModel[distance][0], pBackgroundModel[distance][1]) - - # sum_of_densities = np.zeros(max_value_distance) - # for j in range(max_value_distance): - # if j >= 1: - # sum_of_densities[j] += sum_of_densities[j - 1] - # # sum_of_densities[j] += background_nbinom[distance].pmf(j) - # sum_of_densities[j] += pmf(j, background_nbinom[distance][0], background_nbinom[distance][1]) - - # background_sum_of_densities_dict[distance] = sum_of_densities - - # # background_nbinom[fixateRange] = nbinom(pBackgroundModel[fixateRange][0], pBackgroundModel[fixateRange][1]) - # background_nbinom[fixateRange] = (pBackgroundModel[fixateRange][0], pBackgroundModel[fixateRange][1]) - - # sum_of_densities = np.zeros(max_value) - # for j in range(max_value): - # if j >= 1: - # sum_of_densities[j] += sum_of_densities[j - 1] - # # sum_of_densities[j] += background_nbinom[fixateRange].pmf(j) - # sum_of_densities[j] += pmf(j, background_nbinom[fixateRange][0], background_nbinom[fixateRange][1]) - - # background_sum_of_densities_dict[fixateRange] = sum_of_densities - # # background_nbinom[-fixateRange] = nbinom(pBackgroundModel[-fixateRange][0], pBackgroundModel[-fixateRange][1]) - # background_nbinom[-fixateRange] = (pBackgroundModel[-fixateRange][0], pBackgroundModel[-fixateRange][1]) - - # sum_of_densities = np.zeros(max_value) - # for j in range(max_value): - # if j >= 1: - # sum_of_densities[j] += sum_of_densities[j - 1] - # # sum_of_densities[j] += background_nbinom[-fixateRange].pmf(j) - # sum_of_densities[j] += pmf(j, background_nbinom[-fixateRange][0], background_nbinom[-fixateRange][1]) - - # background_sum_of_densities_dict[-fixateRange] = sum_of_densities - - # min_key = min(background_sum_of_densities_dict) - # max_key = max(background_sum_of_densities_dict) - - # for key in pBackgroundModel.keys(): - # if key in background_sum_of_densities_dict: - # continue - # if key < min_key: - # background_sum_of_densities_dict[key] = background_sum_of_densities_dict[min_key] - # elif key > max_key: - # background_sum_of_densities_dict[key] = background_sum_of_densities_dict[max_key] - - # return background_sum_of_densities_dict - def merge_neighbors(self, pScoresDictionary, pMergeThreshold=1000): if pScoresDictionary is None or len(pScoresDictionary) == 0: log.debug('dict is None or empty') @@ -793,44 +967,118 @@ def merge_neighbors(self, pScoresDictionary, pMergeThreshold=1000): return scores_dict, merged_lines_dict - def readSignificantRegionsFile(self, pSignificantFile, pViewpointIndexStart, pViewpointIndexEnd, pResolution, pRange, pViewpoint): + def readSignificantRegionsFile(self, pFilePath, pInternalIdentifierTriplet, pViewpointIndexStart, pViewpointIndexEnd, pResolution, pRange, pViewpoint): # list of start and end point of regions to highlight - # [[start, end], [start, end]] + + _, interaction_file_data, _ = self.readInteractionFile(pFilePath, pInternalIdentifierTriplet) highlight_areas_list = [] p_values = [] - viewpoint_split = pViewpoint.split('_') - if len(viewpoint_split) == 3: - _, reference_point_start, reference_point_end = viewpoint_split + if len(pViewpoint) == 2: + reference_point_start, reference_point_end = pViewpoint else: - log.debug('viewpoint_split {}, file: {}'.format(viewpoint_split, pSignificantFile)) + log.debug('viewpoint_split {}, file: {} {}'.format(pViewpoint, pFilePath, pInternalIdentifierTriplet)) return None, None - with open(pSignificantFile) as fh: - # skip header - for line in fh.readlines(): - if line.startswith('#'): - continue - _line = line.split('\t') - start = int(_line[1]) - end = int(_line[2]) + for _line in interaction_file_data.values(): + start = int(_line[1]) + end = int(_line[2]) - if int(_line[5]) >= -pRange[0] and int(_line[5]) <= pRange[1]: + if int(_line[5]) >= -pRange[0] and int(_line[5]) <= pRange[1]: - width = (end - start) / pResolution - if int(_line[5]) < 0: - # reference_point_position = reference_point_start - relative_position_genomic_coordinates = start - int(reference_point_start) - viewpointIndex = pViewpointIndexStart - else: - relative_position_genomic_coordinates = start - int(reference_point_end) - viewpointIndex = pViewpointIndexEnd + width = (end - start) / pResolution + if int(_line[5]) < 0: + relative_position_genomic_coordinates = start - int(reference_point_start) + viewpointIndex = pViewpointIndexStart + else: + relative_position_genomic_coordinates = start - int(reference_point_end) + viewpointIndex = pViewpointIndexEnd - relative_position = viewpointIndex + \ - (relative_position_genomic_coordinates / pResolution) - highlight_areas_list.append( - [relative_position, relative_position + width]) - p_values.append([int(relative_position), int(relative_position + width), float(_line[-3])]) + relative_position = viewpointIndex + \ + (relative_position_genomic_coordinates / pResolution) + highlight_areas_list.append( + [relative_position, relative_position + width]) + p_values.append([int(relative_position), int(relative_position + width), float(_line[-3])]) if len(highlight_areas_list) == 0: return None, None + return highlight_areas_list, p_values + + def readTargetHDFFile(self, pFile): + present_genes = {} + targetDict = {} + targetFileHDF5Object = h5py.File(pFile, 'r') + keys_targetFile = list(targetFileHDF5Object.keys()) + log.debug('keys_interactionFile {}'.format(keys_targetFile)) + for outer_matrix in keys_targetFile: + if outer_matrix not in present_genes: + present_genes[outer_matrix] = {} + inner_matrix_object = targetFileHDF5Object[outer_matrix] + keys_inner_matrices = list(inner_matrix_object.keys()) + for inner_matrix in keys_inner_matrices: + if inner_matrix not in present_genes[outer_matrix]: + present_genes[outer_matrix][inner_matrix] = [] + inner_object = inner_matrix_object[inner_matrix] + gene_object = inner_object['genes'] + keys_genes = list(gene_object.keys()) + for gene in keys_genes: + targetDict[gene] = [outer_matrix, inner_matrix, 'genes', gene] + present_genes[outer_matrix][inner_matrix].append(gene) + targetFileHDF5Object.close() + return targetDict, present_genes + + def readAggregatedFileHDF(self, pAggregatedFileName, pInternalPath): + aggregatedFileHDF5Object = h5py.File(pAggregatedFileName, 'r') + + internal_path = '/'.join(pInternalPath) + chromosome = aggregatedFileHDF5Object.get(internal_path + '/' + 'chromosome')[()].decode("utf-8") + + gene_name = aggregatedFileHDF5Object.get(internal_path + '/' + 'gene_name')[()].decode("utf-8") + + start_list = np.array(aggregatedFileHDF5Object[internal_path + '/' + 'start_list'][:]) + end_list = np.array(aggregatedFileHDF5Object[internal_path + '/' + 'end_list'][:]) + relative_distance_list = np.array(aggregatedFileHDF5Object[internal_path + '/' + 'relative_distance_list'][:]) + raw_target_list = np.array(aggregatedFileHDF5Object[internal_path + '/' + 'raw_target_list'][:]) + sum_of_interactions = float(aggregatedFileHDF5Object.get(internal_path + '/' + 'sum_of_interactions')[()]) + aggregatedFileHDF5Object.close() + line_content = [] + data = [] + for i in range(len(start_list)): + line_content.append([chromosome, start_list[i], end_list[i], gene_name, sum_of_interactions, relative_distance_list[i], raw_target_list[i]]) + data.append([sum_of_interactions, raw_target_list[i]]) + + return line_content, data + + def readDifferentialFile(self, pFilePath, pQuadruple): + + differentialFileHDF5Object = h5py.File(pFilePath, 'r') + + internal_path = '/'.join(pQuadruple) + output_list = [] + for item in ['accepted', 'all', 'rejected']: + + try: + item_object = differentialFileHDF5Object[internal_path + '/' + item] + chromosome = item_object.get('chromosome')[()].decode("utf-8") + start_list = np.array(item_object['start_list'][:]) + end_list = np.array(item_object['end_list'][:]) + relative_distance_list = np.array(item_object['relative_distance_list'][:]) + gene = item_object.get('gene')[()].decode("utf-8") + pvalue_list = np.array(item_object['pvalue_list'][:]) + + raw_target_list_1 = np.array(item_object['raw_target_list_1'][:]) + raw_target_list_2 = np.array(item_object['raw_target_list_2'][:]) + sum_of_interactions_1 = float(item_object.get('sum_of_interactions_1')[()]) + sum_of_interactions_2 = float(item_object.get('sum_of_interactions_2')[()]) + + chromosome = [chromosome] * len(start_list) + gene = [gene] * len(start_list) + sum_of_interactions_1 = [sum_of_interactions_1] * len(start_list) + sum_of_interactions_2 = [sum_of_interactions_2] * len(start_list) + output_list.append(zip(chromosome, start_list, end_list, gene, relative_distance_list, sum_of_interactions_1, raw_target_list_1, sum_of_interactions_2, raw_target_list_2, pvalue_list)) + + except Exception as exp: + log.debug('exception {}'.format(str(exp))) + output_list.append([]) + + return output_list diff --git a/hicexplorer/pretrained_classifier_10000_obsexp.BIN b/hicexplorer/pretrained_classifier_10000_obsexp.BIN new file mode 100644 index 00000000..959f4f35 Binary files /dev/null and b/hicexplorer/pretrained_classifier_10000_obsexp.BIN differ diff --git a/hicexplorer/pretrained_classifier_10000_range.BIN b/hicexplorer/pretrained_classifier_10000_range.BIN new file mode 100644 index 00000000..fa1a47cb Binary files /dev/null and b/hicexplorer/pretrained_classifier_10000_range.BIN differ diff --git a/hicexplorer/test/general/test_chicAggregateStatistic.py b/hicexplorer/test/general/test_chicAggregateStatistic.py index 556ecdf0..ef8052ee 100644 --- a/hicexplorer/test/general/test_chicAggregateStatistic.py +++ b/hicexplorer/test/general/test_chicAggregateStatistic.py @@ -2,6 +2,7 @@ from tempfile import NamedTemporaryFile, mkdtemp import os import pytest +import h5py import warnings warnings.simplefilter(action="ignore", category=RuntimeWarning) warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) @@ -33,182 +34,120 @@ def are_files_equal(file1, file2, delta=2, skip=0): def test_regular_mode(): - output_folder = mkdtemp(prefix="output_") - - args = "--interactionFile {} {} --targetFile {} --outFileNameSuffix {} \ - --outputFolder {} -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt ', - ROOT + 'chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt', - 'aggregated.txt', - output_folder, 1).split() + outfile_aggregate = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_aggregate.close() + args = "--interactionFile {} --targetFile {} --outFileName {} \ + -t {}".format(ROOT + 'chicViewpoint/two_matrices.hdf5', + ROOT + 'chicSignificantInteractions/targetFile_dual.hdf5', + outfile_aggregate.name, 1).split() chicAggregateStatistic.main(args) - assert are_files_equal(ROOT + "chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') + aggregateFileH5Object = h5py.File(outfile_aggregate.name, 'r') + assert 'FL-E13-5_chr1_MB-E10-5_chr1' in aggregateFileH5Object + assert 'FL-E13-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'] + assert 'MB-E10-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'] - assert set(os.listdir(ROOT + "chicAggregateStatistic/regular_mode/") - ) == set(os.listdir(output_folder)) + assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'] + assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'] + assert len(aggregateFileH5Object) == 1 + assert aggregateFileH5Object.attrs['type'] == 'aggregate' + + for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1']: + + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]) == 3 + + for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]: + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]) == 7 + for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions'] + + for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1']: + + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]) == 3 + + for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]: + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]) == 7 + for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions'] + + aggregateFileH5Object.close() def test_regular_mode_threads(): - output_folder = mkdtemp(prefix="output_") - - args = "--interactionFile {} {} --targetFile {} --outFileNameSuffix {} \ - --outputFolder {} -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt ', - ROOT + 'chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt', - 'aggregated.txt', - output_folder, 10).split() + outfile_aggregate = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_aggregate.close() + args = "--interactionFile {} --targetFile {} --outFileName {} \ + -t {}".format(ROOT + 'chicViewpoint/two_matrices.hdf5', + ROOT + 'chicSignificantInteractions/targetFile_dual.hdf5', + outfile_aggregate.name, 10).split() chicAggregateStatistic.main(args) - assert are_files_equal(ROOT + "chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') + aggregateFileH5Object = h5py.File(outfile_aggregate.name, 'r') + assert 'FL-E13-5_chr1_MB-E10-5_chr1' in aggregateFileH5Object + assert 'FL-E13-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'] + assert 'MB-E10-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'] - assert set(os.listdir(ROOT + "chicAggregateStatistic/regular_mode/") - ) == set(os.listdir(output_folder)) + assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'] + assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'] + assert len(aggregateFileH5Object) == 1 + assert aggregateFileH5Object.attrs['type'] == 'aggregate' + for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1']: -def test_batch_mode(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]) == 3 - outfile.close() - args = "--interactionFile {} --targetFile {} --outFileNameSuffix {} \ - --outputFolder {} -iff {} -tff {} -w {} -bm -t {}".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicSignificantInteractions/output_5_target_list.txt', - 'aggregated.txt', - output_folder, - ROOT + 'chicViewpoint/output_1', - ROOT + 'chicSignificantInteractions/output_5_target', - outfile.name, 1).split() - chicAggregateStatistic.main(args) - assert are_files_equal( - ROOT + "chicAggregateStatistic/batch_mode_file_names.txt", outfile.name) - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - - assert set(os.listdir(ROOT + "chicAggregateStatistic/batch_mode/") - ) == set(os.listdir(output_folder)) - - -def test_batch_mode_too_many_threads(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - - outfile.close() - args = "--interactionFile {} --targetFile {} --outFileNameSuffix {} \ - --outputFolder {} -iff {} -tff {} -w {} -bm -t {}".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicSignificantInteractions/output_5_target_list.txt', - 'aggregated.txt', - output_folder, - ROOT + 'chicViewpoint/output_1', - ROOT + 'chicSignificantInteractions/output_5_target', - outfile.name, 100).split() - chicAggregateStatistic.main(args) - assert are_files_equal( - ROOT + "chicAggregateStatistic/batch_mode_file_names.txt", outfile.name) - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - - assert set(os.listdir(ROOT + "chicAggregateStatistic/batch_mode/") - ) == set(os.listdir(output_folder)) - - -def test_batch_mode_one_targetfile(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - - outfile.close() - args = "--interactionFile {} --targetFile {} --outFileNameSuffix {} \ - --outputFolder {} -iff {} -w {} -bm -t {}".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicSignificantInteractions/output_5_target_regions.txt', - 'aggregated.txt', - output_folder, - ROOT + 'chicViewpoint/output_1', - outfile.name, 3).split() - chicAggregateStatistic.main(args) - assert are_files_equal( - ROOT + "chicAggregateStatistic/batch_mode_file_names.txt", outfile.name) - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - - assert set(os.listdir(ROOT + "chicAggregateStatistic/batch_mode/") - ) == set(os.listdir(output_folder)) - - -def test_batch_mode_one_targetfile_threads(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - - outfile.close() - args = "--interactionFile {} --targetFile {} --outFileNameSuffix {} \ - --outputFolder {} -iff {} -w {} -bm -t {}".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicSignificantInteractions/output_5_target_regions.txt', - 'aggregated.txt', - output_folder, - ROOT + 'chicViewpoint/output_1', - outfile.name, 20).split() + for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]: + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]) == 7 + for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions'] + + for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1']: + + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]) == 3 + + for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]: + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]) == 7 + for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions'] + + aggregateFileH5Object.close() + + +def test_target_list(): + outfile_aggregate = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_aggregate.close() + args = "--interactionFile {} --targetFile {} --outFileName {} \ + -t {}".format(ROOT + 'chicViewpoint/two_matrices.hdf5', + ROOT + 'chicAggregateStatistic/target_list.bed', + outfile_aggregate.name, 10).split() chicAggregateStatistic.main(args) - assert are_files_equal( - ROOT + "chicAggregateStatistic/batch_mode_file_names.txt", outfile.name) - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt') - - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - assert are_files_equal(ROOT + "chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt') - - assert set(os.listdir(ROOT + "chicAggregateStatistic/batch_mode/") - ) == set(os.listdir(output_folder)) + + aggregateFileH5Object = h5py.File(outfile_aggregate.name, 'r') + assert 'FL-E13-5_chr1_MB-E10-5_chr1' in aggregateFileH5Object + assert 'FL-E13-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'] + assert 'MB-E10-5_chr1' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'] + + assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'] + assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'] + assert len(aggregateFileH5Object) == 1 + assert aggregateFileH5Object.attrs['type'] == 'aggregate' + + for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1']: + + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]) == 3 + + for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome]: + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]) == 7 + for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions'] + + for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1']: + + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]) == 3 + + for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome]: + assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]) == 7 + for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions'] + + aggregateFileH5Object.close() diff --git a/hicexplorer/test/general/test_chicDifferentialTest.py b/hicexplorer/test/general/test_chicDifferentialTest.py index 256d6cc3..9527dc29 100644 --- a/hicexplorer/test/general/test_chicDifferentialTest.py +++ b/hicexplorer/test/general/test_chicDifferentialTest.py @@ -2,6 +2,7 @@ from tempfile import NamedTemporaryFile, mkdtemp import os import pytest +import h5py import warnings warnings.simplefilter(action="ignore", category=RuntimeWarning) warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) @@ -34,154 +35,77 @@ def are_files_equal(file1, file2, delta=2, skip=0): def test_regular_mode_fisher(): - output_folder = mkdtemp(prefix="output_") + outfile_differential = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_differential.close() - args = "--interactionFile {} {} --alpha {} --statisticTest {} --outputFolder {} -t {}\ - ".format(ROOT + 'chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt', - ROOT + 'chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt ', + args = "--aggregatedFile {} --alpha {} --statisticTest {} --outFileName {} -t {}\ + ".format(ROOT + 'chicAggregateStatistic/aggregate.hdf5', 0.5, 'fisher', - output_folder, 1).split() + outfile_differential.name, 1).split() chicDifferentialTest.main(args) - assert are_files_equal(ROOT + "chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt') - assert set(os.listdir(ROOT + "chicDifferentialTest/regular_mode_fisher/") - ) == set(os.listdir(output_folder)) + differentialFileH5Object = h5py.File(outfile_differential.name, 'r') + assert 'FL-E13-5_chr1' in differentialFileH5Object + assert len(differentialFileH5Object) == 1 + assert 'MB-E10-5_chr1' in differentialFileH5Object['FL-E13-5_chr1'] -def test_regular_mode_chi2(): - - output_folder = mkdtemp(prefix="output_") + assert 'genes' in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'] - args = "--interactionFile {} {} --alpha {} --statisticTest {} --outputFolder {} -t {}\ - ".format(ROOT + 'chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt', - ROOT + 'chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt ', - 0.5, 'chi2', - output_folder, 1).split() - chicDifferentialTest.main(args) + assert differentialFileH5Object.attrs['type'] == 'differential' + assert differentialFileH5Object.attrs['alpha'] == 0.5 + assert differentialFileH5Object.attrs['test'] == 'fisher' - assert are_files_equal(ROOT + "chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt') - assert set(os.listdir(ROOT + "chicDifferentialTest/regular_mode_chi2/") - ) == set(os.listdir(output_folder)) + for chromosome in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1']: + assert len(differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome]) == 3 -def test_batch_mode_fisher(): + for gene in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome]: + assert len(differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene]) == 3 + for data in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene]: + assert len(differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene][data]) == 10 + for status in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene][data]: - output_folder = mkdtemp(prefix="output_") - - args = "--interactionFile {} -iff {} --alpha {} --statisticTest {} --outputFolder {} -bm -t {}\ - ".format(ROOT + 'chicAggregateStatistic/batch_mode_file_names.txt', - ROOT + 'chicAggregateStatistic/batch_mode', - 0.5, 'fisher', - output_folder, 1).split() - chicDifferentialTest.main(args) + assert status in ['chromosome', 'end_list', 'gene', 'pvalue_list', 'raw_target_list_1', 'raw_target_list_2', + 'relative_distance_list', 'start_list', 'sum_of_interactions_1', 'sum_of_interactions_2'] - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt') + differentialFileH5Object.close() - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt') - - assert set(os.listdir(ROOT + "chicDifferentialTest/batch_mode_fisher/") - ) == set(os.listdir(output_folder)) - - -def test_batch_mode_chi2(): +def test_regular_mode_chi2(): - output_folder = mkdtemp(prefix="output_") + outfile_differential = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_differential.close() - args = "--interactionFile {} -iff {} --alpha {} --statisticTest {} --outputFolder {} -bm -t {}\ - ".format(ROOT + 'chicAggregateStatistic/batch_mode_file_names.txt', - ROOT + 'chicAggregateStatistic/batch_mode', + args = "--aggregatedFile {} --alpha {} --statisticTest {} --outFileName {} -t {}\ + ".format(ROOT + 'chicAggregateStatistic/aggregate.hdf5', 0.5, 'chi2', - output_folder, 1).split() + outfile_differential.name, 1).split() chicDifferentialTest.main(args) - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt') + differentialFileH5Object = h5py.File(outfile_differential.name, 'r') + assert 'FL-E13-5_chr1' in differentialFileH5Object + assert len(differentialFileH5Object) == 1 - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt') + assert 'MB-E10-5_chr1' in differentialFileH5Object['FL-E13-5_chr1'] - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt') + assert 'genes' in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'] - assert set(os.listdir(ROOT + "chicDifferentialTest/batch_mode_chi2/") - ) == set(os.listdir(output_folder)) + assert differentialFileH5Object.attrs['type'] == 'differential' + assert differentialFileH5Object.attrs['alpha'] == 0.5 + assert differentialFileH5Object.attrs['test'] == 'chi2' + for chromosome in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1']: -def test_batch_mode_fisher_rejected_file(): + assert len(differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome]) == 3 - output_folder = mkdtemp(prefix="output_") - outfile = NamedTemporaryFile(suffix='.txt', delete=False) + for gene in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome]: + assert len(differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene]) == 3 + for data in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene]: + assert len(differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene][data]) == 10 + for status in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][chromosome][gene][data]: - args = "--interactionFile {} -iff {} --alpha {} --statisticTest {} --outputFolder {} -bm --rejectedFileNamesToFile {} -t {}\ - ".format(ROOT + 'chicAggregateStatistic/batch_mode_file_names.txt', - ROOT + 'chicAggregateStatistic/batch_mode', - 0.5, 'fisher', - output_folder, outfile.name, 1 - ).split() - chicDifferentialTest.main(args) + assert status in ['chromosome', 'end_list', 'gene', 'pvalue_list', 'raw_target_list_1', 'raw_target_list_2', + 'relative_distance_list', 'start_list', 'sum_of_interactions_1', 'sum_of_interactions_2'] - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt') - - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt') - - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt') - assert are_files_equal(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt", - output_folder + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt') - - assert are_files_equal( - ROOT + "chicDifferentialTest/rejectedFilesList.txt", outfile.name) - - assert set(os.listdir(ROOT + "chicDifferentialTest/batch_mode_fisher_outfile/") - ) == set(os.listdir(output_folder)) + differentialFileH5Object.close() diff --git a/hicexplorer/test/general/test_chicExportData.py b/hicexplorer/test/general/test_chicExportData.py new file mode 100644 index 00000000..9d5ad002 --- /dev/null +++ b/hicexplorer/test/general/test_chicExportData.py @@ -0,0 +1,383 @@ +from shutil import Error +from hicexplorer import chicExportData + + +from tempfile import NamedTemporaryFile, mkdtemp +import os +import pytest +import tarfile +import pyBigWig +import numpy.testing as nt +import numpy as np +import warnings +warnings.simplefilter(action="ignore", category=RuntimeWarning) +warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) +# mpl.use('agg') +import logging +log = logging.getLogger(__name__) +ROOT = os.path.join(os.path.dirname(os.path.dirname( + os.path.abspath(__file__))), "test_data/cHi-C/") + +tolerance = 50 +DELTA_DECIMAL = 0 + + +def are_files_equal(file1, file2, delta=1, skip=0): + equal = True + if delta: + mismatches = 0 + with open(file1) as textfile1, open(file2) as textfile2: + for i, (x, y) in enumerate(zip(textfile1, textfile2)): + # if x.startswith('File'): + # continue + if i < skip: + continue + if x != y: + if delta: + mismatches += 1 + if mismatches > delta: + equal = False + break + else: + equal = False + break + return equal + + +def are_files_equal_bigwig(pFile1, pFile2, pChromosomeList): + + bw_file1 = pyBigWig.open(pFile1) + bw_file2 = pyBigWig.open(pFile2) + + for chrom in pChromosomeList: + try: + bins_list_file1 = bw_file1.intervals(chrom) + except Exception: + log.debug("Chrom not found: {}", chrom) + try: + bins_list_file2 = bw_file2.intervals(chrom) + except Exception: + log.debug("Chrom not found: {}", chrom) + # sometimes the values are + / - flipped + + if bins_list_file1 is not None and bins_list_file1[0][2] != bins_list_file2[0][2]: + bins_list_file1 = np.array(bins_list_file1) + bins_list_file2 = np.array(bins_list_file2) + bins_list_file1[:][2] *= -1 + if bins_list_file1 is None and bins_list_file2 is None: + return True + nt.assert_array_almost_equal(np.absolute(bins_list_file1), + np.absolute(bins_list_file2), + decimal=DELTA_DECIMAL) + return True + + +def test_interactions_all(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {}".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all').split() + chicExportData.main(args) + + file_obj_new = tarfile.open(outfile.name, "r") + + namelist = file_obj_new.getnames() + assert len(namelist) == 6 + + output_folder_new = mkdtemp(prefix="output_") + output_folder_test_data = mkdtemp(prefix="output_") + + file_obj_new.extractall(output_folder_new) + + file_obj_test_data = tarfile.open(ROOT + 'chicExportData/interaction_all_txt.tar.gz', "r") + file_obj_test_data.extractall(output_folder_test_data) + + files_new = os.listdir(output_folder_new) + files_test_data = os.listdir(output_folder_test_data) + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, output_folder_test_data + '/' + file_test_data, skip=1) + + +# must fail +@pytest.mark.xfail(reason='Test case should fail because of wrong input.') +def test_interaction_bigwig_fail(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {} -oft {}".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all', 'bigwig').split() + chicExportData.main(args) + + +@pytest.mark.xfail(reason='Test case should fail because of wrong input.') +def test_interaction_bigwig_fail_range(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {} -oft {} --range {} {}".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all', 'bigwig', 20000, 200000).split() + chicExportData.main(args) + + +@pytest.mark.xfail(reason='Test case should fail because of wrong input.') +def test_interaction_bigwig_fail_range_background(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {} -oft {} --range {} {} --backgroundModelFile {}".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all', 'bigwig', 20000, 200000, 'background.txt').split() + chicExportData.main(args) + + +@pytest.mark.xfail(reason='Test case should fail because of wrong input.') +def test_significant_one_gene_bigwig_fail(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {} -omn {} -oft {}".format( + ROOT + 'chicSignificantInteractions/significantInteractions_dual.hdf5', outfile.name, 'geneName', 'Eya1', 'bigwig').split() + chicExportData.main(args) + + +@pytest.mark.xfail(reason='Test case should fail because of wrong input.') +def test_target_one_gene_bigwig_fail(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {} -omn {} -oft {}".format( + ROOT + 'chicSignificantInteractions/targetFile_dual.hdf5', outfile.name, 'geneName', 'Eya1', 'bigwig').split() + chicExportData.main(args) + + +def test_interaction_bigwig_all(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {} -oft {} --range {} {} --backgroundModelFile {} --chromosomeSizes {}".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all', 'bigwig', 20000, 200000, ROOT + 'background.txt', ROOT + 'hg19.chrom.sizes').split() + chicExportData.main(args) + file_obj_new = tarfile.open(outfile.name, "r") + + namelist = file_obj_new.getnames() + assert len(namelist) == 12 + + output_folder_new = mkdtemp(prefix="output_") + output_folder_test_data = mkdtemp(prefix="output_") + + file_obj_new.extractall(output_folder_new) + + file_obj_test_data = tarfile.open(ROOT + 'chicExportData/interaction_all_bigwig.tar.gz', "r") + file_obj_test_data.extractall(output_folder_test_data) + namelist = file_obj_test_data.getnames() + assert len(namelist) == 12 + files_new = os.listdir(output_folder_new) + files_test_data = os.listdir(output_folder_test_data) + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal_bigwig(output_folder_new + '/' + file_new, output_folder_test_data + '/' + file_test_data, ['chr1']) + + +def test_interaction_bigwig_oneGene(): + output_folder_new = mkdtemp(prefix="output") + args = "-f {} -o {} -om {} -omn {} -oft {} --range {} {} --backgroundModelFile {} --chromosomeSizes {}".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', output_folder_new + '/data.tar.gz', 'geneName', 'Eya1', 'bigwig', 20000, 200000, ROOT + 'background.txt', ROOT + 'hg19.chrom.sizes').split() + chicExportData.main(args) + files_new = os.listdir(output_folder_new) + + assert len(files_new) == 4 + name_list_oneGene_bigWig = ["background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig", + 'background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig', + 'FL-E13-5_chr1_genes_Eya1.bigwig', + 'MB-E10-5_chr1_genes_Eya1.bigwig'] + files_test_data = name_list_oneGene_bigWig + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal_bigwig(output_folder_new + '/' + file_new, ROOT + '/chicExportData/' + file_test_data, ['chr1']) + + +def test_significant_all(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {}".format( + ROOT + 'chicSignificantInteractions/significantInteractions_dual.hdf5', outfile.name, 'all').split() + chicExportData.main(args) + + file_obj_new = tarfile.open(outfile.name, "r") + + namelist = file_obj_new.getnames() + assert len(namelist) == 6 + + output_folder_new = mkdtemp(prefix="output_") + output_folder_test_data = mkdtemp(prefix="output_") + + file_obj_new.extractall(output_folder_new) + + file_obj_test_data = tarfile.open(ROOT + 'chicExportData/significant_all.tar.gz', "r") + file_obj_test_data.extractall(output_folder_test_data) + + files_new = os.listdir(output_folder_new) + files_test_data = os.listdir(output_folder_test_data) + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, output_folder_test_data + '/' + file_test_data, skip=1) + + +def test_significant_oneGene(): + output_folder_new = mkdtemp(prefix="output") + args = "-f {} -o {} -om {} -omn Eya1".format( + ROOT + 'chicSignificantInteractions/significantInteractions_dual.hdf5', output_folder_new, 'geneName').split() + chicExportData.main(args) + + files_new = os.listdir(output_folder_new) + files_test_data = ['FL-E13-5_chr1_genes_Eya1_significant.txt', 'MB-E10-5_chr1_genes_Eya1_significant.txt'] + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, ROOT + '/chicExportData/' + file_test_data, skip=1) + + +def test_target_all(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {}".format( + ROOT + 'chicSignificantInteractions/targetFile_dual.hdf5', outfile.name, 'all').split() + chicExportData.main(args) + + file_obj_new = tarfile.open(outfile.name, "r") + + namelist = file_obj_new.getnames() + assert len(namelist) == 3 + + output_folder_new = mkdtemp(prefix="output_") + output_folder_test_data = mkdtemp(prefix="output_") + + file_obj_new.extractall(output_folder_new) + + file_obj_test_data = tarfile.open(ROOT + 'chicExportData/target_all.tar.gz', "r") + file_obj_test_data.extractall(output_folder_test_data) + + files_new = os.listdir(output_folder_new) + files_test_data = os.listdir(output_folder_test_data) + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, output_folder_test_data + '/' + file_test_data, skip=1) + + +def test_target_oneGene(): + output_folder_new = mkdtemp(prefix="output") + args = "-f {} -o {} -om {} -omn Eya1".format( + ROOT + 'chicSignificantInteractions/targetFile_dual.hdf5', output_folder_new, 'geneName').split() + chicExportData.main(args) + + files_new = os.listdir(output_folder_new) + files_test_data = ['FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_target.txt'] + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, ROOT + '/chicExportData/' + file_test_data, skip=1) + + +def test_aggregate_all(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {}".format( + ROOT + 'chicAggregateStatistic/aggregate.hdf5', outfile.name, 'all').split() + chicExportData.main(args) + + file_obj_new = tarfile.open(outfile.name, "r") + + namelist = file_obj_new.getnames() + assert len(namelist) == 6 + + output_folder_new = mkdtemp(prefix="output_") + output_folder_test_data = mkdtemp(prefix="output_") + + file_obj_new.extractall(output_folder_new) + + file_obj_test_data = tarfile.open(ROOT + 'chicExportData/aggregate_all.tar.gz', "r") + file_obj_test_data.extractall(output_folder_test_data) + + files_new = os.listdir(output_folder_new) + files_test_data = os.listdir(output_folder_test_data) + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, output_folder_test_data + '/' + file_test_data, skip=1) + + +def test_aggregate_oneGene(): + output_folder_new = mkdtemp(prefix="output") + args = "-f {} -o {} -om {} -omn Eya1".format( + ROOT + 'chicAggregateStatistic/aggregate.hdf5', output_folder_new, 'geneName').split() + chicExportData.main(args) + + files_new = os.listdir(output_folder_new) + files_test_data = ['FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_genes_Eya1_aggregate.txt', + 'FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_genes_Eya1_aggregate.txt'] + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, ROOT + '/chicExportData/' + file_test_data, skip=1) + + +def test_differential_all(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-f {} -o {} -om {}".format( + ROOT + 'chicDifferentialTest/differential.hdf5', outfile.name, 'all').split() + chicExportData.main(args) + + file_obj_new = tarfile.open(outfile.name, "r") + + namelist = file_obj_new.getnames() + assert len(namelist) == 9 + + output_folder_new = mkdtemp(prefix="output_") + output_folder_test_data = mkdtemp(prefix="output_") + + file_obj_new.extractall(output_folder_new) + + file_obj_test_data = tarfile.open(ROOT + 'chicExportData/differential_all.tar.gz', "r") + file_obj_test_data.extractall(output_folder_test_data) + + files_new = os.listdir(output_folder_new) + files_test_data = os.listdir(output_folder_test_data) + + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, output_folder_test_data + '/' + file_test_data, skip=1) + + +def test_differential_one_gene(): + output_folder_new = mkdtemp(prefix="output") + args = "-f {} -o {} -om {} -omn Eya1".format( + ROOT + 'chicDifferentialTest/differential.hdf5', output_folder_new, 'geneName').split() + chicExportData.main(args) + + files_new = os.listdir(output_folder_new) + files_test_data = ['FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_accepted_differential.txt', + 'FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_all_differential.txt', + 'FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_rejected_differential.txt'] + files_new = sorted(files_new) + files_test_data = sorted(files_test_data) + + for file_new, file_test_data in zip(files_new, files_test_data): + assert are_files_equal(output_folder_new + '/' + file_new, ROOT + '/chicExportData/' + file_test_data, skip=1) diff --git a/hicexplorer/test/general/test_chicPlotViewpoint.py b/hicexplorer/test/general/test_chicPlotViewpoint.py index da36dd5e..60e526e9 100644 --- a/hicexplorer/test/general/test_chicPlotViewpoint.py +++ b/hicexplorer/test/general/test_chicPlotViewpoint.py @@ -3,9 +3,13 @@ from matplotlib.testing.exceptions import ImageComparisonFailure import matplotlib as mpl +import matplotlib.pyplot as plt + + from tempfile import NamedTemporaryFile, mkdtemp import os import pytest +import tarfile import warnings warnings.simplefilter(action="ignore", category=RuntimeWarning) warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) @@ -38,162 +42,128 @@ def are_files_equal(file1, file2, delta=1, skip=0): break return equal -# one viewpoint - @pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_one_viewpoint(): - outfile = NamedTemporaryFile(suffix='.png', delete=False) +def test_one_gene(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) outfile.close() - args = "-if {} --range {} {} -o {} -t {}".format( - ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', 200000, 200000, outfile.name, 1).split() + args = "-if {} --range {} {} -o {} -t {} --combinationMode oneGene --combinationName Eya1".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', 200000, 200000, outfile.name, 1).split() chicPlotViewpoint.main(args) - res = compare_images( - ROOT + 'chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png', outfile.name, tolerance) - assert res is None, res - -# n - viewpoints, jpg + file_obj = tarfile.open(outfile.name, "r") + namelist = file_obj.getnames() + assert len(namelist) == 3 + assert 'FL-E13-5_chr1_Eya1.png' in namelist -@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_two_viewpoint_fileformat_dpi(): - outfile = NamedTemporaryFile(suffix='.pdf', delete=False) - outfile.close() - args = "-if {} {} --range {} {} -o {} --dpi {} --outputFormat {} -t {}".format( - ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', - 200000, 200000, outfile.name, 100, 'pdf', 1).split() - chicPlotViewpoint.main(args) + output_folder = mkdtemp(prefix="output_") + file_obj.extractall(output_folder) res = compare_images( - ROOT + 'chicPlotViewpoint/two_viewpoint.pdf', outfile.name, tolerance) + ROOT + 'chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png', output_folder + '/FL-E13-5_chr1_Eya1.png', tolerance) assert res is None, res -# additional background model @pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_two_viewpoint_background(): - outfile = NamedTemporaryFile(suffix='.png', delete=False) +def test_one_gene_background_differential_significant(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) outfile.close() - args = "-if {} {} --range {} {} -o {} -bmf {} -t {}".format( - ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', - 200000, 200000, outfile.name, ROOT + 'background.txt', 1).split() + args = "-if {} --range {} {} -o {} -t {} --combinationMode dual --backgroundModelFile {} --differentialTestResult {} --significantInteractions {} --plotSignificantInteractions".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', 200000, 200000, outfile.name, 1, ROOT + 'background.txt', ROOT + 'chicDifferentialTest/differential.hdf5', ROOT + 'chicSignificantInteractions/significantInteractions_dual.hdf5').split() chicPlotViewpoint.main(args) - res = compare_images( - ROOT + 'chicPlotViewpoint/two_viewpoint_background.png', outfile.name, tolerance) - assert res is None, res + file_obj = tarfile.open(outfile.name, "r") + namelist = file_obj.getnames() + assert len(namelist) == 3 + assert 'FL-E13-5_chr1_MB-E10-5_chr1_Eya1.png' in namelist + assert 'FL-E13-5_chr1_MB-E10-5_chr1_Sox17.png' in namelist + assert 'FL-E13-5_chr1_MB-E10-5_chr1_Tfap2d.png' in namelist -@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_two_viewpoint_background_significant(): - outfile = NamedTemporaryFile(suffix='.png', delete=False) - outfile.close() - args = "-if {} {} --range {} {} -o {} -bmf {} --significantInteractions {} {} -t {}".format( - ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', - 200000, 200000, outfile.name, ROOT + 'background.txt', - ROOT + 'chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt', - ROOT + 'chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt', 1).split() - chicPlotViewpoint.main(args) + output_folder = mkdtemp(prefix="output_") + file_obj.extractall(output_folder) res = compare_images( - ROOT + 'chicPlotViewpoint/two_viewpoint_background_significant.png', outfile.name, tolerance) + ROOT + 'chicPlotViewpoint/background_diff_significant/FL-E13-5_chr1_MB-E10-5_chr1_Eya1.png', output_folder + '/FL-E13-5_chr1_MB-E10-5_chr1_Eya1.png', tolerance) assert res is None, res - - -@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_two_viewpoint_background_differential(): - outfile = NamedTemporaryFile(suffix='.png', delete=False) - outfile.close() - args = "-if {} {} --range {} {} -o {} -bmf {} --differentialTestResult {} -t {}".format( - ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', - 200000, 200000, outfile.name, ROOT + 'background.txt', - ROOT + 'chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt', 1).split() - chicPlotViewpoint.main(args) - res = compare_images( - ROOT + 'chicPlotViewpoint/two_viewpoint_background_differential.png', outfile.name, tolerance) + ROOT + 'chicPlotViewpoint/background_diff_significant/FL-E13-5_chr1_MB-E10-5_chr1_Sox17.png', output_folder + '/FL-E13-5_chr1_MB-E10-5_chr1_Sox17.png', tolerance) assert res is None, res - - -@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_one_viewpoint_colormap_pvalue(): - outfile = NamedTemporaryFile(suffix='.png', delete=False) - outfile.close() - args = "-if {} --range {} {} --pValue --colorMapPvalue {} -o {} --pValue --colorMapPvalue plasma --maxPValue 0.5 --minPValue 0.1 -t {}".format( - ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', 200000, 200000, 'plasma', outfile.name, 1).split() - chicPlotViewpoint.main(args) - res = compare_images( - ROOT + 'chicPlotViewpoint/two_viewpoint_pvalue.png', outfile.name, tolerance) + ROOT + 'chicPlotViewpoint/background_diff_significant/FL-E13-5_chr1_MB-E10-5_chr1_Tfap2d.png', output_folder + '/FL-E13-5_chr1_MB-E10-5_chr1_Tfap2d.png', tolerance) assert res is None, res @pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_one_viewpoint_colormap_pvalue_truncate_zeros(): - outfile = NamedTemporaryFile(suffix='.png', delete=False) +def test_single_significant_pvalue(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) outfile.close() - args = "-if {} --range {} {} --pValue --colorMapPvalue {} -o {} --pValue --colorMapPvalue plasma --maxPValue 0.5 --minPValue 0.1 -t {} --truncateZeroPvalues".format( - ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', 200000, 200000, 'plasma', outfile.name, 1).split() + args = "-if {} --range {} {} -o {} -t {} --combinationMode single --backgroundModelFile {} --significantInteractions {} --pValue --plotSignificantInteractions".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', 200000, 200000, outfile.name, 1, ROOT + 'background.txt', ROOT + 'chicSignificantInteractions/significantInteractions_dual.hdf5').split() chicPlotViewpoint.main(args) - res = compare_images( - ROOT + 'chicPlotViewpoint/two_viewpoint_pvalue.png', outfile.name, tolerance) - assert res is None, res + file_obj = tarfile.open(outfile.name, "r") + namelist = file_obj.getnames() + assert len(namelist) == 6 + assert 'FL-E13-5_chr1_Eya1.png' in namelist + assert 'MB-E10-5_chr1_Eya1.png' in namelist + assert 'FL-E13-5_chr1_Sox17.png' in namelist + assert 'MB-E10-5_chr1_Sox17.png' in namelist + assert 'FL-E13-5_chr1_Tfap2d.png' in namelist + assert 'MB-E10-5_chr1_Tfap2d.png' in namelist -@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_one_viewpoint_per_file_batch_mode(): output_folder = mkdtemp(prefix="output_") - args = "-if {} -iff {} --range {} {} --outputFolder {} -psn {} -bm -t {}".format(ROOT + 'chicViewpoint/fileNames_one_matrix.txt', - ROOT + 'chicViewpoint/output_4', - 200000, 200000, - output_folder, 1, 1).split() - chicPlotViewpoint.main(args) - - res = compare_images(ROOT + 'chicPlotViewpoint/batchMode/one/Eya1_FL-E13-5_chr1_chr1_14300280.png', - output_folder + '/Eya1_FL-E13-5_chr1_chr1_14300280.png', tolerance) + file_obj.extractall(output_folder) + res = compare_images( + ROOT + 'chicPlotViewpoint/background_single_signficant_pvalues/FL-E13-5_chr1_Eya1.png', output_folder + '/FL-E13-5_chr1_Eya1.png', tolerance) assert res is None, res - res = compare_images(ROOT + 'chicPlotViewpoint/batchMode/one/Sox17_FL-E13-5_chr1_chr1_4487435.png', - output_folder + '/Sox17_FL-E13-5_chr1_chr1_4487435.png', tolerance) + res = compare_images( + ROOT + 'chicPlotViewpoint/background_single_signficant_pvalues/MB-E10-5_chr1_Eya1.png', output_folder + '/MB-E10-5_chr1_Eya1.png', tolerance) + assert res is None, res + res = compare_images( + ROOT + 'chicPlotViewpoint/background_single_signficant_pvalues/FL-E13-5_chr1_Sox17.png', output_folder + '/FL-E13-5_chr1_Sox17.png', tolerance) assert res is None, res - res = compare_images(ROOT + 'chicPlotViewpoint/batchMode/one/Tfap2d_FL-E13-5_chr1_chr1_19093103.png', - output_folder + '/Tfap2d_FL-E13-5_chr1_chr1_19093103.png', tolerance) + res = compare_images( + ROOT + 'chicPlotViewpoint/background_single_signficant_pvalues/MB-E10-5_chr1_Sox17.png', output_folder + '/MB-E10-5_chr1_Sox17.png', tolerance) assert res is None, res - assert set(os.listdir(ROOT + "chicPlotViewpoint/batchMode/one") - ) == set(os.listdir(output_folder)) + res = compare_images( + ROOT + 'chicPlotViewpoint/background_single_signficant_pvalues/FL-E13-5_chr1_Tfap2d.png', output_folder + '/FL-E13-5_chr1_Tfap2d.png', tolerance) + assert res is None, res + res = compare_images( + ROOT + 'chicPlotViewpoint/background_single_signficant_pvalues/MB-E10-5_chr1_Tfap2d.png', output_folder + '/MB-E10-5_chr1_Tfap2d.png', tolerance) + assert res is None, res -@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') -def test_two_viewpoints_per_file_batch_mode_significances_differential_pvalue(): - output_folder = mkdtemp(prefix="output_") - args = "-if {} -iff {} --range {} {} --outputFolder {} -psn {} -bm --differentialTestResult {} -diff {} -si {} -siff {} -p -xf {} -bmf {} -t {}".format( - ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicViewpoint/output_1', - 200000, 200000, - output_folder, 2, - ROOT + 'chicDifferentialTest/rejectedFilesList.txt', - ROOT + 'chicDifferentialTest/batch_mode_fisher_outfile/', - ROOT + 'chicSignificantInteractions/output_5_significant_files.txt', - ROOT + 'chicSignificantInteractions/output_5/', - 1.5, - ROOT + 'background.txt', 1).split() +@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') +def test_allGenes(): + outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False) + outfile.close() + args = "-if {} --range {} {} -o {} -t {} --combinationMode allGenes --backgroundModelFile {} --significantInteractions {} --pValue --plotSignificantInteractions".format( + ROOT + 'chicViewpoint/two_matrices.hdf5', 200000, 200000, outfile.name, 1, ROOT + 'background.txt', ROOT + 'chicSignificantInteractions/significantInteractions_dual.hdf5').split() chicPlotViewpoint.main(args) - res = compare_images(ROOT + 'chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png', - output_folder + '/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png', tolerance) + file_obj = tarfile.open(outfile.name, "r") + + namelist = file_obj.getnames() + # assert len(namelist) == 3 + assert 'FL-E13-5_chr1_MB-E10-5_chr1_Eya1.png' in namelist + assert 'FL-E13-5_chr1_MB-E10-5_chr1_Sox17.png' in namelist + assert 'FL-E13-5_chr1_MB-E10-5_chr1_Tfap2d.png' in namelist + + output_folder = mkdtemp(prefix="output_") + + file_obj.extractall(output_folder) + res = compare_images( + ROOT + 'chicPlotViewpoint/allGenes/FL-E13-5_chr1_MB-E10-5_chr1_Eya1.png', output_folder + '/FL-E13-5_chr1_MB-E10-5_chr1_Eya1.png', tolerance) assert res is None, res - res = compare_images(ROOT + 'chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png', - output_folder + '/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png', tolerance) + res = compare_images( + ROOT + 'chicPlotViewpoint/allGenes/FL-E13-5_chr1_MB-E10-5_chr1_Sox17.png', output_folder + '/FL-E13-5_chr1_MB-E10-5_chr1_Sox17.png', tolerance) assert res is None, res - res = compare_images(ROOT + 'chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png', - output_folder + '/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png', tolerance) + res = compare_images( + ROOT + 'chicPlotViewpoint/allGenes/FL-E13-5_chr1_MB-E10-5_chr1_Tfap2d.png', output_folder + '/FL-E13-5_chr1_MB-E10-5_chr1_Tfap2d.png', tolerance) + assert res is None, res - assert set(os.listdir(ROOT + "chicPlotViewpoint/batchMode/two") - ) == set(os.listdir(output_folder)) diff --git a/hicexplorer/test/general/test_chicSignificantInteractions.py b/hicexplorer/test/general/test_chicSignificantInteractions.py index d2d5d709..65e9107b 100644 --- a/hicexplorer/test/general/test_chicSignificantInteractions.py +++ b/hicexplorer/test/general/test_chicSignificantInteractions.py @@ -2,6 +2,7 @@ from tempfile import NamedTemporaryFile, mkdtemp import os import pytest +import h5py import warnings warnings.simplefilter(action="ignore", category=RuntimeWarning) warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) @@ -32,437 +33,286 @@ def are_files_equal(file1, file2, delta=1, skip=0): return equal -def test_xFold_one_interaction_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - 1.5, 0.2, output_folder_target, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_1/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_1_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_loose_pValue_one_interaction_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - 0.5, 0.2, output_folder_target, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_2/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_2_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_loose_pValue_multiple_interaction_files(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} -csn 1 -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - 1.5, 0.2, output_folder_target, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_3/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_3_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_batchMode_xFold_csn_1(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_significant_files_list = NamedTemporaryFile( - suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \ - -suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 1 -t {}".format(ROOT + 'chicViewpoint/fileNames_one_matrix.txt', - ROOT + 'chicViewpoint/output_2', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - 1.5, 0.2, output_folder_target, - outfile_significant_files_list.name, - outfile_target_list.name, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_4_target_list.txt", outfile_target_list.name) - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_4_significant_files.txt", outfile_significant_files_list.name) - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_4/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_4_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_batchMode_loose_pValue_csn_2(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_significant_files_list = NamedTemporaryFile( - suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \ - -suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 2 -t {}".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicViewpoint/output_1', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - 0.5, 0.2, output_folder_target, - outfile_significant_files_list.name, - outfile_target_list.name, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt', skip=4) - - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_target_list.txt", outfile_target_list.name) - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_significant_files.txt", outfile_significant_files_list.name) - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_batchMode_loose_pValue_csn_2_truncate_zeros(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_significant_files_list = NamedTemporaryFile( - suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \ - -suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 2 -t {} --truncateZeroPvalues".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicViewpoint/output_1', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - 0.5, 0.2, output_folder_target, - outfile_significant_files_list.name, - outfile_target_list.name, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt', skip=4) - - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_target_list.txt", outfile_target_list.name) - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_significant_files.txt", outfile_significant_files_list.name) - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_xFold_one_interaction_file_threshold_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - ROOT + 'thresholdFile_xfold.txt', ROOT + 'thresholdFile_pValue.txt', output_folder_target, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_1/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_1_target/") - ) == set(os.listdir(output_folder_target)) +def test_xFold(): + outfile_significant = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_target = NamedTemporaryFile(suffix='.hdf5', delete=False) + # output_folder = mkdtemp(prefix="output_") + # output_folder_target = mkdtemp(prefix="output_target_") -def test_loose_pValue_one_interaction_file_threshold_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - ROOT + 'thresholdFile_loose_pValue.txt', ROOT + 'thresholdFile_pValue.txt', output_folder_target, 1).split() - chicSignificantInteractions.main(args) - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_2/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_2_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_loose_pValue_multiple_interaction_files_threshold_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} -csn 1 -t {}".format(ROOT + 'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - ROOT + 'thresholdFile_xfold.txt', ROOT + 'thresholdFile_pValue.txt', output_folder_target, 1).split() - chicSignificantInteractions.main(args) + outfile_significant.close() + outfile_target.close() - assert are_files_equal(ROOT + "chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_3/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_3_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_batchMode_xFold_csn_1_threshold_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_significant_files_list = NamedTemporaryFile( - suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \ - -suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 1 -t {}".format(ROOT + 'chicViewpoint/fileNames_one_matrix.txt', - ROOT + 'chicViewpoint/output_2', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - ROOT + 'thresholdFile_xfold.txt', ROOT + 'thresholdFile_pValue.txt', output_folder_target, - outfile_significant_files_list.name, - outfile_target_list.name, 1).split() + args = "--interactionFile {} --backgroundModelFile {} --range {} {} --outFileNameSignificant {} --outFileNameTarget {} --xFoldBackground {} --pValue {} -t {} --combinationMode dual".format(ROOT + 'chicViewpoint/two_matrices.hdf5', + ROOT + 'background.txt', + 200000, 200000, outfile_significant.name, + outfile_target.name, 1.5, 0.2, 1).split() chicSignificantInteractions.main(args) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_4_target_list.txt", outfile_target_list.name) - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_4_significant_files.txt", outfile_significant_files_list.name) - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_4/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_4_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_batchMode_loose_pValue_csn_2_threshold_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_significant_files_list = NamedTemporaryFile( - suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \ - -suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 2 -t {}".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicViewpoint/output_1', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - ROOT + 'thresholdFile_loose_pValue.txt', ROOT + 'thresholdFile_pValue.txt', output_folder_target, - outfile_significant_files_list.name, - outfile_target_list.name, 1).split() + significantFileH5Object = h5py.File(outfile_significant.name, 'r') + assert 'FL-E13-5_chr1' in significantFileH5Object + assert 'MB-E10-5_chr1' in significantFileH5Object + assert 'genes' in significantFileH5Object['FL-E13-5_chr1'] + assert 'genes' in significantFileH5Object['MB-E10-5_chr1'] + assert len(significantFileH5Object) == 2 + assert significantFileH5Object.attrs['type'] == 'significant' + assert len(significantFileH5Object.attrs['range']) == 2 + assert significantFileH5Object.attrs['range'][0] == 200000 + assert significantFileH5Object.attrs['range'][1] == 200000 + + # assert significantFileH5Object.attrs['averageContactBin'] == 5 + assert significantFileH5Object.attrs['fixateRange'] == 500000 + assert significantFileH5Object.attrs['mode_preselection'] == 'xfold' + assert significantFileH5Object.attrs['mode_preselection_value'] == 1.5 + + assert significantFileH5Object.attrs['pvalue'] == 0.2 + assert significantFileH5Object.attrs['combinationMode'] == 'dual' + assert significantFileH5Object.attrs['truncateZeroPvalues'] == False + assert significantFileH5Object.attrs['peakInteractionsThreshold'] == 5 + + for chromosome in significantFileH5Object['FL-E13-5_chr1']: + assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome]) == 3 + for gene in significantFileH5Object['FL-E13-5_chr1'][chromosome]: + assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome][gene]) == 12 + for data in significantFileH5Object['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + for chromosome in significantFileH5Object['MB-E10-5_chr1']: + assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome]) == 3 + for gene in significantFileH5Object['MB-E10-5_chr1'][chromosome]: + assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome][gene]) == 12 + for data in significantFileH5Object['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + significantFileH5Object.close() + + targetFileH5Object = h5py.File(outfile_target.name, 'r') + assert 'FL-E13-5_chr1' in targetFileH5Object + assert 'MB-E10-5_chr1' in targetFileH5Object['FL-E13-5_chr1'] + + # assert 'genes' in targetFileH5Object['FL-E13-5_chr1'] + assert len(targetFileH5Object) == 1 + assert len(targetFileH5Object['FL-E13-5_chr1']) == 1 + + assert targetFileH5Object.attrs['type'] == 'target' + assert len(targetFileH5Object.attrs['range']) == 2 + assert targetFileH5Object.attrs['range'][0] == 200000 + assert targetFileH5Object.attrs['range'][1] == 200000 + + # assert targetFileH5Object.attrs['averageContactBin'] == 5 + assert targetFileH5Object.attrs['fixateRange'] == 500000 + assert targetFileH5Object.attrs['mode_preselection'] == 'xfold' + assert targetFileH5Object.attrs['mode_preselection_value'] == 1.5 + + assert targetFileH5Object.attrs['pvalue'] == 0.2 + assert targetFileH5Object.attrs['combinationMode'] == 'dual' + assert targetFileH5Object.attrs['truncateZeroPvalues'] == False + assert targetFileH5Object.attrs['peakInteractionsThreshold'] == 5 + + for matrix in targetFileH5Object['FL-E13-5_chr1']: + assert len(targetFileH5Object['FL-E13-5_chr1'][matrix]) == 2 + + for chromosome in targetFileH5Object['FL-E13-5_chr1'][matrix]: + + assert len(targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome]) == 3 + + for gene in targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome]: + assert len(targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome][gene]) == 5 + for data in targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + targetFileH5Object.close() + + +def test_loose_pvalue(): + outfile_significant = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_target = NamedTemporaryFile(suffix='.hdf5', delete=False) + + # output_folder = mkdtemp(prefix="output_") + # output_folder_target = mkdtemp(prefix="output_target_") + + outfile_significant.close() + outfile_target.close() + + args = "--interactionFile {} --backgroundModelFile {} --range {} {} --outFileNameSignificant {} --outFileNameTarget {} --loosePValue {} --pValue {} -t {} --combinationMode dual".format(ROOT + 'chicViewpoint/two_matrices.hdf5', + ROOT + 'background.txt', + 200000, 200000, outfile_significant.name, + outfile_target.name, 0.5, 0.2, 1).split() chicSignificantInteractions.main(args) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt', skip=4) - - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_target_list.txt", outfile_target_list.name) - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_significant_files.txt", outfile_significant_files_list.name) - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5_target/") - ) == set(os.listdir(output_folder_target)) - - -def test_batchMode_loose_pValue_csn_2_truncate_zeros_threshold_file(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_significant_files_list = NamedTemporaryFile( - suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - output_folder_target = mkdtemp(prefix="output_target_") - - outfile.close() - args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \ - -suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 2 -t {} --truncateZeroPvalues".format(ROOT + 'chicViewpoint/fileNames_two_matrices.txt', - ROOT + 'chicViewpoint/output_1', - ROOT + 'background.txt', - 200000, 200000, - 'output_significant.txt', - output_folder, - ROOT + 'thresholdFile_loose_pValue.txt', ROOT + 'thresholdFile_pValue.txt', output_folder_target, - outfile_significant_files_list.name, - outfile_target_list.name, 1).split() + significantFileH5Object = h5py.File(outfile_significant.name, 'r') + assert 'FL-E13-5_chr1' in significantFileH5Object + assert 'MB-E10-5_chr1' in significantFileH5Object + assert 'genes' in significantFileH5Object['FL-E13-5_chr1'] + assert 'genes' in significantFileH5Object['MB-E10-5_chr1'] + assert len(significantFileH5Object) == 2 + assert significantFileH5Object.attrs['type'] == 'significant' + assert len(significantFileH5Object.attrs['range']) == 2 + assert significantFileH5Object.attrs['range'][0] == 200000 + assert significantFileH5Object.attrs['range'][1] == 200000 + + # assert significantFileH5Object.attrs['averageContactBin'] == 5 + assert significantFileH5Object.attrs['fixateRange'] == 500000 + assert significantFileH5Object.attrs['mode_preselection'] == 'loosePValue' + assert significantFileH5Object.attrs['mode_preselection_value'] == 0.5 + + assert significantFileH5Object.attrs['pvalue'] == 0.2 + assert significantFileH5Object.attrs['combinationMode'] == 'dual' + assert significantFileH5Object.attrs['truncateZeroPvalues'] == False + assert significantFileH5Object.attrs['peakInteractionsThreshold'] == 5 + + for chromosome in significantFileH5Object['FL-E13-5_chr1']: + assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome]) == 3 + for gene in significantFileH5Object['FL-E13-5_chr1'][chromosome]: + assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome][gene]) == 12 + for data in significantFileH5Object['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + for chromosome in significantFileH5Object['MB-E10-5_chr1']: + assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome]) == 3 + for gene in significantFileH5Object['MB-E10-5_chr1'][chromosome]: + assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome][gene]) == 12 + for data in significantFileH5Object['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + significantFileH5Object.close() + + targetFileH5Object = h5py.File(outfile_target.name, 'r') + assert 'FL-E13-5_chr1' in targetFileH5Object + assert 'MB-E10-5_chr1' in targetFileH5Object['FL-E13-5_chr1'] + + # assert 'genes' in targetFileH5Object['FL-E13-5_chr1'] + assert len(targetFileH5Object) == 1 + assert len(targetFileH5Object['FL-E13-5_chr1']) == 1 + + assert targetFileH5Object.attrs['type'] == 'target' + assert len(targetFileH5Object.attrs['range']) == 2 + assert targetFileH5Object.attrs['range'][0] == 200000 + assert targetFileH5Object.attrs['range'][1] == 200000 + + # assert targetFileH5Object.attrs['averageContactBin'] == 5 + assert targetFileH5Object.attrs['fixateRange'] == 500000 + assert targetFileH5Object.attrs['mode_preselection'] == 'loosePValue' + assert targetFileH5Object.attrs['mode_preselection_value'] == 0.5 + + assert targetFileH5Object.attrs['pvalue'] == 0.2 + assert targetFileH5Object.attrs['combinationMode'] == 'dual' + assert targetFileH5Object.attrs['truncateZeroPvalues'] == False + assert targetFileH5Object.attrs['peakInteractionsThreshold'] == 5 + + for matrix in targetFileH5Object['FL-E13-5_chr1']: + assert len(targetFileH5Object['FL-E13-5_chr1'][matrix]) == 2 + + for chromosome in targetFileH5Object['FL-E13-5_chr1'][matrix]: + + assert len(targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome]) == 3 + + for gene in targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome]: + assert len(targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome][gene]) == 5 + for data in targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + targetFileH5Object.close() + + +def test_loose_pvalue_single(): + outfile_significant = NamedTemporaryFile(suffix='.hdf5', delete=False) + outfile_target = NamedTemporaryFile(suffix='.hdf5', delete=False) + + # output_folder = mkdtemp(prefix="output_") + # output_folder_target = mkdtemp(prefix="output_target_") + + outfile_significant.close() + outfile_target.close() + + args = "--interactionFile {} --backgroundModelFile {} --range {} {} --outFileNameSignificant {} --outFileNameTarget {} --loosePValue {} --pValue {} -t {} --combinationMode single".format(ROOT + 'chicViewpoint/two_matrices.hdf5', + ROOT + 'background.txt', + 200000, 200000, outfile_significant.name, + outfile_target.name, 0.5, 0.2, 12).split() chicSignificantInteractions.main(args) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt') - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt') - - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt', skip=4) - assert are_files_equal(ROOT + "chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt", - output_folder_target + '/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt', skip=4) - - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_target_list.txt", outfile_target_list.name) - assert are_files_equal( - ROOT + "chicSignificantInteractions/output_5_significant_files.txt", outfile_significant_files_list.name) - - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5/") - ) == set(os.listdir(output_folder)) - assert set(os.listdir(ROOT + "chicSignificantInteractions/output_5_target/") - ) == set(os.listdir(output_folder_target)) + significantFileH5Object = h5py.File(outfile_significant.name, 'r') + assert 'FL-E13-5_chr1' in significantFileH5Object + assert 'MB-E10-5_chr1' in significantFileH5Object + assert 'genes' in significantFileH5Object['FL-E13-5_chr1'] + assert 'genes' in significantFileH5Object['MB-E10-5_chr1'] + assert len(significantFileH5Object) == 2 + assert significantFileH5Object.attrs['type'] == 'significant' + assert len(significantFileH5Object.attrs['range']) == 2 + assert significantFileH5Object.attrs['range'][0] == 200000 + assert significantFileH5Object.attrs['range'][1] == 200000 + + # assert significantFileH5Object.attrs['averageContactBin'] == 5 + assert significantFileH5Object.attrs['fixateRange'] == 500000 + assert significantFileH5Object.attrs['mode_preselection'] == 'loosePValue' + assert significantFileH5Object.attrs['mode_preselection_value'] == 0.5 + + assert significantFileH5Object.attrs['pvalue'] == 0.2 + assert significantFileH5Object.attrs['combinationMode'] == 'single' + assert significantFileH5Object.attrs['truncateZeroPvalues'] == False + assert significantFileH5Object.attrs['peakInteractionsThreshold'] == 5 + + for chromosome in significantFileH5Object['FL-E13-5_chr1']: + assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome]) == 3 + for gene in significantFileH5Object['FL-E13-5_chr1'][chromosome]: + assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome][gene]) == 12 + for data in significantFileH5Object['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + for chromosome in significantFileH5Object['MB-E10-5_chr1']: + assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome]) == 3 + for gene in significantFileH5Object['MB-E10-5_chr1'][chromosome]: + assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome][gene]) == 12 + for data in significantFileH5Object['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + significantFileH5Object.close() + + targetFileH5Object = h5py.File(outfile_target.name, 'r') + assert 'FL-E13-5_chr1' in targetFileH5Object + assert 'MB-E10-5_chr1' in targetFileH5Object + + # assert 'MB-E10-5_chr1' in targetFileH5Object['FL-E13-5_chr1'] + + # assert 'genes' in targetFileH5Object['FL-E13-5_chr1'] + assert len(targetFileH5Object) == 2 + assert len(targetFileH5Object['FL-E13-5_chr1']) == 2 + assert len(targetFileH5Object['MB-E10-5_chr1']) == 2 + + assert targetFileH5Object.attrs['type'] == 'target' + assert len(targetFileH5Object.attrs['range']) == 2 + assert targetFileH5Object.attrs['range'][0] == 200000 + assert targetFileH5Object.attrs['range'][1] == 200000 + + # assert targetFileH5Object.attrs['averageContactBin'] == 5 + assert targetFileH5Object.attrs['fixateRange'] == 500000 + assert targetFileH5Object.attrs['mode_preselection'] == 'loosePValue' + assert targetFileH5Object.attrs['mode_preselection_value'] == 0.5 + + assert targetFileH5Object.attrs['pvalue'] == 0.2 + assert targetFileH5Object.attrs['combinationMode'] == 'single' + assert targetFileH5Object.attrs['truncateZeroPvalues'] == False + assert targetFileH5Object.attrs['peakInteractionsThreshold'] == 5 + + # for matrix in targetFileH5Object['FL-E13-5_chr1']: + # assert len(targetFileH5Object['FL-E13-5_chr1'][matrix]) == 2 + + for chromosome in targetFileH5Object['FL-E13-5_chr1']: + + assert len(targetFileH5Object['FL-E13-5_chr1'][chromosome]) == 3 + + for gene in targetFileH5Object['FL-E13-5_chr1'][chromosome]: + assert len(targetFileH5Object['FL-E13-5_chr1'][chromosome][gene]) == 5 + for data in targetFileH5Object['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + for chromosome in targetFileH5Object['MB-E10-5_chr1']: + + assert len(targetFileH5Object['MB-E10-5_chr1'][chromosome]) == 3 + + for gene in targetFileH5Object['MB-E10-5_chr1'][chromosome]: + assert len(targetFileH5Object['MB-E10-5_chr1'][chromosome][gene]) == 5 + for data in targetFileH5Object['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + targetFileH5Object.close() diff --git a/hicexplorer/test/general/test_chicViewpoint.py b/hicexplorer/test/general/test_chicViewpoint.py index 00b41fa1..4a67fc4e 100644 --- a/hicexplorer/test/general/test_chicViewpoint.py +++ b/hicexplorer/test/general/test_chicViewpoint.py @@ -2,6 +2,7 @@ from tempfile import NamedTemporaryFile, mkdtemp import os import pytest +import h5py import warnings warnings.simplefilter(action="ignore", category=RuntimeWarning) warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) @@ -16,8 +17,6 @@ def are_files_equal(file1, file2, delta=1, skip=0): mismatches = 0 with open(file1) as textfile1, open(file2) as textfile2: for i, (x, y) in enumerate(zip(textfile1, textfile2)): - # if x.startswith('File'): - # continue if i < skip: continue if x != y: @@ -33,144 +32,68 @@ def are_files_equal(file1, file2, delta=1, skip=0): def test_two_matrices(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") + outfile = NamedTemporaryFile(suffix='.hdf5', delete=False) outfile.close() args = "--matrices {} {} --referencePoints {} --backgroundModel {} --range {} {} -o {} -t {}".format(ROOT + 'FL-E13-5_chr1.cool', ROOT + 'MB-E10-5_chr1.cool', ROOT + 'referencePoints_chicViewpoint.bed', ROOT + 'background.txt', 200000, 200000, - output_folder, 1).split() + outfile.name, 1).split() chicViewpoint.main(args) - assert are_files_equal(ROOT + "chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - - assert set(os.listdir(ROOT + "chicViewpoint/output_1/") - ) == set(os.listdir(output_folder)) + interactionFileH5Object = h5py.File(outfile.name, 'r') + assert 'FL-E13-5_chr1' in interactionFileH5Object + assert 'MB-E10-5_chr1' in interactionFileH5Object + assert 'genes' in interactionFileH5Object['FL-E13-5_chr1'] + assert 'genes' in interactionFileH5Object['MB-E10-5_chr1'] + assert len(interactionFileH5Object) == 2 + assert interactionFileH5Object.attrs['type'] == 'interactions' + assert len(interactionFileH5Object.attrs['range']) == 2 + assert interactionFileH5Object.attrs['range'][0] == 200000 + assert interactionFileH5Object.attrs['range'][1] == 200000 + assert interactionFileH5Object.attrs['averageContactBin'] == 5 + assert interactionFileH5Object.attrs['fixateRange'] == 500000 + for chromosome in interactionFileH5Object['FL-E13-5_chr1']: + assert len(interactionFileH5Object['FL-E13-5_chr1'][chromosome]) == 3 + for gene in interactionFileH5Object['FL-E13-5_chr1'][chromosome]: + assert len(interactionFileH5Object['FL-E13-5_chr1'][chromosome][gene]) == 12 + for data in interactionFileH5Object['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] + + for chromosome in interactionFileH5Object['MB-E10-5_chr1']: + assert len(interactionFileH5Object['MB-E10-5_chr1'][chromosome]) == 3 + for gene in interactionFileH5Object['MB-E10-5_chr1'][chromosome]: + assert len(interactionFileH5Object['MB-E10-5_chr1'][chromosome][gene]) == 12 + for data in interactionFileH5Object['MB-E10-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] def test_one_matrix(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - output_folder = mkdtemp(prefix="output_") + outfile = NamedTemporaryFile(suffix='.hdf5', delete=False) outfile.close() args = "--matrices {} --referencePoints {} --backgroundModel {} --range {} {} -o {} -t {}".format(ROOT + 'FL-E13-5_chr1.cool', ROOT + 'referencePoints_chicViewpoint.bed', ROOT + 'background.txt', 200000, 200000, - output_folder, 1).split() - chicViewpoint.main(args) - - assert are_files_equal(ROOT + "chicViewpoint/output_2/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_2/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - - assert set(os.listdir(ROOT + "chicViewpoint/output_2/") - ) == set(os.listdir(output_folder)) - - -def test_two_matrices_writeFileName(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_name_list = NamedTemporaryFile(suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - outfile.close() - args = "--matrices {} {} --referencePoints {} --backgroundModel {} --range {} {} -o {} -w {} -t {} --decimalPlaces {}".format(ROOT + 'FL-E13-5_chr1.cool', - ROOT + 'MB-E10-5_chr1.cool', - ROOT + 'referencePoints_chicViewpoint.bed', - ROOT + 'background.txt', - 200000, 200000, - output_folder, outfile_name_list.name, 1, 5).split() + outfile.name, 1).split() chicViewpoint.main(args) - assert are_files_equal( - ROOT + "chicViewpoint/fileNames_two_matrices.txt", outfile_name_list.name) - - assert are_files_equal(ROOT + "chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - - assert set(os.listdir(ROOT + "chicViewpoint/output_3/") - ) == set(os.listdir(output_folder)) - - -def test_one_matrix_writeFileName(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_name_list = NamedTemporaryFile(suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - outfile.close() - args = "--matrices {} --referencePoints {} --backgroundModel {} --range {} {} -o {} -w {} -t {}".format(ROOT + 'FL-E13-5_chr1.cool', - ROOT + 'referencePoints_chicViewpoint.bed', - ROOT + 'background.txt', - 200000, 200000, - output_folder, outfile_name_list.name, 1).split() - chicViewpoint.main(args) - assert are_files_equal( - ROOT + "chicViewpoint/fileNames_one_matrix.txt", outfile_name_list.name) - - assert are_files_equal(ROOT + "chicViewpoint/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - - assert set(os.listdir(ROOT + "chicViewpoint/output_4/") - ) == set(os.listdir(output_folder)) - - -@pytest.mark.xfail -def test_two_matrices_writeFileName_crash(): - outfile = NamedTemporaryFile(suffix='.txt', delete=False) - outfile_name_list = NamedTemporaryFile(suffix='.txt', delete=False) - - output_folder = mkdtemp(prefix="output_") - outfile.close() - args = "--matrices {} {} --referencePoints {} --backgroundModel {} --range {} {} -o {} -w {} -t {} --decimalPlaces {}".format(ROOT + 'FL-E13-5_chr1.cool', - ROOT + 'MB-E10-5_chr1.cool', - ROOT + 'referencePoints_chicViewpoint_crash.bed', - ROOT + 'background.txt', - 200000, 200000, - output_folder, outfile_name_list.name, 1, 5).split() - chicViewpoint.main(args) - assert are_files_equal( - ROOT + "chicViewpoint/fileNames_two_matrices.txt", outfile_name_list.name) - - assert are_files_equal(ROOT + "chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt", - output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt", - output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt', skip=4) - assert are_files_equal(ROOT + "chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt", - output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt', skip=4) - assert set(os.listdir(ROOT + "chicViewpoint/output_3/") - ) == set(os.listdir(output_folder)) + interactionFileH5Object = h5py.File(outfile.name, 'r') + assert 'FL-E13-5_chr1' in interactionFileH5Object + assert len(interactionFileH5Object) == 1 + + assert 'genes' in interactionFileH5Object['FL-E13-5_chr1'] + + assert interactionFileH5Object.attrs['type'] == 'interactions' + assert len(interactionFileH5Object.attrs['range']) == 2 + assert interactionFileH5Object.attrs['range'][0] == 200000 + assert interactionFileH5Object.attrs['range'][1] == 200000 + assert interactionFileH5Object.attrs['averageContactBin'] == 5 + assert interactionFileH5Object.attrs['fixateRange'] == 500000 + for chromosome in interactionFileH5Object['FL-E13-5_chr1']: + assert len(interactionFileH5Object['FL-E13-5_chr1'][chromosome]) == 3 + for gene in interactionFileH5Object['FL-E13-5_chr1'][chromosome]: + assert len(interactionFileH5Object['FL-E13-5_chr1'][chromosome][gene]) == 12 + for data in interactionFileH5Object['FL-E13-5_chr1'][chromosome][gene]: + assert data in ['chromosome', 'end_list', 'gene', 'interaction_data_list', 'pvalue', 'raw', 'reference_point_end', 'reference_point_start', 'relative_position_list', 'start_list', 'sum_of_interactions', 'xfold'] diff --git a/hicexplorer/test/general/test_hicAdjustMatrix.py b/hicexplorer/test/general/test_hicAdjustMatrix.py index d8c202e7..9441c09d 100644 --- a/hicexplorer/test/general/test_hicAdjustMatrix.py +++ b/hicexplorer/test/general/test_hicAdjustMatrix.py @@ -148,3 +148,43 @@ def test_remove(): np.assert_equal(test.cut_intervals, new.cut_intervals) os.unlink(outfile.name) + + +def test_remove_inter(): + outfile = NamedTemporaryFile( + suffix='.cool', prefix='test_matrix', delete=True) + outfile.close() + args = "--matrix {} --outFileName {} --chromosomes 1 2 3 {} --action {} --interIntraHandling {} ".format( + ROOT + 'hicAdjustMatrix/gm12878_1_2_3.cool', + outfile.name, + ROOT + 'hicAdjustMatrix/remove.bed', + "keep", "inter").split() + + compute(hicAdjustMatrix.main, args, 5) + test = hm.hiCMatrix( + ROOT + "hicAdjustMatrix/inter-removed.cool") + new = hm.hiCMatrix(outfile.name) + np.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=5) + np.assert_equal(test.cut_intervals, new.cut_intervals) + + os.unlink(outfile.name) + + +def test_remove_intra(): + outfile = NamedTemporaryFile( + suffix='.cool', prefix='test_matrix', delete=True) + outfile.close() + args = "--matrix {} --outFileName {} --chromosomes 1 2 3 {} --action {} --interIntraHandling {} ".format( + ROOT + 'hicAdjustMatrix/gm12878_1_2_3.cool', + outfile.name, + ROOT + 'hicAdjustMatrix/remove.bed', + "keep", "intra").split() + + compute(hicAdjustMatrix.main, args, 5) + test = hm.hiCMatrix( + ROOT + "hicAdjustMatrix/intra-removed.cool") + new = hm.hiCMatrix(outfile.name) + np.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=5) + np.assert_equal(test.cut_intervals, new.cut_intervals) + + os.unlink(outfile.name) diff --git a/hicexplorer/test/general/test_hicAggregateContacts.py b/hicexplorer/test/general/test_hicAggregateContacts.py index 241d81ba..96132921 100755 --- a/hicexplorer/test/general/test_hicAggregateContacts.py +++ b/hicexplorer/test/general/test_hicAggregateContacts.py @@ -126,7 +126,7 @@ def test_hicAggregateContacts_all(): outfile_aggregate_matrix = NamedTemporaryFile(suffix='.tab', prefix='hicaggregate_test_', delete=False) args = "--matrix {root}/Li_et_al_2015.h5 --BED {root}/hicAggregateContacts/test_regions.bed " \ "--outFileName {out_agg} --numberOfBins 30 --disable_bbox_tight --dpi 100 "\ - "--mode all --range 50000:900000 --outFilePrefixMatrix {out_mat}".\ + "--mode all --outFilePrefixMatrix {out_mat} --keep_outlier".\ format(root=ROOT, out_agg=outfile_aggregate_plots.name, out_mat=outfile_aggregate_matrix.name) test_image_agg = ROOT + 'hicAggregateContacts/master_aggregate_all.png' @@ -324,7 +324,7 @@ def test_hicAggregateContacts_row_wise_intra_perChr(): args = "--matrix {root}/Li_et_al_2015.h5 --BED {root}/hicAggregateContacts/bed1_row-wise.bed " \ "--BED2 {root}/hicAggregateContacts/bed2_row-wise.bed "\ "--outFileName {out_agg} --numberOfBins 30 --row_wise "\ - "--range 50000:6000000 --dpi 100 --mode intra-chr --perChr ".\ + "--range 50000:6000000 --dpi 100 --mode intra-chr --perChr --keep_outlier".\ format(root=ROOT, out_agg=outfile_aggregate_row_wise.name) test_image_agg_row_wise = ROOT + 'hicAggregateContacts/master_aggregate_row_wise_intra_perChr.png' diff --git a/hicexplorer/test/general/test_hicBuildMatrix.py b/hicexplorer/test/general/test_hicBuildMatrix.py index e4031f52..2008faaa 100644 --- a/hicexplorer/test/general/test_hicBuildMatrix.py +++ b/hicexplorer/test/general/test_hicBuildMatrix.py @@ -94,6 +94,38 @@ def test_build_matrix_restriction_enzyme(capsys): # os.unlink("/tmp/test.bam") +def test_build_matrix_restriction_enzyme_region(capsys): + outfile = NamedTemporaryFile(suffix='.h5', delete=False) + outfile.close() + outfile_bam = NamedTemporaryFile(suffix='.bam', delete=False) + outfile.close() + qc_folder = mkdtemp(prefix="testQC_") + args = "-s {} {} --outFileName {} -bs 5000 -b {} --QCfolder {} --threads 4 --danglingSequence GATC AGCT --restrictionSequence GATC AAGCTT -rs {} {} --region {}".format(sam_R1, sam_R2, + outfile.name, outfile_bam.name, + qc_folder, dpnii_file, ROOT + 'hicFindRestSite/hindIII.bed', 'chr3R').split() + # hicBuildMatrix.main(args) + compute(hicBuildMatrix.main, args, 5) + + test = hm.hiCMatrix(ROOT + "small_test_matrix_parallel_two_rc_chr3R.h5") + new = hm.hiCMatrix(outfile.name) + + # print('test.cut_intervals {}'.format(test.cut_intervals)) + # print('new.cut_intervals {}'.format(new.cut_intervals)) + nt.assert_equal(test.matrix.data, new.matrix.data) + nt.assert_equal(len(test.cut_intervals), len(new.cut_intervals)) + + # print("MATRIX NAME:", outfile.name) + print(set(os.listdir(ROOT + "QC_region/"))) + assert are_files_equal(ROOT + "QC_region/QC.log", qc_folder + "/QC.log") + assert set(os.listdir(ROOT + "QC_region/")) == set(os.listdir(qc_folder)) + + # accept delta of 60 kb, file size is around 4.5 MB + assert abs(os.path.getsize(ROOT + "build_region.bam") - os.path.getsize(outfile_bam.name)) < 64000 + + os.unlink(outfile.name) + shutil.rmtree(qc_folder) + + def test_build_matrix_chromosome_sizes(capsys): outfile = NamedTemporaryFile(suffix='.h5', delete=False) outfile.close() diff --git a/hicexplorer/test/general/test_hicCompareMatrices.py b/hicexplorer/test/general/test_hicCompareMatrices.py new file mode 100644 index 00000000..0ad91b8c --- /dev/null +++ b/hicexplorer/test/general/test_hicCompareMatrices.py @@ -0,0 +1,56 @@ +import warnings +warnings.simplefilter(action="ignore", category=RuntimeWarning) +warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) +from hicexplorer import hicCompareMatrices +from hicmatrix import HiCMatrix as hm +from tempfile import NamedTemporaryFile +import os +import numpy.testing as nt +from hicexplorer.test.test_compute_function import compute + + +ROOT = os.path.join(os.path.dirname( + os.path.dirname(os.path.abspath(__file__))), "test_data/") + + +# I doubled the values in ./hicexplorer/test/test_data/hicConvertFormat/small_test_matrix_chr4.cool +# hicNormalize -m ./hicexplorer/test/test_data/small_test_matrix.cool --normalize multiplicative -mv 2 -o ./hicexplorer/test/test_data/hicCompareMatrices/small_test_matrix_twice.cool + +def test_hicCompareMatrices_doubleMinusOneEqual0(): + outfile = NamedTemporaryFile(suffix='.cool', delete=False) + outfile.close() + + args = "--matrices {} {} --outFileName {} " \ + "--operation diff" \ + .format(ROOT + "hicCompareMatrices/small_test_matrix_twice.cool", + ROOT + "small_test_matrix.cool", + outfile.name).split() + + compute(hicCompareMatrices.main, args, 5) + input = hm.hiCMatrix( + ROOT + "small_test_matrix.cool") + new = hm.hiCMatrix(outfile.name) + nt.assert_equal([], new.matrix.data) + nt.assert_equal(input.cut_intervals, new.cut_intervals) + + os.unlink(outfile.name) + + +def test_hicCompareMatrices_noNorm_doubleMinusOneEqualOne(): + outfile = NamedTemporaryFile(suffix='.cool', delete=False) + outfile.close() + + args = "--matrices {} {} --outFileName {} " \ + "--operation diff --noNorm" \ + .format(ROOT + "hicCompareMatrices/small_test_matrix_twice.cool", + ROOT + "small_test_matrix.cool", + outfile.name).split() + + compute(hicCompareMatrices.main, args, 5) + input = hm.hiCMatrix( + ROOT + "small_test_matrix.cool") + new = hm.hiCMatrix(outfile.name) + nt.assert_equal(input.matrix.data, new.matrix.data) + nt.assert_equal(input.cut_intervals, new.cut_intervals) + + os.unlink(outfile.name) diff --git a/hicexplorer/test/general/test_hicConvertFormat.py b/hicexplorer/test/general/test_hicConvertFormat.py index 1c56cfaf..a3f49a04 100644 --- a/hicexplorer/test/general/test_hicConvertFormat.py +++ b/hicexplorer/test/general/test_hicConvertFormat.py @@ -14,7 +14,6 @@ from hicexplorer.test.test_compute_function import compute REMOVE_OUTPUT = True -# DIFF = 60 DELTA_DECIMAL = 0 ROOT = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "test_data/hicConvertFormat") @@ -29,7 +28,6 @@ def test_hicConvertFormat_h5_to_cool(): outfile.close() args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat cool".format(original_matrix_h5, outfile.name).split() - # hicConvertFormat.main(args) compute(hicConvertFormat.main, args, 5) test = hm.hiCMatrix(original_matrix_cool) @@ -43,7 +41,6 @@ def test_hicConvertFormat_h5_to_cool_enforce_integer(): outfile.close() args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat cool ".format(original_matrix_h5, outfile.name).split() - # hicConvertFormat.main(args) compute(hicConvertFormat.main, args, 5) test = hm.hiCMatrix(original_matrix_cool) @@ -58,7 +55,6 @@ def test_hicConvertFormat_h5_to_homer(): outfile.close() args = "--matrices {} --outFileName {} --inputFormat cool --outputFormat homer ".format(original_matrix_cool_chr4, outfile.name).split() - # hicConvertFormat.main(args) compute(hicConvertFormat.main, args, 5) test = hm.hiCMatrix(original_matrix_cool_chr4) @@ -82,10 +78,17 @@ def test_hicConvertFormat_h5_to_ginteractions(): outfile.close() args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat ginteractions ".format(original_matrix_h5, outfile.name).split() - # hicConvertFormat.main(args) compute(hicConvertFormat.main, args, 5) - # os.unlink(outfile.name) + +def test_hicConvertFormat_h5_to_hicpro(): + outfile = NamedTemporaryFile(suffix='.hicpro', delete=False) + outfile_bed = NamedTemporaryFile(suffix='.bed', delete=False) + + outfile.close() + + args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat hicpro --bedFileHicpro {}".format(original_matrix_h5, outfile.name, outfile_bed.name).split() + compute(hicConvertFormat.main, args, 5) def test_hicConvertFormat_h5_to_mcool(): @@ -93,28 +96,22 @@ def test_hicConvertFormat_h5_to_mcool(): outfile.close() args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat mcool -r 10000 100000 200000 ".format(original_matrix_h5, outfile.name).split() - # hicConvertFormat.main(args) compute(hicConvertFormat.main, args, 5) new1 = hm.hiCMatrix(outfile.name + '::/resolutions/10000') # noqa: F841 new2 = hm.hiCMatrix(outfile.name + '::/resolutions/100000') # noqa: F841 new3 = hm.hiCMatrix(outfile.name + '::/resolutions/200000') # noqa: F841 - # os.unlink(outfile.name) - def test_hicConvertFormat_cool_to_h5(): - # original_matrix = '' outfile = NamedTemporaryFile(suffix='.h5', delete=False) outfile.close() args = "--matrices {} --outFileName {} --inputFormat cool --outputFormat h5".format(original_matrix_cool, outfile.name).split() - # hicConvertFormat.main(args) compute(hicConvertFormat.main, args, 5) test = hm.hiCMatrix(original_matrix_h5) - # print(outfile.name) new = hm.hiCMatrix(outfile.name) nt.assert_array_almost_equal(test.matrix.data, new.matrix.data, decimal=DELTA_DECIMAL) @@ -126,11 +123,8 @@ def test_hicConvertFormat_hicpro_to_cool(): hicprofile = ROOT + '/test_matrix.hicpro' bedfile = ROOT + '/test_matrix.bed' args = "--matrices {} --outFileName {} --inputFormat hicpro --outputFormat cool --bedFileHicpro {}".format(hicprofile, outfile.name, bedfile).split() - # hicConvertFormat.main(args) compute(hicConvertFormat.main, args, 5) - # test = hm.hiCMatrix(original_matrix_cool) - # print(outfile.name) new = hm.hiCMatrix(outfile.name) matrixFileHandlerInput = MatrixFileHandler(pFileType='hicpro', pMatrixFile=hicprofile, @@ -141,3 +135,22 @@ def test_hicConvertFormat_hicpro_to_cool(): new.matrix = triu(new.matrix) nt.assert_array_almost_equal(new.matrix.data, _matrix.data, decimal=0) + + +def test_hicConvertFormat_2D_text_to_cool(): + + outfile = NamedTemporaryFile(suffix='.cool', delete=False) + outfile.close() + text_2d = ROOT + '/GSM1436265_RAD21_ENCFF002EMQ.txt' + args = "--matrices {} --outFileName {} --inputFormat 2D-text --outputFormat cool -r 10000 --chromosomeSizes {}".format(text_2d, outfile.name, ROOT + '/hg19.chrom.sizes').split() + compute(hicConvertFormat.main, args, 5) + + new = hm.hiCMatrix(outfile.name) + + matrixFileHandlerInput = MatrixFileHandler(pFileType='cool', pMatrixFile=ROOT + '/2dtexttocool.cool') + + _matrix, cut_intervals, nan_bins, \ + distance_counts, correction_factors = matrixFileHandlerInput.load() + + new.matrix = triu(new.matrix) + nt.assert_array_almost_equal(new.matrix.data, _matrix.data, decimal=0) diff --git a/hicexplorer/test/general/test_hicCorrectMatrix.py b/hicexplorer/test/general/test_hicCorrectMatrix.py index 65ba9aab..e6324847 100644 --- a/hicexplorer/test/general/test_hicCorrectMatrix.py +++ b/hicexplorer/test/general/test_hicCorrectMatrix.py @@ -60,17 +60,19 @@ def test_correct_matrix_KR_cool(): outfile.close() args = "correct --matrix {} --correctionMethod KR "\ - "--outFileName {} ".format(ROOT + "small_test_matrix.cool", + "--outFileName {} ".format(ROOT + "hicCorrectMatrix/gm12878_raw_values.cool", outfile.name).split() # hicCorrectMatrix.main(args) compute(hicCorrectMatrix.main, args, 5) - test = hm.hiCMatrix(ROOT + "hicCorrectMatrix/kr_full.cool") + test = hm.hiCMatrix(ROOT + "hicCorrectMatrix/gm12878_KR.cool") new = hm.hiCMatrix(outfile.name) - nt.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=5) + assert 3000000000 < new.matrix.sum() // 2 < 3688003604 + # nt.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=5) # nt.assert_almost_equal(test.correction_factors, new.correction_factors, decimal=5) nt.assert_equal(test.cut_intervals, new.cut_intervals) + # nt.assert_equal(test., new.cut_intervals) os.unlink(outfile.name) @@ -80,14 +82,14 @@ def test_correct_matrix_KR_partial_cool(): outfile.close() args = "correct --matrix {} --correctionMethod KR --chromosomes "\ - "chrUextra chr3LHet --outFileName {} ".format(ROOT + "small_test_matrix.cool", - outfile.name).split() + " 3 --outFileName {} ".format(ROOT + "hicCorrectMatrix/gm12878_raw_values.cool", + outfile.name).split() # hicCorrectMatrix.main(args) compute(hicCorrectMatrix.main, args, 5) test = hm.hiCMatrix(ROOT + "hicCorrectMatrix/kr_partial.cool") new = hm.hiCMatrix(outfile.name) - nt.assert_almost_equal(test.matrix.data, new.matrix.data, decimal=5) + nt.assert_allclose(test.matrix.data, new.matrix.data, rtol=1.0) nt.assert_equal(test.cut_intervals, new.cut_intervals) os.unlink(outfile.name) diff --git a/hicexplorer/test/general/test_hicCorrelate.py b/hicexplorer/test/general/test_hicCorrelate.py index 19e693ad..5491bae4 100644 --- a/hicexplorer/test/general/test_hicCorrelate.py +++ b/hicexplorer/test/general/test_hicCorrelate.py @@ -41,9 +41,9 @@ def test_correlate_chromosomes(): args = "--matrices {} {} --labels 'first' 'second' " \ " --method spearman --log1p --colorMap jet "\ "--outFileNameHeatmap {} --outFileNameScatter {} " \ - "--chromosomes chrUextra chr3LHet".format(ROOT + "hicCorrectMatrix/small_test_matrix_ICEcorrected_chrUextra_chr3LHet.h5", - ROOT + "hicCorrectMatrix/small_test_matrix_ICEcorrected_chrUextra_chr3LHet.h5", - outfile_heatmap.name, outfile_scatter.name).split() + "--chromosomes chrUextra chr3LHet --plotNumbers".format(ROOT + "hicCorrectMatrix/small_test_matrix_ICEcorrected_chrUextra_chr3LHet.h5", + ROOT + "hicCorrectMatrix/small_test_matrix_ICEcorrected_chrUextra_chr3LHet.h5", + outfile_heatmap.name, outfile_scatter.name).split() hicCorrelate.main(args) # compute(hicCorrelate.main, args, 5) diff --git a/hicexplorer/test/general/test_hicDifferentialTAD.py b/hicexplorer/test/general/test_hicDifferentialTAD.py index 84dbe682..9318bc07 100644 --- a/hicexplorer/test/general/test_hicDifferentialTAD.py +++ b/hicexplorer/test/general/test_hicDifferentialTAD.py @@ -4,6 +4,8 @@ import pytest import logging log = logging.getLogger(__name__) +import pandas as pd +from pybedtools import BedTool from hicexplorer import hicDifferentialTAD from hicexplorer.test.test_compute_function import compute @@ -25,8 +27,8 @@ def are_files_equal(file1, file2, delta=1, skip=0, eps=0.1): mismatches = 0 - if delta: - mismatches = 0 + # if delta: + # mismatches = 0 with open(file1) as textfile1, open(file2) as textfile2: for i, (x, y) in enumerate(zip(textfile1, textfile2)): if i < skip: @@ -34,19 +36,43 @@ def are_files_equal(file1, file2, delta=1, skip=0, eps=0.1): if x.startswith('File'): continue if x != y: - if delta: - mismatches += 1 - if mismatches > delta: - break - else: + # if delta: + mismatches += 1 + if mismatches > delta: break - if mismatches < delta: + # else: + # break + if mismatches <= delta: return True else: - log.debug('mismatches: {}'.format(mismatches)) + print('mismatches: {}'.format(mismatches)) return False +def all_tads_present(pOriginTADs, pAccepted, pRejected): + + original_tads = pd.read_csv(pOriginTADs, sep='\t', header=None)[[0, 1, 2]] + accepted_tads = pd.read_csv(pAccepted, sep='\t', header=None, skiprows=4)[[0, 1, 2]] + rejected_tads = pd.read_csv(pRejected, sep='\t', header=None, skiprows=4)[[0, 1, 2]] + + original_tads_bedtool = BedTool.from_dataframe(original_tads) + accepted_tads_bedtool = BedTool.from_dataframe(accepted_tads) + rejected_tads_bedtool = BedTool.from_dataframe(rejected_tads) + + x = original_tads_bedtool.intersect(accepted_tads_bedtool, c=True).to_dataframe() + y = original_tads_bedtool.intersect(rejected_tads_bedtool, c=True).to_dataframe() + + mask_x = x['name'] >= 1 + mask_y = y['name'] >= 1 + + # print(x) + # print(mask_x.sum()) + # print(mask_y.sum()) + + return mask_x.sum() + mask_y.sum() + # selection = (mask_x) & (mask_y) + + def test_cool_all_single_core(): outfile_pref = NamedTemporaryFile(prefix='differential_tad', delete=True) @@ -56,10 +82,25 @@ def test_cool_all_single_core(): ROOT + "untreated_R1_domains.bed", 1, outfile_pref.name, 'all', 'all' ).split() - compute(hicDifferentialTAD.main, args, 5) + # compute(hicDifferentialTAD.main, args, 5) + hicDifferentialTAD.main(args) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_all_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_all_rejected.diff_tad', delta=5, skip=4) + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_rejected.diff_tad', delta=0, skip=4) def test_cool_all_multi_core(): @@ -73,8 +114,23 @@ def test_cool_all_multi_core(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_all_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_all_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_rejected.diff_tad', delta=0, skip=4) # intra-TAD', 'left-inter-TAD', 'right-inter-TAD', 'all' @@ -89,8 +145,23 @@ def test_cool_all_single_core_intra_TAD(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_intra-TAD_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_intra-TAD_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_intra-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_intra-TAD_rejected.diff_tad', delta=0, skip=4) def test_cool_all_multi_core_intra_TAD(): @@ -104,8 +175,23 @@ def test_cool_all_multi_core_intra_TAD(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_intra-TAD_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_intra-TAD_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_intra-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_intra-TAD_rejected.diff_tad', delta=0, skip=4) # 'left-inter-TAD' @@ -120,8 +206,23 @@ def test_cool_all_single_core_left_inter_TAD(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_left_inter-TAD_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_left_inter-TAD_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_left_inter-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_left_inter-TAD_rejected.diff_tad', delta=0, skip=4) def test_cool_all_multi_core_left_inter_TAD(): @@ -131,12 +232,27 @@ def test_cool_all_multi_core_left_inter_TAD(): ROOT + "GSM2644945_Untreated-R1.100000_chr1.cool", ROOT + "GSM2644947_Auxin2days-R1.100000_chr1.cool", ROOT + "untreated_R1_domains.bed", - 4, outfile_pref.name, 'left-inter-TAD', 'all' + 11, outfile_pref.name, 'left-inter-TAD', 'all' ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_left_inter-TAD_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_left_inter-TAD_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_left_inter-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_left_inter-TAD_rejected.diff_tad', delta=0, skip=4) # 'left-inter-TAD' @@ -151,8 +267,23 @@ def test_cool_all_single_core_right_inter_TAD(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_right_inter-TAD_t1_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_right_inter-TAD_t1_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_right_inter-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_right_inter-TAD_rejected.diff_tad', delta=0, skip=4) def test_cool_all_multi_core_right_inter_TAD(): @@ -166,8 +297,23 @@ def test_cool_all_multi_core_right_inter_TAD(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_right_inter-TAD_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_right_inter-TAD_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_right_inter-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_right_inter-TAD_rejected.diff_tad', delta=0, skip=4) # 'left-inter-TAD' @@ -182,8 +328,23 @@ def test_cool_one_single_core_right_inter_TAD(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_one_reject_right_inter-TAD_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_one_reject_right_inter-TAD_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_one_right_inter-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_one_right_inter-TAD_rejected.diff_tad', delta=0, skip=4) def test_cool_one_multi_core_right_inter_TAD(): @@ -197,8 +358,23 @@ def test_cool_one_multi_core_right_inter_TAD(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_one_reject_right_inter-TAD_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_one_reject_right_inter-TAD_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_one_right_inter-TAD_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_one_right_inter-TAD_rejected.diff_tad', delta=0, skip=4) def test_h5_all_single_core_one(): @@ -212,8 +388,23 @@ def test_h5_all_single_core_one(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_one_reject_all_h5_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_one_reject_all_h5_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_one_h5_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_one_h5_rejected.diff_tad', delta=0, skip=4) def test_h5_all_multi_core_all(): @@ -227,8 +418,23 @@ def test_h5_all_multi_core_all(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_all__t4_h5_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_all__t4_h5_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_h5_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_h5_rejected.diff_tad', delta=0, skip=4) @pytest.mark.xfail(reason='Access of a chromosome which is not in the matrix.') @@ -268,8 +474,24 @@ def test_cool_all_multi_core_all_multichr_chromosome(): ).split() compute(hicDifferentialTAD.main, args, 5) - assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'mode_all_reject_all__t4_cool_multi_chromosomes_accepted.diff_tad', delta=5, skip=4) - assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'mode_all_reject_all__t4_cool_multi_chromosomes_rejected.diff_tad', delta=5, skip=4) + # test only on the line numbers + with open(ROOT + "untreated_R1_domains_chr1_chr2.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains_chr1_chr2.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'multichromosome_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'multichromosome_rejected.diff_tad', delta=0, skip=4) + # mode_all_reject_all__t4_cool_multi_chromosomes_rejected.diff_tad @@ -282,4 +504,23 @@ def test_cool_all_one_core_all_multichr_chromosome(): ROOT + "untreated_R1_domains_chr1_chr2.bed", 1, outfile_pref.name, 'all', 'all' ).split() - compute(hicDifferentialTAD.main, args, 5) + compute(hicDifferentialTAD.main, args, 7) + + # test only on the line numbers + with open(ROOT + "untreated_R1_domains_chr1_chr2.bed", 'r') as file: + number_of_tads = len(file.readlines()) + + with open(outfile_pref.name + '_accepted.diff_tad', 'r') as file: + number_output_tads = len(file.readlines()) + with open(outfile_pref.name + '_rejected.diff_tad', 'r') as file: + number_output_tads += len(file.readlines()) + + number_output_tads -= 8 + assert number_of_tads == number_output_tads + + # test on the intersection to exclude the case of duplicated lines + assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains_chr1_chr2.bed", outfile_pref.name + '_accepted.diff_tad', outfile_pref.name + '_rejected.diff_tad') + # assert number_of_tads == all_tads_present(ROOT + "untreated_R1_domains_chr1_chr2.bed", ROOT + 'mode_all_reject_all__t4_cool_multi_chromosomes_accepted.diff_tad', ROOT + 'mode_all_reject_all__t4_cool_multi_chromosomes_rejected.diff_tad') + + assert are_files_equal(outfile_pref.name + '_accepted.diff_tad', ROOT + 'multichromosome_accepted.diff_tad', delta=0, skip=4) + assert are_files_equal(outfile_pref.name + '_rejected.diff_tad', ROOT + 'multichromosome_rejected.diff_tad', delta=0, skip=4) diff --git a/hicexplorer/test/general/test_hicFindRestSite.py b/hicexplorer/test/general/test_hicFindRestSite.py index 8cf0e2a2..fb8bc4d9 100644 --- a/hicexplorer/test/general/test_hicFindRestSite.py +++ b/hicexplorer/test/general/test_hicFindRestSite.py @@ -50,3 +50,23 @@ def test_fasta(): assert are_files_equal(ROOT + "hindIII_chrM.bed", outfile.name, skip=0) + + +def test_fasta_gz_two_patterns(): + outfile = NamedTemporaryFile(suffix='.bed', delete=False) + outfile.close() + args = "-f {} -p {} {} -o {}".format(ROOT + 'dm3_chrM.fasta.gz', 'AAGCTT', 'GATC', outfile.name).split() + hicFindRestSite.main(args) + + assert are_files_equal(ROOT + "hindIII_DpnII.bed", + outfile.name, skip=0) + + +def test_fasta_two_patterns(): + outfile = NamedTemporaryFile(suffix='.bed', delete=False) + outfile.close() + args = "-f {} -p {} {} -o {}".format(ROOT + 'dm3_chrM.fasta', 'AAGCTT', 'GATC', outfile.name).split() + hicFindRestSite.main(args) + + assert are_files_equal(ROOT + "hindIII_DpnII.bed", + outfile.name, skip=0) diff --git a/hicexplorer/test/general/test_hicHyperoptDetectLoops.py b/hicexplorer/test/general/test_hicHyperoptDetectLoops.py index e8bab716..240ca626 100644 --- a/hicexplorer/test/general/test_hicHyperoptDetectLoops.py +++ b/hicexplorer/test/general/test_hicHyperoptDetectLoops.py @@ -22,29 +22,44 @@ def are_files_equal(file1, file2, delta=None): equal = True - if delta: - mismatches = 0 + # if delta: + mismatches = 0 with open(file1) as textfile1, open(file2) as textfile2: for x, y in zip(textfile1, textfile2): if x.startswith('File'): continue if x != y: - if delta: - mismatches += 1 - if mismatches > delta: - equal = False - break - else: - equal = False - break + mismatches += 1 + if mismatches > delta: + return False return equal def test_main(): outfile = NamedTemporaryFile(suffix='.txt', delete=True) - + outfile.close() args = "--matrix {} -p {} -ml {} -r {} --runs {} -o {}".format( ROOT + "hicDetectLoops/GSE63525_GM12878_insitu_primary_2_5mb.cool", ROOT + 'hicHyperoptDectedLoops/ctcf_sorted.bed', 3210, 10000, 2, outfile.name).split() hicHyperoptDetectLoops.main(args) - are_files_equal(outfile.name, ROOT + 'hicHyperoptDetectLoops/hyperopt_result.txt', delta=2) + assert are_files_equal(outfile.name, ROOT + 'hicHyperoptDetectLoops/hyperopt_result.txt', delta=2) + + +def test_main_add(): + outfile = NamedTemporaryFile(suffix='.txt', delete=True) + outfile.close() + args = "--matrix {} -p {} -ml {} -r {} --runs {} -o {} -cl {}".format( + ROOT + "hicDetectLoops/GSE63525_GM12878_insitu_primary_2_5mb.cool", + ROOT + 'hicHyperoptDectedLoops/ctcf_sorted.bed', 3210, 10000, 2, outfile.name, 'add').split() + hicHyperoptDetectLoops.main(args) + assert are_files_equal(outfile.name, ROOT + 'hicHyperoptDetectLoops/hyperopt_result.txt', delta=2) + + +def test_main_remove(): + outfile = NamedTemporaryFile(suffix='.txt', delete=True) + outfile.close() + args = "--matrix {} -p {} -ml {} -r {} --runs {} -o {} -cl {}".format( + ROOT + "hicDetectLoops/GSE63525_GM12878_insitu_primary_2_5mb.cool", + ROOT + 'hicHyperoptDectedLoops/ctcf_sorted.bed', 3210, 10000, 2, outfile.name, 'remove').split() + hicHyperoptDetectLoops.main(args) + assert are_files_equal(outfile.name, ROOT + 'hicHyperoptDetectLoops/hyperopt_result.txt', delta=2) diff --git a/hicexplorer/test/general/test_hicInterIntraTAD.py b/hicexplorer/test/general/test_hicInterIntraTAD.py new file mode 100644 index 00000000..9aea0d97 --- /dev/null +++ b/hicexplorer/test/general/test_hicInterIntraTAD.py @@ -0,0 +1,57 @@ +import os +import sys +from tempfile import NamedTemporaryFile +from tempfile import mkdtemp +from psutil import virtual_memory +import subprocess +import pytest +import logging +log = logging.getLogger(__name__) + +import matplotlib as mpl +mpl.use('agg') +from matplotlib.testing.compare import compare_images +from matplotlib.testing.exceptions import ImageComparisonFailure +from hicexplorer import hicInterIntraTAD, hicMergeDomains +from hicexplorer.test.test_compute_function import compute + +mem = virtual_memory() +memory = mem.total / 2**30 + +# memory in GB the test computer needs to have to run the test case +LOW_MEMORY = 2 +MID_MEMORY = 4 +HIGH_MEMORY = 120 + +REMOVE_OUTPUT = True + +ROOT = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "test_data/") + + +def are_files_equal(file1, file2, delta=None): + equal = True + mismatches = 0 + with open(file1) as textfile1, open(file2) as textfile2: + for x, y in zip(textfile1, textfile2): + if x.startswith('File'): + continue + if x != y: + mismatches += 1 + if mismatches > delta: + equal = False + break + return equal + + +@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') +def test_main(): + outfile = NamedTemporaryFile(suffix='.txt', delete=True) + outfile_plot = NamedTemporaryFile(suffix='.png', delete=True) + + args = "-m {} --tadDomains {} --threads {} --outFileNameRatioPlot {} -o {}".format( + ROOT + 'hicInterIntraTAD/GSM2644947_Auxin2days-R1.100000_chr1_chr2.cool', + ROOT + 'hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed', 5, outfile_plot.name, outfile.name).split() + compute(hicInterIntraTAD.main, args, 5) + are_files_equal(outfile.name, ROOT + 'hicInterIntraTAD/output_test.txt', delta=2) + res = compare_images(ROOT + 'hicInterIntraTAD/ratio.png', outfile_plot.name, tol=40) + assert res is None, res diff --git a/hicexplorer/test/general/test_hicPCA.py b/hicexplorer/test/general/test_hicPCA.py index 2e6f6098..c29f5596 100644 --- a/hicexplorer/test/general/test_hicPCA.py +++ b/hicexplorer/test/general/test_hicPCA.py @@ -74,10 +74,10 @@ def test_pca_bedgraph_lieberman(): pca1.close() pca2.close() matrix = ROOT + "small_test_matrix_50kb_res.h5" - args = "--matrix {} --outputFileName {} {} -f bedgraph -noe 2 --method lieberman"\ + args = "--matrix {} --outputFileName {} {} -f bedgraph --whichEigenvectors 1 2 --method lieberman"\ .format(matrix, pca1.name, pca2.name).split() - # hicPCA.main(args) - compute(hicPCA.main, args, 5) + hicPCA.main(args) + # compute(hicPCA.main, args, 5) assert are_files_equal(ROOT + "hicPCA/pca1.bedgraph", pca1.name) assert are_files_equal(ROOT + "hicPCA/pca2.bedgraph", pca2.name) @@ -92,7 +92,7 @@ def test_pca_bedgraph_lieberman_ignore_masked_bins(): pca1.close() pca2.close() matrix = ROOT + "small_test_matrix_50kb_res.h5" - args = "--matrix {} --outputFileName {} {} -f bedgraph -noe 2 \ + args = "--matrix {} --outputFileName {} {} -f bedgraph --whichEigenvectors 1 2 \ --ignoreMaskedBins --method lieberman".format(matrix, pca1.name, pca2.name).split() # hicPCA.main(args) compute(hicPCA.main, args, 5) @@ -111,7 +111,7 @@ def test_pca_bigwig_lieberman(): pca1.close() pca2.close() matrix = ROOT + "small_test_matrix_50kb_res.h5" - args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2 --method lieberman"\ + args = "--matrix {} --outputFileName {} {} -f bigwig --whichEigenvectors 1 2 --method lieberman"\ .format(matrix, pca1.name, pca2.name).split() # hicPCA.main(args) compute(hicPCA.main, args, 5) @@ -137,7 +137,7 @@ def test_pca_bedgraph_lieberman_gene_density(): matrix = ROOT + "small_test_matrix.h5" gene_track = ROOT + 'dm3_genes.bed.gz' chromosomes = 'chrX chrXHet' - args = "--matrix {} --outputFileName {} {} -f bedgraph -noe 2 --method lieberman \ + args = "--matrix {} --outputFileName {} {} -f bedgraph --whichEigenvectors 1 2 --method lieberman \ --extraTrack {} --chromosomes {}"\ .format(matrix, pca1.name, pca2.name, gene_track, chromosomes).split() # hicPCA.main(args) @@ -159,7 +159,7 @@ def test_pca_bigwig_lieberman_gene_density(): matrix = ROOT + "small_test_matrix.h5" gene_track = ROOT + 'dm3_genes.bed.gz' chromosomes = 'chrX chrXHet' - args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2 --method lieberman \ + args = "--matrix {} --outputFileName {} {} -f bigwig --whichEigenvectors 1 2 --method lieberman \ --extraTrack {} --chromosomes {}"\ .format(matrix, pca1.name, pca2.name, gene_track, chromosomes).split() # hicPCA.main(args) @@ -187,7 +187,7 @@ def test_pca_bigwig_lieberman_gene_density_intermediate_matrices(): matrix = ROOT + "small_test_matrix.h5" gene_track = ROOT + 'dm3_genes.bed.gz' chromosomes = 'chrX chrXHet' - args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2 --method lieberman \ + args = "--matrix {} --outputFileName {} {} -f bigwig --whichEigenvectors 1 2 --method lieberman \ --extraTrack {} --chromosomes {} --pearsonMatrix {} --obsexpMatrix {}"\ .format(matrix, pca1.name, pca2.name, gene_track, chromosomes, pearson_matrix.name, obs_exp_matrix.name).split() @@ -235,7 +235,7 @@ def test_pca_bigwig_gene_density_intermediate_matrices_norm(): matrix = ROOT + "small_test_matrix.h5" gene_track = ROOT + 'dm3_genes.bed.gz' chromosomes = 'chrX chrXHet' - args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2 \ + args = "--matrix {} --outputFileName {} {} -f bigwig --whichEigenvectors 1 2 \ --extraTrack {} --chromosomes {} --pearsonMatrix {} --obsexpMatrix {} \ --method dist_norm --ligation_factor"\ .format(matrix, pca1.name, pca2.name, gene_track, chromosomes, @@ -291,7 +291,7 @@ def test_pca_bigwig_lieberman_histoneMark_track(): matrix = ROOT + "small_test_matrix.h5" extra_track = ROOT + 'bigwig_chrx_2e6_5e6.bw' chromosomes = 'chrX ' - args = "--matrix {} --outputFileName {} {} -f bigwig -noe 2 --method lieberman \ + args = "--matrix {} --outputFileName {} {} -f bigwig --whichEigenvectors 1 2 --method lieberman \ --extraTrack {} --chromosomes {}"\ .format(matrix, pca1.name, pca2.name, extra_track, chromosomes).split() # hicPCA.main(args) @@ -315,7 +315,7 @@ def test_pca_bedgraph_lieberman_histoneMark_track(): matrix = ROOT + "small_test_matrix.h5" extra_track = ROOT + 'bigwig_chrx_2e6_5e6.bw' chromosomes = 'chrX ' - args = "--matrix {} --outputFileName {} {} -f bedgraph -noe 2 --method lieberman \ + args = "--matrix {} --outputFileName {} {} -f bedgraph --whichEigenvectors 1 2 --method lieberman \ --extraTrack {} --chromosomes {}"\ .format(matrix, pca1.name, pca2.name, extra_track, chromosomes).split() # hicPCA.main(args) @@ -327,3 +327,26 @@ def test_pca_bedgraph_lieberman_histoneMark_track(): os.unlink(pca1.name) os.unlink(pca2.name) + + +def test_pca_extratrack_extends_chromosomesize(): + pca1 = NamedTemporaryFile(suffix='.bw', delete=False) + pca2 = NamedTemporaryFile(suffix='.bw', delete=False) + + pca1.close() + pca2.close() + matrix = ROOT + "hicPCA/mm9_reduced_chr1.cool" + extra_track = ROOT + 'hicPCA/mm9_genes_sorted.bed12' + + args = "--matrix {} --outputFileName {} {} -f bigwig --whichEigenvectors 1 2 --method lieberman \ + --extraTrack {}"\ + .format(matrix, pca1.name, pca2.name, extra_track).split() + # hicPCA.main(args) + compute(hicPCA.main, args, 5) + chrom_list = ['chr1'] + assert are_files_equal_bigwig(ROOT + "hicPCA/pca_reduced_mm9_1.bw", + pca1.name, chrom_list) + assert are_files_equal_bigwig(ROOT + "hicPCA/pca_reduced_mm9_2.bw", + pca2.name, chrom_list) + os.unlink(pca1.name) + os.unlink(pca2.name) diff --git a/hicexplorer/test/general/test_hicPlotDistVsCounts.py b/hicexplorer/test/general/test_hicPlotDistVsCounts.py index 73effc17..4e9b7730 100644 --- a/hicexplorer/test/general/test_hicPlotDistVsCounts.py +++ b/hicexplorer/test/general/test_hicPlotDistVsCounts.py @@ -14,52 +14,54 @@ ROOT = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "test_data/") matrix = ROOT + 'small_test_matrix_50kb_res.h5' -outfile = NamedTemporaryFile(suffix='.png', prefix='plotFile', delete=False) -outFileData = NamedTemporaryFile(suffix='.txt', prefix='dataFile', delete=True) def test_plot(): outfile = NamedTemporaryFile(suffix='.png', prefix='plotFile', delete=False) matrix = ROOT + 'small_test_matrix_50kb_res.h5' - args = "--matrices {} --plotFile {} --plotsize 6 4".format(matrix, outfile.name).split() + args = "--matrices {} --plotFile {} --plotsize 8 4".format(matrix, outfile.name).split() hicPlotDistVsCounts.main(args) # local computer: test passes with delta of 3000 # travis: needs to be at least 4500 to pass # I love this voodoo :( + # After changing the plotsize, let see if 2000 works for both... size_new = os.path.getsize(outfile.name) size_reference = os.path.getsize(ROOT + 'hicPlotDistVsCounts/dist_vs_counts.png',) - assert abs(size_new - size_reference) < 5000 + assert abs(size_new - size_reference) < 2000 - os.remove(outfile.name) + # os.remove(outfile.name) @pytest.mark.parametrize("matrices", [matrix]) # required -@pytest.mark.parametrize("plotFile", [outfile]) # required -@pytest.mark.parametrize("labels", [None, ['label_1', 'label_2']]) # don't know if this will work +@pytest.mark.parametrize("labels", ['', '--labels label_1 label_2']) # don't know if this will work @pytest.mark.parametrize("plotsize1, plotsize2", [[6, 4], [6, 5]]) # (6, 5 is default) @pytest.mark.parametrize("perchr", ['--perchr', '']) # Not sure if this works due to store_True option of argparse -@pytest.mark.parametrize("outFileData", [outFileData]) @pytest.mark.parametrize("skipDiagonal", ['--skipDiagonal', '']) # not sure if this will work, see comment on perchr -@pytest.mark.parametrize("maxdepth", [int(3e6)]) # default is 3e6 +@pytest.mark.parametrize("maxdepth", [int(3e6), '1000000']) # default is 3e6 @pytest.mark.parametrize("chromosomeExclude", ['chrX']) -def test_trivial_run(matrices, plotFile, labels, plotsize1, plotsize2, perchr, outFileData, skipDiagonal, maxdepth, chromosomeExclude): +def test_trivial_run(matrices, labels, plotsize1, plotsize2, perchr, skipDiagonal, maxdepth, chromosomeExclude): """ Simple test for general behaviour with all commandline args. """ - args = "--matrices {} --plotFile {} --labels {} --plotsize {} {} {} --outFileData {} --maxdepth {} --chromosomeExclude {}".format( + outfile_new = NamedTemporaryFile(suffix='.png', prefix='plotFile', delete=False) + outFileData_new = NamedTemporaryFile(suffix='.txt', prefix='dataFile', delete=False) + args = "--matrices {} --plotFile {} {} --plotsize {} {} {} --outFileData {} --maxdepth {} --chromosomeExclude {}".format( matrices, - plotFile.name, + outfile_new.name, labels, plotsize1, plotsize2, perchr, - outFileData.name, + outFileData_new.name, maxdepth, chromosomeExclude, ).split() + # with open("test.txt", 'a') as fo: + # fo.write(str(args)) + # fo.write("\n") # hicPlotDistVsCounts.main(args) compute(hicPlotDistVsCounts.main, args, 5) diff --git a/hicexplorer/test/general/test_hicPlotMatrix.py b/hicexplorer/test/general/test_hicPlotMatrix.py index b441309c..26a14d18 100644 --- a/hicexplorer/test/general/test_hicPlotMatrix.py +++ b/hicexplorer/test/general/test_hicPlotMatrix.py @@ -609,3 +609,21 @@ def test_hicPlotMatrix_bigwig_multiple_chr_matrix_pruned(): assert res is None, res if REMOVE_OUTPUT: os.remove(outfile.name) + + +@pytest.mark.xfail(raises=ImageComparisonFailure, reason='Matplotlib plots for reasons a different image size.') +@pytest.mark.skipif(LOW_MEMORY > memory, + reason="Travis has too less memory to run it.") +def test_hicPlotMatrix_plot_tads(): + + outfile = NamedTemporaryFile(suffix='.png', prefix='hicexplorer_test', delete=False) + + args = "--matrix {} --disable_tight_layout " \ + "--outFileName {} --tads {} --region {}".format(ROOT + "small_test_matrix.h5", outfile.name, ROOT + "find_TADs/None/multiNone_domains.bed", 'chr3L:1300000-4220000').split() + # hicexplorer.hicPlotMatrix.main(args) + compute(hicexplorer.hicPlotMatrix.main, args, 5) + + res = compare_images(ROOT + "hicPlotMatrix" + '/plot_tads.png', outfile.name, tol=tolerance) + assert res is None, res + if REMOVE_OUTPUT: + os.remove(outfile.name) diff --git a/hicexplorer/test/general/test_hicTADClassifier.py b/hicexplorer/test/general/test_hicTADClassifier.py new file mode 100644 index 00000000..deab5971 --- /dev/null +++ b/hicexplorer/test/general/test_hicTADClassifier.py @@ -0,0 +1,257 @@ +from hicexplorer import hicTADClassifier +from hicexplorer.test.test_compute_function import compute +from hicexplorer.lib.tadClassifier import TADClassifier +import math +import pandas as pd +import numpy as np +import numpy.testing as nt +import os +import shutil +from tempfile import mkdtemp, NamedTemporaryFile +from hicmatrix import HiCMatrix as hm +import warnings +warnings.simplefilter(action="ignore", category=RuntimeWarning) +warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) + +# from hicexplorer.test.test_compute_function import compute + + +ROOT = os.path.join( + os.path.dirname( + os.path.dirname( + os.path.abspath(__file__))), + "test_data/hicTADClassifier/") +# ROOT = 'test_data/hicTADClassifier/' + + +def test_MP_Domain_Data(): + + protein_df = TADClassifier.MP_Domain_Data.readProtein( + ROOT + 'unittest.regionPeak', None) + assert protein_df.shape == (28, 6) and protein_df.iloc[0, 0] == 'chr1' + + domain_df = TADClassifier.MP_Domain_Data.read_domain_file( + ROOT + 'unittest_tads.bed') + assert domain_df.shape == (11, 9) and domain_df.iloc[0, 0] == 'chr1' + + domain_protein = TADClassifier.MP_Domain_Data.check_domains_against_protein( + domain_df, protein_df, 10000, threshold=1.0) + assert len(domain_protein) >= 1 and np.nanmin( + domain_protein['signal_value']) >= 1.0 + + tad_dict = TADClassifier.MP_Domain_Data.build_tad_dictionary(domain_df, [ + 'chr1']) + assert tad_dict['chr1'][1060000] + + domain_df_2 = TADClassifier.MP_Domain_Data.read_domain_file( + ROOT + 'unittest_tads_2.bed') + matrix_2 = TADClassifier.MP_Matrix( + ROOT + 'unittest_matrix_2.cool', method='range') + + domain_dict_2 = TADClassifier.MP_Domain_Data.build_tad_dictionary(domain_df_2, [ + 'chr1']) + is_boundary_2 = matrix_2.get_boundary_positions(domain_dict_2) + + assert (is_boundary_2[is_boundary_2].shape[0] == 62 and is_boundary_2.shape == ( + 2000,) and is_boundary_2[778] == True and is_boundary_2[779] == False) + + +def test_MP_Matrix(): + + matrix = TADClassifier.MP_Matrix( + ROOT + 'unittest_matrix.cool', method='range') + assert ( + matrix.numpy_matrix.shape == ( + 500, + 500) and + matrix.numpy_matrix.max() <= 1 and matrix.numpy_matrix.min() >= 0) + + X_unittest = pd.read_csv(ROOT + 'X_unittest.csv') + y_unittest = pd.read_csv(ROOT + 'y_unittest.csv') + X_unittest = X_unittest.to_numpy() + y_unittest = y_unittest.to_numpy()[:, 0] + + # unselect border cases + X_unittest = TADClassifier.MP_Matrix.unselect_border_cases(X_unittest, 2) + y_unittest = TADClassifier.MP_Matrix.unselect_border_cases_list( + y_unittest, 2) + assert (X_unittest.shape == (2, 8) and y_unittest.shape == (2,)) + + # get positions + positions = matrix.get_positions() + assert (positions.shape == (500, 3) and positions[0, 0] == 'chr1') + + # build features + matrix_2 = hm.hiCMatrix(ROOT + 'unittest_matrix_2.cool') + features = TADClassifier.MP_Matrix.build_features( + matrix_2.matrix, 2) + test_value = 37.03932717672038 + + assert (features.shape == (2000, + 15) and math.isclose(features[10, + 3], + test_value, + rel_tol=1e-5) and math.isclose(np.array(matrix_2.getMatrix())[8, + 8], + features[10, + 0], + rel_tol=1e-5)) + + +def test_MP_Classifier(): + + X_unittest = pd.read_csv(ROOT + 'X_unittest.csv') + y_unittest = pd.read_csv(ROOT + 'y_unittest.csv') + X_impure = X_unittest.copy(deep=True).to_numpy() + X_unittest = X_unittest.to_numpy() + y_unittest = y_unittest.to_numpy()[:, 0] + + # impute + X_impure[2, 2] = np.nan + X_imputed = TADClassifier.MP_Classifier.impute(X_impure, fill_value=-1.0) + assert (X_imputed[2, 2] == -1.0 and X_imputed[3, 3] == 43.0) + + # resample + X, y = TADClassifier.MP_Classifier.resample( + X_unittest, y_unittest, method='undersample_random', passed_method=None, threads=4) + assert y[y == True].shape == y[y == False].shape + + X, y = TADClassifier.MP_Classifier.resample( + X_unittest, y_unittest, method='undersample_cluster_centroids', passed_method=None, threads=4) + assert y[y == True].shape == y[y == False].shape + + # resample_test + positions = np.zeros((5, 3)) + positions, X, y = TADClassifier.MP_Classifier.resample_test( + positions, X_unittest, y_unittest, threads=4) + assert y[y == True].shape == y[y == False].shape + + +# def test_get_domains(): + +# # get_domains +# y_unittest = pd.read_csv( +# ROOT + 'y_unittest.csv', +# header=None).to_numpy()[ +# :, +# 0].astype(bool) +# positions_unittest = pd.read_csv( +# ROOT + 'positions_unittest.csv', +# header=None).to_numpy() + +# domain_df = TADClassifier.get_domains(positions_unittest, y_unittest) + +# print(domain_df.head) +# assert domain_df['Chrom'].iloc[0] == 'chr1' and domain_df['Start'].iloc[0] == 20000 + + +def test_hicTADClassifier(): + outfile = NamedTemporaryFile(suffix='.bed', delete=False) + outfile.close() + + args = ['--matrices', + ROOT + 'gm12878_chr1.cool', + '--out_file', + outfile.name, + '-n', + 'range', + '--saved_classifier', + ROOT + 'trained_model.bin.BIN', + '--threads', + '4' + ] + hicTADClassifier.main(args) + # compute(hicTADClassifier.main, args, 1) + domain_df = TADClassifier.MP_Domain_Data.read_domain_file( + outfile.name) + assert domain_df['Chrom'].iloc[0] == 1 + + +def test_hicTADClassifier_two_matrices(): + # args = ['--matrices', + # ROOT + 'unittest_matrix_2.cool', + # '--out_file', + # test_folder + 'domains_test.bed', + # '-n', + # 'obs_exp', + # '--saved_classifier', + # 'unittest_classifier.data', + # '--unselect_border_cases', + # 'True', + # '--threads', + # '4' + # ] + # + # compute(main, args, 1) + # domain_df = TADClassifier.MP_Domain_Data.read_domain_file(test_folder + 'domains_test.bed') + # assert domain_df['Chrom'].iloc[0] = 'chr1' + outfile_2 = NamedTemporaryFile(suffix='.bed', delete=False) + outfile_2.close() + outfile_3 = NamedTemporaryFile(suffix='.bed', delete=False) + outfile_3.close() + args = ['--matrices', + ROOT + 'gm12878_chr1.cool', + ROOT + 'gm12878_chr1.cool', + '--out_file', + outfile_2.name, + outfile_3.name, + '-n', + 'range', + '--saved_classifier', + ROOT + 'trained_model.bin.BIN', + '--unselect_border_cases', + # 'True', + '--threads', + '4' + ] + print(args) + hicTADClassifier.main(args) + # compute(hicTADClassifier.main, args, 1) + domain_df = TADClassifier.MP_Domain_Data.read_domain_file( + outfile_2.name) + assert domain_df['Chrom'].iloc[0] == 1 + domain_df_3 = TADClassifier.MP_Domain_Data.read_domain_file( + outfile_3.name) + assert domain_df_3['Chrom'].iloc[0] == 1 + + # shutil.rmtree(test_folder) + + +def test_hicTADClassifier_load_model_obs_exp(): + outfile = NamedTemporaryFile(suffix='.bed', delete=False) + outfile.close() + + args = ['--matrices', + ROOT + 'gm12878_chr1.cool', + '--out_file', + outfile.name, + '-n', + 'obs_exp', + '--threads', + '4' + ] + hicTADClassifier.main(args) + # compute(hicTADClassifier.main, args, 1) + domain_df = TADClassifier.MP_Domain_Data.read_domain_file( + outfile.name) + assert domain_df['Chrom'].iloc[0] == 1 + + +# def test_hicTADClassifier_load_model_range(): +# outfile = NamedTemporaryFile(suffix='.bed', delete=False) +# outfile.close() + +# args = ['--matrices', +# ROOT + 'gm12878_chr1.cool', +# '--out_file', +# outfile.name, +# '-n', +# 'range', +# '--threads', +# '4' +# ] +# hicTADClassifier.main(args) +# # compute(hicTADClassifier.main, args, 1) +# domain_df = TADClassifier.MP_Domain_Data.read_domain_file( +# outfile.name) +# assert domain_df['Chrom'].iloc[0] == 1 diff --git a/hicexplorer/test/general/test_hicTrainTADClassifier.py b/hicexplorer/test/general/test_hicTrainTADClassifier.py new file mode 100644 index 00000000..0e7f1968 --- /dev/null +++ b/hicexplorer/test/general/test_hicTrainTADClassifier.py @@ -0,0 +1,105 @@ +from hicexplorer import hicTrainTADClassifier +from hicexplorer.test.test_compute_function import compute +# from hicexplorer.lib.tadClassifier import TADClassifier +import numpy.testing as nt +import os +import shutil +from tempfile import mkdtemp +import tempfile +from hicmatrix import HiCMatrix +import warnings +warnings.simplefilter(action="ignore", category=RuntimeWarning) +warnings.simplefilter(action="ignore", category=PendingDeprecationWarning) + +# from hicexplorer.test.test_compute_function import compute + + +ROOT = os.path.join( + os.path.dirname( + os.path.dirname( + os.path.abspath(__file__))), + "test_data/hicTADClassifier/") +# ROOT = 'test_data/hicTADClassifier/' + + +def test_hicTrainClassifier_train_test(): + + test_folder = mkdtemp(prefix="testfolder_hicTrainClassifier") + print(tempfile.gettempdir()) + + args = ['--mode', + 'train_test', + '--domain_file', + ROOT + 'unittest_domains.bed', + '--matrices', + ROOT + 'gm12878_chr1.cool', + '--out_file', + test_folder + 'train_test.txt', + '-n', + 'obs_exp', + '-r', + '10000', + '--estimators_per_step', + '10'] + # '--chrPrefixProtein', 'remove'] + # hicTrainTADClassifier.main(args) + compute(hicTrainTADClassifier.main, args, 5) + f = open(test_folder + 'train_test.txt', "r") + assert f.readline().split()[0] == 'accuracy' + +# def test_hicTrainClassifier_train_new(): + args = ['--mode', + 'train_new', + '--domain_file', + ROOT + 'unittest_domains.bed', + '--matrices', + ROOT + 'gm12878_chr1.cool', + '--out_file', + test_folder + 'unittest_classifier_new', + '-n', + 'range', + '-r', + '10000', + '--estimators_per_step', + '10'] + + compute(hicTrainTADClassifier.main, args, 5) + # if estimator is build will be checked by the next run + + args = ['--mode', + 'train_existing', + '--domain_file', + ROOT + 'unittest_domains.bed', + '--matrices', + ROOT + 'gm12878_chr1.cool', + '--out_file', + test_folder + 'unittest_classifier_new', + '-n', + 'range', + '-r', + '10000', + '--saved_classifier', + test_folder + 'unittest_classifier_new.BIN'] + + compute(hicTrainTADClassifier.main, args, 5) + + args = ['--mode', + 'predict_test', + '--domain_file', + ROOT + 'unittest_domains.bed', + '--matrices', + ROOT + 'gm12878_chr1.cool', + '--out_file', + test_folder + 'predict_test', + '-n', + 'range', + '-r', + '10000', + '--saved_classifier', + test_folder + 'unittest_classifier_new.BIN'] + + compute(hicTrainTADClassifier.main, args, 5) + f = open(test_folder + 'predict_test_results.txt', "r") + assert f.readline().split()[0] == 'accuracy' + +# shutil.rmtree(test_folder) diff --git a/hicexplorer/test/general/test_hicValidateLocations.py b/hicexplorer/test/general/test_hicValidateLocations.py index dd7a2575..e0a729d8 100644 --- a/hicexplorer/test/general/test_hicValidateLocations.py +++ b/hicexplorer/test/general/test_hicValidateLocations.py @@ -44,10 +44,9 @@ def test_loop_narrow_peak(): outfile = NamedTemporaryFile(suffix='out', delete=True) outfile.close() - args = "--data {} --protein {} --method {} --outFileName {} -r {} --addChrPrefixLoops".format(ROOT + 'loops_1.bedgraph', - ROOT + 'GSM935376_hg19_Gm12878_Smc3.narrowPeak', - 'loops', outfile.name, 10000).split() - # hicValidateLocations.main(args) + args = "--data {} --validationData {} --validationType {} --method {} --outFileName {} -r {} --chrPrefixLoops {} ".format(ROOT + 'loops_1.bedgraph', + ROOT + 'GSM935376_hg19_Gm12878_Smc3.narrowPeak', 'bed', + 'loops', outfile.name, 10000, 'add').split() compute(hicValidateLocations.main, args, 5) assert are_files_equal( ROOT + 'overlap_smc3_matched_locations', outfile.name + '_matched_locations') @@ -59,16 +58,31 @@ def test_loop_broad_peak(): outfile = NamedTemporaryFile(suffix='out', delete=True) outfile.close() - args = "--data {} --protein {} --method {} --outFileName {} -r {} --addChrPrefixLoops".format(ROOT + 'loops_1.bedgraph', - ROOT + 'GSM733752_hg19_ctcf_GM12878.broadPeak', - 'loops', outfile.name, 10000).split() - # hicValidateLocations.main(args) + args = "--data {} --validationData {} --validationType {} --method {} --outFileName {} -r {} --chrPrefixProtein {} ".format(ROOT + 'loops_1.bedgraph', + ROOT + 'GSM733752_hg19_ctcf_GM12878.broadPeak', 'bed', + 'loops', outfile.name, 10000, 'remove').split() compute(hicValidateLocations.main, args, 5) - # print(outfile.name + '_matched_locations') print(open(outfile.name + '_matched_locations', "r").read(1000)) print(open(outfile.name + '_statistics', "r").read(1000)) assert are_files_equal( ROOT + 'overlap_ctcf_matched_locations', outfile.name + '_matched_locations') assert are_files_equal(ROOT + 'overlap_ctcf_statistics', outfile.name + '_statistics', skip=3) + + +def test_loop_cool(): + outfile = NamedTemporaryFile(suffix='out', delete=True) + outfile.close() + + args = "--data {} --validationData {} --validationType {} --method {} --outFileName {} -r {} --chrPrefixLoop {} ".format(ROOT + 'loops_1.bedgraph', + ROOT + 'GSM1436265_RAD21_ENCFF002EMQ_10kb.cool', 'cool', + 'loops', outfile.name, 10000, 'add').split() + compute(hicValidateLocations.main, args, 5) + + print(open(outfile.name + '_matched_locations', "r").read(1000)) + print(open(outfile.name + '_statistics', "r").read(1000)) + assert are_files_equal( + ROOT + 'overlap_rad21_cool_matched_locations', outfile.name + '_matched_locations') + assert are_files_equal(ROOT + 'overlap_rad21_cool_statistics', + outfile.name + '_statistics', skip=3) diff --git a/hicexplorer/test/test_data/QC_multi_restriction/QC.log b/hicexplorer/test/test_data/QC_multi_restriction/QC.log index 13fee336..b1e866a8 100644 --- a/hicexplorer/test/test_data/QC_multi_restriction/QC.log +++ b/hicexplorer/test/test_data/QC_multi_restriction/QC.log @@ -12,8 +12,8 @@ One mate not unique 3603 (3.60) Low mapping quality 34877 (34.88) # count (percentage w.r.t. mappable, unique and high quality pairs) -dangling end GATC 54 (0.10) -dangling end AGCT 246 (0.47) +dangling end GATC (restriction sequence GATC) 54 (0.10) +dangling end AGCT (restriction sequence AAGCTT) 246 (0.47) self ligation (removed) 12147 (23.04) One mate not close to rest site 0 (0.00) same fragment 2946 (5.59) diff --git a/hicexplorer/test/test_data/QC_rc_multiple/QC.log b/hicexplorer/test/test_data/QC_rc_multiple/QC.log index a7792774..17b6933f 100644 --- a/hicexplorer/test/test_data/QC_rc_multiple/QC.log +++ b/hicexplorer/test/test_data/QC_rc_multiple/QC.log @@ -12,8 +12,8 @@ One mate not unique 3603 (3.60) Low mapping quality 34877 (34.88) # count (percentage w.r.t. mappable, unique and high quality pairs) -dangling end GATC 54 (0.10) -dangling end AGCT 246 (0.47) +dangling end GATC (restriction sequence GATC) 54 (0.10) +dangling end AGCT (restriction sequence AAGCTT) 246 (0.47) self ligation (removed) 12228 (23.19) One mate not close to rest site 67 (0.13) same fragment 2933 (5.56) diff --git a/hicexplorer/test/test_data/QC_region/QC.log b/hicexplorer/test/test_data/QC_region/QC.log new file mode 100644 index 00000000..2a6b1f29 --- /dev/null +++ b/hicexplorer/test/test_data/QC_region/QC.log @@ -0,0 +1,30 @@ + +File /tmp/tmpmzka3uhk.h5 +Sequenced reads 99983 +Min rest. site distance 300 +Max library insert size 1000 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 52726 (52.73) +Hi-C contacts 7987 (7.99) +One mate unmapped 8777 (8.78) +One mate not unique 3603 (3.60) +Low mapping quality 34877 (34.88) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +dangling end GATC (restriction sequence GATC) 11 (0.02) +dangling end AGCT (restriction sequence AAGCTT) 59 (0.11) +self ligation (removed) 0 (0.00) +One mate not close to rest site 40906 (77.58) +same fragment 3751 (7.11) +self circle 0 (0.00) +duplicated pairs 12 (0.02) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 0 (0.00) +Intra short range (< 20kb) 2145 (26.86) +Intra long range (>= 20kb) 5842 (73.14) +Read pair type: inward pairs 1806 (22.61) +Read pair type: outward pairs 2447 (30.64) +Read pair type: left pairs 1865 (23.35) +Read pair type: right pairs 1869 (23.40) diff --git a/hicexplorer/test/test_data/QC_region/QC_table.txt b/hicexplorer/test/test_data/QC_region/QC_table.txt new file mode 100644 index 00000000..d2d2b651 --- /dev/null +++ b/hicexplorer/test/test_data/QC_region/QC_table.txt @@ -0,0 +1,2 @@ +File Sequenced reads Min rest. site distance Max library insert size Pairs mappable, unique and high quality Hi-C contacts One mate unmapped One mate not unique Low mapping quality dangling end GATC dangling end AGCT self ligation (removed) One mate not close to rest site same fragment self circle duplicated pairs inter chromosomal Intra short range (< 20kb) Intra long range (>= 20kb) Read pair type: inward pairs Read pair type: outward pairs Read pair type: left pairs Read pair type: right pairs +/tmp/tmpmzka3uhk.h5 99983 300 1000 52726 7987 8777 3603 34877 11 59 0 40906 3751 0 12 0 2145 5842 1806 2447 1865 1869 diff --git a/hicexplorer/test/test_data/QC_region/discarded_table.txt b/hicexplorer/test/test_data/QC_region/discarded_table.txt new file mode 100644 index 00000000..b6943e11 --- /dev/null +++ b/hicexplorer/test/test_data/QC_region/discarded_table.txt @@ -0,0 +1,2 @@ +File One mate not close to rest site One mate not close to rest site % dangling end GATC % dangling end AGCT % duplicated pairs duplicated pairs % same fragment same fragment % self circle self circle % self ligation (removed) self ligation (removed) % +/tmp/tmpmzka3uhk.h5 40906 0.7758221750180176 0.0002086257254485453 0.001118992527405834 12 0.00022759170048932214 3751 0.07114137237795395 0 0.0 0 0.0 diff --git a/hicexplorer/test/test_data/QC_region/distance.png b/hicexplorer/test/test_data/QC_region/distance.png new file mode 100644 index 00000000..ed074148 Binary files /dev/null and b/hicexplorer/test/test_data/QC_region/distance.png differ diff --git a/hicexplorer/test/test_data/QC_region/distance_table.txt b/hicexplorer/test/test_data/QC_region/distance_table.txt new file mode 100644 index 00000000..bab49f93 --- /dev/null +++ b/hicexplorer/test/test_data/QC_region/distance_table.txt @@ -0,0 +1,2 @@ +File inter chromosomal inter chromosomal % Intra short range (< 20kb) Intra short range (< 20kb) % Intra long range (>= 20kb) Intra long range (>= 20kb) % +/tmp/tmpmzka3uhk.h5 0 0.0 2145 0.2685614122949793 5842 0.7314385877050207 diff --git a/hicexplorer/test/test_data/QC_region/hicQC.html b/hicexplorer/test/test_data/QC_region/hicQC.html new file mode 100644 index 00000000..ac3e9c72 --- /dev/null +++ b/hicexplorer/test/test_data/QC_region/hicQC.html @@ -0,0 +1,236 @@ + + + + + HiCExplorer QC report + + + + + + + +
+
+
+

HiCExplorer QC report

+
+ +

Pairs sequenced

+ Pairs sequenced + +

Unmappable and non-unique pairs

+ Unmappable and non-unique + +

This figure contains the fraction of reads, with respect to the total number of reads, + that did not map, that have a low quality score or that didn't map uniquely to the genome. + +

Unmappable and non-unique table

+ + + + + + + + + + + + +
Hi-C contacts Hi-C contacts_% Low mapping quality Low mapping quality_% One mate not unique One mate not unique_% One mate unmapped One mate unmapped_%
File
/tmp/tmpmzka3uhk.h57,9877.99%34,87734.88%3,6033.60%8,7778.78%
+ Download table (tab separated) + +

Pairs discarded

+ Pairs discarded + +

This figure contains the fraction read pairs (with respect to mappable reads) that were discarded + when building the Hi-C matrix.

+
+
Dangling ends
+
These are reads that start with the restriction site and constitute reads that were digested but no ligated.
+
Same fragment
+
These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in + between. These read pairs are not valid Hi-C pairs
+
Self circle
+
self circles are defined as pairs within 25kb with 'outward' read orientation
+
Self ligation
+
These are read pairs with a restriction site in between that are within 800 bp.
+
+ +

Discarded pairs table

+ + + + + + + + + + + + + + + + +
One mate not close to rest site One mate not close to rest site % dangling end GATC % dangling end AGCT % duplicated pairs duplicated pairs % same fragment same fragment % self circle self circle % self ligation (removed) self ligation (removed) %
File
/tmp/tmpmzka3uhk.h540,90677.58%0.02%0.11%120.02%3,7517.11%0.00%0.00%0.00%0.00%
+ Download table (tab separated) + +

Contact distance

+ Contact distance + +

Contact distance table

+ + + + + + + + + + +
inter chromosomal inter chromosomal % Intra short range (< 20kb) Intra short range (< 20kb) % Intra long range (>= 20kb) Intra long range (>= 20kb) %
File
/tmp/tmpmzka3uhk.h50.00%0.00%2,14526.86%5,84273.14%
+ Download table (tab separated) + +

Read orientation

+ Contact distance + +

Read orientation table

+ + + + + + + + + + + + +
Read pair type: inward pairs Read pair type: inward pairs % Read pair type: outward pairs Read pair type: outward pairs % Read pair type: left pairs Read pair type: left pairs % Read pair type: right pairs Read pair type: right pairs %
File
/tmp/tmpmzka3uhk.h51,80622.61%2,44730.64%1,86523.35%1,86923.40%
+ Download table (tab separated) + +

Number of reads table

+ + + + + + + + + + + + + + + + + + + + + + + + +
Sequenced reads Pairs mappable, unique and high quality Hi-C contacts One mate unmapped One mate not unique Low mapping quality dangling end GATC dangling end AGCT self ligation (removed) One mate not close to rest site same fragment self circle duplicated pairs inter chromosomal Intra short range (< 20kb) Intra long range (>= 20kb) Read pair type: inward pairs Read pair type: outward pairs Read pair type: left pairs Read pair type: right pairs
File
/tmp/tmpmzka3uhk.h5999835272679878777360334877115904090637510120214558421806244718651869
+ + Download table (tab separated) +
+
+
+ + diff --git a/hicexplorer/test/test_data/QC_region/pairs_discarded.png b/hicexplorer/test/test_data/QC_region/pairs_discarded.png new file mode 100644 index 00000000..dff5bbc6 Binary files /dev/null and b/hicexplorer/test/test_data/QC_region/pairs_discarded.png differ diff --git a/hicexplorer/test/test_data/QC_region/pairs_sequenced.png b/hicexplorer/test/test_data/QC_region/pairs_sequenced.png new file mode 100644 index 00000000..d7e7e854 Binary files /dev/null and b/hicexplorer/test/test_data/QC_region/pairs_sequenced.png differ diff --git a/hicexplorer/test/test_data/QC_region/read_orientation.png b/hicexplorer/test/test_data/QC_region/read_orientation.png new file mode 100644 index 00000000..37915156 Binary files /dev/null and b/hicexplorer/test/test_data/QC_region/read_orientation.png differ diff --git a/hicexplorer/test/test_data/QC_region/read_orientation_table.txt b/hicexplorer/test/test_data/QC_region/read_orientation_table.txt new file mode 100644 index 00000000..b1348da7 --- /dev/null +++ b/hicexplorer/test/test_data/QC_region/read_orientation_table.txt @@ -0,0 +1,2 @@ +File Read pair type: inward pairs Read pair type: inward pairs % Read pair type: outward pairs Read pair type: outward pairs % Read pair type: left pairs Read pair type: left pairs % Read pair type: right pairs Read pair type: right pairs % +/tmp/tmpmzka3uhk.h5 1806 0.22611744084136723 2447 0.3063728558908226 1865 0.23350444472267434 1869 0.23400525854513585 diff --git a/hicexplorer/test/test_data/QC_region/unmapable_table.txt b/hicexplorer/test/test_data/QC_region/unmapable_table.txt new file mode 100644 index 00000000..5a51411c --- /dev/null +++ b/hicexplorer/test/test_data/QC_region/unmapable_table.txt @@ -0,0 +1,2 @@ +File Hi-C contacts Hi-C contacts_% Low mapping quality Low mapping quality_% One mate not unique One mate not unique_% One mate unmapped One mate unmapped_% +/tmp/tmpmzka3uhk.h5 7987 0.07988358020863547 34877 0.3488293009811668 3603 0.036036126141444046 8777 0.08778492343698428 diff --git a/hicexplorer/test/test_data/QC_region/unmappable_and_non_unique.png b/hicexplorer/test/test_data/QC_region/unmappable_and_non_unique.png new file mode 100644 index 00000000..97889f8d Binary files /dev/null and b/hicexplorer/test/test_data/QC_region/unmappable_and_non_unique.png differ diff --git a/hicexplorer/test/test_data/build_region.bam b/hicexplorer/test/test_data/build_region.bam new file mode 100644 index 00000000..dc2a537a Binary files /dev/null and b/hicexplorer/test/test_data/build_region.bam differ diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/aggregate.hdf5 b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/aggregate.hdf5 new file mode 100644 index 00000000..29d06b18 Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/aggregate.hdf5 differ diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt deleted file mode 100644 index 2b4a5298..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt +++ /dev/null @@ -1,7 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 14274000 14279000 Eya1 673.0 -22000 7.00000 -chr1 14290000 14439000 Eya1 673.0 138000 523.00000 -chr1 14444000 14467000 Eya1 673.0 166000 10.00000 -chr1 14476000 14501000 Eya1 673.0 200000 30.25000 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt deleted file mode 100644 index 24e1d1e8..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt +++ /dev/null @@ -1,5 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 19077000 19118000 Tfap2d 472.0 24000 349.00000 -chr1 19120000 19274000 Tfap2d 472.0 180000 86.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt deleted file mode 100644 index 80fc36ec..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt +++ /dev/null @@ -1,5 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 4480000 4549000 Sox17 810.0 61000 640.00000 -chr1 4555000 4688000 Sox17 810.0 200000 73.18333 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt deleted file mode 100644 index d37b6557..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt +++ /dev/null @@ -1,7 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 14274000 14279000 Eya1 832.0 -22000 0.00000 -chr1 14290000 14439000 Eya1 832.0 138000 645.00000 -chr1 14444000 14467000 Eya1 832.0 166000 25.00000 -chr1 14476000 14501000 Eya1 832.0 200000 26.15000 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt deleted file mode 100644 index 9e2066fb..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt +++ /dev/null @@ -1,5 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 19077000 19118000 Tfap2d 800.0 24000 534.00000 -chr1 19120000 19274000 Tfap2d 800.0 180000 214.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt deleted file mode 100644 index 3172b5a4..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt +++ /dev/null @@ -1,5 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 4480000 4549000 Sox17 978.0 61000 798.00000 -chr1 4555000 4688000 Sox17 978.0 200000 82.93333 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt deleted file mode 100644 index 404ada15..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt +++ /dev/null @@ -1,6 +0,0 @@ -FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt -MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt -FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt -MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt -FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt -MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt deleted file mode 100644 index 4ba4288f..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt +++ /dev/null @@ -1,4 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3.1 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 14331000 14344000 Eya1 673.0 43000 11.20000 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt deleted file mode 100644 index ac3196bc..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt +++ /dev/null @@ -1,4 +0,0 @@ -# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3.1 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Sum of interactions Relative distance Raw target -chr1 14331000 14344000 Eya1 832.0 43000 22.80000 diff --git a/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/target_list.bed b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/target_list.bed new file mode 100644 index 00000000..a3dfba94 --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicAggregateStatistic/target_list.bed @@ -0,0 +1,8 @@ +chr1 4480000 4549000 +chr1 4555000 4688000 +chr1 14274000 14279000 +chr1 14290000 14439000 +chr1 14444000 14467000 +chr1 14476000 14501000 +chr1 19077000 19118000 +chr1 19120000 19274000 \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt deleted file mode 100644 index 425fb673..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 0.97540 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt deleted file mode 100644 index bc3dcc4f..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt +++ /dev/null @@ -1,13 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335 -chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.05733 -chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.18635 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt deleted file mode 100644 index a69bc28b..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt +++ /dev/null @@ -1,14 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335 -chr1 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 0.97540 -chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.05733 -chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.18635 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt deleted file mode 100644 index e201da4d..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt deleted file mode 100644 index e66d0406..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 19077000 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25577 -chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00599 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt deleted file mode 100644 index e66d0406..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 19077000 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25577 -chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00599 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt deleted file mode 100644 index 2bc72a7b..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.65155 -chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.70460 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt deleted file mode 100644 index ff528bb3..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt deleted file mode 100644 index 2bc72a7b..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.65155 -chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.70460 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt deleted file mode 100644 index a5faca03..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 1.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt deleted file mode 100644 index a4a41119..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt +++ /dev/null @@ -1,13 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 -chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.06013 -chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.22603 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt deleted file mode 100644 index 25c91b77..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt +++ /dev/null @@ -1,14 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 -chr1 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 1.00000 -chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.06013 -chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.22603 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt deleted file mode 100644 index 29111010..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt deleted file mode 100644 index 7e6ce05e..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 19077000 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25983 -chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00595 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt deleted file mode 100644 index 7e6ce05e..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 19077000 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25983 -chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00595 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt deleted file mode 100644 index 75457de9..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.66923 -chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.67655 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt deleted file mode 100644 index e14c8063..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt deleted file mode 100644 index 75457de9..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.66923 -chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.67655 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt deleted file mode 100644 index a5faca03..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 1.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt deleted file mode 100644 index a4a41119..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt +++ /dev/null @@ -1,13 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 -chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.06013 -chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.22603 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt deleted file mode 100644 index 25c91b77..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt +++ /dev/null @@ -1,14 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366 -chr1 14290000 14439000 Eya1 138000 673.00000 523.00000 832.00000 645.00000 1.00000 -chr1 14444000 14467000 Eya1 166000 673.00000 10.00000 832.00000 25.00000 0.06013 -chr1 14476000 14501000 Eya1 200000 673.00000 30.25000 832.00000 26.15000 0.22603 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt deleted file mode 100644 index 29111010..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt deleted file mode 100644 index 7e6ce05e..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 19077000 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25983 -chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00595 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt deleted file mode 100644 index 7e6ce05e..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 19077000 19118000 Tfap2d 24000 472.00000 349.00000 800.00000 534.00000 0.25983 -chr1 19120000 19274000 Tfap2d 180000 472.00000 86.00000 800.00000 214.00000 0.00595 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt deleted file mode 100644 index 75457de9..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.66923 -chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.67655 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt deleted file mode 100644 index e14c8063..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt deleted file mode 100644 index 75457de9..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt +++ /dev/null @@ -1,12 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.4.3-dev -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 4480000 4549000 Sox17 61000 810.00000 640.00000 978.00000 798.00000 0.66923 -chr1 4555000 4688000 Sox17 200000 810.00000 73.18333 978.00000 82.93333 0.67655 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/differential.hdf5 b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/differential.hdf5 new file mode 100644 index 00000000..05483635 Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/differential.hdf5 differ diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt deleted file mode 100644 index 1d92d5ed..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1 -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt deleted file mode 100644 index 3092649d..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1 -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14331000 14344000 Eya1 43000 673.00000 11.20000 832.00000 22.80000 0.17177 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt deleted file mode 100644 index 3092649d..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1 -# This file contains the p-values computed by chi2 test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14331000 14344000 Eya1 43000 673.00000 11.20000 832.00000 22.80000 0.17177 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt deleted file mode 100644 index a4e20071..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1 -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt deleted file mode 100644 index ed71d182..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1 -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14331000 14344000 Eya1 43000 673.00000 11.20000 832.00000 22.80000 0.23380 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt deleted file mode 100644 index ed71d182..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3.1 -# This file contains the p-values computed by fisher test -# To test the smoothed (float) values they were rounded up to the next integer -# -# Alpha level 0.5 -# Degrees of freedom 1 -# -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value -chr1 14331000 14344000 Eya1 43000 673.00000 11.20000 832.00000 22.80000 0.23380 diff --git a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/rejectedFilesList.txt b/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/rejectedFilesList.txt deleted file mode 100644 index 4fb09601..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicDifferentialTest/rejectedFilesList.txt +++ /dev/null @@ -1,3 +0,0 @@ -FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt -FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt -FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_genes_Eya1_aggregate.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_genes_Eya1_aggregate.txt new file mode 100644 index 00000000..3a788852 --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_genes_Eya1_aggregate.txt @@ -0,0 +1,9 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 14274000 14278000 Eya1 673.000000000000 -23000 5.600000000000 +chr1 14295000 14298000 Eya1 673.000000000000 -3000 44.400000000000 +chr1 14314000 14319000 Eya1 673.000000000000 18000 24.200000000000 +chr1 14426000 14432000 Eya1 673.000000000000 131000 2.400000000000 +chr1 14447000 14455000 Eya1 673.000000000000 154000 4.400000000000 +chr1 14460000 14465000 Eya1 673.000000000000 164000 3.200000000000 +chr1 14480000 14488000 Eya1 673.000000000000 187000 7.600000000000 +chr1 14491000 14501000 Eya1 673.000000000000 200000 20.650000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_genes_Eya1_aggregate.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_genes_Eya1_aggregate.txt new file mode 100644 index 00000000..d7db30de --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_genes_Eya1_aggregate.txt @@ -0,0 +1,9 @@ +# Chromosome Start End Gene Sum of interactions Relative position Raw +chr1 14274000 14278000 Eya1 832.000000000000 -23000 0.000000000000 +chr1 14295000 14298000 Eya1 832.000000000000 -3000 49.800000000000 +chr1 14314000 14319000 Eya1 832.000000000000 18000 23.400000000000 +chr1 14426000 14432000 Eya1 832.000000000000 131000 9.000000000000 +chr1 14447000 14455000 Eya1 832.000000000000 154000 12.400000000000 +chr1 14460000 14465000 Eya1 832.000000000000 164000 7.600000000000 +chr1 14480000 14488000 Eya1 832.000000000000 187000 3.200000000000 +chr1 14491000 14501000 Eya1 832.000000000000 200000 18.750000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_accepted_differential.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_accepted_differential.txt new file mode 100644 index 00000000..00e113db --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_accepted_differential.txt @@ -0,0 +1,3 @@ +# Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14295000 14298000 Eya1 -3000 673.000000000000 44.400000000000 832.000000000000 49.800000000000 0.670801771179 +chr1 14460000 14465000 Eya1 164000 673.000000000000 3.200000000000 832.000000000000 7.600000000000 0.564250349826 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_all_differential.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_all_differential.txt new file mode 100644 index 00000000..cfd5cf87 --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_all_differential.txt @@ -0,0 +1,9 @@ +# Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14278000 Eya1 -23000 673.000000000000 5.600000000000 832.000000000000 0.000000000000 0.008134451704 +chr1 14295000 14298000 Eya1 -3000 673.000000000000 44.400000000000 832.000000000000 49.800000000000 0.670801771179 +chr1 14314000 14319000 Eya1 18000 673.000000000000 24.200000000000 832.000000000000 23.400000000000 0.385952554141 +chr1 14426000 14432000 Eya1 131000 673.000000000000 2.400000000000 832.000000000000 9.000000000000 0.245228952263 +chr1 14447000 14455000 Eya1 154000 673.000000000000 4.400000000000 832.000000000000 12.400000000000 0.232102031454 +chr1 14460000 14465000 Eya1 164000 673.000000000000 3.200000000000 832.000000000000 7.600000000000 0.564250349826 +chr1 14480000 14488000 Eya1 187000 673.000000000000 7.600000000000 832.000000000000 3.200000000000 0.151571165731 +chr1 14491000 14501000 Eya1 200000 673.000000000000 20.650000000000 832.000000000000 18.750000000000 0.338670136491 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_rejected_differential.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_rejected_differential.txt new file mode 100644 index 00000000..69a9c3a0 --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_rejected_differential.txt @@ -0,0 +1,7 @@ +# Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value +chr1 14274000 14278000 Eya1 -23000 673.000000000000 5.600000000000 832.000000000000 0.000000000000 0.008134451704 +chr1 14314000 14319000 Eya1 18000 673.000000000000 24.200000000000 832.000000000000 23.400000000000 0.385952554141 +chr1 14426000 14432000 Eya1 131000 673.000000000000 2.400000000000 832.000000000000 9.000000000000 0.245228952263 +chr1 14447000 14455000 Eya1 154000 673.000000000000 4.400000000000 832.000000000000 12.400000000000 0.232102031454 +chr1 14480000 14488000 Eya1 187000 673.000000000000 7.600000000000 832.000000000000 3.200000000000 0.151571165731 +chr1 14491000 14501000 Eya1 200000 673.000000000000 20.650000000000 832.000000000000 18.750000000000 0.338670136491 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_target.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_target.txt new file mode 100644 index 00000000..72906d35 --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_target.txt @@ -0,0 +1,8 @@ +chr1 14274000 14278000 +chr1 14295000 14298000 +chr1 14314000 14319000 +chr1 14426000 14432000 +chr1 14447000 14455000 +chr1 14460000 14465000 +chr1 14480000 14488000 +chr1 14491000 14501000 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_genes_Eya1.bigwig b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_genes_Eya1.bigwig new file mode 100644 index 00000000..00d49b89 Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_genes_Eya1.bigwig differ diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_genes_Eya1_significant.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_genes_Eya1_significant.txt new file mode 100644 index 00000000..4ae41399 --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/FL-E13-5_chr1_genes_Eya1_significant.txt @@ -0,0 +1,7 @@ +# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw +chr1 14274000 14278000 Eya1 673.000000000000 -26000 0.008320950966 0.007037698679 7.811125758170 5.600000000000 +chr1 14296000 14298000 Eya1 673.000000000000 -3000 0.057949479941 0.104215728599 3.781355935916 39.000000000000 +chr1 14314000 14316000 Eya1 673.000000000000 14000 0.015156017831 0.048507853154 3.190333935010 10.200000000000 +chr1 14317000 14319000 Eya1 673.000000000000 17000 0.014561664190 0.034914431882 3.517090338584 9.800000000000 +chr1 14480000 14488000 Eya1 673.000000000000 184000 0.011292719168 0.000000010481 19.285082946462 7.600000000000 +chr1 14491000 14501000 Eya1 673.000000000000 200000 0.030683506686 0.000000000000 56.967824833429 20.650000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/MB-E10-5_chr1_genes_Eya1.bigwig b/hicexplorer/test/test_data/cHi-C/chicExportData/MB-E10-5_chr1_genes_Eya1.bigwig new file mode 100644 index 00000000..e6e108c8 Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicExportData/MB-E10-5_chr1_genes_Eya1.bigwig differ diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/MB-E10-5_chr1_genes_Eya1_significant.txt b/hicexplorer/test/test_data/cHi-C/chicExportData/MB-E10-5_chr1_genes_Eya1_significant.txt new file mode 100644 index 00000000..48ccfcfb --- /dev/null +++ b/hicexplorer/test/test_data/cHi-C/chicExportData/MB-E10-5_chr1_genes_Eya1_significant.txt @@ -0,0 +1,6 @@ +# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw +chr1 14295000 14298000 Eya1 832.000000000000 -3000 0.059855769231 0.058592411666 4.790153125993 49.800000000000 +chr1 14426000 14432000 Eya1 832.000000000000 130000 0.010817307692 0.000000429856 13.723515822111 9.000000000000 +chr1 14447000 14455000 Eya1 832.000000000000 149000 0.014903846154 0.000000000000 22.364938939273 12.400000000000 +chr1 14460000 14465000 Eya1 832.000000000000 162000 0.009134615385 0.000004098864 12.153660299090 7.600000000000 +chr1 14491000 14501000 Eya1 832.000000000000 200000 0.022536057692 0.000000000000 41.397571634330 18.750000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicExportData/aggregate_all.tar.gz b/hicexplorer/test/test_data/cHi-C/chicExportData/aggregate_all.tar.gz new file mode 100644 index 00000000..f403ac11 Binary files 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a/hicexplorer/test/test_data/cHi-C/chicPlotViewpoint/two_viewpoint_background_significant.png and /dev/null differ diff --git a/hicexplorer/test/test_data/cHi-C/chicPlotViewpoint/two_viewpoint_pdf.png b/hicexplorer/test/test_data/cHi-C/chicPlotViewpoint/two_viewpoint_pdf.png deleted file mode 100644 index c4d475b9..00000000 Binary files a/hicexplorer/test/test_data/cHi-C/chicPlotViewpoint/two_viewpoint_pdf.png and /dev/null differ diff --git a/hicexplorer/test/test_data/cHi-C/chicPlotViewpoint/two_viewpoint_pvalue.png b/hicexplorer/test/test_data/cHi-C/chicPlotViewpoint/two_viewpoint_pvalue.png deleted file mode 100644 index aae5fba1..00000000 Binary files a/hicexplorer/test/test_data/cHi-C/chicPlotViewpoint/two_viewpoint_pvalue.png and /dev/null differ diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt deleted file mode 100644 index 97df7c97..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt +++ /dev/null @@ -1,8 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.00703769867936687721 7.81112575817000021061 5.59999999999999964473 -chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864070004 3.78135593591500018817 39.00000000000000000000 -chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.04850785315391703545 3.19033393500999995496 10.19999999999999928946 -chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.03491443188205700654 3.51709033858399999772 9.80000000000000071054 -chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000001048074382837 19.28508294646199772160 7.59999999999999875655 -chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000000011102 56.96782483342801128856 20.64999999999999857891 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt deleted file mode 100644 index 85692c87..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt +++ /dev/null @@ -1,8 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1 -# /tmp/output_target_8dty7wuh/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed -# Mode: x-fold background with 1.5 -# Used p-value: 0.2 -# -chr1 14274000 14278000 -chr1 14296000 14298000 -chr1 14314000 14319000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt deleted file mode 100644 index b9113b59..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt +++ /dev/null @@ -1,8 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00284160000885902431 9.15400589712000112286 7.00000000000000000000 -chr1 14295000 14372000 Eya1 673.0 -1000 0.73997028231099992723 0.00004780944416038491 71.55022378473699973256 497.99999999999977262632 -chr1 14391000 14404000 Eya1 673.0 99000 0.01485884100899999803 0.00001657170147506548 12.71460890380599906280 10.00000000000000000000 -chr1 14405000 14431000 Eya1 673.0 126000 0.01485884100399999762 0.00000000021609136702 16.50018487636599928692 10.00000000000000532907 -chr1 14447000 14465000 Eya1 673.0 150000 0.01485884100799999760 0.00000000084501772246 20.98645213257099939597 10.00000000000000177636 -chr1 14476000 14501000 Eya1 673.0 200000 0.04494799405200000653 0.00000000000000011102 81.22289233532099217427 30.24999999999999644729 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt deleted file mode 100644 index cb9804d7..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt +++ /dev/null @@ -1,10 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev -# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed -# Mode: loose p-value with 0.5 -# Used p-value: 0.2 -# -chr1 14274000 14279000 -chr1 14285000 14308000 -chr1 14310000 14322000 -chr1 14361000 14395000 -chr1 14491000 14500000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt deleted file mode 100644 index 97df7c97..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt +++ /dev/null @@ -1,8 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.00703769867936687721 7.81112575817000021061 5.59999999999999964473 -chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864070004 3.78135593591500018817 39.00000000000000000000 -chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.04850785315391703545 3.19033393500999995496 10.19999999999999928946 -chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.03491443188205700654 3.51709033858399999772 9.80000000000000071054 -chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000001048074382837 19.28508294646199772160 7.59999999999999875655 -chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000000011102 56.96782483342801128856 20.64999999999999857891 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt deleted file mode 100644 index e10ebebe..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt +++ /dev/null @@ -1,7 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 14295000 14298000 Eya1 832.0 -3000 0.05985576923100000002 0.05859241166597439765 4.79015312599299925012 49.79999999999999715783 -chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602988210 13.72351582211000042832 9.00000000000000000000 -chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000003774758 22.36493893927400122834 12.39999999999999857891 -chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00000409886448993202 12.15366029908999934150 7.59999999999999964473 -chr1 14491000 14501000 Eya1 832.0 200000 0.02253605769199999720 0.00000000000000011102 41.39757163433100117800 18.75000000000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt deleted file mode 100644 index 6c4d34ec..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt +++ /dev/null @@ -1,8 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1 -# /tmp/output_target_dodw19_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed -# Mode: x-fold background with 1.5 -# Used p-value: 0.2 -# -chr1 14274000 14278000 -chr1 14296000 14298000 -chr1 14314000 14319000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt deleted file mode 100644 index d01b8016..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt +++ /dev/null @@ -1,6 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1 -# /tmp/output_target_dodw19_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed -# Mode: x-fold background with 1.5 -# Used p-value: 0.2 -# -chr1 14295000 14298000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt deleted file mode 100644 index 97df7c97..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt +++ /dev/null @@ -1,8 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.00703769867936687721 7.81112575817000021061 5.59999999999999964473 -chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864070004 3.78135593591500018817 39.00000000000000000000 -chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.04850785315391703545 3.19033393500999995496 10.19999999999999928946 -chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.03491443188205700654 3.51709033858399999772 9.80000000000000071054 -chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000001048074382837 19.28508294646199772160 7.59999999999999875655 -chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000000011102 56.96782483342801128856 20.64999999999999857891 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt deleted file mode 100644 index 175f1573..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt +++ /dev/null @@ -1,10 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 19089000 19091000 Tfap2d 472.0 -3000 0.06101694915199999680 0.18037846472445218104 4.06818820852600016025 28.80000000000000071054 -chr1 19104000 19106000 Tfap2d 472.0 11000 0.02245762711799999950 0.10196541156059013566 3.62722049649999966903 10.59999999999999964473 -chr1 19109000 19114000 Tfap2d 472.0 18000 0.03940677966200000631 0.00062015947456495191 9.61739201792699915927 18.60000000000000142109 -chr1 19125000 19129000 Tfap2d 472.0 33000 0.01652542372999999884 0.00444026967424504537 7.28507499155399962376 7.79999999999999982236 -chr1 19133000 19138000 Tfap2d 472.0 41000 0.01949152542399999744 0.00034288349714106658 9.72184228688099949522 9.19999999999999928946 -chr1 19197000 19202000 Tfap2d 472.0 108000 0.01059322033899999863 0.00398884532051024809 10.24326734149200035517 5.00000000000000000000 -chr1 19227000 19233000 Tfap2d 472.0 137000 0.01186440677899999914 0.00127166209953588627 14.41899403645599875290 5.59999999999999964473 -chr1 19254000 19261000 Tfap2d 472.0 163000 0.01355932203300000069 0.00002168738798669079 19.68794216164500454624 6.39999999999999946709 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt deleted file mode 100644 index 40c9ccf9..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt +++ /dev/null @@ -1,8 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 4509000 4515000 Sox17 810.0 23000 0.03432098765399999724 0.00000105351171875157 11.55191083898800030738 27.80000000000000071054 -chr1 4561000 4567000 Sox17 810.0 75000 0.01432098765400000029 0.00000044101966734100 11.23656007944399881637 11.59999999999999964473 -chr1 4585000 4590000 Sox17 810.0 98000 0.00987654320999999807 0.00037019878415900376 8.98479195802099894763 8.00000000000000000000 -chr1 4652000 4658000 Sox17 810.0 169000 0.00740740740700000008 0.00005538687174377888 11.12107213938599947767 6.00000000000000000000 -chr1 4499000 4500000 Sox17 810.0 12000 0.00987654320999999981 0.15859163588059255190 1.65903762227799989049 8.00000000000000000000 -chr1 4501000 4502000 Sox17 810.0 14000 0.00765432098799999957 0.16880410287101188516 1.57677828943600006895 6.20000000000000017764 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt deleted file mode 100644 index 5fd7539a..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt +++ /dev/null @@ -1,3 +0,0 @@ -FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt -FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt -FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt deleted file mode 100644 index 3477ec07..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt +++ /dev/null @@ -1,8 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1 -# /tmp/output_target_83sqy1lg/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed -# Mode: x-fold background with 1.5 -# Used p-value: 0.2 -# -chr1 14274000 14278000 -chr1 14296000 14298000 -chr1 14314000 14319000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt deleted file mode 100644 index 9dbdf330..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt +++ /dev/null @@ -1,11 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1 -# /tmp/output_target_83sqy1lg/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed -# Mode: x-fold background with 1.5 -# Used p-value: 0.2 -# -chr1 19089000 19091000 -chr1 19097000 19098000 -chr1 19104000 19106000 -chr1 19109000 19114000 -chr1 19125000 19129000 -chr1 19227000 19233000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.txt deleted file mode 100644 index 2d3d2465..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.txt +++ /dev/null @@ -1,9 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3.1 -# /tmp/output_target_83sqy1lg/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed -# Mode: x-fold background with 1.5 -# Used p-value: 0.2 -# -chr1 4484000 4485000 -chr1 4499000 4502000 -chr1 4509000 4515000 -chr1 4585000 4590000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target_list.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target_list.txt deleted file mode 100644 index a5c93b6c..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_4_target_list.txt +++ /dev/null @@ -1,3 +0,0 @@ -FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.txt -FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt -FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt deleted file mode 100644 index b9113b59..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt +++ /dev/null @@ -1,8 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00284160000885902431 9.15400589712000112286 7.00000000000000000000 -chr1 14295000 14372000 Eya1 673.0 -1000 0.73997028231099992723 0.00004780944416038491 71.55022378473699973256 497.99999999999977262632 -chr1 14391000 14404000 Eya1 673.0 99000 0.01485884100899999803 0.00001657170147506548 12.71460890380599906280 10.00000000000000000000 -chr1 14405000 14431000 Eya1 673.0 126000 0.01485884100399999762 0.00000000021609136702 16.50018487636599928692 10.00000000000000532907 -chr1 14447000 14465000 Eya1 673.0 150000 0.01485884100799999760 0.00000000084501772246 20.98645213257099939597 10.00000000000000177636 -chr1 14476000 14501000 Eya1 673.0 200000 0.04494799405200000653 0.00000000000000011102 81.22289233532099217427 30.24999999999999644729 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt deleted file mode 100644 index 8d872b69..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt +++ /dev/null @@ -1,10 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 19088000 19093000 Tfap2d 472.0 -1000 0.25550847457600001089 0.11635169910476195199 8.11832748109999968733 120.59999999999999431566 -chr1 19094000 19118000 Tfap2d 472.0 1000 0.38686440678100009194 0.03474409585293225522 32.83428528261499934615 182.60000000000005115908 -chr1 19124000 19141000 Tfap2d 472.0 33000 0.04661016949300000184 0.00000002462477854959 22.39995010446000023308 22.00000000000000000000 -chr1 19143000 19150000 Tfap2d 472.0 52000 0.01059322034000000079 0.01821075341789391011 7.00310519245599927274 5.00000000000000000000 -chr1 19153000 19185000 Tfap2d 472.0 65000 0.03177966102100000800 0.00000000020590662508 24.96572554191800108470 14.99999999999999467093 -chr1 19186000 19210000 Tfap2d 472.0 108000 0.03177966101800000498 0.00000007308534966111 29.45424687062300250773 15.00000000000000000000 -chr1 19215000 19251000 Tfap2d 472.0 137000 0.04237288135900001140 0.00000000012967626972 56.40252329690899557590 19.99999999999999644729 -chr1 19252000 19264000 Tfap2d 472.0 163000 0.01694915254200000249 0.00000130986798663191 24.34766306781100198009 8.00000000000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt deleted file mode 100644 index 25a1964d..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt +++ /dev/null @@ -1,9 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 4480000 4518000 Sox17 810.0 0 0.76049382715799984656 0.00000000602330973987 45.61581246979399395514 616.00000000000011368684 -chr1 4520000 4549000 Sox17 810.0 44000 0.02962962962900000247 0.00000000000001332268 17.03851209048299963911 24.00000000000000710543 -chr1 4557000 4578000 Sox17 810.0 75000 0.02592592592600001522 0.00000000000051858517 20.41795056780900097237 21.00000000000000355271 -chr1 4582000 4590000 Sox17 810.0 98000 0.01111111110999999860 0.00013740149648666655 9.96981855628800062163 9.00000000000000000000 -chr1 4592000 4634000 Sox17 810.0 116000 0.02839506171900002887 0.00000000000000011102 32.07927393785299585716 22.99999999999999289457 -chr1 4641000 4670000 Sox17 810.0 169000 0.01604938270900000546 0.00000000034415081895 23.33313824700799798961 12.99999999999999644729 -chr1 4671000 4688000 Sox17 810.0 191000 0.00763374485400000052 0.00000023615040700697 14.23725687309200438335 6.18333333333300050327 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt deleted file mode 100644 index 040294b3..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt +++ /dev/null @@ -1,5 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 14290000 14439000 Eya1 832.0 -1000 0.77524038462200028921 0.00000214655292485322 124.40376311550902244107 645.00000000000000000000 -chr1 14444000 14467000 Eya1 832.0 149000 0.03004807692100000191 0.00000000000000011102 43.43355247431500032462 25.00000000000000000000 -chr1 14484000 14501000 Eya1 832.0 200000 0.02902644230799999656 0.00000000000000011102 53.10190206687700253951 24.15000000000000213163 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt deleted file mode 100644 index c358c001..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt +++ /dev/null @@ -1,6 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 19077000 19083000 Tfap2d 800.0 -15000 0.01875000000000000278 0.00087756598335464453 9.05078678760400023862 15.00000000000000000000 -chr1 19084000 19118000 Tfap2d 800.0 0 0.64874999999999971578 0.00000017949046560162 44.36507725070399033029 518.99999999999988631316 -chr1 19120000 19249000 Tfap2d 800.0 105000 0.25625000000000008882 0.00000000000000011102 244.06286621622496113559 204.99999999999994315658 -chr1 19258000 19274000 Tfap2d 800.0 169000 0.01000000000000000021 0.00000195299526528636 14.62211731845800244400 8.00000000000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt deleted file mode 100644 index 098160b8..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt +++ /dev/null @@ -1,8 +0,0 @@ -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target -chr1 4480000 4549000 Sox17 978.0 0 0.81595092025199977837 0.00000000000956168478 62.24249077437998067808 797.99999999999988631316 -chr1 4555000 4575000 Sox17 978.0 78000 0.02147239264300000727 0.00000000000005484502 17.04008783523400438753 21.00000000000000000000 -chr1 4577000 4591000 Sox17 978.0 93000 0.00715746421499999924 0.00023632212134716557 6.23881980673299985085 6.99999999999999911182 -chr1 4599000 4632000 Sox17 978.0 128000 0.01738241309700000112 0.00000000000000011102 20.66516512408400174650 16.99999999999999289457 -chr1 4634000 4662000 Sox17 978.0 169000 0.01635991820800000371 0.00000000000171385128 23.27331220218900398322 15.99999999999999644729 -chr1 4663000 4688000 Sox17 978.0 200000 0.02242672120499999977 0.00000000000000011102 39.41625174041998747043 21.93333333333300316781 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt deleted file mode 100644 index 8202840b..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt +++ /dev/null @@ -1,6 +0,0 @@ -FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt -MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt -FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt -MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt -FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt -MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt deleted file mode 100644 index 0054fe74..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt +++ /dev/null @@ -1,9 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3-dev -# /tmp/output_target_yw5bwpmm/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt -# Mode: loose p-value with 0.5 -# Used p-value: 0.2 -# -chr1 14274000 14279000 -chr1 14290000 14439000 -chr1 14444000 14467000 -chr1 14476000 14501000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt deleted file mode 100644 index f3cfd652..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt +++ /dev/null @@ -1,7 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3-dev -# /tmp/output_target_yw5bwpmm/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt -# Mode: loose p-value with 0.5 -# Used p-value: 0.2 -# -chr1 19077000 19118000 -chr1 19120000 19274000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt deleted file mode 100644 index 1e39785c..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt +++ /dev/null @@ -1,7 +0,0 @@ -# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3-dev -# /tmp/output_target_yw5bwpmm/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt -# Mode: loose p-value with 0.5 -# Used p-value: 0.2 -# -chr1 4480000 4549000 -chr1 4555000 4688000 diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target_list.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target_list.txt deleted file mode 100644 index 376cf264..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target_list.txt +++ /dev/null @@ -1,3 +0,0 @@ -FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt -FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt -FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target_regions.txt b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target_regions.txt deleted file mode 100644 index 6b510fc2..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/output_5_target_regions.txt +++ /dev/null @@ -1,8 +0,0 @@ -chr1 4480000 4549000 -chr1 4555000 4688000 -chr1 14274000 14279000 -chr1 14290000 14439000 -chr1 14444000 14467000 -chr1 14476000 14501000 -chr1 19077000 19118000 -chr1 19120000 19274000 \ No newline at end of file diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 new file mode 100644 index 00000000..3ff3d1fa Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 differ diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 new file mode 100644 index 00000000..722e65d6 Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 differ diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 new file mode 100644 index 00000000..9ef1ca90 Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 differ diff --git a/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 new file mode 100644 index 00000000..68dc3ce2 Binary files /dev/null and b/hicexplorer/test/test_data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 differ diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt deleted file mode 100644 index f6af4efe..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 14100000 14101000 Eya1 673.0 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14101000 14102000 Eya1 673.0 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14102000 14103000 Eya1 673.0 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14103000 14104000 Eya1 673.0 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14104000 14105000 Eya1 673.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14105000 14106000 Eya1 673.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14106000 14107000 Eya1 673.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14107000 14108000 Eya1 673.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14108000 14109000 Eya1 673.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14109000 14110000 Eya1 673.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14110000 14111000 Eya1 673.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14111000 14112000 Eya1 673.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14112000 14113000 Eya1 673.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14113000 14114000 Eya1 673.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14114000 14115000 Eya1 673.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14115000 14116000 Eya1 673.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14116000 14117000 Eya1 673.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14117000 14118000 Eya1 673.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14118000 14119000 Eya1 673.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14119000 14120000 Eya1 673.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14120000 14121000 Eya1 673.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14121000 14122000 Eya1 673.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14122000 14123000 Eya1 673.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14123000 14124000 Eya1 673.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14124000 14125000 Eya1 673.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14125000 14126000 Eya1 673.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14126000 14127000 Eya1 673.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14127000 14128000 Eya1 673.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14128000 14129000 Eya1 673.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14129000 14130000 Eya1 673.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14130000 14131000 Eya1 673.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14131000 14132000 Eya1 673.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14132000 14133000 Eya1 673.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14133000 14134000 Eya1 673.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14134000 14135000 Eya1 673.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14135000 14136000 Eya1 673.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14136000 14137000 Eya1 673.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14137000 14138000 Eya1 673.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14138000 14139000 Eya1 673.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14139000 14140000 Eya1 673.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14140000 14141000 Eya1 673.0 -160000 0.000891530461 0.012107544045 4.242405017910 0.600000000000 -chr1 14141000 14142000 Eya1 673.0 -159000 0.000891530461 0.012107544045 4.789812097144 0.600000000000 -chr1 14142000 14143000 Eya1 673.0 -158000 0.000891530461 0.012107544045 4.303889149198 0.600000000000 -chr1 14143000 14144000 Eya1 673.0 -157000 0.000891530461 0.012107544045 4.367181637306 0.600000000000 -chr1 14144000 14145000 Eya1 673.0 -156000 0.000891530461 0.012107544045 5.120143967809 0.600000000000 -chr1 14145000 14146000 Eya1 673.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14146000 14147000 Eya1 673.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14147000 14148000 Eya1 673.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14148000 14149000 Eya1 673.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14149000 14150000 Eya1 673.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14150000 14151000 Eya1 673.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14151000 14152000 Eya1 673.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14152000 14153000 Eya1 673.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14153000 14154000 Eya1 673.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14154000 14155000 Eya1 673.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14155000 14156000 Eya1 673.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14156000 14157000 Eya1 673.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14157000 14158000 Eya1 673.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14158000 14159000 Eya1 673.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14159000 14160000 Eya1 673.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14160000 14161000 Eya1 673.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14161000 14162000 Eya1 673.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14162000 14163000 Eya1 673.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14163000 14164000 Eya1 673.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14164000 14165000 Eya1 673.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14165000 14166000 Eya1 673.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14166000 14167000 Eya1 673.0 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14167000 14168000 Eya1 673.0 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14168000 14169000 Eya1 673.0 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14169000 14170000 Eya1 673.0 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14170000 14171000 Eya1 673.0 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14171000 14172000 Eya1 673.0 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14172000 14173000 Eya1 673.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14173000 14174000 Eya1 673.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14174000 14175000 Eya1 673.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14175000 14176000 Eya1 673.0 -125000 0.000297176820 0.042850447268 0.916568982282 0.200000000000 -chr1 14176000 14177000 Eya1 673.0 -124000 0.000297176820 0.042850447268 0.908160092485 0.200000000000 -chr1 14177000 14178000 Eya1 673.0 -123000 0.000297176820 0.042850447268 0.798302018335 0.200000000000 -chr1 14178000 14179000 Eya1 673.0 -122000 0.000297176820 0.042850447268 0.925135047590 0.200000000000 -chr1 14179000 14180000 Eya1 673.0 -121000 0.000297176820 0.042850447268 0.883834378206 0.200000000000 -chr1 14180000 14181000 Eya1 673.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14181000 14182000 Eya1 673.0 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14182000 14183000 Eya1 673.0 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14183000 14184000 Eya1 673.0 -117000 0.000297176820 0.042850447268 0.860777829009 0.200000000000 -chr1 14184000 14185000 Eya1 673.0 -116000 0.000297176820 0.042850447268 0.791915602137 0.200000000000 -chr1 14185000 14186000 Eya1 673.0 -115000 0.000297176820 0.042850447268 0.761457309513 0.200000000000 -chr1 14186000 14187000 Eya1 673.0 -114000 0.000297176820 0.042850447268 0.811388936776 0.200000000000 -chr1 14187000 14188000 Eya1 673.0 -113000 0.000297176820 0.042850447268 0.891796850153 0.200000000000 -chr1 14188000 14189000 Eya1 673.0 -112000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14189000 14190000 Eya1 673.0 -111000 0.000297176820 0.042850447268 1.064402690160 0.200000000000 -chr1 14190000 14191000 Eya1 673.0 -110000 0.000297176820 0.042850447268 1.207188418049 0.200000000000 -chr1 14191000 14192000 Eya1 673.0 -109000 0.000297176820 0.042850447268 1.010096430089 0.200000000000 -chr1 14192000 14193000 Eya1 673.0 -108000 0.000297176820 0.042850447268 0.951821635672 0.200000000000 -chr1 14193000 14194000 Eya1 673.0 -107000 0.000297176820 0.042850447268 0.824912085835 0.200000000000 -chr1 14194000 14195000 Eya1 673.0 -106000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14195000 14196000 Eya1 673.0 -105000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14196000 14197000 Eya1 673.0 -104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14197000 14198000 Eya1 673.0 -103000 0.001188707281 0.006261619191 5.424079472832 0.800000000000 -chr1 14198000 14199000 Eya1 673.0 -102000 0.001188707281 0.006261619191 5.499413910652 0.800000000000 -chr1 14199000 14200000 Eya1 673.0 -101000 0.001188707281 0.006261619191 5.822908849742 0.800000000000 -chr1 14200000 14201000 Eya1 673.0 -100000 0.001188707281 0.006261619191 4.888367915554 0.800000000000 -chr1 14201000 14202000 Eya1 673.0 -99000 0.001188707281 0.006261619191 4.499520464782 0.800000000000 -chr1 14202000 14203000 Eya1 673.0 -98000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14203000 14204000 Eya1 673.0 -97000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14204000 14205000 Eya1 673.0 -96000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14205000 14206000 Eya1 673.0 -95000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14206000 14207000 Eya1 673.0 -94000 0.000594353640 0.023000625561 1.546710160135 0.400000000000 -chr1 14207000 14208000 Eya1 673.0 -93000 0.000594353640 0.023000625561 1.488563161197 0.400000000000 -chr1 14208000 14209000 Eya1 673.0 -92000 0.000594353640 0.023000625561 1.093806079608 0.400000000000 -chr1 14209000 14210000 Eya1 673.0 -91000 0.000594353640 0.023000625561 1.031140105862 0.400000000000 -chr1 14210000 14211000 Eya1 673.0 -90000 0.000594353640 0.023000625561 1.020509795419 0.400000000000 -chr1 14211000 14212000 Eya1 673.0 -89000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14212000 14213000 Eya1 673.0 -88000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14213000 14214000 Eya1 673.0 -87000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14214000 14215000 Eya1 673.0 -86000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14215000 14216000 Eya1 673.0 -85000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14216000 14217000 Eya1 673.0 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14217000 14218000 Eya1 673.0 -83000 0.000594353640 0.023000625561 1.466510373460 0.400000000000 -chr1 14218000 14219000 Eya1 673.0 -82000 0.000594353640 0.023000625561 1.546710160135 0.400000000000 -chr1 14219000 14220000 Eya1 673.0 -81000 0.000594353640 0.023000625561 1.816320184969 0.400000000000 -chr1 14220000 14221000 Eya1 673.0 -80000 0.000594353640 0.023000625561 2.106158514412 0.400000000000 -chr1 14221000 14222000 Eya1 673.0 -79000 0.000594353640 0.023000625561 1.885513335312 0.400000000000 -chr1 14222000 14223000 Eya1 673.0 -78000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14223000 14224000 Eya1 673.0 -77000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14224000 14225000 Eya1 673.0 -76000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14225000 14226000 Eya1 673.0 -75000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14226000 14227000 Eya1 673.0 -74000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14227000 14228000 Eya1 673.0 -73000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14228000 14229000 Eya1 673.0 -72000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14229000 14230000 Eya1 673.0 -71000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14230000 14231000 Eya1 673.0 -70000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14231000 14232000 Eya1 673.0 -69000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14232000 14233000 Eya1 673.0 -68000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14233000 14234000 Eya1 673.0 -67000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14234000 14235000 Eya1 673.0 -66000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14235000 14236000 Eya1 673.0 -65000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14236000 14237000 Eya1 673.0 -64000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14237000 14238000 Eya1 673.0 -63000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14238000 14239000 Eya1 673.0 -62000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14239000 14240000 Eya1 673.0 -61000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14240000 14241000 Eya1 673.0 -60000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14241000 14242000 Eya1 673.0 -59000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14242000 14243000 Eya1 673.0 -58000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14243000 14244000 Eya1 673.0 -57000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14244000 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14451000 Eya1 673.0 150000 0.001188707281 0.000000000000 1.721555655524 0.800000000000 -chr1 14451000 14452000 Eya1 673.0 151000 0.001188707281 0.000000000000 1.816320187745 0.800000000000 -chr1 14452000 14453000 Eya1 673.0 152000 0.000594353640 0.000000000000 0.879906224076 0.400000000000 -chr1 14453000 14454000 Eya1 673.0 153000 0.000594353640 0.000000000000 0.887797759777 0.400000000000 -chr1 14454000 14455000 Eya1 673.0 154000 0.000891530461 0.000000000000 1.356019866146 0.600000000000 -chr1 14455000 14456000 Eya1 673.0 155000 0.000594353640 0.000000000000 0.876012833675 0.400000000000 -chr1 14456000 14457000 Eya1 673.0 156000 0.000594353640 0.000000000000 0.876012833675 0.400000000000 -chr1 14457000 14458000 Eya1 673.0 157000 0.000594353640 0.000000000000 0.821489212945 0.400000000000 -chr1 14458000 14459000 Eya1 673.0 158000 0.001188707281 0.000000000000 1.583831204275 0.800000000000 -chr1 14459000 14460000 Eya1 673.0 159000 0.000594353640 0.000000000000 0.770345916308 0.400000000000 -chr1 14460000 14461000 Eya1 673.0 160000 0.001188707281 0.000000000000 1.517079697070 0.800000000000 -chr1 14461000 14462000 Eya1 673.0 161000 0.001188707281 0.000000000000 1.429450544260 0.800000000000 -chr1 14462000 14463000 Eya1 673.0 162000 0.001188707281 0.000000000000 1.616154290340 0.800000000000 -chr1 14463000 14464000 Eya1 673.0 163000 0.000594353640 0.000000000000 0.821489212945 0.400000000000 -chr1 14464000 14465000 Eya1 673.0 164000 0.000594353640 0.000000000000 0.857051516792 0.400000000000 -chr1 14465000 14466000 Eya1 673.0 165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14466000 14467000 Eya1 673.0 166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14467000 14468000 Eya1 673.0 167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14468000 14469000 Eya1 673.0 168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14469000 14470000 Eya1 673.0 169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14470000 14471000 Eya1 673.0 170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14471000 14472000 Eya1 673.0 171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14472000 14473000 Eya1 673.0 172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14473000 14474000 Eya1 673.0 173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14474000 14475000 Eya1 673.0 174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14475000 14476000 Eya1 673.0 175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14476000 14477000 Eya1 673.0 176000 0.000297176820 0.000000000000 0.421231702882 0.200000000000 -chr1 14477000 14478000 Eya1 673.0 177000 0.000297176820 0.000000000000 0.449952046478 0.200000000000 -chr1 14478000 14479000 Eya1 673.0 178000 0.000594353640 0.000000000000 0.933862738240 0.400000000000 -chr1 14479000 14480000 Eya1 673.0 179000 0.000594353640 0.000000000000 0.951821637197 0.400000000000 -chr1 14480000 14481000 Eya1 673.0 180000 0.001485884101 0.000000000000 2.512422592521 1.000000000000 -chr1 14481000 14482000 Eya1 673.0 181000 0.001188707281 0.000000000000 2.020192860178 0.800000000000 -chr1 14482000 14483000 Eya1 673.0 182000 0.001188707281 0.000000000000 2.128805380321 0.800000000000 -chr1 14483000 14484000 Eya1 673.0 183000 0.001783060921 0.000000000000 3.093420317586 1.200000000000 -chr1 14484000 14485000 Eya1 673.0 184000 0.002080237741 0.000000000000 3.380127570538 1.400000000000 -chr1 14485000 14486000 Eya1 673.0 185000 0.001188707281 0.000000000000 1.903643274393 0.800000000000 -chr1 14486000 14487000 Eya1 673.0 186000 0.001188707281 0.000000000000 2.106158514412 0.800000000000 -chr1 14487000 14488000 Eya1 673.0 187000 0.001188707281 0.000000000000 2.140312436513 0.800000000000 -chr1 14488000 14489000 Eya1 673.0 188000 0.000594353640 0.000000000000 1.058710697124 0.400000000000 -chr1 14489000 14490000 Eya1 673.0 189000 0.000297176820 0.000000000000 0.575520059550 0.200000000000 -chr1 14490000 14491000 Eya1 673.0 190000 0.000297176820 0.000000000000 0.578885673960 0.200000000000 -chr1 14491000 14492000 Eya1 673.0 191000 0.002080237741 0.000000000000 3.849589730333 1.400000000000 -chr1 14492000 14493000 Eya1 673.0 192000 0.003268945022 0.000000000000 5.982878858272 2.200000000000 -chr1 14493000 14494000 Eya1 673.0 193000 0.002971768202 0.000000000000 5.892229182196 2.000000000000 -chr1 14494000 14495000 Eya1 673.0 194000 0.003268945022 0.000000000000 6.294126893758 2.200000000000 -chr1 14495000 14496000 Eya1 673.0 195000 0.003268945022 0.000000000000 6.680269651133 2.200000000000 -chr1 14496000 14497000 Eya1 673.0 196000 0.002971768202 0.000000000000 6.072972410121 2.000000000000 -chr1 14497000 14498000 Eya1 673.0 197000 0.002080237741 0.000000000000 3.937080406684 1.400000000000 -chr1 14498000 14499000 Eya1 673.0 198000 0.002971768202 0.000000000000 4.852424033528 2.000000000000 -chr1 14499000 14500000 Eya1 673.0 199000 0.003343239227 0.000000000000 5.830530441735 2.250000000000 -chr1 14500000 14501000 Eya1 673.0 200000 0.004457652303 0.000000000000 7.575723225668 3.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt deleted file mode 100644 index fbac2858..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 18893000 18894000 Tfap2d 472.0 -200000 0.001412429379 0.009736859396 8.554173074049 0.666666666667 -chr1 18894000 18895000 Tfap2d 472.0 -199000 0.001059322034 0.016726462474 5.040852007510 0.500000000000 -chr1 18895000 18896000 Tfap2d 472.0 -198000 0.000847457627 0.023000625561 3.282415254892 0.400000000000 -chr1 18896000 18897000 Tfap2d 472.0 -197000 0.000847457627 0.023000625561 3.136530131373 0.400000000000 -chr1 18897000 18898000 Tfap2d 472.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18898000 18899000 Tfap2d 472.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18899000 18900000 Tfap2d 472.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18900000 18901000 Tfap2d 472.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18901000 18902000 Tfap2d 472.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18902000 18903000 Tfap2d 472.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18903000 18904000 Tfap2d 472.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18904000 18905000 Tfap2d 472.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18905000 18906000 Tfap2d 472.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18906000 18907000 Tfap2d 472.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18907000 18908000 Tfap2d 472.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18908000 18909000 Tfap2d 472.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18909000 18910000 Tfap2d 472.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18910000 18911000 Tfap2d 472.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18911000 18912000 Tfap2d 472.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18912000 18913000 Tfap2d 472.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18913000 18914000 Tfap2d 472.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18914000 18915000 Tfap2d 472.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18915000 18916000 Tfap2d 472.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18916000 18917000 Tfap2d 472.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18917000 18918000 Tfap2d 472.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18918000 18919000 Tfap2d 472.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18919000 18920000 Tfap2d 472.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18920000 18921000 Tfap2d 472.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18921000 18922000 Tfap2d 472.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18922000 18923000 Tfap2d 472.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18923000 18924000 Tfap2d 472.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18924000 18925000 Tfap2d 472.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18925000 18926000 Tfap2d 472.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18926000 18927000 Tfap2d 472.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18927000 18928000 Tfap2d 472.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18928000 18929000 Tfap2d 472.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18929000 18930000 Tfap2d 472.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18930000 18931000 Tfap2d 472.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18931000 18932000 Tfap2d 472.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18932000 18933000 Tfap2d 472.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18933000 18934000 Tfap2d 472.0 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18934000 18935000 Tfap2d 472.0 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18935000 18936000 Tfap2d 472.0 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18936000 18937000 Tfap2d 472.0 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18937000 18938000 Tfap2d 472.0 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18938000 18939000 Tfap2d 472.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18939000 18940000 Tfap2d 472.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18940000 18941000 Tfap2d 472.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18941000 18942000 Tfap2d 472.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18942000 18943000 Tfap2d 472.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18943000 18944000 Tfap2d 472.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18944000 18945000 Tfap2d 472.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18945000 18946000 Tfap2d 472.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18946000 18947000 Tfap2d 472.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18947000 18948000 Tfap2d 472.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18948000 18949000 Tfap2d 472.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18949000 18950000 Tfap2d 472.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18950000 18951000 Tfap2d 472.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18951000 18952000 Tfap2d 472.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18952000 18953000 Tfap2d 472.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18953000 18954000 Tfap2d 472.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18954000 18955000 Tfap2d 472.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18955000 18956000 Tfap2d 472.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18956000 18957000 Tfap2d 472.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18957000 18958000 Tfap2d 472.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18958000 18959000 Tfap2d 472.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18959000 18960000 Tfap2d 472.0 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18960000 18961000 Tfap2d 472.0 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18961000 18962000 Tfap2d 472.0 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18962000 18963000 Tfap2d 472.0 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18963000 18964000 Tfap2d 472.0 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18964000 18965000 Tfap2d 472.0 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18965000 18966000 Tfap2d 472.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18966000 18967000 Tfap2d 472.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18967000 18968000 Tfap2d 472.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18968000 18969000 Tfap2d 472.0 -125000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18969000 18970000 Tfap2d 472.0 -124000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18970000 18971000 Tfap2d 472.0 -123000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18971000 18972000 Tfap2d 472.0 -122000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18972000 18973000 Tfap2d 472.0 -121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18973000 18974000 Tfap2d 472.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18974000 18975000 Tfap2d 472.0 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18975000 18976000 Tfap2d 472.0 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18976000 18977000 Tfap2d 472.0 -117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18977000 18978000 Tfap2d 472.0 -116000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18978000 18979000 Tfap2d 472.0 -115000 0.001271186441 0.012107544045 3.257165906583 0.600000000000 -chr1 18979000 18980000 Tfap2d 472.0 -114000 0.001271186441 0.012107544045 3.470750557945 0.600000000000 -chr1 18980000 18981000 Tfap2d 472.0 -113000 0.001271186441 0.012107544045 3.814698814531 0.600000000000 -chr1 18981000 18982000 Tfap2d 472.0 -112000 0.001271186441 0.012107544045 4.602517039860 0.600000000000 -chr1 18982000 18983000 Tfap2d 472.0 -111000 0.001271186441 0.012107544045 4.553027608970 0.600000000000 -chr1 18983000 18984000 Tfap2d 472.0 -110000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18984000 18985000 Tfap2d 472.0 -109000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18985000 18986000 Tfap2d 472.0 -108000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18986000 18987000 Tfap2d 472.0 -107000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18987000 18988000 Tfap2d 472.0 -106000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18988000 18989000 Tfap2d 472.0 -105000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18989000 18990000 Tfap2d 472.0 -104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18990000 18991000 Tfap2d 472.0 -103000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18991000 18992000 Tfap2d 472.0 -102000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18992000 18993000 Tfap2d 472.0 -101000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18993000 18994000 Tfap2d 472.0 -100000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18994000 18995000 Tfap2d 472.0 -99000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18995000 18996000 Tfap2d 472.0 -98000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18996000 18997000 Tfap2d 472.0 -97000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18997000 18998000 Tfap2d 472.0 -96000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18998000 18999000 Tfap2d 472.0 -95000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18999000 19000000 Tfap2d 472.0 -94000 0.000423728814 0.042850447268 1.102686374757 0.200000000000 -chr1 19000000 19001000 Tfap2d 472.0 -93000 0.000423728814 0.042850447268 1.061231999455 0.200000000000 -chr1 19001000 19002000 Tfap2d 472.0 -92000 0.000423728814 0.042850447268 0.779800308873 0.200000000000 -chr1 19002000 19003000 Tfap2d 472.0 -91000 0.000423728814 0.042850447268 0.735124249200 0.200000000000 -chr1 19003000 19004000 Tfap2d 472.0 -90000 0.000423728814 0.042850447268 0.727545648641 0.200000000000 -chr1 19004000 19005000 Tfap2d 472.0 -89000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19005000 19006000 Tfap2d 472.0 -88000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19006000 19007000 Tfap2d 472.0 -87000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19007000 19008000 Tfap2d 472.0 -86000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19008000 19009000 Tfap2d 472.0 -85000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19009000 19010000 Tfap2d 472.0 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19010000 19011000 Tfap2d 472.0 -83000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19011000 19012000 Tfap2d 472.0 -82000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19012000 19013000 Tfap2d 472.0 -81000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19013000 19014000 Tfap2d 472.0 -80000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19014000 19015000 Tfap2d 472.0 -79000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19015000 19016000 Tfap2d 472.0 -78000 0.000423728814 0.042850447268 1.238104000914 0.200000000000 -chr1 19016000 19017000 Tfap2d 472.0 -77000 0.000423728814 0.042850447268 0.980165665600 0.200000000000 -chr1 19017000 19018000 Tfap2d 472.0 -76000 0.000423728814 0.042850447268 0.934727521861 0.200000000000 -chr1 19018000 19019000 Tfap2d 472.0 -75000 0.000423728814 0.042850447268 1.022781564413 0.200000000000 -chr1 19019000 19020000 Tfap2d 472.0 -74000 0.000423728814 0.042850447268 1.001020254378 0.200000000000 -chr1 19020000 19021000 Tfap2d 472.0 -73000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19021000 19022000 Tfap2d 472.0 -72000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19022000 19023000 Tfap2d 472.0 -71000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19023000 19024000 Tfap2d 472.0 -70000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19024000 19025000 Tfap2d 472.0 -69000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19025000 19026000 Tfap2d 472.0 -68000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19026000 19027000 Tfap2d 472.0 -67000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19027000 19028000 Tfap2d 472.0 -66000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19028000 19029000 Tfap2d 472.0 -65000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19029000 19030000 Tfap2d 472.0 -64000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19030000 19031000 Tfap2d 472.0 -63000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19031000 19032000 Tfap2d 472.0 -62000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19032000 19033000 Tfap2d 472.0 -61000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19033000 19034000 Tfap2d 472.0 -60000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19034000 19035000 Tfap2d 472.0 -59000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19035000 19036000 Tfap2d 472.0 -58000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19036000 19037000 Tfap2d 472.0 -57000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19037000 19038000 Tfap2d 472.0 -56000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19038000 19039000 Tfap2d 472.0 -55000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19039000 19040000 Tfap2d 472.0 -54000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19040000 19041000 Tfap2d 472.0 -53000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19041000 19042000 Tfap2d 472.0 -52000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19042000 19043000 Tfap2d 472.0 -51000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19043000 19044000 Tfap2d 472.0 -50000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19044000 19045000 Tfap2d 472.0 -49000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19045000 19046000 Tfap2d 472.0 -48000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19046000 19047000 Tfap2d 472.0 -47000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19047000 19048000 Tfap2d 472.0 -46000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19048000 19049000 Tfap2d 472.0 -45000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19049000 19050000 Tfap2d 472.0 -44000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19050000 19051000 Tfap2d 472.0 -43000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19051000 19052000 Tfap2d 472.0 -42000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19052000 19053000 Tfap2d 472.0 -41000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19053000 19054000 Tfap2d 472.0 -40000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19054000 19055000 Tfap2d 472.0 -39000 0.000423728814 0.042850447268 0.571432615421 0.200000000000 -chr1 19055000 19056000 Tfap2d 472.0 -38000 0.000423728814 0.042850447268 0.624530335872 0.200000000000 -chr1 19056000 19057000 Tfap2d 472.0 -37000 0.000423728814 0.042850447268 0.551343187379 0.200000000000 -chr1 19057000 19058000 Tfap2d 472.0 -36000 0.000423728814 0.042850447268 0.566842795180 0.200000000000 -chr1 19058000 19059000 Tfap2d 472.0 -35000 0.000423728814 0.042850447268 0.593041411154 0.200000000000 -chr1 19059000 19060000 Tfap2d 472.0 -34000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19060000 19061000 Tfap2d 472.0 -33000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19061000 19062000 Tfap2d 472.0 -32000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19062000 19063000 Tfap2d 472.0 -31000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19063000 19064000 Tfap2d 472.0 -30000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19064000 19065000 Tfap2d 472.0 -29000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19065000 19066000 Tfap2d 472.0 -28000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19066000 19067000 Tfap2d 472.0 -27000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19067000 19068000 Tfap2d 472.0 -26000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19068000 19069000 Tfap2d 472.0 -25000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19069000 19070000 Tfap2d 472.0 -24000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19070000 19071000 Tfap2d 472.0 -23000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19071000 19072000 Tfap2d 472.0 -22000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19072000 19073000 Tfap2d 472.0 -21000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19073000 19074000 Tfap2d 472.0 -20000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19074000 19075000 Tfap2d 472.0 -19000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19075000 19076000 Tfap2d 472.0 -18000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19076000 19077000 Tfap2d 472.0 -17000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19077000 19078000 Tfap2d 472.0 -16000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19078000 19079000 Tfap2d 472.0 -15000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19079000 19080000 Tfap2d 472.0 -14000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19080000 19081000 Tfap2d 472.0 -13000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19081000 19082000 Tfap2d 472.0 -12000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19082000 19083000 Tfap2d 472.0 -11000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19083000 19084000 Tfap2d 472.0 -10000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19084000 19085000 Tfap2d 472.0 -9000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19085000 19086000 Tfap2d 472.0 -8000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19086000 19087000 Tfap2d 472.0 -7000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19087000 19088000 Tfap2d 472.0 -6000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19088000 19089000 Tfap2d 472.0 -5000 0.008474576271 0.000000032703 1.449115563952 4.000000000000 -chr1 19089000 19090000 Tfap2d 472.0 -4000 0.022881355932 0.000000000000 2.298482575464 10.800000000000 -chr1 19090000 19091000 Tfap2d 472.0 -3000 0.038135593220 0.000000000000 1.769705633062 18.000000000000 -chr1 19091000 19092000 Tfap2d 472.0 -2000 0.089830508475 0.000000000000 1.342839718965 42.400000000000 -chr1 19092000 19093000 Tfap2d 472.0 -1000 0.096186440678 0.000000000000 1.258183989657 45.400000000000 -chr1 19093000 19094000 Tfap2d 472.0 0 0.097033898305 0.573211350056 1.219741990578 45.800000000000 -chr1 19094000 19095000 Tfap2d 472.0 1000 0.088559322034 0.000000000000 1.131750082102 41.800000000000 -chr1 19095000 19096000 Tfap2d 472.0 2000 0.079237288136 0.000000000000 1.158236837774 37.400000000000 -chr1 19096000 19097000 Tfap2d 472.0 3000 0.030084745763 0.000000000000 1.213515835692 14.200000000000 -chr1 19097000 19098000 Tfap2d 472.0 4000 0.025423728814 0.000000000000 1.625145146017 12.000000000000 -chr1 19098000 19099000 Tfap2d 472.0 5000 0.017796610169 0.000000000000 1.469519570887 8.400000000000 -chr1 19099000 19100000 Tfap2d 472.0 6000 0.012288135593 0.000000000000 1.174511283228 5.800000000000 -chr1 19100000 19101000 Tfap2d 472.0 7000 0.009745762712 0.000000000000 1.020530866525 4.600000000000 -chr1 19101000 19102000 Tfap2d 472.0 8000 0.010169491525 0.000000000000 1.167282061499 4.800000000000 -chr1 19102000 19103000 Tfap2d 472.0 9000 0.011440677966 0.000000000000 1.429438900967 5.400000000000 -chr1 19103000 19104000 Tfap2d 472.0 10000 0.010593220339 0.000000000000 1.461721788921 5.000000000000 -chr1 19104000 19105000 Tfap2d 472.0 11000 0.012288135593 0.000000000000 1.918974131188 5.800000000000 -chr1 19105000 19106000 Tfap2d 472.0 12000 0.010169491525 0.000000000000 1.708246365312 4.800000000000 -chr1 19106000 19107000 Tfap2d 472.0 13000 0.007203389831 0.000000000000 1.341221660736 3.400000000000 -chr1 19107000 19108000 Tfap2d 472.0 14000 0.007203389831 0.000000000000 1.483887168230 3.400000000000 -chr1 19108000 19109000 Tfap2d 472.0 15000 0.006355932203 0.000000000000 1.367673022577 3.000000000000 -chr1 19109000 19110000 Tfap2d 472.0 16000 0.008050847458 0.000000000000 1.767787252797 3.800000000000 -chr1 19110000 19111000 Tfap2d 472.0 17000 0.006779661017 0.000000000000 1.614225657668 3.200000000000 -chr1 19111000 19112000 Tfap2d 472.0 18000 0.009745762712 0.000000000000 2.388748113765 4.600000000000 -chr1 19112000 19113000 Tfap2d 472.0 19000 0.007203389831 0.000000000000 1.810902302517 3.400000000000 -chr1 19113000 19114000 Tfap2d 472.0 20000 0.007627118644 0.000000000000 2.035728691180 3.600000000000 -chr1 19114000 19115000 Tfap2d 472.0 21000 0.003813559322 0.000000000000 1.046371254994 1.800000000000 -chr1 19115000 19116000 Tfap2d 472.0 22000 0.003813559322 0.000000000000 1.090381719525 1.800000000000 -chr1 19116000 19117000 Tfap2d 472.0 23000 0.000847457627 0.000000000000 0.270649771714 0.400000000000 -chr1 19117000 19118000 Tfap2d 472.0 24000 0.000423728814 0.000000000000 0.137835796800 0.200000000000 -chr1 19118000 19119000 Tfap2d 472.0 25000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19119000 19120000 Tfap2d 472.0 26000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19120000 19121000 Tfap2d 472.0 27000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19121000 19122000 Tfap2d 472.0 28000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19122000 19123000 Tfap2d 472.0 29000 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19132000 19133000 Tfap2d 472.0 39000 0.001694915254 0.000000000000 0.865913226679 0.800000000000 -chr1 19133000 19134000 Tfap2d 472.0 40000 0.003389830508 0.000000000000 1.629366302482 1.600000000000 -chr1 19134000 19135000 Tfap2d 472.0 41000 0.004237288136 0.000000000000 2.072597002974 2.000000000000 -chr1 19135000 19136000 Tfap2d 472.0 42000 0.004237288136 0.000000000000 2.045563129814 2.000000000000 -chr1 19136000 19137000 Tfap2d 472.0 43000 0.004237288136 0.000000000000 2.135307956640 2.000000000000 -chr1 19137000 19138000 Tfap2d 472.0 44000 0.003389830508 0.000000000000 1.839007894971 1.600000000000 -chr1 19138000 19139000 Tfap2d 472.0 45000 0.001694915254 0.000000000000 1.020932050432 0.800000000000 -chr1 19139000 19140000 Tfap2d 472.0 46000 0.000847457627 0.000000000000 0.511390782515 0.400000000000 -chr1 19140000 19141000 Tfap2d 472.0 47000 0.000423728814 0.000000000000 0.267825153582 0.200000000000 -chr1 19141000 19142000 Tfap2d 472.0 48000 0.000000000000 1.000000000000 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19161000 19162000 Tfap2d 472.0 68000 0.002118644068 0.000000000000 1.759898452895 1.000000000000 -chr1 19162000 19163000 Tfap2d 472.0 69000 0.001694915254 0.000000000000 1.394013391721 0.800000000000 -chr1 19163000 19164000 Tfap2d 472.0 70000 0.000423728814 0.000000000000 0.341752677703 0.200000000000 -chr1 19164000 19165000 Tfap2d 472.0 71000 0.000847457627 0.000000000000 0.661095344113 0.400000000000 -chr1 19165000 19166000 Tfap2d 472.0 72000 0.000423728814 0.000000000000 0.337664726984 0.200000000000 -chr1 19166000 19167000 Tfap2d 472.0 73000 0.000423728814 0.000000000000 0.349365979986 0.200000000000 -chr1 19167000 19168000 Tfap2d 472.0 74000 0.000423728814 0.000000000000 0.336056799968 0.200000000000 -chr1 19168000 19169000 Tfap2d 472.0 75000 0.000423728814 0.000000000000 0.327479944218 0.200000000000 -chr1 19169000 19170000 Tfap2d 472.0 76000 0.000423728814 0.000000000000 0.325216257950 0.200000000000 -chr1 19170000 19171000 Tfap2d 472.0 77000 0.000847457627 0.000000000000 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19190000 19191000 Tfap2d 472.0 97000 0.001694915254 0.000000000000 1.373662831110 0.800000000000 -chr1 19191000 19192000 Tfap2d 472.0 98000 0.001271186441 0.000000000000 1.005775695846 0.600000000000 -chr1 19192000 19193000 Tfap2d 472.0 99000 0.001271186441 0.000000000000 1.080182571018 0.600000000000 -chr1 19193000 19194000 Tfap2d 472.0 100000 0.000847457627 0.000000000000 0.804238495376 0.400000000000 -chr1 19194000 19195000 Tfap2d 472.0 101000 0.000847457627 0.000000000000 0.860633267502 0.400000000000 -chr1 19195000 19196000 Tfap2d 472.0 102000 0.000847457627 0.000000000000 0.837648996932 0.400000000000 -chr1 19196000 19197000 Tfap2d 472.0 103000 0.000847457627 0.000000000000 0.925533481613 0.400000000000 -chr1 19197000 19198000 Tfap2d 472.0 104000 0.001694915254 0.000000000000 1.764298198693 0.800000000000 -chr1 19198000 19199000 Tfap2d 472.0 105000 0.002118644068 0.000000000000 2.112931975945 1.000000000000 -chr1 19199000 19200000 Tfap2d 472.0 106000 0.002118644068 0.000000000000 2.063506666181 1.000000000000 -chr1 19200000 19201000 Tfap2d 472.0 107000 0.002118644068 0.000000000000 1.982357527016 1.000000000000 -chr1 19201000 19202000 Tfap2d 472.0 108000 0.002542372881 0.000000000000 2.320172973657 1.200000000000 -chr1 19202000 19203000 Tfap2d 472.0 109000 0.001271186441 0.000000000000 1.202930590359 0.600000000000 -chr1 19203000 19204000 Tfap2d 472.0 110000 0.000847457627 0.000000000000 0.830257976313 0.400000000000 -chr1 19204000 19205000 Tfap2d 472.0 111000 0.001271186441 0.000000000000 1.179475119064 0.600000000000 -chr1 19205000 19206000 Tfap2d 472.0 112000 0.001694915254 0.000000000000 1.613072639333 0.800000000000 -chr1 19206000 19207000 Tfap2d 472.0 113000 0.001271186441 0.000000000000 1.241734803255 0.600000000000 -chr1 19207000 19208000 Tfap2d 472.0 114000 0.000847457627 0.000000000000 0.815860439041 0.400000000000 -chr1 19208000 19209000 Tfap2d 472.0 115000 0.000847457627 0.000000000000 0.822996244685 0.400000000000 -chr1 19209000 19210000 Tfap2d 472.0 116000 0.000423728814 0.000000000000 0.473637100575 0.200000000000 -chr1 19210000 19211000 Tfap2d 472.0 117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19211000 19212000 Tfap2d 472.0 118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19212000 19213000 Tfap2d 472.0 119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19213000 19214000 Tfap2d 472.0 120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19214000 19215000 Tfap2d 472.0 121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19215000 19216000 Tfap2d 472.0 122000 0.000847457627 0.000000000000 0.953674702560 0.400000000000 -chr1 19216000 19217000 Tfap2d 472.0 123000 0.000847457627 0.000000000000 0.973405903461 0.400000000000 -chr1 19217000 19218000 Tfap2d 472.0 124000 0.000847457627 0.000000000000 1.034020922346 0.400000000000 -chr1 19218000 19219000 Tfap2d 472.0 125000 0.000847457627 0.000000000000 1.129150847963 0.400000000000 -chr1 19219000 19220000 Tfap2d 472.0 126000 0.001271186441 0.000000000000 1.579968536413 0.600000000000 -chr1 19220000 19221000 Tfap2d 472.0 127000 0.000847457627 0.000000000000 1.077434014837 0.400000000000 -chr1 19221000 19222000 Tfap2d 472.0 128000 0.000847457627 0.000000000000 1.129150847963 0.400000000000 -chr1 19222000 19223000 Tfap2d 472.0 129000 0.000847457627 0.000000000000 1.089913945607 0.400000000000 -chr1 19223000 19224000 Tfap2d 472.0 130000 0.000847457627 0.000000000000 1.019089212169 0.400000000000 -chr1 19224000 19225000 Tfap2d 472.0 131000 0.000423728814 0.000000000000 0.553505317542 0.200000000000 -chr1 19225000 19226000 Tfap2d 472.0 132000 0.000423728814 0.000000000000 0.566842795180 0.200000000000 -chr1 19226000 19227000 Tfap2d 472.0 133000 0.000423728814 0.000000000000 0.511390782207 0.200000000000 -chr1 19227000 19228000 Tfap2d 472.0 134000 0.001271186441 0.000000000000 1.597854972809 0.600000000000 -chr1 19228000 19229000 Tfap2d 472.0 135000 0.001694915254 0.000000000000 2.231523414735 0.800000000000 -chr1 19229000 19230000 Tfap2d 472.0 136000 0.002118644068 0.000000000000 2.556953911034 1.000000000000 -chr1 19230000 19231000 Tfap2d 472.0 137000 0.002542372881 0.000000000000 2.861024107679 1.200000000000 -chr1 19231000 19232000 Tfap2d 472.0 138000 0.002542372881 0.000000000000 3.183695998364 1.200000000000 -chr1 19232000 19233000 Tfap2d 472.0 139000 0.001694915254 0.000000000000 1.987941631835 0.800000000000 -chr1 19233000 19234000 Tfap2d 472.0 140000 0.001271186441 0.000000000000 1.339973315587 0.600000000000 -chr1 19234000 19235000 Tfap2d 472.0 141000 0.000847457627 0.000000000000 0.963439290036 0.400000000000 -chr1 19235000 19236000 Tfap2d 472.0 142000 0.000423728814 0.000000000000 0.538717007419 0.200000000000 -chr1 19236000 19237000 Tfap2d 472.0 143000 0.001271186441 0.000000000000 1.539751155194 0.600000000000 -chr1 19237000 19238000 Tfap2d 472.0 144000 0.001271186441 0.000000000000 1.749717221137 0.600000000000 -chr1 19238000 19239000 Tfap2d 472.0 145000 0.001271186441 0.000000000000 2.117157840635 0.600000000000 -chr1 19239000 19240000 Tfap2d 472.0 146000 0.001694915254 0.000000000000 2.601730063600 0.800000000000 -chr1 19240000 19241000 Tfap2d 472.0 147000 0.001271186441 0.000000000000 1.857155998658 0.600000000000 -chr1 19241000 19242000 Tfap2d 472.0 148000 0.000423728814 0.000000000000 0.641562981525 0.200000000000 -chr1 19242000 19243000 Tfap2d 472.0 149000 0.000423728814 0.000000000000 0.659550728811 0.200000000000 -chr1 19243000 19244000 Tfap2d 472.0 150000 0.000847457627 0.000000000000 1.227337877296 0.400000000000 -chr1 19244000 19245000 Tfap2d 472.0 151000 0.001271186441 0.000000000000 1.942346641449 0.600000000000 -chr1 19245000 19246000 Tfap2d 472.0 152000 0.001271186441 0.000000000000 1.881918078824 0.600000000000 -chr1 19246000 19247000 Tfap2d 472.0 153000 0.002118644068 0.000000000000 3.164660446662 1.000000000000 -chr1 19247000 19248000 Tfap2d 472.0 154000 0.002118644068 0.000000000000 3.222462464392 1.000000000000 -chr1 19248000 19249000 Tfap2d 472.0 155000 0.001694915254 0.000000000000 2.498121343489 0.800000000000 -chr1 19249000 19250000 Tfap2d 472.0 156000 0.000847457627 0.000000000000 1.249060671745 0.400000000000 -chr1 19250000 19251000 Tfap2d 472.0 157000 0.000847457627 0.000000000000 1.171318305746 0.400000000000 -chr1 19251000 19252000 Tfap2d 472.0 158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19252000 19253000 Tfap2d 472.0 159000 0.000847457627 0.000000000000 1.098395766262 0.400000000000 -chr1 19253000 19254000 Tfap2d 472.0 160000 0.000847457627 0.000000000000 1.081562114542 0.400000000000 -chr1 19254000 19255000 Tfap2d 472.0 161000 0.001694915254 0.000000000000 2.038178424337 0.800000000000 -chr1 19255000 19256000 Tfap2d 472.0 162000 0.001694915254 0.000000000000 2.304389486014 0.800000000000 -chr1 19256000 19257000 Tfap2d 472.0 163000 0.002542372881 0.000000000000 3.513954917238 1.200000000000 -chr1 19257000 19258000 Tfap2d 472.0 164000 0.002118644068 0.000000000000 3.055061815685 1.000000000000 -chr1 19258000 19259000 Tfap2d 472.0 165000 0.002118644068 0.000000000000 3.252162579500 1.000000000000 -chr1 19259000 19260000 Tfap2d 472.0 166000 0.001694915254 0.000000000000 2.822877120847 0.800000000000 -chr1 19260000 19261000 Tfap2d 472.0 167000 0.001694915254 0.000000000000 2.701317818024 0.800000000000 -chr1 19261000 19262000 Tfap2d 472.0 168000 0.000847457627 0.000000000000 1.312966101957 0.400000000000 -chr1 19262000 19263000 Tfap2d 472.0 169000 0.000423728814 0.000000000000 0.593041411154 0.200000000000 -chr1 19263000 19264000 Tfap2d 472.0 170000 0.000423728814 0.000000000000 0.573755512251 0.200000000000 -chr1 19264000 19265000 Tfap2d 472.0 171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19265000 19266000 Tfap2d 472.0 172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19266000 19267000 Tfap2d 472.0 173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19267000 19268000 Tfap2d 472.0 174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19268000 19269000 Tfap2d 472.0 175000 0.000423728814 0.000000000000 0.608378689139 0.200000000000 -chr1 19269000 19270000 Tfap2d 472.0 176000 0.000423728814 0.000000000000 0.600612152627 0.200000000000 -chr1 19270000 19271000 Tfap2d 472.0 177000 0.000423728814 0.000000000000 0.641562981525 0.200000000000 -chr1 19271000 19272000 Tfap2d 472.0 178000 0.000423728814 0.000000000000 0.665772905546 0.200000000000 -chr1 19272000 19273000 Tfap2d 472.0 179000 0.000423728814 0.000000000000 0.678576230756 0.200000000000 -chr1 19273000 19274000 Tfap2d 472.0 180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19274000 19275000 Tfap2d 472.0 181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19275000 19276000 Tfap2d 472.0 182000 0.000423728814 0.000000000000 0.758837934828 0.200000000000 -chr1 19276000 19277000 Tfap2d 472.0 183000 0.000423728814 0.000000000000 0.735124249200 0.200000000000 -chr1 19277000 19278000 Tfap2d 472.0 184000 0.000423728814 0.000000000000 0.688506614701 0.200000000000 -chr1 19278000 19279000 Tfap2d 472.0 185000 0.000423728814 0.000000000000 0.678576230756 0.200000000000 -chr1 19279000 19280000 Tfap2d 472.0 186000 0.000423728814 0.000000000000 0.750765190784 0.200000000000 -chr1 19280000 19281000 Tfap2d 472.0 187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19281000 19282000 Tfap2d 472.0 188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19282000 19283000 Tfap2d 472.0 189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19283000 19284000 Tfap2d 472.0 190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19284000 19285000 Tfap2d 472.0 191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19285000 19286000 Tfap2d 472.0 192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19286000 19287000 Tfap2d 472.0 193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19287000 19288000 Tfap2d 472.0 194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19288000 19289000 Tfap2d 472.0 195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19289000 19290000 Tfap2d 472.0 196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19290000 19291000 Tfap2d 472.0 197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19291000 19292000 Tfap2d 472.0 198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19292000 19293000 Tfap2d 472.0 199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19293000 19294000 Tfap2d 472.0 200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt deleted file mode 100644 index cdb1a506..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 4287000 4288000 Sox17 810.0 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4288000 4289000 Sox17 810.0 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4289000 4290000 Sox17 810.0 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4290000 4291000 Sox17 810.0 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4291000 4292000 Sox17 810.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4292000 4293000 Sox17 810.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4293000 4294000 Sox17 810.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4294000 4295000 Sox17 810.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4295000 4296000 Sox17 810.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4296000 4297000 Sox17 810.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4297000 4298000 Sox17 810.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4298000 4299000 Sox17 810.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4299000 4300000 Sox17 810.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4300000 4301000 Sox17 810.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4301000 4302000 Sox17 810.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4302000 4303000 Sox17 810.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4303000 4304000 Sox17 810.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4304000 4305000 Sox17 810.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4305000 4306000 Sox17 810.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4306000 4307000 Sox17 810.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4307000 4308000 Sox17 810.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4308000 4309000 Sox17 810.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4309000 4310000 Sox17 810.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4310000 4311000 Sox17 810.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4311000 4312000 Sox17 810.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4312000 4313000 Sox17 810.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4313000 4314000 Sox17 810.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4314000 4315000 Sox17 810.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4315000 4316000 Sox17 810.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4316000 4317000 Sox17 810.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4317000 4318000 Sox17 810.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4318000 4319000 Sox17 810.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4319000 4320000 Sox17 810.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4320000 4321000 Sox17 810.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4321000 4322000 Sox17 810.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4322000 4323000 Sox17 810.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4323000 4324000 Sox17 810.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4324000 4325000 Sox17 810.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4325000 4326000 Sox17 810.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4326000 4327000 Sox17 810.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4327000 4328000 Sox17 810.0 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4328000 4329000 Sox17 810.0 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4329000 4330000 Sox17 810.0 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4330000 4331000 Sox17 810.0 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4331000 4332000 Sox17 810.0 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4332000 4333000 Sox17 810.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4333000 4334000 Sox17 810.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4334000 4335000 Sox17 810.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4335000 4336000 Sox17 810.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4336000 4337000 Sox17 810.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4337000 4338000 Sox17 810.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4338000 4339000 Sox17 810.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4339000 4340000 Sox17 810.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4340000 4341000 Sox17 810.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4341000 4342000 Sox17 810.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4342000 4343000 Sox17 810.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4343000 4344000 Sox17 810.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4344000 4345000 Sox17 810.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4345000 4346000 Sox17 810.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4346000 4347000 Sox17 810.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4347000 4348000 Sox17 810.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4348000 4349000 Sox17 810.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4349000 4350000 Sox17 810.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4350000 4351000 Sox17 810.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4351000 4352000 Sox17 810.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4352000 4353000 Sox17 810.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4353000 4354000 Sox17 810.0 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4354000 4355000 Sox17 810.0 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4355000 4356000 Sox17 810.0 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4356000 4357000 Sox17 810.0 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4357000 4358000 Sox17 810.0 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4358000 4359000 Sox17 810.0 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4359000 4360000 Sox17 810.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4360000 4361000 Sox17 810.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4361000 4362000 Sox17 810.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4362000 4363000 Sox17 810.0 -125000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4363000 4364000 Sox17 810.0 -124000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4364000 4365000 Sox17 810.0 -123000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4365000 4366000 Sox17 810.0 -122000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4366000 4367000 Sox17 810.0 -121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4367000 4368000 Sox17 810.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4368000 4369000 Sox17 810.0 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4369000 4370000 Sox17 810.0 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4370000 4371000 Sox17 810.0 -117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4371000 4372000 Sox17 810.0 -116000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4372000 4373000 Sox17 810.0 -115000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4373000 4374000 Sox17 810.0 -114000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4374000 4375000 Sox17 810.0 -113000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4375000 4376000 Sox17 810.0 -112000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4376000 4377000 Sox17 810.0 -111000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4377000 4378000 Sox17 810.0 -110000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4378000 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4676000 Sox17 810.0 188000 0.000493827160 0.000000000000 0.879644813784 0.400000000000 -chr1 4676000 4677000 Sox17 810.0 189000 0.000246913580 0.000000000000 0.478179012441 0.200000000000 -chr1 4677000 4678000 Sox17 810.0 190000 0.000246913580 0.000000000000 0.480975380957 0.200000000000 -chr1 4678000 4679000 Sox17 810.0 191000 0.000740740741 0.000000000000 1.370779835192 0.600000000000 -chr1 4679000 4680000 Sox17 810.0 192000 0.000740740741 0.000000000000 1.355716320410 0.600000000000 -chr1 4680000 4681000 Sox17 810.0 193000 0.000740740741 0.000000000000 1.468692681340 0.600000000000 -chr1 4681000 4682000 Sox17 810.0 194000 0.000740740741 0.000000000000 1.426244915656 0.600000000000 -chr1 4682000 4683000 Sox17 810.0 195000 0.000740740741 0.000000000000 1.513744604449 0.600000000000 -chr1 4683000 4684000 Sox17 810.0 196000 0.000493827160 0.000000000000 1.009163069632 0.400000000000 -chr1 4684000 4685000 Sox17 810.0 197000 0.000493827160 0.000000000000 0.934622615061 0.400000000000 -chr1 4685000 4686000 Sox17 810.0 198000 0.000246913580 0.000000000000 0.403170540070 0.200000000000 -chr1 4686000 4687000 Sox17 810.0 199000 0.000308641975 0.000000000000 0.538264332961 0.250000000000 -chr1 4687000 4688000 Sox17 810.0 200000 0.000411522634 0.000000000000 0.699377466512 0.333333333333 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt deleted file mode 100644 index d1e1cd88..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 14100000 14101000 Eya1 832.0 -200000 0.000400641026 0.028365821799 2.426424093120 0.333333333333 -chr1 14101000 14102000 Eya1 832.0 -199000 0.000300480769 0.036748857670 1.429857059822 0.250000000000 -chr1 14102000 14103000 Eya1 832.0 -198000 0.000240384615 0.042850447268 0.931069711724 0.200000000000 -chr1 14103000 14104000 Eya1 832.0 -197000 0.000240384615 0.042850447268 0.889688835341 0.200000000000 -chr1 14104000 14105000 Eya1 832.0 -196000 0.000240384615 0.042850447268 0.976487746811 0.200000000000 -chr1 14105000 14106000 Eya1 832.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14106000 14107000 Eya1 832.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14107000 14108000 Eya1 832.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14108000 14109000 Eya1 832.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14109000 14110000 Eya1 832.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14110000 14111000 Eya1 832.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14111000 14112000 Eya1 832.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14112000 14113000 Eya1 832.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14113000 14114000 Eya1 832.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14114000 14115000 Eya1 832.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14115000 14116000 Eya1 832.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14116000 14117000 Eya1 832.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14117000 14118000 Eya1 832.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14118000 14119000 Eya1 832.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14119000 14120000 Eya1 832.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14120000 14121000 Eya1 832.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14121000 14122000 Eya1 832.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14122000 14123000 Eya1 832.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14123000 14124000 Eya1 832.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14124000 14125000 Eya1 832.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14125000 14126000 Eya1 832.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14126000 14127000 Eya1 832.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14127000 14128000 Eya1 832.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14128000 14129000 Eya1 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-chr1 14138000 14139000 Eya1 832.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14139000 14140000 Eya1 832.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14140000 14141000 Eya1 832.0 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14141000 14142000 Eya1 832.0 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14142000 14143000 Eya1 832.0 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14143000 14144000 Eya1 832.0 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14144000 14145000 Eya1 832.0 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14145000 14146000 Eya1 832.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14146000 14147000 Eya1 832.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14147000 14148000 Eya1 832.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14148000 14149000 Eya1 832.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14149000 14150000 Eya1 832.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14150000 14151000 Eya1 832.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14151000 14152000 Eya1 832.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14152000 14153000 Eya1 832.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14153000 14154000 Eya1 832.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14154000 14155000 Eya1 832.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14155000 14156000 Eya1 832.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14156000 14157000 Eya1 832.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14157000 14158000 Eya1 832.0 -143000 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14167000 14168000 Eya1 832.0 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14168000 14169000 Eya1 832.0 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14169000 14170000 Eya1 832.0 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14170000 14171000 Eya1 832.0 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14171000 14172000 Eya1 832.0 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14172000 14173000 Eya1 832.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14173000 14174000 Eya1 832.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14174000 14175000 Eya1 832.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14175000 14176000 Eya1 832.0 -125000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14176000 14177000 Eya1 832.0 -124000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14177000 14178000 Eya1 832.0 -123000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14178000 14179000 Eya1 832.0 -122000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14179000 14180000 Eya1 832.0 -121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14180000 14181000 Eya1 832.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14181000 14182000 Eya1 832.0 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14182000 14183000 Eya1 832.0 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14183000 14184000 Eya1 832.0 -117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14184000 14185000 Eya1 832.0 -116000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14185000 14186000 Eya1 832.0 -115000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14186000 14187000 Eya1 832.0 -114000 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14196000 14197000 Eya1 832.0 -104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14197000 14198000 Eya1 832.0 -103000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14198000 14199000 Eya1 832.0 -102000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14199000 14200000 Eya1 832.0 -101000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14200000 14201000 Eya1 832.0 -100000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14201000 14202000 Eya1 832.0 -99000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14202000 14203000 Eya1 832.0 -98000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14203000 14204000 Eya1 832.0 -97000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14204000 14205000 Eya1 832.0 -96000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14205000 14206000 Eya1 832.0 -95000 0.000000000000 1.000000000000 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0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14216000 14217000 Eya1 832.0 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14217000 14218000 Eya1 832.0 -83000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14218000 14219000 Eya1 832.0 -82000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14219000 14220000 Eya1 832.0 -81000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14220000 14221000 Eya1 832.0 -80000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14221000 14222000 Eya1 832.0 -79000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14222000 14223000 Eya1 832.0 -78000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14223000 14224000 Eya1 832.0 -77000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14224000 14225000 Eya1 832.0 -76000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14225000 14226000 Eya1 832.0 -75000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14226000 14227000 Eya1 832.0 -74000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14227000 14228000 Eya1 832.0 -73000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14228000 14229000 Eya1 832.0 -72000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14229000 14230000 Eya1 832.0 -71000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14230000 14231000 Eya1 832.0 -70000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14231000 14232000 Eya1 832.0 -69000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14232000 14233000 Eya1 832.0 -68000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14233000 14234000 Eya1 832.0 -67000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14234000 14235000 Eya1 832.0 -66000 0.000000000000 1.000000000000 0.000000000000 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14265000 Eya1 832.0 -36000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14265000 14266000 Eya1 832.0 -35000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14266000 14267000 Eya1 832.0 -34000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14267000 14268000 Eya1 832.0 -33000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14268000 14269000 Eya1 832.0 -32000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14269000 14270000 Eya1 832.0 -31000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14270000 14271000 Eya1 832.0 -30000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14271000 14272000 Eya1 832.0 -29000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14272000 14273000 Eya1 832.0 -28000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14273000 14274000 Eya1 832.0 -27000 0.000000000000 1.000000000000 0.000000000000 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14314000 Eya1 832.0 13000 0.005528846154 0.000000000000 1.029433141187 4.600000000000 -chr1 14314000 14315000 Eya1 832.0 14000 0.005528846154 0.000000000000 1.138933759778 4.600000000000 -chr1 14315000 14316000 Eya1 832.0 15000 0.006250000000 0.000000000000 1.344878472201 5.200000000000 -chr1 14316000 14317000 Eya1 832.0 16000 0.005048076923 0.000000000000 1.108445549704 4.200000000000 -chr1 14317000 14318000 Eya1 832.0 17000 0.006009615385 0.000000000000 1.430879113618 5.000000000000 -chr1 14318000 14319000 Eya1 832.0 18000 0.005288461538 0.000000000000 1.296235389493 4.400000000000 -chr1 14319000 14320000 Eya1 832.0 19000 0.004567307692 0.000000000000 1.148202195205 3.800000000000 -chr1 14320000 14321000 Eya1 832.0 20000 0.003605769231 0.000000000000 0.962403788298 3.000000000000 -chr1 14321000 14322000 Eya1 832.0 21000 0.004326923077 0.000000000000 1.187228923935 3.600000000000 -chr1 14322000 14323000 Eya1 832.0 22000 0.003365384615 0.000000000000 0.962238568726 2.800000000000 -chr1 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14383000 Eya1 832.0 82000 0.001442307692 0.000000000000 1.241426282299 1.200000000000 -chr1 14383000 14384000 Eya1 832.0 83000 0.001201923077 0.000000000000 0.905791800808 1.000000000000 -chr1 14384000 14385000 Eya1 832.0 84000 0.000721153846 0.000000000000 0.511097841780 0.600000000000 -chr1 14385000 14386000 Eya1 832.0 85000 0.000961538462 0.000000000000 0.680016944466 0.800000000000 -chr1 14386000 14387000 Eya1 832.0 86000 0.001682692308 0.000000000000 1.306536052373 1.400000000000 -chr1 14387000 14388000 Eya1 832.0 87000 0.000961538462 0.000000000000 0.711751068273 0.800000000000 -chr1 14388000 14389000 Eya1 832.0 88000 0.000961538462 0.000000000000 0.707037485005 0.800000000000 -chr1 14389000 14390000 Eya1 832.0 89000 0.001201923077 0.000000000000 0.976487746018 1.000000000000 -chr1 14390000 14391000 Eya1 832.0 90000 0.001201923077 0.000000000000 0.983685444445 1.000000000000 -chr1 14391000 14392000 Eya1 832.0 91000 0.000721153846 0.000000000000 0.566547135970 0.600000000000 -chr1 14392000 14393000 Eya1 832.0 92000 0.000721153846 0.000000000000 0.635492025580 0.600000000000 -chr1 14393000 14394000 Eya1 832.0 93000 0.000961538462 0.000000000000 0.879912034881 0.800000000000 -chr1 14394000 14395000 Eya1 832.0 94000 0.000961538462 0.000000000000 0.806770732420 0.800000000000 -chr1 14395000 14396000 Eya1 832.0 95000 0.000721153846 0.000000000000 0.580231849042 0.600000000000 -chr1 14396000 14397000 Eya1 832.0 96000 0.000721153846 0.000000000000 0.563887290240 0.600000000000 -chr1 14397000 14398000 Eya1 832.0 97000 0.000721153846 0.000000000000 0.584467118044 0.600000000000 -chr1 14398000 14399000 Eya1 832.0 98000 0.000480769231 0.000000000000 0.380389525993 0.400000000000 -chr1 14399000 14400000 Eya1 832.0 99000 0.000240384615 0.000000000000 0.204265293878 0.200000000000 -chr1 14400000 14401000 Eya1 832.0 100000 0.000721153846 0.000000000000 0.684376027315 0.600000000000 -chr1 14401000 14402000 Eya1 832.0 101000 0.000480769231 0.000000000000 0.488243872910 0.400000000000 -chr1 14402000 14403000 Eya1 832.0 102000 0.000721153846 0.000000000000 0.712807079120 0.600000000000 -chr1 14403000 14404000 Eya1 832.0 103000 0.000721153846 0.000000000000 0.787593395411 0.600000000000 -chr1 14404000 14405000 Eya1 832.0 104000 0.000961538462 0.000000000000 1.000899939643 0.800000000000 -chr1 14405000 14406000 Eya1 832.0 105000 0.000961538462 0.000000000000 0.958946050621 0.800000000000 -chr1 14406000 14407000 Eya1 832.0 106000 0.001201923077 0.000000000000 1.170643204852 1.000000000000 -chr1 14407000 14408000 Eya1 832.0 107000 0.000961538462 0.000000000000 0.899685339184 0.800000000000 -chr1 14408000 14409000 Eya1 832.0 108000 0.001201923077 0.000000000000 1.096876646200 1.000000000000 -chr1 14409000 14410000 Eya1 832.0 109000 0.000961538462 0.000000000000 0.909909036298 0.800000000000 -chr1 14410000 14411000 Eya1 832.0 110000 0.000480769231 0.000000000000 0.471011736562 0.400000000000 -chr1 14411000 14412000 Eya1 832.0 111000 0.000480769231 0.000000000000 0.446083538620 0.400000000000 -chr1 14412000 14413000 Eya1 832.0 112000 0.000480769231 0.000000000000 0.457554258272 0.400000000000 -chr1 14413000 14414000 Eya1 832.0 113000 0.000240384615 0.000000000000 0.234815235231 0.200000000000 -chr1 14414000 14415000 Eya1 832.0 114000 0.000480769231 0.000000000000 0.462843902917 0.400000000000 -chr1 14415000 14416000 Eya1 832.0 115000 0.000480769231 0.000000000000 0.466892100350 0.400000000000 -chr1 14416000 14417000 Eya1 832.0 116000 0.000240384615 0.000000000000 0.268697970519 0.200000000000 -chr1 14417000 14418000 Eya1 832.0 117000 0.000240384615 0.000000000000 0.274219161738 0.200000000000 -chr1 14418000 14419000 Eya1 832.0 118000 0.000480769231 0.000000000000 0.556055522474 0.400000000000 -chr1 14419000 14420000 Eya1 832.0 119000 0.000240384615 0.000000000000 0.271430492274 0.200000000000 -chr1 14420000 14421000 Eya1 832.0 120000 0.000480769231 0.000000000000 0.535598630183 0.400000000000 -chr1 14421000 14422000 Eya1 832.0 121000 0.000480769231 0.000000000000 0.526789442119 0.400000000000 -chr1 14422000 14423000 Eya1 832.0 122000 0.000480769231 0.000000000000 0.541026994721 0.400000000000 -chr1 14423000 14424000 Eya1 832.0 123000 0.000240384615 0.000000000000 0.276110328386 0.200000000000 -chr1 14424000 14425000 Eya1 832.0 124000 0.000480769231 0.000000000000 0.586608023254 0.400000000000 -chr1 14425000 14426000 Eya1 832.0 125000 0.000240384615 0.000000000000 0.320287980913 0.200000000000 -chr1 14426000 14427000 Eya1 832.0 126000 0.001682692308 0.000000000000 2.091432710060 1.400000000000 -chr1 14427000 14428000 Eya1 832.0 127000 0.001923076923 0.000000000000 2.444946418284 1.600000000000 -chr1 14428000 14429000 Eya1 832.0 128000 0.001923076923 0.000000000000 2.562303847300 1.600000000000 -chr1 14429000 14430000 Eya1 832.0 129000 0.001682692308 0.000000000000 2.164107978537 1.400000000000 -chr1 14430000 14431000 Eya1 832.0 130000 0.002403846154 0.000000000000 2.890685746055 2.000000000000 -chr1 14431000 14432000 Eya1 832.0 131000 0.001201923077 0.000000000000 1.570039121874 1.000000000000 -chr1 14432000 14433000 Eya1 832.0 132000 0.000961538462 0.000000000000 1.286297112140 0.800000000000 -chr1 14433000 14434000 Eya1 832.0 133000 0.000961538462 0.000000000000 1.160463698084 0.800000000000 -chr1 14434000 14435000 Eya1 832.0 134000 0.001442307692 0.000000000000 1.812950834534 1.200000000000 -chr1 14435000 14436000 Eya1 832.0 135000 0.000721153846 0.000000000000 0.949470299058 0.600000000000 -chr1 14436000 14437000 Eya1 832.0 136000 0.000480769231 0.000000000000 0.580231849042 0.400000000000 -chr1 14437000 14438000 Eya1 832.0 137000 0.000480769231 0.000000000000 0.541026994721 0.400000000000 -chr1 14438000 14439000 Eya1 832.0 138000 0.000480769231 0.000000000000 0.602045076614 0.400000000000 -chr1 14439000 14440000 Eya1 832.0 139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14440000 14441000 Eya1 832.0 140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14441000 14442000 Eya1 832.0 141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14442000 14443000 Eya1 832.0 142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14443000 14444000 Eya1 832.0 143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14444000 14445000 Eya1 832.0 144000 0.000240384615 0.000000000000 0.330876012971 0.200000000000 -chr1 14445000 14446000 Eya1 832.0 145000 0.000961538462 0.000000000000 1.601439905096 0.800000000000 -chr1 14446000 14447000 Eya1 832.0 146000 0.000961538462 0.000000000000 1.475981478388 0.800000000000 -chr1 14447000 14448000 Eya1 832.0 147000 0.001442307692 0.000000000000 2.107157767708 1.200000000000 -chr1 14448000 14449000 Eya1 832.0 148000 0.001682692308 0.000000000000 2.547745301633 1.400000000000 -chr1 14449000 14450000 Eya1 832.0 149000 0.002163461538 0.000000000000 3.367513817293 1.800000000000 -chr1 14450000 14451000 Eya1 832.0 150000 0.002163461538 0.000000000000 3.133251984828 1.800000000000 -chr1 14451000 14452000 Eya1 832.0 151000 0.002163461538 0.000000000000 3.305724572467 1.800000000000 -chr1 14452000 14453000 Eya1 832.0 152000 0.002163461538 0.000000000000 3.202879807229 1.800000000000 -chr1 14453000 14454000 Eya1 832.0 153000 0.001923076923 0.000000000000 2.872537943893 1.600000000000 -chr1 14454000 14455000 Eya1 832.0 154000 0.001201923077 0.000000000000 1.828127744223 1.000000000000 -chr1 14455000 14456000 Eya1 832.0 155000 0.000480769231 0.000000000000 0.708601727240 0.400000000000 -chr1 14456000 14457000 Eya1 832.0 156000 0.000721153846 0.000000000000 1.062902590860 0.600000000000 -chr1 14457000 14458000 Eya1 832.0 157000 0.000240384615 0.000000000000 0.332248942495 0.200000000000 -chr1 14458000 14459000 Eya1 832.0 158000 0.000721153846 0.000000000000 0.960863942738 0.600000000000 -chr1 14459000 14460000 Eya1 832.0 159000 0.000721153846 0.000000000000 0.934692551098 0.600000000000 -chr1 14460000 14461000 Eya1 832.0 160000 0.001682692308 0.000000000000 2.147524775510 1.400000000000 -chr1 14461000 14462000 Eya1 832.0 161000 0.001923076923 0.000000000000 2.312548596844 1.600000000000 -chr1 14462000 14463000 Eya1 832.0 162000 0.002163461538 0.000000000000 2.941420233350 1.800000000000 -chr1 14463000 14464000 Eya1 832.0 163000 0.001682692308 0.000000000000 2.325742597467 1.400000000000 -chr1 14464000 14465000 Eya1 832.0 164000 0.001682692308 0.000000000000 2.426424095919 1.400000000000 -chr1 14465000 14466000 Eya1 832.0 165000 0.000721153846 0.000000000000 1.106986108791 0.600000000000 -chr1 14466000 14467000 Eya1 832.0 166000 0.000240384615 0.000000000000 0.400359976274 0.200000000000 -chr1 14467000 14468000 Eya1 832.0 167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14468000 14469000 Eya1 832.0 168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14469000 14470000 Eya1 832.0 169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14470000 14471000 Eya1 832.0 170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14471000 14472000 Eya1 832.0 171000 0.000480769231 0.000000000000 0.659028767461 0.400000000000 -chr1 14472000 14473000 Eya1 832.0 172000 0.000480769231 0.000000000000 0.618316565296 0.400000000000 -chr1 14473000 14474000 Eya1 832.0 173000 0.000480769231 0.000000000000 0.630488151323 0.400000000000 -chr1 14474000 14475000 Eya1 832.0 174000 0.000480769231 0.000000000000 0.667266626197 0.400000000000 -chr1 14475000 14476000 Eya1 832.0 175000 0.000480769231 0.000000000000 0.690275820369 0.400000000000 -chr1 14476000 14477000 Eya1 832.0 176000 0.000240384615 0.000000000000 0.340731894279 0.200000000000 -chr1 14477000 14478000 Eya1 832.0 177000 0.000480769231 0.000000000000 0.727927229038 0.400000000000 -chr1 14478000 14479000 Eya1 832.0 178000 0.000480769231 0.000000000000 0.755396181293 0.400000000000 -chr1 14479000 14480000 Eya1 832.0 179000 0.000480769231 0.000000000000 0.769923031050 0.400000000000 -chr1 14480000 14481000 Eya1 832.0 180000 0.000480769231 0.000000000000 0.812913656138 0.400000000000 -chr1 14481000 14482000 Eya1 832.0 181000 0.000240384615 0.000000000000 0.408530587410 0.200000000000 -chr1 14482000 14483000 Eya1 832.0 182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14483000 14484000 Eya1 832.0 183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14484000 14485000 Eya1 832.0 184000 0.000240384615 0.000000000000 0.390595098725 0.200000000000 -chr1 14485000 14486000 Eya1 832.0 185000 0.000961538462 0.000000000000 1.539846062099 0.800000000000 -chr1 14486000 14487000 Eya1 832.0 186000 0.000961538462 0.000000000000 1.703659471393 0.800000000000 -chr1 14487000 14488000 Eya1 832.0 187000 0.000961538462 0.000000000000 1.731286381939 0.800000000000 -chr1 14488000 14489000 Eya1 832.0 188000 0.001201923077 0.000000000000 2.140962437394 1.000000000000 -chr1 14489000 14490000 Eya1 832.0 189000 0.001442307692 0.000000000000 2.793209135173 1.200000000000 -chr1 14490000 14491000 Eya1 832.0 190000 0.000721153846 0.000000000000 1.404771845823 0.600000000000 -chr1 14491000 14492000 Eya1 832.0 191000 0.001442307692 0.000000000000 2.669066506024 1.200000000000 -chr1 14492000 14493000 Eya1 832.0 192000 0.002403846154 0.000000000000 4.399560174407 2.000000000000 -chr1 14493000 14494000 Eya1 832.0 193000 0.002163461538 0.000000000000 4.289571172663 1.800000000000 -chr1 14494000 14495000 Eya1 832.0 194000 0.001682692308 0.000000000000 3.239907320421 1.400000000000 -chr1 14495000 14496000 Eya1 832.0 195000 0.002163461538 0.000000000000 4.421153111551 1.800000000000 -chr1 14496000 14497000 Eya1 832.0 196000 0.001682692308 0.000000000000 3.438674642317 1.400000000000 -chr1 14497000 14498000 Eya1 832.0 197000 0.001442307692 0.000000000000 2.729727108893 1.200000000000 -chr1 14498000 14499000 Eya1 832.0 198000 0.002644230769 0.000000000000 4.317607586564 2.200000000000 -chr1 14499000 14500000 Eya1 832.0 199000 0.003305288462 0.000000000000 5.764345200343 2.750000000000 -chr1 14500000 14501000 Eya1 832.0 200000 0.003605769231 0.000000000000 6.127958811148 3.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt deleted file mode 100644 index 76a80051..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 18893000 18894000 Tfap2d 800.0 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18894000 18895000 Tfap2d 800.0 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18895000 18896000 Tfap2d 800.0 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18896000 18897000 Tfap2d 800.0 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18897000 18898000 Tfap2d 800.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18898000 18899000 Tfap2d 800.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18899000 18900000 Tfap2d 800.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18900000 18901000 Tfap2d 800.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18901000 18902000 Tfap2d 800.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18902000 18903000 Tfap2d 800.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18903000 18904000 Tfap2d 800.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18904000 18905000 Tfap2d 800.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18905000 18906000 Tfap2d 800.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18906000 18907000 Tfap2d 800.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18907000 18908000 Tfap2d 800.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18908000 18909000 Tfap2d 800.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18909000 18910000 Tfap2d 800.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18910000 18911000 Tfap2d 800.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18911000 18912000 Tfap2d 800.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18912000 18913000 Tfap2d 800.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18913000 18914000 Tfap2d 800.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18914000 18915000 Tfap2d 800.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18915000 18916000 Tfap2d 800.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18916000 18917000 Tfap2d 800.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18917000 18918000 Tfap2d 800.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18918000 18919000 Tfap2d 800.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18919000 18920000 Tfap2d 800.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18920000 18921000 Tfap2d 800.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18921000 18922000 Tfap2d 800.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18922000 18923000 Tfap2d 800.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18923000 18924000 Tfap2d 800.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18924000 18925000 Tfap2d 800.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18925000 18926000 Tfap2d 800.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18926000 18927000 Tfap2d 800.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18927000 18928000 Tfap2d 800.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18928000 18929000 Tfap2d 800.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18929000 18930000 Tfap2d 800.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18930000 18931000 Tfap2d 800.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18931000 18932000 Tfap2d 800.0 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0.000000000000 -chr1 18941000 18942000 Tfap2d 800.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18942000 18943000 Tfap2d 800.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18943000 18944000 Tfap2d 800.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18944000 18945000 Tfap2d 800.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18945000 18946000 Tfap2d 800.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18946000 18947000 Tfap2d 800.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18947000 18948000 Tfap2d 800.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18948000 18949000 Tfap2d 800.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18949000 18950000 Tfap2d 800.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18950000 18951000 Tfap2d 800.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18951000 18952000 Tfap2d 800.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18952000 18953000 Tfap2d 800.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18953000 18954000 Tfap2d 800.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18954000 18955000 Tfap2d 800.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18955000 18956000 Tfap2d 800.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18956000 18957000 Tfap2d 800.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18957000 18958000 Tfap2d 800.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18958000 18959000 Tfap2d 800.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18959000 18960000 Tfap2d 800.0 -134000 0.000000000000 1.000000000000 0.000000000000 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0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19008000 19009000 Tfap2d 800.0 -85000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19009000 19010000 Tfap2d 800.0 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19010000 19011000 Tfap2d 800.0 -83000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19011000 19012000 Tfap2d 800.0 -82000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19012000 19013000 Tfap2d 800.0 -81000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19013000 19014000 Tfap2d 800.0 -80000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19014000 19015000 Tfap2d 800.0 -79000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19015000 19016000 Tfap2d 800.0 -78000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19016000 19017000 Tfap2d 800.0 -77000 0.000250000000 0.042850447268 0.578297742704 0.200000000000 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19037000 Tfap2d 800.0 -57000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19037000 19038000 Tfap2d 800.0 -56000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19038000 19039000 Tfap2d 800.0 -55000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19039000 19040000 Tfap2d 800.0 -54000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19040000 19041000 Tfap2d 800.0 -53000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19041000 19042000 Tfap2d 800.0 -52000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19042000 19043000 Tfap2d 800.0 -51000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19043000 19044000 Tfap2d 800.0 -50000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19044000 19045000 Tfap2d 800.0 -49000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19045000 19046000 Tfap2d 800.0 -48000 0.000000000000 1.000000000000 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800.0 -38000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19056000 19057000 Tfap2d 800.0 -37000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19057000 19058000 Tfap2d 800.0 -36000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19058000 19059000 Tfap2d 800.0 -35000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19059000 19060000 Tfap2d 800.0 -34000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19060000 19061000 Tfap2d 800.0 -33000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19061000 19062000 Tfap2d 800.0 -32000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19062000 19063000 Tfap2d 800.0 -31000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19063000 19064000 Tfap2d 800.0 -30000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19064000 19065000 Tfap2d 800.0 -29000 0.000000000000 1.000000000000 0.000000000000 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0.001500000000 0.000000000000 0.766333205611 1.200000000000 -chr1 19133000 19134000 Tfap2d 800.0 40000 0.002000000000 0.000000000000 0.961326118464 1.600000000000 -chr1 19134000 19135000 Tfap2d 800.0 41000 0.002250000000 0.000000000000 1.100549008579 1.800000000000 -chr1 19135000 19136000 Tfap2d 800.0 42000 0.002500000000 0.000000000000 1.206882246590 2.000000000000 -chr1 19136000 19137000 Tfap2d 800.0 43000 0.003500000000 0.000000000000 1.763764372185 2.800000000000 -chr1 19137000 19138000 Tfap2d 800.0 44000 0.003250000000 0.000000000000 1.763148819303 2.600000000000 -chr1 19138000 19139000 Tfap2d 800.0 45000 0.002500000000 0.000000000000 1.505874774387 2.000000000000 -chr1 19139000 19140000 Tfap2d 800.0 46000 0.002250000000 0.000000000000 1.357742527578 1.800000000000 -chr1 19140000 19141000 Tfap2d 800.0 47000 0.001750000000 0.000000000000 1.106117884292 1.400000000000 -chr1 19141000 19142000 Tfap2d 800.0 48000 0.000750000000 0.000000000000 0.481357659034 0.600000000000 -chr1 19142000 19143000 Tfap2d 800.0 49000 0.001000000000 0.000000000000 0.617995361700 0.800000000000 -chr1 19143000 19144000 Tfap2d 800.0 50000 0.000500000000 0.000000000000 0.309572025986 0.400000000000 -chr1 19144000 19145000 Tfap2d 800.0 51000 0.001000000000 0.000000000000 0.627306026353 0.800000000000 -chr1 19145000 19146000 Tfap2d 800.0 52000 0.001000000000 0.000000000000 0.613442909647 0.800000000000 -chr1 19146000 19147000 Tfap2d 800.0 53000 0.001000000000 0.000000000000 0.641810212045 0.800000000000 -chr1 19147000 19148000 Tfap2d 800.0 54000 0.000750000000 0.000000000000 0.523741352272 0.600000000000 -chr1 19148000 19149000 Tfap2d 800.0 55000 0.001000000000 0.000000000000 0.708722340602 0.800000000000 -chr1 19149000 19150000 Tfap2d 800.0 56000 0.000500000000 0.000000000000 0.355875534288 0.400000000000 -chr1 19150000 19151000 Tfap2d 800.0 57000 0.000500000000 0.000000000000 0.365240679736 0.400000000000 -chr1 19151000 19152000 Tfap2d 800.0 58000 0.000750000000 0.000000000000 0.546662198984 0.600000000000 -chr1 19152000 19153000 Tfap2d 800.0 59000 0.000500000000 0.000000000000 0.361279284049 0.400000000000 -chr1 19153000 19154000 Tfap2d 800.0 60000 0.000250000000 0.000000000000 0.171700773197 0.200000000000 -chr1 19154000 19155000 Tfap2d 800.0 61000 0.000500000000 0.000000000000 0.352113636434 0.400000000000 -chr1 19155000 19156000 Tfap2d 800.0 62000 0.000500000000 0.000000000000 0.376809389136 0.400000000000 -chr1 19156000 19157000 Tfap2d 800.0 63000 0.000250000000 0.000000000000 0.183829746101 0.200000000000 -chr1 19157000 19158000 Tfap2d 800.0 64000 0.000250000000 0.000000000000 0.184644955624 0.200000000000 -chr1 19158000 19159000 Tfap2d 800.0 65000 0.001000000000 0.000000000000 0.780092506053 0.800000000000 -chr1 19159000 19160000 Tfap2d 800.0 66000 0.000750000000 0.000000000000 0.640575961628 0.600000000000 -chr1 19160000 19161000 Tfap2d 800.0 67000 0.000750000000 0.000000000000 0.612315257231 0.600000000000 -chr1 19161000 19162000 Tfap2d 800.0 68000 0.001000000000 0.000000000000 0.830672069766 0.800000000000 -chr1 19162000 19163000 Tfap2d 800.0 69000 0.001000000000 0.000000000000 0.822467901115 0.800000000000 -chr1 19163000 19164000 Tfap2d 800.0 70000 0.000500000000 0.000000000000 0.403268159690 0.400000000000 -chr1 19164000 19165000 Tfap2d 800.0 71000 0.000750000000 0.000000000000 0.585069379540 0.600000000000 -chr1 19165000 19166000 Tfap2d 800.0 72000 0.001000000000 0.000000000000 0.796888755682 0.800000000000 -chr1 19166000 19167000 Tfap2d 800.0 73000 0.000750000000 0.000000000000 0.618377784575 0.600000000000 -chr1 19167000 19168000 Tfap2d 800.0 74000 0.001000000000 0.000000000000 0.793094047924 0.800000000000 -chr1 19168000 19169000 Tfap2d 800.0 75000 0.000750000000 0.000000000000 0.579639501265 0.600000000000 -chr1 19169000 19170000 Tfap2d 800.0 76000 0.001000000000 0.000000000000 0.767510368762 0.800000000000 -chr1 19170000 19171000 Tfap2d 800.0 77000 0.001500000000 0.000000000000 1.115288504340 1.200000000000 -chr1 19171000 19172000 Tfap2d 800.0 78000 0.001500000000 0.000000000000 1.227639434667 1.200000000000 -chr1 19172000 19173000 Tfap2d 800.0 79000 0.001250000000 0.000000000000 1.038340087208 1.000000000000 -chr1 19173000 19174000 Tfap2d 800.0 80000 0.001250000000 0.000000000000 1.092846128960 1.000000000000 -chr1 19174000 19175000 Tfap2d 800.0 81000 0.000750000000 0.000000000000 0.638937659923 0.600000000000 -chr1 19175000 19176000 Tfap2d 800.0 82000 0.000500000000 0.000000000000 0.430361111197 0.400000000000 -chr1 19176000 19177000 Tfap2d 800.0 83000 0.000750000000 0.000000000000 0.565214083704 0.600000000000 -chr1 19177000 19178000 Tfap2d 800.0 84000 0.000750000000 0.000000000000 0.531541755451 0.600000000000 -chr1 19178000 19179000 Tfap2d 800.0 85000 0.001000000000 0.000000000000 0.707217622245 0.800000000000 -chr1 19179000 19180000 Tfap2d 800.0 86000 0.001250000000 0.000000000000 0.970569638906 1.000000000000 -chr1 19180000 19181000 Tfap2d 800.0 87000 0.001500000000 0.000000000000 1.110331666506 1.200000000000 -chr1 19181000 19182000 Tfap2d 800.0 88000 0.001750000000 0.000000000000 1.286808222709 1.400000000000 -chr1 19182000 19183000 Tfap2d 800.0 89000 0.002000000000 0.000000000000 1.624875609374 1.600000000000 -chr1 19183000 19184000 Tfap2d 800.0 90000 0.002250000000 0.000000000000 1.841459152001 1.800000000000 -chr1 19184000 19185000 Tfap2d 800.0 91000 0.002000000000 0.000000000000 1.571224057089 1.600000000000 -chr1 19185000 19186000 Tfap2d 800.0 92000 0.001250000000 0.000000000000 1.101519511005 1.000000000000 -chr1 19186000 19187000 Tfap2d 800.0 93000 0.000750000000 0.000000000000 0.686331387207 0.600000000000 -chr1 19187000 19188000 Tfap2d 800.0 94000 0.000750000000 0.000000000000 0.629281171287 0.600000000000 -chr1 19188000 19189000 Tfap2d 800.0 95000 0.001500000000 0.000000000000 1.206882246008 1.200000000000 -chr1 19189000 19190000 Tfap2d 800.0 96000 0.002000000000 0.000000000000 1.563847418266 1.600000000000 -chr1 19190000 19191000 Tfap2d 800.0 97000 0.002000000000 0.000000000000 1.620922140709 1.600000000000 -chr1 19191000 19192000 Tfap2d 800.0 98000 0.002500000000 0.000000000000 1.978025535164 2.000000000000 -chr1 19192000 19193000 Tfap2d 800.0 99000 0.003250000000 0.000000000000 2.761666773237 2.600000000000 -chr1 19193000 19194000 Tfap2d 800.0 100000 0.002250000000 0.000000000000 2.135253205224 1.800000000000 -chr1 19194000 19195000 Tfap2d 800.0 101000 0.002250000000 0.000000000000 2.284981325218 1.800000000000 -chr1 19195000 19196000 Tfap2d 800.0 102000 0.004000000000 0.000000000000 3.953703265520 3.200000000000 -chr1 19196000 19197000 Tfap2d 800.0 103000 0.003500000000 0.000000000000 3.822453279063 2.800000000000 -chr1 19197000 19198000 Tfap2d 800.0 104000 0.004250000000 0.000000000000 4.423977733223 3.400000000000 -chr1 19198000 19199000 Tfap2d 800.0 105000 0.005250000000 0.000000000000 5.235845436391 4.200000000000 -chr1 19199000 19200000 Tfap2d 800.0 106000 0.004750000000 0.000000000000 4.626381945577 3.800000000000 -chr1 19200000 19201000 Tfap2d 800.0 107000 0.003000000000 0.000000000000 2.807018258254 2.400000000000 -chr1 19201000 19202000 Tfap2d 800.0 108000 0.003750000000 0.000000000000 3.422255136144 3.000000000000 -chr1 19202000 19203000 Tfap2d 800.0 109000 0.003250000000 0.000000000000 3.075492542686 2.600000000000 -chr1 19203000 19204000 Tfap2d 800.0 110000 0.002750000000 0.000000000000 2.694187133136 2.200000000000 -chr1 19204000 19205000 Tfap2d 800.0 111000 0.003750000000 0.000000000000 3.479451601239 3.000000000000 -chr1 19205000 19206000 Tfap2d 800.0 112000 0.003750000000 0.000000000000 3.568923214524 3.000000000000 -chr1 19206000 19207000 Tfap2d 800.0 113000 0.004000000000 0.000000000000 3.907325514242 3.200000000000 -chr1 19207000 19208000 Tfap2d 800.0 114000 0.003000000000 0.000000000000 2.888145954204 2.400000000000 -chr1 19208000 19209000 Tfap2d 800.0 115000 0.002250000000 0.000000000000 2.185055029640 1.800000000000 -chr1 19209000 19210000 Tfap2d 800.0 116000 0.002000000000 0.000000000000 2.235567114714 1.600000000000 -chr1 19210000 19211000 Tfap2d 800.0 117000 0.003250000000 0.000000000000 3.707443066693 2.600000000000 -chr1 19211000 19212000 Tfap2d 800.0 118000 0.002750000000 0.000000000000 3.180637588552 2.200000000000 -chr1 19212000 19213000 Tfap2d 800.0 119000 0.003000000000 0.000000000000 3.387452543582 2.400000000000 -chr1 19213000 19214000 Tfap2d 800.0 120000 0.003250000000 0.000000000000 3.620646740040 2.600000000000 -chr1 19214000 19215000 Tfap2d 800.0 121000 0.003250000000 0.000000000000 3.561096628728 2.600000000000 -chr1 19215000 19216000 Tfap2d 800.0 122000 0.004000000000 0.000000000000 4.501344596082 3.200000000000 -chr1 19216000 19217000 Tfap2d 800.0 123000 0.003750000000 0.000000000000 4.307321122815 3.000000000000 -chr1 19217000 19218000 Tfap2d 800.0 124000 0.004500000000 0.000000000000 5.490651097659 3.600000000000 -chr1 19218000 19219000 Tfap2d 800.0 125000 0.004250000000 0.000000000000 5.662691502533 3.400000000000 -chr1 19219000 19220000 Tfap2d 800.0 126000 0.004250000000 0.000000000000 5.282361473408 3.400000000000 -chr1 19220000 19221000 Tfap2d 800.0 127000 0.003500000000 0.000000000000 4.449802481277 2.800000000000 -chr1 19221000 19222000 Tfap2d 800.0 128000 0.003250000000 0.000000000000 4.330293501937 2.600000000000 -chr1 19222000 19223000 Tfap2d 800.0 129000 0.002500000000 0.000000000000 3.215246139541 2.000000000000 -chr1 19223000 19224000 Tfap2d 800.0 130000 0.004500000000 0.000000000000 5.411363716616 3.600000000000 -chr1 19224000 19225000 Tfap2d 800.0 131000 0.003750000000 0.000000000000 4.898522060247 3.000000000000 -chr1 19225000 19226000 Tfap2d 800.0 132000 0.002750000000 0.000000000000 3.678809740720 2.200000000000 -chr1 19226000 19227000 Tfap2d 800.0 133000 0.003000000000 0.000000000000 3.620646738024 2.400000000000 -chr1 19227000 19228000 Tfap2d 800.0 134000 0.003250000000 0.000000000000 4.085182547149 2.600000000000 -chr1 19228000 19229000 Tfap2d 800.0 135000 0.002000000000 0.000000000000 2.633197629387 1.600000000000 -chr1 19229000 19230000 Tfap2d 800.0 136000 0.003250000000 0.000000000000 3.922367299526 2.600000000000 -chr1 19230000 19231000 Tfap2d 800.0 137000 0.003250000000 0.000000000000 3.657342484316 2.600000000000 -chr1 19231000 19232000 Tfap2d 800.0 138000 0.003500000000 0.000000000000 4.382888157748 2.800000000000 -chr1 19232000 19233000 Tfap2d 800.0 139000 0.003750000000 0.000000000000 4.398320860434 3.000000000000 -chr1 19233000 19234000 Tfap2d 800.0 140000 0.003500000000 0.000000000000 3.689393195582 2.800000000000 -chr1 19234000 19235000 Tfap2d 800.0 141000 0.002750000000 0.000000000000 3.126360496166 2.200000000000 -chr1 19235000 19236000 Tfap2d 800.0 142000 0.002500000000 0.000000000000 3.178430343770 2.000000000000 -chr1 19236000 19237000 Tfap2d 800.0 143000 0.002250000000 0.000000000000 2.725359544693 1.800000000000 -chr1 19237000 19238000 Tfap2d 800.0 144000 0.001250000000 0.000000000000 1.720555267451 1.000000000000 -chr1 19238000 19239000 Tfap2d 800.0 145000 0.000750000000 0.000000000000 1.249123125975 0.600000000000 -chr1 19239000 19240000 Tfap2d 800.0 146000 0.000500000000 0.000000000000 0.767510368762 0.400000000000 -chr1 19240000 19241000 Tfap2d 800.0 147000 0.000500000000 0.000000000000 0.730481359472 0.400000000000 -chr1 19241000 19242000 Tfap2d 800.0 148000 0.000750000000 0.000000000000 1.135566477299 0.600000000000 -chr1 19242000 19243000 Tfap2d 800.0 149000 0.001000000000 0.000000000000 1.556539719993 0.800000000000 -chr1 19243000 19244000 Tfap2d 800.0 150000 0.001000000000 0.000000000000 1.448258695209 0.800000000000 -chr1 19244000 19245000 Tfap2d 800.0 151000 0.001250000000 0.000000000000 1.909974197425 1.000000000000 -chr1 19245000 19246000 Tfap2d 800.0 152000 0.001250000000 0.000000000000 1.850552777510 1.000000000000 -chr1 19246000 19247000 Tfap2d 800.0 153000 0.000750000000 0.000000000000 1.120289798118 0.600000000000 -chr1 19247000 19248000 Tfap2d 800.0 154000 0.000500000000 0.000000000000 0.760501141597 0.400000000000 -chr1 19248000 19249000 Tfap2d 800.0 155000 0.000500000000 0.000000000000 0.736945796329 0.400000000000 -chr1 19249000 19250000 Tfap2d 800.0 156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19250000 19251000 Tfap2d 800.0 157000 0.000250000000 0.000000000000 0.345538900195 0.200000000000 -chr1 19251000 19252000 Tfap2d 800.0 158000 0.000250000000 0.000000000000 0.333099500149 0.200000000000 -chr1 19252000 19253000 Tfap2d 800.0 159000 0.000250000000 0.000000000000 0.324026751047 0.200000000000 -chr1 19253000 19254000 Tfap2d 800.0 160000 0.000250000000 0.000000000000 0.319060823790 0.200000000000 -chr1 19254000 19255000 Tfap2d 800.0 161000 0.000250000000 0.000000000000 0.300631317590 0.200000000000 -chr1 19255000 19256000 Tfap2d 800.0 162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19256000 19257000 Tfap2d 800.0 163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19257000 19258000 Tfap2d 800.0 164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19258000 19259000 Tfap2d 800.0 165000 0.000250000000 0.000000000000 0.383755184381 0.200000000000 -chr1 19259000 19260000 Tfap2d 800.0 166000 0.000500000000 0.000000000000 0.832748750650 0.400000000000 -chr1 19260000 19261000 Tfap2d 800.0 167000 0.000750000000 0.000000000000 1.195333134476 0.600000000000 -chr1 19261000 19262000 Tfap2d 800.0 168000 0.000750000000 0.000000000000 1.161975000232 0.600000000000 -chr1 19262000 19263000 Tfap2d 800.0 169000 0.001000000000 0.000000000000 1.399577730324 0.800000000000 -chr1 19263000 19264000 Tfap2d 800.0 170000 0.000750000000 0.000000000000 1.015547256684 0.600000000000 -chr1 19264000 19265000 Tfap2d 800.0 171000 0.000750000000 0.000000000000 1.028084877240 0.600000000000 -chr1 19265000 19266000 Tfap2d 800.0 172000 0.000500000000 0.000000000000 0.643049227908 0.400000000000 -chr1 19266000 19267000 Tfap2d 800.0 173000 0.000750000000 0.000000000000 0.983561516064 0.600000000000 -chr1 19267000 19268000 Tfap2d 800.0 174000 0.000500000000 0.000000000000 0.693957291245 0.400000000000 -chr1 19268000 19269000 Tfap2d 800.0 175000 0.000750000000 0.000000000000 1.076830279776 0.600000000000 -chr1 19269000 19270000 Tfap2d 800.0 176000 0.000750000000 0.000000000000 1.063083510150 0.600000000000 -chr1 19270000 19271000 Tfap2d 800.0 177000 0.000750000000 0.000000000000 1.135566477299 0.600000000000 -chr1 19271000 19272000 Tfap2d 800.0 178000 0.000500000000 0.000000000000 0.785612028545 0.400000000000 -chr1 19272000 19273000 Tfap2d 800.0 179000 0.000500000000 0.000000000000 0.800719952292 0.400000000000 -chr1 19273000 19274000 Tfap2d 800.0 180000 0.000250000000 0.000000000000 0.422715101192 0.200000000000 -chr1 19274000 19275000 Tfap2d 800.0 181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19275000 19276000 Tfap2d 800.0 182000 0.000250000000 0.000000000000 0.447714381549 0.200000000000 -chr1 19276000 19277000 Tfap2d 800.0 183000 0.000250000000 0.000000000000 0.433723307028 0.200000000000 -chr1 19277000 19278000 Tfap2d 800.0 184000 0.000750000000 0.000000000000 1.218656708021 0.600000000000 -chr1 19278000 19279000 Tfap2d 800.0 185000 0.000750000000 0.000000000000 1.201079928437 0.600000000000 -chr1 19279000 19280000 Tfap2d 800.0 186000 0.000750000000 0.000000000000 1.328854387687 0.600000000000 -chr1 19280000 19281000 Tfap2d 800.0 187000 0.000500000000 0.000000000000 0.900268918608 0.400000000000 -chr1 19281000 19282000 Tfap2d 800.0 188000 0.000500000000 0.000000000000 0.890640373956 0.400000000000 -chr1 19282000 19283000 Tfap2d 800.0 189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19283000 19284000 Tfap2d 800.0 190000 0.000250000000 0.000000000000 0.486987573219 0.200000000000 -chr1 19284000 19285000 Tfap2d 800.0 191000 0.000250000000 0.000000000000 0.462638194377 0.200000000000 -chr1 19285000 19286000 Tfap2d 800.0 192000 0.000250000000 0.000000000000 0.457554258138 0.200000000000 -chr1 19286000 19287000 Tfap2d 800.0 193000 0.000500000000 0.000000000000 0.991367559904 0.400000000000 -chr1 19287000 19288000 Tfap2d 800.0 194000 0.000500000000 0.000000000000 0.962715318068 0.400000000000 -chr1 19288000 19289000 Tfap2d 800.0 195000 0.000250000000 0.000000000000 0.510888804001 0.200000000000 -chr1 19289000 19290000 Tfap2d 800.0 196000 0.000250000000 0.000000000000 0.510888804001 0.200000000000 -chr1 19290000 19291000 Tfap2d 800.0 197000 0.000250000000 0.000000000000 0.473152698875 0.200000000000 -chr1 19291000 19292000 Tfap2d 800.0 198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19292000 19293000 Tfap2d 800.0 199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19293000 19294000 Tfap2d 800.0 200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt deleted file mode 100644 index 0aecad21..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 4287000 4288000 Sox17 978.0 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4288000 4289000 Sox17 978.0 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4289000 4290000 Sox17 978.0 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4290000 4291000 Sox17 978.0 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4291000 4292000 Sox17 978.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4292000 4293000 Sox17 978.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4293000 4294000 Sox17 978.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4294000 4295000 Sox17 978.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4295000 4296000 Sox17 978.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4296000 4297000 Sox17 978.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4297000 4298000 Sox17 978.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4298000 4299000 Sox17 978.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4299000 4300000 Sox17 978.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4300000 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0.400000000000 -chr1 14480000 14481000 Eya1 673.0 180000 0.001485884101 0.000000000000 2.512422592521 1.000000000000 -chr1 14481000 14482000 Eya1 673.0 181000 0.001188707281 0.000000000000 2.020192860178 0.800000000000 -chr1 14482000 14483000 Eya1 673.0 182000 0.001188707281 0.000000000000 2.128805380321 0.800000000000 -chr1 14483000 14484000 Eya1 673.0 183000 0.001783060921 0.000000000000 3.093420317586 1.200000000000 -chr1 14484000 14485000 Eya1 673.0 184000 0.002080237741 0.000000000000 3.380127570538 1.400000000000 -chr1 14485000 14486000 Eya1 673.0 185000 0.001188707281 0.000000000000 1.903643274393 0.800000000000 -chr1 14486000 14487000 Eya1 673.0 186000 0.001188707281 0.000000000000 2.106158514412 0.800000000000 -chr1 14487000 14488000 Eya1 673.0 187000 0.001188707281 0.000000000000 2.140312436513 0.800000000000 -chr1 14488000 14489000 Eya1 673.0 188000 0.000594353640 0.000000000000 1.058710697124 0.400000000000 -chr1 14489000 14490000 Eya1 673.0 189000 0.000297176820 0.000000000000 0.575520059550 0.200000000000 -chr1 14490000 14491000 Eya1 673.0 190000 0.000297176820 0.000000000000 0.578885673960 0.200000000000 -chr1 14491000 14492000 Eya1 673.0 191000 0.002080237741 0.000000000000 3.849589730333 1.400000000000 -chr1 14492000 14493000 Eya1 673.0 192000 0.003268945022 0.000000000000 5.982878858272 2.200000000000 -chr1 14493000 14494000 Eya1 673.0 193000 0.002971768202 0.000000000000 5.892229182196 2.000000000000 -chr1 14494000 14495000 Eya1 673.0 194000 0.003268945022 0.000000000000 6.294126893758 2.200000000000 -chr1 14495000 14496000 Eya1 673.0 195000 0.003268945022 0.000000000000 6.680269651133 2.200000000000 -chr1 14496000 14497000 Eya1 673.0 196000 0.002971768202 0.000000000000 6.072972410121 2.000000000000 -chr1 14497000 14498000 Eya1 673.0 197000 0.002080237741 0.000000000000 3.937080406684 1.400000000000 -chr1 14498000 14499000 Eya1 673.0 198000 0.002971768202 0.000000000000 4.852424033528 2.000000000000 -chr1 14499000 14500000 Eya1 673.0 199000 0.003343239227 0.000000000000 5.830530441735 2.250000000000 -chr1 14500000 14501000 Eya1 673.0 200000 0.004457652303 0.000000000000 7.575723225668 3.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_2/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_2/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt deleted file mode 100644 index fbac2858..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_2/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 18893000 18894000 Tfap2d 472.0 -200000 0.001412429379 0.009736859396 8.554173074049 0.666666666667 -chr1 18894000 18895000 Tfap2d 472.0 -199000 0.001059322034 0.016726462474 5.040852007510 0.500000000000 -chr1 18895000 18896000 Tfap2d 472.0 -198000 0.000847457627 0.023000625561 3.282415254892 0.400000000000 -chr1 18896000 18897000 Tfap2d 472.0 -197000 0.000847457627 0.023000625561 3.136530131373 0.400000000000 -chr1 18897000 18898000 Tfap2d 472.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18898000 18899000 Tfap2d 472.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18899000 18900000 Tfap2d 472.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18900000 18901000 Tfap2d 472.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18901000 18902000 Tfap2d 472.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18902000 18903000 Tfap2d 472.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18903000 18904000 Tfap2d 472.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18904000 18905000 Tfap2d 472.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18905000 18906000 Tfap2d 472.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18906000 18907000 Tfap2d 472.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18907000 18908000 Tfap2d 472.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18908000 18909000 Tfap2d 472.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18909000 18910000 Tfap2d 472.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18910000 18911000 Tfap2d 472.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18911000 18912000 Tfap2d 472.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18912000 18913000 Tfap2d 472.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18913000 18914000 Tfap2d 472.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18914000 18915000 Tfap2d 472.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18915000 18916000 Tfap2d 472.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18916000 18917000 Tfap2d 472.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18917000 18918000 Tfap2d 472.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18918000 18919000 Tfap2d 472.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18919000 18920000 Tfap2d 472.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18920000 18921000 Tfap2d 472.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18921000 18922000 Tfap2d 472.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18922000 18923000 Tfap2d 472.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18923000 18924000 Tfap2d 472.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18924000 18925000 Tfap2d 472.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18925000 18926000 Tfap2d 472.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18926000 18927000 Tfap2d 472.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18927000 18928000 Tfap2d 472.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18928000 18929000 Tfap2d 472.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18929000 18930000 Tfap2d 472.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18930000 18931000 Tfap2d 472.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18931000 18932000 Tfap2d 472.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18932000 18933000 Tfap2d 472.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18933000 18934000 Tfap2d 472.0 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18934000 18935000 Tfap2d 472.0 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18935000 18936000 Tfap2d 472.0 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18936000 18937000 Tfap2d 472.0 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18937000 18938000 Tfap2d 472.0 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18938000 18939000 Tfap2d 472.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18939000 18940000 Tfap2d 472.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18940000 18941000 Tfap2d 472.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18941000 18942000 Tfap2d 472.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18942000 18943000 Tfap2d 472.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18943000 18944000 Tfap2d 472.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18944000 18945000 Tfap2d 472.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18945000 18946000 Tfap2d 472.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18946000 18947000 Tfap2d 472.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18947000 18948000 Tfap2d 472.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18948000 18949000 Tfap2d 472.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18949000 18950000 Tfap2d 472.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18950000 18951000 Tfap2d 472.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18951000 18952000 Tfap2d 472.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18952000 18953000 Tfap2d 472.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18953000 18954000 Tfap2d 472.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18954000 18955000 Tfap2d 472.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18955000 18956000 Tfap2d 472.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18956000 18957000 Tfap2d 472.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18957000 18958000 Tfap2d 472.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18958000 18959000 Tfap2d 472.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18959000 18960000 Tfap2d 472.0 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18960000 18961000 Tfap2d 472.0 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18961000 18962000 Tfap2d 472.0 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18962000 18963000 Tfap2d 472.0 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18963000 18964000 Tfap2d 472.0 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18964000 18965000 Tfap2d 472.0 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18965000 18966000 Tfap2d 472.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18966000 18967000 Tfap2d 472.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18967000 18968000 Tfap2d 472.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18968000 18969000 Tfap2d 472.0 -125000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18969000 18970000 Tfap2d 472.0 -124000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18970000 18971000 Tfap2d 472.0 -123000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18971000 18972000 Tfap2d 472.0 -122000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18972000 18973000 Tfap2d 472.0 -121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18973000 18974000 Tfap2d 472.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18974000 18975000 Tfap2d 472.0 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18975000 18976000 Tfap2d 472.0 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18976000 18977000 Tfap2d 472.0 -117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18977000 18978000 Tfap2d 472.0 -116000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18978000 18979000 Tfap2d 472.0 -115000 0.001271186441 0.012107544045 3.257165906583 0.600000000000 -chr1 18979000 18980000 Tfap2d 472.0 -114000 0.001271186441 0.012107544045 3.470750557945 0.600000000000 -chr1 18980000 18981000 Tfap2d 472.0 -113000 0.001271186441 0.012107544045 3.814698814531 0.600000000000 -chr1 18981000 18982000 Tfap2d 472.0 -112000 0.001271186441 0.012107544045 4.602517039860 0.600000000000 -chr1 18982000 18983000 Tfap2d 472.0 -111000 0.001271186441 0.012107544045 4.553027608970 0.600000000000 -chr1 18983000 18984000 Tfap2d 472.0 -110000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18984000 18985000 Tfap2d 472.0 -109000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18985000 18986000 Tfap2d 472.0 -108000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18986000 18987000 Tfap2d 472.0 -107000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18987000 18988000 Tfap2d 472.0 -106000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18988000 18989000 Tfap2d 472.0 -105000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18989000 18990000 Tfap2d 472.0 -104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18990000 18991000 Tfap2d 472.0 -103000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18991000 18992000 Tfap2d 472.0 -102000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18992000 18993000 Tfap2d 472.0 -101000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18993000 18994000 Tfap2d 472.0 -100000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18994000 18995000 Tfap2d 472.0 -99000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18995000 18996000 Tfap2d 472.0 -98000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18996000 18997000 Tfap2d 472.0 -97000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18997000 18998000 Tfap2d 472.0 -96000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18998000 18999000 Tfap2d 472.0 -95000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18999000 19000000 Tfap2d 472.0 -94000 0.000423728814 0.042850447268 1.102686374757 0.200000000000 -chr1 19000000 19001000 Tfap2d 472.0 -93000 0.000423728814 0.042850447268 1.061231999455 0.200000000000 -chr1 19001000 19002000 Tfap2d 472.0 -92000 0.000423728814 0.042850447268 0.779800308873 0.200000000000 -chr1 19002000 19003000 Tfap2d 472.0 -91000 0.000423728814 0.042850447268 0.735124249200 0.200000000000 -chr1 19003000 19004000 Tfap2d 472.0 -90000 0.000423728814 0.042850447268 0.727545648641 0.200000000000 -chr1 19004000 19005000 Tfap2d 472.0 -89000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19005000 19006000 Tfap2d 472.0 -88000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19006000 19007000 Tfap2d 472.0 -87000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19007000 19008000 Tfap2d 472.0 -86000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19008000 19009000 Tfap2d 472.0 -85000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19009000 19010000 Tfap2d 472.0 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19010000 19011000 Tfap2d 472.0 -83000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19011000 19012000 Tfap2d 472.0 -82000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19012000 19013000 Tfap2d 472.0 -81000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19013000 19014000 Tfap2d 472.0 -80000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19014000 19015000 Tfap2d 472.0 -79000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19015000 19016000 Tfap2d 472.0 -78000 0.000423728814 0.042850447268 1.238104000914 0.200000000000 -chr1 19016000 19017000 Tfap2d 472.0 -77000 0.000423728814 0.042850447268 0.980165665600 0.200000000000 -chr1 19017000 19018000 Tfap2d 472.0 -76000 0.000423728814 0.042850447268 0.934727521861 0.200000000000 -chr1 19018000 19019000 Tfap2d 472.0 -75000 0.000423728814 0.042850447268 1.022781564413 0.200000000000 -chr1 19019000 19020000 Tfap2d 472.0 -74000 0.000423728814 0.042850447268 1.001020254378 0.200000000000 -chr1 19020000 19021000 Tfap2d 472.0 -73000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19021000 19022000 Tfap2d 472.0 -72000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19022000 19023000 Tfap2d 472.0 -71000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19023000 19024000 Tfap2d 472.0 -70000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19024000 19025000 Tfap2d 472.0 -69000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19025000 19026000 Tfap2d 472.0 -68000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19026000 19027000 Tfap2d 472.0 -67000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19027000 19028000 Tfap2d 472.0 -66000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19028000 19029000 Tfap2d 472.0 -65000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19029000 19030000 Tfap2d 472.0 -64000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19030000 19031000 Tfap2d 472.0 -63000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19031000 19032000 Tfap2d 472.0 -62000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19032000 19033000 Tfap2d 472.0 -61000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19033000 19034000 Tfap2d 472.0 -60000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19034000 19035000 Tfap2d 472.0 -59000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19035000 19036000 Tfap2d 472.0 -58000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19036000 19037000 Tfap2d 472.0 -57000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19037000 19038000 Tfap2d 472.0 -56000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19038000 19039000 Tfap2d 472.0 -55000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19039000 19040000 Tfap2d 472.0 -54000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19040000 19041000 Tfap2d 472.0 -53000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19041000 19042000 Tfap2d 472.0 -52000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19042000 19043000 Tfap2d 472.0 -51000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19043000 19044000 Tfap2d 472.0 -50000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19044000 19045000 Tfap2d 472.0 -49000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19045000 19046000 Tfap2d 472.0 -48000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19046000 19047000 Tfap2d 472.0 -47000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19047000 19048000 Tfap2d 472.0 -46000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19048000 19049000 Tfap2d 472.0 -45000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19049000 19050000 Tfap2d 472.0 -44000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19050000 19051000 Tfap2d 472.0 -43000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19051000 19052000 Tfap2d 472.0 -42000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19052000 19053000 Tfap2d 472.0 -41000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19053000 19054000 Tfap2d 472.0 -40000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19054000 19055000 Tfap2d 472.0 -39000 0.000423728814 0.042850447268 0.571432615421 0.200000000000 -chr1 19055000 19056000 Tfap2d 472.0 -38000 0.000423728814 0.042850447268 0.624530335872 0.200000000000 -chr1 19056000 19057000 Tfap2d 472.0 -37000 0.000423728814 0.042850447268 0.551343187379 0.200000000000 -chr1 19057000 19058000 Tfap2d 472.0 -36000 0.000423728814 0.042850447268 0.566842795180 0.200000000000 -chr1 19058000 19059000 Tfap2d 472.0 -35000 0.000423728814 0.042850447268 0.593041411154 0.200000000000 -chr1 19059000 19060000 Tfap2d 472.0 -34000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19060000 19061000 Tfap2d 472.0 -33000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19061000 19062000 Tfap2d 472.0 -32000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19062000 19063000 Tfap2d 472.0 -31000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19063000 19064000 Tfap2d 472.0 -30000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19064000 19065000 Tfap2d 472.0 -29000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19065000 19066000 Tfap2d 472.0 -28000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19066000 19067000 Tfap2d 472.0 -27000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19067000 19068000 Tfap2d 472.0 -26000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19068000 19069000 Tfap2d 472.0 -25000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19069000 19070000 Tfap2d 472.0 -24000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19070000 19071000 Tfap2d 472.0 -23000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19071000 19072000 Tfap2d 472.0 -22000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19072000 19073000 Tfap2d 472.0 -21000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19073000 19074000 Tfap2d 472.0 -20000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19074000 19075000 Tfap2d 472.0 -19000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19075000 19076000 Tfap2d 472.0 -18000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19076000 19077000 Tfap2d 472.0 -17000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19077000 19078000 Tfap2d 472.0 -16000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19078000 19079000 Tfap2d 472.0 -15000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19079000 19080000 Tfap2d 472.0 -14000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19080000 19081000 Tfap2d 472.0 -13000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19081000 19082000 Tfap2d 472.0 -12000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19082000 19083000 Tfap2d 472.0 -11000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19083000 19084000 Tfap2d 472.0 -10000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 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1.219741990578 45.800000000000 -chr1 19094000 19095000 Tfap2d 472.0 1000 0.088559322034 0.000000000000 1.131750082102 41.800000000000 -chr1 19095000 19096000 Tfap2d 472.0 2000 0.079237288136 0.000000000000 1.158236837774 37.400000000000 -chr1 19096000 19097000 Tfap2d 472.0 3000 0.030084745763 0.000000000000 1.213515835692 14.200000000000 -chr1 19097000 19098000 Tfap2d 472.0 4000 0.025423728814 0.000000000000 1.625145146017 12.000000000000 -chr1 19098000 19099000 Tfap2d 472.0 5000 0.017796610169 0.000000000000 1.469519570887 8.400000000000 -chr1 19099000 19100000 Tfap2d 472.0 6000 0.012288135593 0.000000000000 1.174511283228 5.800000000000 -chr1 19100000 19101000 Tfap2d 472.0 7000 0.009745762712 0.000000000000 1.020530866525 4.600000000000 -chr1 19101000 19102000 Tfap2d 472.0 8000 0.010169491525 0.000000000000 1.167282061499 4.800000000000 -chr1 19102000 19103000 Tfap2d 472.0 9000 0.011440677966 0.000000000000 1.429438900967 5.400000000000 -chr1 19103000 19104000 Tfap2d 472.0 10000 0.010593220339 0.000000000000 1.461721788921 5.000000000000 -chr1 19104000 19105000 Tfap2d 472.0 11000 0.012288135593 0.000000000000 1.918974131188 5.800000000000 -chr1 19105000 19106000 Tfap2d 472.0 12000 0.010169491525 0.000000000000 1.708246365312 4.800000000000 -chr1 19106000 19107000 Tfap2d 472.0 13000 0.007203389831 0.000000000000 1.341221660736 3.400000000000 -chr1 19107000 19108000 Tfap2d 472.0 14000 0.007203389831 0.000000000000 1.483887168230 3.400000000000 -chr1 19108000 19109000 Tfap2d 472.0 15000 0.006355932203 0.000000000000 1.367673022577 3.000000000000 -chr1 19109000 19110000 Tfap2d 472.0 16000 0.008050847458 0.000000000000 1.767787252797 3.800000000000 -chr1 19110000 19111000 Tfap2d 472.0 17000 0.006779661017 0.000000000000 1.614225657668 3.200000000000 -chr1 19111000 19112000 Tfap2d 472.0 18000 0.009745762712 0.000000000000 2.388748113765 4.600000000000 -chr1 19112000 19113000 Tfap2d 472.0 19000 0.007203389831 0.000000000000 1.810902302517 3.400000000000 -chr1 19113000 19114000 Tfap2d 472.0 20000 0.007627118644 0.000000000000 2.035728691180 3.600000000000 -chr1 19114000 19115000 Tfap2d 472.0 21000 0.003813559322 0.000000000000 1.046371254994 1.800000000000 -chr1 19115000 19116000 Tfap2d 472.0 22000 0.003813559322 0.000000000000 1.090381719525 1.800000000000 -chr1 19116000 19117000 Tfap2d 472.0 23000 0.000847457627 0.000000000000 0.270649771714 0.400000000000 -chr1 19117000 19118000 Tfap2d 472.0 24000 0.000423728814 0.000000000000 0.137835796800 0.200000000000 -chr1 19118000 19119000 Tfap2d 472.0 25000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19119000 19120000 Tfap2d 472.0 26000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19120000 19121000 Tfap2d 472.0 27000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19121000 19122000 Tfap2d 472.0 28000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19122000 19123000 Tfap2d 472.0 29000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19123000 19124000 Tfap2d 472.0 30000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19124000 19125000 Tfap2d 472.0 31000 0.002118644068 0.000000000000 0.852317970687 1.000000000000 -chr1 19125000 19126000 Tfap2d 472.0 32000 0.003813559322 0.000000000000 1.599867384629 1.800000000000 -chr1 19126000 19127000 Tfap2d 472.0 33000 0.004237288136 0.000000000000 1.807219666460 2.000000000000 -chr1 19127000 19128000 Tfap2d 472.0 34000 0.004237288136 0.000000000000 1.884430653326 2.000000000000 -chr1 19128000 19129000 Tfap2d 472.0 35000 0.004237288136 0.000000000000 1.993557287139 2.000000000000 -chr1 19129000 19130000 Tfap2d 472.0 36000 0.002118644068 0.000000000000 1.024266008409 1.000000000000 -chr1 19130000 19131000 Tfap2d 472.0 37000 0.000847457627 0.000000000000 0.420070999751 0.400000000000 -chr1 19131000 19132000 Tfap2d 472.0 38000 0.000847457627 0.000000000000 0.430316633970 0.400000000000 -chr1 19132000 19133000 Tfap2d 472.0 39000 0.001694915254 0.000000000000 0.865913226679 0.800000000000 -chr1 19133000 19134000 Tfap2d 472.0 40000 0.003389830508 0.000000000000 1.629366302482 1.600000000000 -chr1 19134000 19135000 Tfap2d 472.0 41000 0.004237288136 0.000000000000 2.072597002974 2.000000000000 -chr1 19135000 19136000 Tfap2d 472.0 42000 0.004237288136 0.000000000000 2.045563129814 2.000000000000 -chr1 19136000 19137000 Tfap2d 472.0 43000 0.004237288136 0.000000000000 2.135307956640 2.000000000000 -chr1 19137000 19138000 Tfap2d 472.0 44000 0.003389830508 0.000000000000 1.839007894971 1.600000000000 -chr1 19138000 19139000 Tfap2d 472.0 45000 0.001694915254 0.000000000000 1.020932050432 0.800000000000 -chr1 19139000 19140000 Tfap2d 472.0 46000 0.000847457627 0.000000000000 0.511390782515 0.400000000000 -chr1 19140000 19141000 Tfap2d 472.0 47000 0.000423728814 0.000000000000 0.267825153582 0.200000000000 -chr1 19141000 19142000 Tfap2d 472.0 48000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19142000 19143000 Tfap2d 472.0 49000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19143000 19144000 Tfap2d 472.0 50000 0.000423728814 0.000000000000 0.262349174564 0.200000000000 -chr1 19144000 19145000 Tfap2d 472.0 51000 0.001271186441 0.000000000000 0.797422914856 0.600000000000 -chr1 19145000 19146000 Tfap2d 472.0 52000 0.002118644068 0.000000000000 1.299667181455 1.000000000000 -chr1 19146000 19147000 Tfap2d 472.0 53000 0.002118644068 0.000000000000 1.359767398401 1.000000000000 -chr1 19147000 19148000 Tfap2d 472.0 54000 0.002118644068 0.000000000000 1.479495345400 1.000000000000 -chr1 19148000 19149000 Tfap2d 472.0 55000 0.001694915254 0.000000000000 1.201224306105 0.800000000000 -chr1 19149000 19150000 Tfap2d 472.0 56000 0.000847457627 0.000000000000 0.603178871675 0.400000000000 -chr1 19150000 19151000 Tfap2d 472.0 57000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19151000 19152000 Tfap2d 472.0 58000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19152000 19153000 Tfap2d 472.0 59000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19153000 19154000 Tfap2d 472.0 60000 0.000423728814 0.000000000000 0.291018259656 0.200000000000 -chr1 19154000 19155000 Tfap2d 472.0 61000 0.001694915254 0.000000000000 1.193605547234 0.800000000000 -chr1 19155000 19156000 Tfap2d 472.0 62000 0.001694915254 0.000000000000 1.277319963174 0.800000000000 -chr1 19156000 19157000 Tfap2d 472.0 63000 0.001694915254 0.000000000000 1.246303363398 0.800000000000 -chr1 19157000 19158000 Tfap2d 472.0 64000 0.002118644068 0.000000000000 1.564787759528 1.000000000000 -chr1 19158000 19159000 Tfap2d 472.0 65000 0.002966101695 0.000000000000 2.313833704394 1.400000000000 -chr1 19159000 19160000 Tfap2d 472.0 66000 0.001694915254 0.000000000000 1.447629291815 0.800000000000 -chr1 19160000 19161000 Tfap2d 472.0 67000 0.002118644068 0.000000000000 1.729704116472 1.000000000000 -chr1 19161000 19162000 Tfap2d 472.0 68000 0.002118644068 0.000000000000 1.759898452895 1.000000000000 -chr1 19162000 19163000 Tfap2d 472.0 69000 0.001694915254 0.000000000000 1.394013391721 0.800000000000 -chr1 19163000 19164000 Tfap2d 472.0 70000 0.000423728814 0.000000000000 0.341752677703 0.200000000000 -chr1 19164000 19165000 Tfap2d 472.0 71000 0.000847457627 0.000000000000 0.661095344113 0.400000000000 -chr1 19165000 19166000 Tfap2d 472.0 72000 0.000423728814 0.000000000000 0.337664726984 0.200000000000 -chr1 19166000 19167000 Tfap2d 472.0 73000 0.000423728814 0.000000000000 0.349365979986 0.200000000000 -chr1 19167000 19168000 Tfap2d 472.0 74000 0.000423728814 0.000000000000 0.336056799968 0.200000000000 -chr1 19168000 19169000 Tfap2d 472.0 75000 0.000423728814 0.000000000000 0.327479944218 0.200000000000 -chr1 19169000 19170000 Tfap2d 472.0 76000 0.000423728814 0.000000000000 0.325216257950 0.200000000000 -chr1 19170000 19171000 Tfap2d 472.0 77000 0.000847457627 0.000000000000 0.630106499627 0.400000000000 -chr1 19171000 19172000 Tfap2d 472.0 78000 0.000847457627 0.000000000000 0.693581601507 0.400000000000 -chr1 19172000 19173000 Tfap2d 472.0 79000 0.000847457627 0.000000000000 0.703959381158 0.400000000000 -chr1 19173000 19174000 Tfap2d 472.0 80000 0.000847457627 0.000000000000 0.740912629804 0.400000000000 -chr1 19174000 19175000 Tfap2d 472.0 81000 0.000847457627 0.000000000000 0.721963457541 0.400000000000 -chr1 19175000 19176000 Tfap2d 472.0 82000 0.000423728814 0.000000000000 0.364712806099 0.200000000000 -chr1 19176000 19177000 Tfap2d 472.0 83000 0.000423728814 0.000000000000 0.319329990793 0.200000000000 -chr1 19177000 19178000 Tfap2d 472.0 84000 0.000423728814 0.000000000000 0.300306076526 0.200000000000 -chr1 19178000 19179000 Tfap2d 472.0 85000 0.000423728814 0.000000000000 0.299668484002 0.200000000000 -chr1 19179000 19180000 Tfap2d 472.0 86000 0.000423728814 0.000000000000 0.329006657256 0.200000000000 -chr1 19180000 19181000 Tfap2d 472.0 87000 0.000847457627 0.000000000000 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0.001694915254 0.000000000000 1.373662831110 0.800000000000 -chr1 19191000 19192000 Tfap2d 472.0 98000 0.001271186441 0.000000000000 1.005775695846 0.600000000000 -chr1 19192000 19193000 Tfap2d 472.0 99000 0.001271186441 0.000000000000 1.080182571018 0.600000000000 -chr1 19193000 19194000 Tfap2d 472.0 100000 0.000847457627 0.000000000000 0.804238495376 0.400000000000 -chr1 19194000 19195000 Tfap2d 472.0 101000 0.000847457627 0.000000000000 0.860633267502 0.400000000000 -chr1 19195000 19196000 Tfap2d 472.0 102000 0.000847457627 0.000000000000 0.837648996932 0.400000000000 -chr1 19196000 19197000 Tfap2d 472.0 103000 0.000847457627 0.000000000000 0.925533481613 0.400000000000 -chr1 19197000 19198000 Tfap2d 472.0 104000 0.001694915254 0.000000000000 1.764298198693 0.800000000000 -chr1 19198000 19199000 Tfap2d 472.0 105000 0.002118644068 0.000000000000 2.112931975945 1.000000000000 -chr1 19199000 19200000 Tfap2d 472.0 106000 0.002118644068 0.000000000000 2.063506666181 1.000000000000 -chr1 19200000 19201000 Tfap2d 472.0 107000 0.002118644068 0.000000000000 1.982357527016 1.000000000000 -chr1 19201000 19202000 Tfap2d 472.0 108000 0.002542372881 0.000000000000 2.320172973657 1.200000000000 -chr1 19202000 19203000 Tfap2d 472.0 109000 0.001271186441 0.000000000000 1.202930590359 0.600000000000 -chr1 19203000 19204000 Tfap2d 472.0 110000 0.000847457627 0.000000000000 0.830257976313 0.400000000000 -chr1 19204000 19205000 Tfap2d 472.0 111000 0.001271186441 0.000000000000 1.179475119064 0.600000000000 -chr1 19205000 19206000 Tfap2d 472.0 112000 0.001694915254 0.000000000000 1.613072639333 0.800000000000 -chr1 19206000 19207000 Tfap2d 472.0 113000 0.001271186441 0.000000000000 1.241734803255 0.600000000000 -chr1 19207000 19208000 Tfap2d 472.0 114000 0.000847457627 0.000000000000 0.815860439041 0.400000000000 -chr1 19208000 19209000 Tfap2d 472.0 115000 0.000847457627 0.000000000000 0.822996244685 0.400000000000 -chr1 19209000 19210000 Tfap2d 472.0 116000 0.000423728814 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19220000 Tfap2d 472.0 126000 0.001271186441 0.000000000000 1.579968536413 0.600000000000 -chr1 19220000 19221000 Tfap2d 472.0 127000 0.000847457627 0.000000000000 1.077434014837 0.400000000000 -chr1 19221000 19222000 Tfap2d 472.0 128000 0.000847457627 0.000000000000 1.129150847963 0.400000000000 -chr1 19222000 19223000 Tfap2d 472.0 129000 0.000847457627 0.000000000000 1.089913945607 0.400000000000 -chr1 19223000 19224000 Tfap2d 472.0 130000 0.000847457627 0.000000000000 1.019089212169 0.400000000000 -chr1 19224000 19225000 Tfap2d 472.0 131000 0.000423728814 0.000000000000 0.553505317542 0.200000000000 -chr1 19225000 19226000 Tfap2d 472.0 132000 0.000423728814 0.000000000000 0.566842795180 0.200000000000 -chr1 19226000 19227000 Tfap2d 472.0 133000 0.000423728814 0.000000000000 0.511390782207 0.200000000000 -chr1 19227000 19228000 Tfap2d 472.0 134000 0.001271186441 0.000000000000 1.597854972809 0.600000000000 -chr1 19228000 19229000 Tfap2d 472.0 135000 0.001694915254 0.000000000000 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472.0 145000 0.001271186441 0.000000000000 2.117157840635 0.600000000000 -chr1 19239000 19240000 Tfap2d 472.0 146000 0.001694915254 0.000000000000 2.601730063600 0.800000000000 -chr1 19240000 19241000 Tfap2d 472.0 147000 0.001271186441 0.000000000000 1.857155998658 0.600000000000 -chr1 19241000 19242000 Tfap2d 472.0 148000 0.000423728814 0.000000000000 0.641562981525 0.200000000000 -chr1 19242000 19243000 Tfap2d 472.0 149000 0.000423728814 0.000000000000 0.659550728811 0.200000000000 -chr1 19243000 19244000 Tfap2d 472.0 150000 0.000847457627 0.000000000000 1.227337877296 0.400000000000 -chr1 19244000 19245000 Tfap2d 472.0 151000 0.001271186441 0.000000000000 1.942346641449 0.600000000000 -chr1 19245000 19246000 Tfap2d 472.0 152000 0.001271186441 0.000000000000 1.881918078824 0.600000000000 -chr1 19246000 19247000 Tfap2d 472.0 153000 0.002118644068 0.000000000000 3.164660446662 1.000000000000 -chr1 19247000 19248000 Tfap2d 472.0 154000 0.002118644068 0.000000000000 3.222462464392 1.000000000000 -chr1 19248000 19249000 Tfap2d 472.0 155000 0.001694915254 0.000000000000 2.498121343489 0.800000000000 -chr1 19249000 19250000 Tfap2d 472.0 156000 0.000847457627 0.000000000000 1.249060671745 0.400000000000 -chr1 19250000 19251000 Tfap2d 472.0 157000 0.000847457627 0.000000000000 1.171318305746 0.400000000000 -chr1 19251000 19252000 Tfap2d 472.0 158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19252000 19253000 Tfap2d 472.0 159000 0.000847457627 0.000000000000 1.098395766262 0.400000000000 -chr1 19253000 19254000 Tfap2d 472.0 160000 0.000847457627 0.000000000000 1.081562114542 0.400000000000 -chr1 19254000 19255000 Tfap2d 472.0 161000 0.001694915254 0.000000000000 2.038178424337 0.800000000000 -chr1 19255000 19256000 Tfap2d 472.0 162000 0.001694915254 0.000000000000 2.304389486014 0.800000000000 -chr1 19256000 19257000 Tfap2d 472.0 163000 0.002542372881 0.000000000000 3.513954917238 1.200000000000 -chr1 19257000 19258000 Tfap2d 472.0 164000 0.002118644068 0.000000000000 3.055061815685 1.000000000000 -chr1 19258000 19259000 Tfap2d 472.0 165000 0.002118644068 0.000000000000 3.252162579500 1.000000000000 -chr1 19259000 19260000 Tfap2d 472.0 166000 0.001694915254 0.000000000000 2.822877120847 0.800000000000 -chr1 19260000 19261000 Tfap2d 472.0 167000 0.001694915254 0.000000000000 2.701317818024 0.800000000000 -chr1 19261000 19262000 Tfap2d 472.0 168000 0.000847457627 0.000000000000 1.312966101957 0.400000000000 -chr1 19262000 19263000 Tfap2d 472.0 169000 0.000423728814 0.000000000000 0.593041411154 0.200000000000 -chr1 19263000 19264000 Tfap2d 472.0 170000 0.000423728814 0.000000000000 0.573755512251 0.200000000000 -chr1 19264000 19265000 Tfap2d 472.0 171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19265000 19266000 Tfap2d 472.0 172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19266000 19267000 Tfap2d 472.0 173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19267000 19268000 Tfap2d 472.0 174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19268000 19269000 Tfap2d 472.0 175000 0.000423728814 0.000000000000 0.608378689139 0.200000000000 -chr1 19269000 19270000 Tfap2d 472.0 176000 0.000423728814 0.000000000000 0.600612152627 0.200000000000 -chr1 19270000 19271000 Tfap2d 472.0 177000 0.000423728814 0.000000000000 0.641562981525 0.200000000000 -chr1 19271000 19272000 Tfap2d 472.0 178000 0.000423728814 0.000000000000 0.665772905546 0.200000000000 -chr1 19272000 19273000 Tfap2d 472.0 179000 0.000423728814 0.000000000000 0.678576230756 0.200000000000 -chr1 19273000 19274000 Tfap2d 472.0 180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19274000 19275000 Tfap2d 472.0 181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19275000 19276000 Tfap2d 472.0 182000 0.000423728814 0.000000000000 0.758837934828 0.200000000000 -chr1 19276000 19277000 Tfap2d 472.0 183000 0.000423728814 0.000000000000 0.735124249200 0.200000000000 -chr1 19277000 19278000 Tfap2d 472.0 184000 0.000423728814 0.000000000000 0.688506614701 0.200000000000 -chr1 19278000 19279000 Tfap2d 472.0 185000 0.000423728814 0.000000000000 0.678576230756 0.200000000000 -chr1 19279000 19280000 Tfap2d 472.0 186000 0.000423728814 0.000000000000 0.750765190784 0.200000000000 -chr1 19280000 19281000 Tfap2d 472.0 187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19281000 19282000 Tfap2d 472.0 188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19282000 19283000 Tfap2d 472.0 189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19283000 19284000 Tfap2d 472.0 190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19284000 19285000 Tfap2d 472.0 191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19285000 19286000 Tfap2d 472.0 192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19286000 19287000 Tfap2d 472.0 193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19287000 19288000 Tfap2d 472.0 194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19288000 19289000 Tfap2d 472.0 195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19289000 19290000 Tfap2d 472.0 196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19290000 19291000 Tfap2d 472.0 197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19291000 19292000 Tfap2d 472.0 198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19292000 19293000 Tfap2d 472.0 199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19293000 19294000 Tfap2d 472.0 200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_2/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_2/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt deleted file mode 100644 index cdb1a506..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_2/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 4287000 4288000 Sox17 810.0 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4288000 4289000 Sox17 810.0 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4289000 4290000 Sox17 810.0 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4290000 4291000 Sox17 810.0 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4291000 4292000 Sox17 810.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4292000 4293000 Sox17 810.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4293000 4294000 Sox17 810.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4294000 4295000 Sox17 810.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4295000 4296000 Sox17 810.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4296000 4297000 Sox17 810.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4297000 4298000 Sox17 810.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4298000 4299000 Sox17 810.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4299000 4300000 Sox17 810.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4300000 4301000 Sox17 810.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4301000 4302000 Sox17 810.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4302000 4303000 Sox17 810.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4303000 4304000 Sox17 810.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4304000 4305000 Sox17 810.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4305000 4306000 Sox17 810.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4306000 4307000 Sox17 810.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4307000 4308000 Sox17 810.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4308000 4309000 Sox17 810.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4309000 4310000 Sox17 810.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4310000 4311000 Sox17 810.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4311000 4312000 Sox17 810.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4312000 4313000 Sox17 810.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4313000 4314000 Sox17 810.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4314000 4315000 Sox17 810.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4315000 4316000 Sox17 810.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4316000 4317000 Sox17 810.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4317000 4318000 Sox17 810.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4318000 4319000 Sox17 810.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4319000 4320000 Sox17 810.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4320000 4321000 Sox17 810.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4321000 4322000 Sox17 810.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4322000 4323000 Sox17 810.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4323000 4324000 Sox17 810.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4324000 4325000 Sox17 810.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4325000 4326000 Sox17 810.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4326000 4327000 Sox17 810.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4327000 4328000 Sox17 810.0 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4328000 4329000 Sox17 810.0 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4329000 4330000 Sox17 810.0 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4330000 4331000 Sox17 810.0 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4331000 4332000 Sox17 810.0 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4332000 4333000 Sox17 810.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4333000 4334000 Sox17 810.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4334000 4335000 Sox17 810.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4335000 4336000 Sox17 810.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4336000 4337000 Sox17 810.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4337000 4338000 Sox17 810.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4338000 4339000 Sox17 810.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4339000 4340000 Sox17 810.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4340000 4341000 Sox17 810.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4341000 4342000 Sox17 810.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4342000 4343000 Sox17 810.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4343000 4344000 Sox17 810.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4344000 4345000 Sox17 810.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4345000 4346000 Sox17 810.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4346000 4347000 Sox17 810.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4347000 4348000 Sox17 810.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4348000 4349000 Sox17 810.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4349000 4350000 Sox17 810.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4350000 4351000 Sox17 810.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4351000 4352000 Sox17 810.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4352000 4353000 Sox17 810.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4353000 4354000 Sox17 810.0 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4354000 4355000 Sox17 810.0 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4355000 4356000 Sox17 810.0 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4356000 4357000 Sox17 810.0 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4357000 4358000 Sox17 810.0 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4358000 4359000 Sox17 810.0 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4359000 4360000 Sox17 810.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4360000 4361000 Sox17 810.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4361000 4362000 Sox17 810.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4362000 4363000 Sox17 810.0 -125000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4363000 4364000 Sox17 810.0 -124000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4364000 4365000 Sox17 810.0 -123000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4365000 4366000 Sox17 810.0 -122000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4366000 4367000 Sox17 810.0 -121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4367000 4368000 Sox17 810.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4368000 4369000 Sox17 810.0 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4369000 4370000 Sox17 810.0 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4370000 4371000 Sox17 810.0 -117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4371000 4372000 Sox17 810.0 -116000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4372000 4373000 Sox17 810.0 -115000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4373000 4374000 Sox17 810.0 -114000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4374000 4375000 Sox17 810.0 -113000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4375000 4376000 Sox17 810.0 -112000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4376000 4377000 Sox17 810.0 -111000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4377000 4378000 Sox17 810.0 -110000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4378000 4379000 Sox17 810.0 -109000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4379000 4380000 Sox17 810.0 -108000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4380000 4381000 Sox17 810.0 -107000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4381000 4382000 Sox17 810.0 -106000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4382000 4383000 Sox17 810.0 -105000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4383000 4384000 Sox17 810.0 -104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4384000 4385000 Sox17 810.0 -103000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4385000 4386000 Sox17 810.0 -102000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4386000 4387000 Sox17 810.0 -101000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4387000 4388000 Sox17 810.0 -100000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4388000 4389000 Sox17 810.0 -99000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4389000 4390000 Sox17 810.0 -98000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4390000 4391000 Sox17 810.0 -97000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4391000 4392000 Sox17 810.0 -96000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4392000 4393000 Sox17 810.0 -95000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4393000 4394000 Sox17 810.0 -94000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4394000 4395000 Sox17 810.0 -93000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4395000 4396000 Sox17 810.0 -92000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4396000 4397000 Sox17 810.0 -91000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4397000 4398000 Sox17 810.0 -90000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4398000 4399000 Sox17 810.0 -89000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4399000 4400000 Sox17 810.0 -88000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4400000 4401000 Sox17 810.0 -87000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4401000 4402000 Sox17 810.0 -86000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4402000 4403000 Sox17 810.0 -85000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4403000 4404000 Sox17 810.0 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4404000 4405000 Sox17 810.0 -83000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4405000 4406000 Sox17 810.0 -82000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4406000 4407000 Sox17 810.0 -81000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4407000 4408000 Sox17 810.0 -80000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4408000 4409000 Sox17 810.0 -79000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4409000 4410000 Sox17 810.0 -78000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4410000 4411000 Sox17 810.0 -77000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4411000 4412000 Sox17 810.0 -76000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4412000 4413000 Sox17 810.0 -75000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4413000 4414000 Sox17 810.0 -74000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4414000 4415000 Sox17 810.0 -73000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4415000 4416000 Sox17 810.0 -72000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4416000 4417000 Sox17 810.0 -71000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4417000 4418000 Sox17 810.0 -70000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4418000 4419000 Sox17 810.0 -69000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4419000 4420000 Sox17 810.0 -68000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4420000 4421000 Sox17 810.0 -67000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4421000 4422000 Sox17 810.0 -66000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4422000 4423000 Sox17 810.0 -65000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4423000 4424000 Sox17 810.0 -64000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4424000 4425000 Sox17 810.0 -63000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4425000 4426000 Sox17 810.0 -62000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4426000 4427000 Sox17 810.0 -61000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4427000 4428000 Sox17 810.0 -60000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4428000 4429000 Sox17 810.0 -59000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4429000 4430000 Sox17 810.0 -58000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4430000 4431000 Sox17 810.0 -57000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4431000 4432000 Sox17 810.0 -56000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4432000 4433000 Sox17 810.0 -55000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4433000 4434000 Sox17 810.0 -54000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4434000 4435000 Sox17 810.0 -53000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4435000 4436000 Sox17 810.0 -52000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4436000 4437000 Sox17 810.0 -51000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4437000 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0.001481481481 0.000000000000 2.295259259717 1.200000000000 -chr1 4656000 4657000 Sox17 810.0 169000 0.001728395062 0.000000000000 2.419023237597 1.400000000000 -chr1 4657000 4658000 Sox17 810.0 170000 0.001234567901 0.000000000000 1.671682727052 1.000000000000 -chr1 4658000 4659000 Sox17 810.0 171000 0.000987654321 0.000000000000 1.353856628464 0.800000000000 -chr1 4659000 4660000 Sox17 810.0 172000 0.000987654321 0.000000000000 1.270220697103 0.800000000000 -chr1 4660000 4661000 Sox17 810.0 173000 0.000493827160 0.000000000000 0.647612520865 0.400000000000 -chr1 4661000 4662000 Sox17 810.0 174000 0.000246913580 0.000000000000 0.342694958640 0.200000000000 -chr1 4662000 4663000 Sox17 810.0 175000 0.000246913580 0.000000000000 0.354512026264 0.200000000000 -chr1 4663000 4664000 Sox17 810.0 176000 0.000246913580 0.000000000000 0.349986340790 0.200000000000 -chr1 4664000 4665000 Sox17 810.0 177000 0.000246913580 0.000000000000 0.373849046024 0.200000000000 -chr1 4665000 4666000 Sox17 810.0 178000 0.000493827160 0.000000000000 0.775913114612 0.400000000000 -chr1 4666000 4667000 Sox17 810.0 179000 0.000246913580 0.000000000000 0.395417260391 0.200000000000 -chr1 4667000 4668000 Sox17 810.0 180000 0.000246913580 0.000000000000 0.417496396239 0.200000000000 -chr1 4668000 4669000 Sox17 810.0 181000 0.000246913580 0.000000000000 0.419626479907 0.200000000000 -chr1 4669000 4670000 Sox17 810.0 182000 0.000246913580 0.000000000000 0.442187043505 0.200000000000 -chr1 4670000 4671000 Sox17 810.0 183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4671000 4672000 Sox17 810.0 184000 0.000246913580 0.000000000000 0.401203854492 0.200000000000 -chr1 4672000 4673000 Sox17 810.0 185000 0.000246913580 0.000000000000 0.395417260391 0.200000000000 -chr1 4673000 4674000 Sox17 810.0 186000 0.000246913580 0.000000000000 0.437482925987 0.200000000000 -chr1 4674000 4675000 Sox17 810.0 187000 0.000246913580 0.000000000000 0.444577243757 0.200000000000 -chr1 4675000 4676000 Sox17 810.0 188000 0.000493827160 0.000000000000 0.879644813784 0.400000000000 -chr1 4676000 4677000 Sox17 810.0 189000 0.000246913580 0.000000000000 0.478179012441 0.200000000000 -chr1 4677000 4678000 Sox17 810.0 190000 0.000246913580 0.000000000000 0.480975380957 0.200000000000 -chr1 4678000 4679000 Sox17 810.0 191000 0.000740740741 0.000000000000 1.370779835192 0.600000000000 -chr1 4679000 4680000 Sox17 810.0 192000 0.000740740741 0.000000000000 1.355716320410 0.600000000000 -chr1 4680000 4681000 Sox17 810.0 193000 0.000740740741 0.000000000000 1.468692681340 0.600000000000 -chr1 4681000 4682000 Sox17 810.0 194000 0.000740740741 0.000000000000 1.426244915656 0.600000000000 -chr1 4682000 4683000 Sox17 810.0 195000 0.000740740741 0.000000000000 1.513744604449 0.600000000000 -chr1 4683000 4684000 Sox17 810.0 196000 0.000493827160 0.000000000000 1.009163069632 0.400000000000 -chr1 4684000 4685000 Sox17 810.0 197000 0.000493827160 0.000000000000 0.934622615061 0.400000000000 -chr1 4685000 4686000 Sox17 810.0 198000 0.000246913580 0.000000000000 0.403170540070 0.200000000000 -chr1 4686000 4687000 Sox17 810.0 199000 0.000308641975 0.000000000000 0.538264332961 0.250000000000 -chr1 4687000 4688000 Sox17 810.0 200000 0.000411522634 0.000000000000 0.699377466512 0.333333333333 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt deleted file mode 100644 index 15212e5d..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 14100000 14101000 Eya1 673.0 -200000 0.00000 1.00000 0.00000 0.00000 -chr1 14101000 14102000 Eya1 673.0 -199000 0.00000 1.00000 0.00000 0.00000 -chr1 14102000 14103000 Eya1 673.0 -198000 0.00000 1.00000 0.00000 0.00000 -chr1 14103000 14104000 Eya1 673.0 -197000 0.00000 1.00000 0.00000 0.00000 -chr1 14104000 14105000 Eya1 673.0 -196000 0.00000 1.00000 0.00000 0.00000 -chr1 14105000 14106000 Eya1 673.0 -195000 0.00000 1.00000 0.00000 0.00000 -chr1 14106000 14107000 Eya1 673.0 -194000 0.00000 1.00000 0.00000 0.00000 -chr1 14107000 14108000 Eya1 673.0 -193000 0.00000 1.00000 0.00000 0.00000 -chr1 14108000 14109000 Eya1 673.0 -192000 0.00000 1.00000 0.00000 0.00000 -chr1 14109000 14110000 Eya1 673.0 -191000 0.00000 1.00000 0.00000 0.00000 -chr1 14110000 14111000 Eya1 673.0 -190000 0.00000 1.00000 0.00000 0.00000 -chr1 14111000 14112000 Eya1 673.0 -189000 0.00000 1.00000 0.00000 0.00000 -chr1 14112000 14113000 Eya1 673.0 -188000 0.00000 1.00000 0.00000 0.00000 -chr1 14113000 14114000 Eya1 673.0 -187000 0.00000 1.00000 0.00000 0.00000 -chr1 14114000 14115000 Eya1 673.0 -186000 0.00000 1.00000 0.00000 0.00000 -chr1 14115000 14116000 Eya1 673.0 -185000 0.00000 1.00000 0.00000 0.00000 -chr1 14116000 14117000 Eya1 673.0 -184000 0.00000 1.00000 0.00000 0.00000 -chr1 14117000 14118000 Eya1 673.0 -183000 0.00000 1.00000 0.00000 0.00000 -chr1 14118000 14119000 Eya1 673.0 -182000 0.00000 1.00000 0.00000 0.00000 -chr1 14119000 14120000 Eya1 673.0 -181000 0.00000 1.00000 0.00000 0.00000 -chr1 14120000 14121000 Eya1 673.0 -180000 0.00000 1.00000 0.00000 0.00000 -chr1 14121000 14122000 Eya1 673.0 -179000 0.00000 1.00000 0.00000 0.00000 -chr1 14122000 14123000 Eya1 673.0 -178000 0.00000 1.00000 0.00000 0.00000 -chr1 14123000 14124000 Eya1 673.0 -177000 0.00000 1.00000 0.00000 0.00000 -chr1 14124000 14125000 Eya1 673.0 -176000 0.00000 1.00000 0.00000 0.00000 -chr1 14125000 14126000 Eya1 673.0 -175000 0.00000 1.00000 0.00000 0.00000 -chr1 14126000 14127000 Eya1 673.0 -174000 0.00000 1.00000 0.00000 0.00000 -chr1 14127000 14128000 Eya1 673.0 -173000 0.00000 1.00000 0.00000 0.00000 -chr1 14128000 14129000 Eya1 673.0 -172000 0.00000 1.00000 0.00000 0.00000 -chr1 14129000 14130000 Eya1 673.0 -171000 0.00000 1.00000 0.00000 0.00000 -chr1 14130000 14131000 Eya1 673.0 -170000 0.00000 1.00000 0.00000 0.00000 -chr1 14131000 14132000 Eya1 673.0 -169000 0.00000 1.00000 0.00000 0.00000 -chr1 14132000 14133000 Eya1 673.0 -168000 0.00000 1.00000 0.00000 0.00000 -chr1 14133000 14134000 Eya1 673.0 -167000 0.00000 1.00000 0.00000 0.00000 -chr1 14134000 14135000 Eya1 673.0 -166000 0.00000 1.00000 0.00000 0.00000 -chr1 14135000 14136000 Eya1 673.0 -165000 0.00000 1.00000 0.00000 0.00000 -chr1 14136000 14137000 Eya1 673.0 -164000 0.00000 1.00000 0.00000 0.00000 -chr1 14137000 14138000 Eya1 673.0 -163000 0.00000 1.00000 0.00000 0.00000 -chr1 14138000 14139000 Eya1 673.0 -162000 0.00000 1.00000 0.00000 0.00000 -chr1 14139000 14140000 Eya1 673.0 -161000 0.00000 1.00000 0.00000 0.00000 -chr1 14140000 14141000 Eya1 673.0 -160000 0.00089 0.01211 4.24241 0.60000 -chr1 14141000 14142000 Eya1 673.0 -159000 0.00089 0.01211 4.78981 0.60000 -chr1 14142000 14143000 Eya1 673.0 -158000 0.00089 0.01211 4.30389 0.60000 -chr1 14143000 14144000 Eya1 673.0 -157000 0.00089 0.01211 4.36718 0.60000 -chr1 14144000 14145000 Eya1 673.0 -156000 0.00089 0.01211 5.12014 0.60000 -chr1 14145000 14146000 Eya1 673.0 -155000 0.00000 1.00000 0.00000 0.00000 -chr1 14146000 14147000 Eya1 673.0 -154000 0.00000 1.00000 0.00000 0.00000 -chr1 14147000 14148000 Eya1 673.0 -153000 0.00000 1.00000 0.00000 0.00000 -chr1 14148000 14149000 Eya1 673.0 -152000 0.00000 1.00000 0.00000 0.00000 -chr1 14149000 14150000 Eya1 673.0 -151000 0.00000 1.00000 0.00000 0.00000 -chr1 14150000 14151000 Eya1 673.0 -150000 0.00000 1.00000 0.00000 0.00000 -chr1 14151000 14152000 Eya1 673.0 -149000 0.00000 1.00000 0.00000 0.00000 -chr1 14152000 14153000 Eya1 673.0 -148000 0.00000 1.00000 0.00000 0.00000 -chr1 14153000 14154000 Eya1 673.0 -147000 0.00000 1.00000 0.00000 0.00000 -chr1 14154000 14155000 Eya1 673.0 -146000 0.00000 1.00000 0.00000 0.00000 -chr1 14155000 14156000 Eya1 673.0 -145000 0.00000 1.00000 0.00000 0.00000 -chr1 14156000 14157000 Eya1 673.0 -144000 0.00000 1.00000 0.00000 0.00000 -chr1 14157000 14158000 Eya1 673.0 -143000 0.00000 1.00000 0.00000 0.00000 -chr1 14158000 14159000 Eya1 673.0 -142000 0.00000 1.00000 0.00000 0.00000 -chr1 14159000 14160000 Eya1 673.0 -141000 0.00000 1.00000 0.00000 0.00000 -chr1 14160000 14161000 Eya1 673.0 -140000 0.00000 1.00000 0.00000 0.00000 -chr1 14161000 14162000 Eya1 673.0 -139000 0.00000 1.00000 0.00000 0.00000 -chr1 14162000 14163000 Eya1 673.0 -138000 0.00000 1.00000 0.00000 0.00000 -chr1 14163000 14164000 Eya1 673.0 -137000 0.00000 1.00000 0.00000 0.00000 -chr1 14164000 14165000 Eya1 673.0 -136000 0.00000 1.00000 0.00000 0.00000 -chr1 14165000 14166000 Eya1 673.0 -135000 0.00000 1.00000 0.00000 0.00000 -chr1 14166000 14167000 Eya1 673.0 -134000 0.00000 1.00000 0.00000 0.00000 -chr1 14167000 14168000 Eya1 673.0 -133000 0.00000 1.00000 0.00000 0.00000 -chr1 14168000 14169000 Eya1 673.0 -132000 0.00000 1.00000 0.00000 0.00000 -chr1 14169000 14170000 Eya1 673.0 -131000 0.00000 1.00000 0.00000 0.00000 -chr1 14170000 14171000 Eya1 673.0 -130000 0.00000 1.00000 0.00000 0.00000 -chr1 14171000 14172000 Eya1 673.0 -129000 0.00000 1.00000 0.00000 0.00000 -chr1 14172000 14173000 Eya1 673.0 -128000 0.00000 1.00000 0.00000 0.00000 -chr1 14173000 14174000 Eya1 673.0 -127000 0.00000 1.00000 0.00000 0.00000 -chr1 14174000 14175000 Eya1 673.0 -126000 0.00000 1.00000 0.00000 0.00000 -chr1 14175000 14176000 Eya1 673.0 -125000 0.00030 0.04285 0.91657 0.20000 -chr1 14176000 14177000 Eya1 673.0 -124000 0.00030 0.04285 0.90816 0.20000 -chr1 14177000 14178000 Eya1 673.0 -123000 0.00030 0.04285 0.79830 0.20000 -chr1 14178000 14179000 Eya1 673.0 -122000 0.00030 0.04285 0.92514 0.20000 -chr1 14179000 14180000 Eya1 673.0 -121000 0.00030 0.04285 0.88383 0.20000 -chr1 14180000 14181000 Eya1 673.0 -120000 0.00000 1.00000 0.00000 0.00000 -chr1 14181000 14182000 Eya1 673.0 -119000 0.00000 1.00000 0.00000 0.00000 -chr1 14182000 14183000 Eya1 673.0 -118000 0.00000 1.00000 0.00000 0.00000 -chr1 14183000 14184000 Eya1 673.0 -117000 0.00030 0.04285 0.86078 0.20000 -chr1 14184000 14185000 Eya1 673.0 -116000 0.00030 0.04285 0.79192 0.20000 -chr1 14185000 14186000 Eya1 673.0 -115000 0.00030 0.04285 0.76146 0.20000 -chr1 14186000 14187000 Eya1 673.0 -114000 0.00030 0.04285 0.81139 0.20000 -chr1 14187000 14188000 Eya1 673.0 -113000 0.00030 0.04285 0.89180 0.20000 -chr1 14188000 14189000 Eya1 673.0 -112000 0.00000 1.00000 0.00000 0.00000 -chr1 14189000 14190000 Eya1 673.0 -111000 0.00030 0.04285 1.06440 0.20000 -chr1 14190000 14191000 Eya1 673.0 -110000 0.00030 0.04285 1.20719 0.20000 -chr1 14191000 14192000 Eya1 673.0 -109000 0.00030 0.04285 1.01010 0.20000 -chr1 14192000 14193000 Eya1 673.0 -108000 0.00030 0.04285 0.95182 0.20000 -chr1 14193000 14194000 Eya1 673.0 -107000 0.00030 0.04285 0.82491 0.20000 -chr1 14194000 14195000 Eya1 673.0 -106000 0.00000 1.00000 0.00000 0.00000 -chr1 14195000 14196000 Eya1 673.0 -105000 0.00000 1.00000 0.00000 0.00000 -chr1 14196000 14197000 Eya1 673.0 -104000 0.00000 1.00000 0.00000 0.00000 -chr1 14197000 14198000 Eya1 673.0 -103000 0.00119 0.00626 5.42408 0.80000 -chr1 14198000 14199000 Eya1 673.0 -102000 0.00119 0.00626 5.49941 0.80000 -chr1 14199000 14200000 Eya1 673.0 -101000 0.00119 0.00626 5.82291 0.80000 -chr1 14200000 14201000 Eya1 673.0 -100000 0.00119 0.00626 4.88837 0.80000 -chr1 14201000 14202000 Eya1 673.0 -99000 0.00119 0.00626 4.49952 0.80000 -chr1 14202000 14203000 Eya1 673.0 -98000 0.00000 1.00000 0.00000 0.00000 -chr1 14203000 14204000 Eya1 673.0 -97000 0.00000 1.00000 0.00000 0.00000 -chr1 14204000 14205000 Eya1 673.0 -96000 0.00000 1.00000 0.00000 0.00000 -chr1 14205000 14206000 Eya1 673.0 -95000 0.00000 1.00000 0.00000 0.00000 -chr1 14206000 14207000 Eya1 673.0 -94000 0.00059 0.02300 1.54671 0.40000 -chr1 14207000 14208000 Eya1 673.0 -93000 0.00059 0.02300 1.48856 0.40000 -chr1 14208000 14209000 Eya1 673.0 -92000 0.00059 0.02300 1.09381 0.40000 -chr1 14209000 14210000 Eya1 673.0 -91000 0.00059 0.02300 1.03114 0.40000 -chr1 14210000 14211000 Eya1 673.0 -90000 0.00059 0.02300 1.02051 0.40000 -chr1 14211000 14212000 Eya1 673.0 -89000 0.00000 1.00000 0.00000 0.00000 -chr1 14212000 14213000 Eya1 673.0 -88000 0.00000 1.00000 0.00000 0.00000 -chr1 14213000 14214000 Eya1 673.0 -87000 0.00000 1.00000 0.00000 0.00000 -chr1 14214000 14215000 Eya1 673.0 -86000 0.00000 1.00000 0.00000 0.00000 -chr1 14215000 14216000 Eya1 673.0 -85000 0.00000 1.00000 0.00000 0.00000 -chr1 14216000 14217000 Eya1 673.0 -84000 0.00000 1.00000 0.00000 0.00000 -chr1 14217000 14218000 Eya1 673.0 -83000 0.00059 0.02300 1.46651 0.40000 -chr1 14218000 14219000 Eya1 673.0 -82000 0.00059 0.02300 1.54671 0.40000 -chr1 14219000 14220000 Eya1 673.0 -81000 0.00059 0.02300 1.81632 0.40000 -chr1 14220000 14221000 Eya1 673.0 -80000 0.00059 0.02300 2.10616 0.40000 -chr1 14221000 14222000 Eya1 673.0 -79000 0.00059 0.02300 1.88551 0.40000 -chr1 14222000 14223000 Eya1 673.0 -78000 0.00000 1.00000 0.00000 0.00000 -chr1 14223000 14224000 Eya1 673.0 -77000 0.00000 1.00000 0.00000 0.00000 -chr1 14224000 14225000 Eya1 673.0 -76000 0.00000 1.00000 0.00000 0.00000 -chr1 14225000 14226000 Eya1 673.0 -75000 0.00000 1.00000 0.00000 0.00000 -chr1 14226000 14227000 Eya1 673.0 -74000 0.00000 1.00000 0.00000 0.00000 -chr1 14227000 14228000 Eya1 673.0 -73000 0.00000 1.00000 0.00000 0.00000 -chr1 14228000 14229000 Eya1 673.0 -72000 0.00000 1.00000 0.00000 0.00000 -chr1 14229000 14230000 Eya1 673.0 -71000 0.00000 1.00000 0.00000 0.00000 -chr1 14230000 14231000 Eya1 673.0 -70000 0.00000 1.00000 0.00000 0.00000 -chr1 14231000 14232000 Eya1 673.0 -69000 0.00000 1.00000 0.00000 0.00000 -chr1 14232000 14233000 Eya1 673.0 -68000 0.00000 1.00000 0.00000 0.00000 -chr1 14233000 14234000 Eya1 673.0 -67000 0.00000 1.00000 0.00000 0.00000 -chr1 14234000 14235000 Eya1 673.0 -66000 0.00000 1.00000 0.00000 0.00000 -chr1 14235000 14236000 Eya1 673.0 -65000 0.00000 1.00000 0.00000 0.00000 -chr1 14236000 14237000 Eya1 673.0 -64000 0.00000 1.00000 0.00000 0.00000 -chr1 14237000 14238000 Eya1 673.0 -63000 0.00000 1.00000 0.00000 0.00000 -chr1 14238000 14239000 Eya1 673.0 -62000 0.00000 1.00000 0.00000 0.00000 -chr1 14239000 14240000 Eya1 673.0 -61000 0.00000 1.00000 0.00000 0.00000 -chr1 14240000 14241000 Eya1 673.0 -60000 0.00000 1.00000 0.00000 0.00000 -chr1 14241000 14242000 Eya1 673.0 -59000 0.00000 1.00000 0.00000 0.00000 -chr1 14242000 14243000 Eya1 673.0 -58000 0.00000 1.00000 0.00000 0.00000 -chr1 14243000 14244000 Eya1 673.0 -57000 0.00000 1.00000 0.00000 0.00000 -chr1 14244000 14245000 Eya1 673.0 -56000 0.00000 1.00000 0.00000 0.00000 -chr1 14245000 14246000 Eya1 673.0 -55000 0.00000 1.00000 0.00000 0.00000 -chr1 14246000 14247000 Eya1 673.0 -54000 0.00000 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-chr1 14491000 14492000 Eya1 673.0 191000 0.00208 0.00000 3.84959 1.40000 -chr1 14492000 14493000 Eya1 673.0 192000 0.00327 0.00000 5.98288 2.20000 -chr1 14493000 14494000 Eya1 673.0 193000 0.00297 0.00000 5.89223 2.00000 -chr1 14494000 14495000 Eya1 673.0 194000 0.00327 0.00000 6.29413 2.20000 -chr1 14495000 14496000 Eya1 673.0 195000 0.00327 0.00000 6.68027 2.20000 -chr1 14496000 14497000 Eya1 673.0 196000 0.00297 0.00000 6.07297 2.00000 -chr1 14497000 14498000 Eya1 673.0 197000 0.00208 0.00000 3.93708 1.40000 -chr1 14498000 14499000 Eya1 673.0 198000 0.00297 0.00000 4.85242 2.00000 -chr1 14499000 14500000 Eya1 673.0 199000 0.00334 0.00000 5.83053 2.25000 -chr1 14500000 14501000 Eya1 673.0 200000 0.00446 0.00000 7.57572 3.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt deleted file mode 100644 index a49c7be2..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 18893000 18894000 Tfap2d 472.0 -200000 0.00141 0.00974 8.55417 0.66667 -chr1 18894000 18895000 Tfap2d 472.0 -199000 0.00106 0.01673 5.04085 0.50000 -chr1 18895000 18896000 Tfap2d 472.0 -198000 0.00085 0.02300 3.28242 0.40000 -chr1 18896000 18897000 Tfap2d 472.0 -197000 0.00085 0.02300 3.13653 0.40000 -chr1 18897000 18898000 Tfap2d 472.0 -196000 0.00000 1.00000 0.00000 0.00000 -chr1 18898000 18899000 Tfap2d 472.0 -195000 0.00000 1.00000 0.00000 0.00000 -chr1 18899000 18900000 Tfap2d 472.0 -194000 0.00000 1.00000 0.00000 0.00000 -chr1 18900000 18901000 Tfap2d 472.0 -193000 0.00000 1.00000 0.00000 0.00000 -chr1 18901000 18902000 Tfap2d 472.0 -192000 0.00000 1.00000 0.00000 0.00000 -chr1 18902000 18903000 Tfap2d 472.0 -191000 0.00000 1.00000 0.00000 0.00000 -chr1 18903000 18904000 Tfap2d 472.0 -190000 0.00000 1.00000 0.00000 0.00000 -chr1 18904000 18905000 Tfap2d 472.0 -189000 0.00000 1.00000 0.00000 0.00000 -chr1 18905000 18906000 Tfap2d 472.0 -188000 0.00000 1.00000 0.00000 0.00000 -chr1 18906000 18907000 Tfap2d 472.0 -187000 0.00000 1.00000 0.00000 0.00000 -chr1 18907000 18908000 Tfap2d 472.0 -186000 0.00000 1.00000 0.00000 0.00000 -chr1 18908000 18909000 Tfap2d 472.0 -185000 0.00000 1.00000 0.00000 0.00000 -chr1 18909000 18910000 Tfap2d 472.0 -184000 0.00000 1.00000 0.00000 0.00000 -chr1 18910000 18911000 Tfap2d 472.0 -183000 0.00000 1.00000 0.00000 0.00000 -chr1 18911000 18912000 Tfap2d 472.0 -182000 0.00000 1.00000 0.00000 0.00000 -chr1 18912000 18913000 Tfap2d 472.0 -181000 0.00000 1.00000 0.00000 0.00000 -chr1 18913000 18914000 Tfap2d 472.0 -180000 0.00000 1.00000 0.00000 0.00000 -chr1 18914000 18915000 Tfap2d 472.0 -179000 0.00000 1.00000 0.00000 0.00000 -chr1 18915000 18916000 Tfap2d 472.0 -178000 0.00000 1.00000 0.00000 0.00000 -chr1 18916000 18917000 Tfap2d 472.0 -177000 0.00000 1.00000 0.00000 0.00000 -chr1 18917000 18918000 Tfap2d 472.0 -176000 0.00000 1.00000 0.00000 0.00000 -chr1 18918000 18919000 Tfap2d 472.0 -175000 0.00000 1.00000 0.00000 0.00000 -chr1 18919000 18920000 Tfap2d 472.0 -174000 0.00000 1.00000 0.00000 0.00000 -chr1 18920000 18921000 Tfap2d 472.0 -173000 0.00000 1.00000 0.00000 0.00000 -chr1 18921000 18922000 Tfap2d 472.0 -172000 0.00000 1.00000 0.00000 0.00000 -chr1 18922000 18923000 Tfap2d 472.0 -171000 0.00000 1.00000 0.00000 0.00000 -chr1 18923000 18924000 Tfap2d 472.0 -170000 0.00000 1.00000 0.00000 0.00000 -chr1 18924000 18925000 Tfap2d 472.0 -169000 0.00000 1.00000 0.00000 0.00000 -chr1 18925000 18926000 Tfap2d 472.0 -168000 0.00000 1.00000 0.00000 0.00000 -chr1 18926000 18927000 Tfap2d 472.0 -167000 0.00000 1.00000 0.00000 0.00000 -chr1 18927000 18928000 Tfap2d 472.0 -166000 0.00000 1.00000 0.00000 0.00000 -chr1 18928000 18929000 Tfap2d 472.0 -165000 0.00000 1.00000 0.00000 0.00000 -chr1 18929000 18930000 Tfap2d 472.0 -164000 0.00000 1.00000 0.00000 0.00000 -chr1 18930000 18931000 Tfap2d 472.0 -163000 0.00000 1.00000 0.00000 0.00000 -chr1 18931000 18932000 Tfap2d 472.0 -162000 0.00000 1.00000 0.00000 0.00000 -chr1 18932000 18933000 Tfap2d 472.0 -161000 0.00000 1.00000 0.00000 0.00000 -chr1 18933000 18934000 Tfap2d 472.0 -160000 0.00000 1.00000 0.00000 0.00000 -chr1 18934000 18935000 Tfap2d 472.0 -159000 0.00000 1.00000 0.00000 0.00000 -chr1 18935000 18936000 Tfap2d 472.0 -158000 0.00000 1.00000 0.00000 0.00000 -chr1 18936000 18937000 Tfap2d 472.0 -157000 0.00000 1.00000 0.00000 0.00000 -chr1 18937000 18938000 Tfap2d 472.0 -156000 0.00000 1.00000 0.00000 0.00000 -chr1 18938000 18939000 Tfap2d 472.0 -155000 0.00000 1.00000 0.00000 0.00000 -chr1 18939000 18940000 Tfap2d 472.0 -154000 0.00000 1.00000 0.00000 0.00000 -chr1 18940000 18941000 Tfap2d 472.0 -153000 0.00000 1.00000 0.00000 0.00000 -chr1 18941000 18942000 Tfap2d 472.0 -152000 0.00000 1.00000 0.00000 0.00000 -chr1 18942000 18943000 Tfap2d 472.0 -151000 0.00000 1.00000 0.00000 0.00000 -chr1 18943000 18944000 Tfap2d 472.0 -150000 0.00000 1.00000 0.00000 0.00000 -chr1 18944000 18945000 Tfap2d 472.0 -149000 0.00000 1.00000 0.00000 0.00000 -chr1 18945000 18946000 Tfap2d 472.0 -148000 0.00000 1.00000 0.00000 0.00000 -chr1 18946000 18947000 Tfap2d 472.0 -147000 0.00000 1.00000 0.00000 0.00000 -chr1 18947000 18948000 Tfap2d 472.0 -146000 0.00000 1.00000 0.00000 0.00000 -chr1 18948000 18949000 Tfap2d 472.0 -145000 0.00000 1.00000 0.00000 0.00000 -chr1 18949000 18950000 Tfap2d 472.0 -144000 0.00000 1.00000 0.00000 0.00000 -chr1 18950000 18951000 Tfap2d 472.0 -143000 0.00000 1.00000 0.00000 0.00000 -chr1 18951000 18952000 Tfap2d 472.0 -142000 0.00000 1.00000 0.00000 0.00000 -chr1 18952000 18953000 Tfap2d 472.0 -141000 0.00000 1.00000 0.00000 0.00000 -chr1 18953000 18954000 Tfap2d 472.0 -140000 0.00000 1.00000 0.00000 0.00000 -chr1 18954000 18955000 Tfap2d 472.0 -139000 0.00000 1.00000 0.00000 0.00000 -chr1 18955000 18956000 Tfap2d 472.0 -138000 0.00000 1.00000 0.00000 0.00000 -chr1 18956000 18957000 Tfap2d 472.0 -137000 0.00000 1.00000 0.00000 0.00000 -chr1 18957000 18958000 Tfap2d 472.0 -136000 0.00000 1.00000 0.00000 0.00000 -chr1 18958000 18959000 Tfap2d 472.0 -135000 0.00000 1.00000 0.00000 0.00000 -chr1 18959000 18960000 Tfap2d 472.0 -134000 0.00000 1.00000 0.00000 0.00000 -chr1 18960000 18961000 Tfap2d 472.0 -133000 0.00000 1.00000 0.00000 0.00000 -chr1 18961000 18962000 Tfap2d 472.0 -132000 0.00000 1.00000 0.00000 0.00000 -chr1 18962000 18963000 Tfap2d 472.0 -131000 0.00000 1.00000 0.00000 0.00000 -chr1 18963000 18964000 Tfap2d 472.0 -130000 0.00000 1.00000 0.00000 0.00000 -chr1 18964000 18965000 Tfap2d 472.0 -129000 0.00000 1.00000 0.00000 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0.00000 -chr1 18978000 18979000 Tfap2d 472.0 -115000 0.00127 0.01211 3.25717 0.60000 -chr1 18979000 18980000 Tfap2d 472.0 -114000 0.00127 0.01211 3.47075 0.60000 -chr1 18980000 18981000 Tfap2d 472.0 -113000 0.00127 0.01211 3.81470 0.60000 -chr1 18981000 18982000 Tfap2d 472.0 -112000 0.00127 0.01211 4.60252 0.60000 -chr1 18982000 18983000 Tfap2d 472.0 -111000 0.00127 0.01211 4.55303 0.60000 -chr1 18983000 18984000 Tfap2d 472.0 -110000 0.00000 1.00000 0.00000 0.00000 -chr1 18984000 18985000 Tfap2d 472.0 -109000 0.00000 1.00000 0.00000 0.00000 -chr1 18985000 18986000 Tfap2d 472.0 -108000 0.00000 1.00000 0.00000 0.00000 -chr1 18986000 18987000 Tfap2d 472.0 -107000 0.00000 1.00000 0.00000 0.00000 -chr1 18987000 18988000 Tfap2d 472.0 -106000 0.00000 1.00000 0.00000 0.00000 -chr1 18988000 18989000 Tfap2d 472.0 -105000 0.00000 1.00000 0.00000 0.00000 -chr1 18989000 18990000 Tfap2d 472.0 -104000 0.00000 1.00000 0.00000 0.00000 -chr1 18990000 18991000 Tfap2d 472.0 -103000 0.00000 1.00000 0.00000 0.00000 -chr1 18991000 18992000 Tfap2d 472.0 -102000 0.00000 1.00000 0.00000 0.00000 -chr1 18992000 18993000 Tfap2d 472.0 -101000 0.00000 1.00000 0.00000 0.00000 -chr1 18993000 18994000 Tfap2d 472.0 -100000 0.00000 1.00000 0.00000 0.00000 -chr1 18994000 18995000 Tfap2d 472.0 -99000 0.00000 1.00000 0.00000 0.00000 -chr1 18995000 18996000 Tfap2d 472.0 -98000 0.00000 1.00000 0.00000 0.00000 -chr1 18996000 18997000 Tfap2d 472.0 -97000 0.00000 1.00000 0.00000 0.00000 -chr1 18997000 18998000 Tfap2d 472.0 -96000 0.00000 1.00000 0.00000 0.00000 -chr1 18998000 18999000 Tfap2d 472.0 -95000 0.00000 1.00000 0.00000 0.00000 -chr1 18999000 19000000 Tfap2d 472.0 -94000 0.00042 0.04285 1.10269 0.20000 -chr1 19000000 19001000 Tfap2d 472.0 -93000 0.00042 0.04285 1.06123 0.20000 -chr1 19001000 19002000 Tfap2d 472.0 -92000 0.00042 0.04285 0.77980 0.20000 -chr1 19002000 19003000 Tfap2d 472.0 -91000 0.00042 0.04285 0.73512 0.20000 -chr1 19003000 19004000 Tfap2d 472.0 -90000 0.00042 0.04285 0.72755 0.20000 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19017000 19018000 Tfap2d 472.0 -76000 0.00042 0.04285 0.93473 0.20000 -chr1 19018000 19019000 Tfap2d 472.0 -75000 0.00042 0.04285 1.02278 0.20000 -chr1 19019000 19020000 Tfap2d 472.0 -74000 0.00042 0.04285 1.00102 0.20000 -chr1 19020000 19021000 Tfap2d 472.0 -73000 0.00000 1.00000 0.00000 0.00000 -chr1 19021000 19022000 Tfap2d 472.0 -72000 0.00000 1.00000 0.00000 0.00000 -chr1 19022000 19023000 Tfap2d 472.0 -71000 0.00000 1.00000 0.00000 0.00000 -chr1 19023000 19024000 Tfap2d 472.0 -70000 0.00000 1.00000 0.00000 0.00000 -chr1 19024000 19025000 Tfap2d 472.0 -69000 0.00000 1.00000 0.00000 0.00000 -chr1 19025000 19026000 Tfap2d 472.0 -68000 0.00000 1.00000 0.00000 0.00000 -chr1 19026000 19027000 Tfap2d 472.0 -67000 0.00000 1.00000 0.00000 0.00000 -chr1 19027000 19028000 Tfap2d 472.0 -66000 0.00000 1.00000 0.00000 0.00000 -chr1 19028000 19029000 Tfap2d 472.0 -65000 0.00000 1.00000 0.00000 0.00000 -chr1 19029000 19030000 Tfap2d 472.0 -64000 0.00000 1.00000 0.00000 0.00000 -chr1 19030000 19031000 Tfap2d 472.0 -63000 0.00000 1.00000 0.00000 0.00000 -chr1 19031000 19032000 Tfap2d 472.0 -62000 0.00000 1.00000 0.00000 0.00000 -chr1 19032000 19033000 Tfap2d 472.0 -61000 0.00000 1.00000 0.00000 0.00000 -chr1 19033000 19034000 Tfap2d 472.0 -60000 0.00000 1.00000 0.00000 0.00000 -chr1 19034000 19035000 Tfap2d 472.0 -59000 0.00000 1.00000 0.00000 0.00000 -chr1 19035000 19036000 Tfap2d 472.0 -58000 0.00000 1.00000 0.00000 0.00000 -chr1 19036000 19037000 Tfap2d 472.0 -57000 0.00000 1.00000 0.00000 0.00000 -chr1 19037000 19038000 Tfap2d 472.0 -56000 0.00000 1.00000 0.00000 0.00000 -chr1 19038000 19039000 Tfap2d 472.0 -55000 0.00000 1.00000 0.00000 0.00000 -chr1 19039000 19040000 Tfap2d 472.0 -54000 0.00000 1.00000 0.00000 0.00000 -chr1 19040000 19041000 Tfap2d 472.0 -53000 0.00000 1.00000 0.00000 0.00000 -chr1 19041000 19042000 Tfap2d 472.0 -52000 0.00000 1.00000 0.00000 0.00000 -chr1 19042000 19043000 Tfap2d 472.0 -51000 0.00000 1.00000 0.00000 0.00000 -chr1 19043000 19044000 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-chr1 19096000 19097000 Tfap2d 472.0 3000 0.03008 0.00000 1.21352 14.20000 -chr1 19097000 19098000 Tfap2d 472.0 4000 0.02542 0.00000 1.62515 12.00000 -chr1 19098000 19099000 Tfap2d 472.0 5000 0.01780 0.00000 1.46952 8.40000 -chr1 19099000 19100000 Tfap2d 472.0 6000 0.01229 0.00000 1.17451 5.80000 -chr1 19100000 19101000 Tfap2d 472.0 7000 0.00975 0.00000 1.02053 4.60000 -chr1 19101000 19102000 Tfap2d 472.0 8000 0.01017 0.00000 1.16728 4.80000 -chr1 19102000 19103000 Tfap2d 472.0 9000 0.01144 0.00000 1.42944 5.40000 -chr1 19103000 19104000 Tfap2d 472.0 10000 0.01059 0.00000 1.46172 5.00000 -chr1 19104000 19105000 Tfap2d 472.0 11000 0.01229 0.00000 1.91897 5.80000 -chr1 19105000 19106000 Tfap2d 472.0 12000 0.01017 0.00000 1.70825 4.80000 -chr1 19106000 19107000 Tfap2d 472.0 13000 0.00720 0.00000 1.34122 3.40000 -chr1 19107000 19108000 Tfap2d 472.0 14000 0.00720 0.00000 1.48389 3.40000 -chr1 19108000 19109000 Tfap2d 472.0 15000 0.00636 0.00000 1.36767 3.00000 -chr1 19109000 19110000 Tfap2d 472.0 16000 0.00805 0.00000 1.76779 3.80000 -chr1 19110000 19111000 Tfap2d 472.0 17000 0.00678 0.00000 1.61423 3.20000 -chr1 19111000 19112000 Tfap2d 472.0 18000 0.00975 0.00000 2.38875 4.60000 -chr1 19112000 19113000 Tfap2d 472.0 19000 0.00720 0.00000 1.81090 3.40000 -chr1 19113000 19114000 Tfap2d 472.0 20000 0.00763 0.00000 2.03573 3.60000 -chr1 19114000 19115000 Tfap2d 472.0 21000 0.00381 0.00000 1.04637 1.80000 -chr1 19115000 19116000 Tfap2d 472.0 22000 0.00381 0.00000 1.09038 1.80000 -chr1 19116000 19117000 Tfap2d 472.0 23000 0.00085 0.00000 0.27065 0.40000 -chr1 19117000 19118000 Tfap2d 472.0 24000 0.00042 0.00000 0.13784 0.20000 -chr1 19118000 19119000 Tfap2d 472.0 25000 0.00000 1.00000 0.00000 0.00000 -chr1 19119000 19120000 Tfap2d 472.0 26000 0.00000 1.00000 0.00000 0.00000 -chr1 19120000 19121000 Tfap2d 472.0 27000 0.00000 1.00000 0.00000 0.00000 -chr1 19121000 19122000 Tfap2d 472.0 28000 0.00000 1.00000 0.00000 0.00000 -chr1 19122000 19123000 Tfap2d 472.0 29000 0.00000 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-chr1 19136000 19137000 Tfap2d 472.0 43000 0.00424 0.00000 2.13531 2.00000 -chr1 19137000 19138000 Tfap2d 472.0 44000 0.00339 0.00000 1.83901 1.60000 -chr1 19138000 19139000 Tfap2d 472.0 45000 0.00169 0.00000 1.02093 0.80000 -chr1 19139000 19140000 Tfap2d 472.0 46000 0.00085 0.00000 0.51139 0.40000 -chr1 19140000 19141000 Tfap2d 472.0 47000 0.00042 0.00000 0.26783 0.20000 -chr1 19141000 19142000 Tfap2d 472.0 48000 0.00000 1.00000 0.00000 0.00000 -chr1 19142000 19143000 Tfap2d 472.0 49000 0.00000 1.00000 0.00000 0.00000 -chr1 19143000 19144000 Tfap2d 472.0 50000 0.00042 0.00000 0.26235 0.20000 -chr1 19144000 19145000 Tfap2d 472.0 51000 0.00127 0.00000 0.79742 0.60000 -chr1 19145000 19146000 Tfap2d 472.0 52000 0.00212 0.00000 1.29967 1.00000 -chr1 19146000 19147000 Tfap2d 472.0 53000 0.00212 0.00000 1.35977 1.00000 -chr1 19147000 19148000 Tfap2d 472.0 54000 0.00212 0.00000 1.47950 1.00000 -chr1 19148000 19149000 Tfap2d 472.0 55000 0.00169 0.00000 1.20122 0.80000 -chr1 19149000 19150000 Tfap2d 472.0 56000 0.00085 0.00000 0.60318 0.40000 -chr1 19150000 19151000 Tfap2d 472.0 57000 0.00000 1.00000 0.00000 0.00000 -chr1 19151000 19152000 Tfap2d 472.0 58000 0.00000 1.00000 0.00000 0.00000 -chr1 19152000 19153000 Tfap2d 472.0 59000 0.00000 1.00000 0.00000 0.00000 -chr1 19153000 19154000 Tfap2d 472.0 60000 0.00042 0.00000 0.29102 0.20000 -chr1 19154000 19155000 Tfap2d 472.0 61000 0.00169 0.00000 1.19361 0.80000 -chr1 19155000 19156000 Tfap2d 472.0 62000 0.00169 0.00000 1.27732 0.80000 -chr1 19156000 19157000 Tfap2d 472.0 63000 0.00169 0.00000 1.24630 0.80000 -chr1 19157000 19158000 Tfap2d 472.0 64000 0.00212 0.00000 1.56479 1.00000 -chr1 19158000 19159000 Tfap2d 472.0 65000 0.00297 0.00000 2.31383 1.40000 -chr1 19159000 19160000 Tfap2d 472.0 66000 0.00169 0.00000 1.44763 0.80000 -chr1 19160000 19161000 Tfap2d 472.0 67000 0.00212 0.00000 1.72970 1.00000 -chr1 19161000 19162000 Tfap2d 472.0 68000 0.00212 0.00000 1.75990 1.00000 -chr1 19162000 19163000 Tfap2d 472.0 69000 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0.20000 -chr1 19176000 19177000 Tfap2d 472.0 83000 0.00042 0.00000 0.31933 0.20000 -chr1 19177000 19178000 Tfap2d 472.0 84000 0.00042 0.00000 0.30031 0.20000 -chr1 19178000 19179000 Tfap2d 472.0 85000 0.00042 0.00000 0.29967 0.20000 -chr1 19179000 19180000 Tfap2d 472.0 86000 0.00042 0.00000 0.32901 0.20000 -chr1 19180000 19181000 Tfap2d 472.0 87000 0.00085 0.00000 0.62731 0.40000 -chr1 19181000 19182000 Tfap2d 472.0 88000 0.00085 0.00000 0.62315 0.40000 -chr1 19182000 19183000 Tfap2d 472.0 89000 0.00085 0.00000 0.68851 0.40000 -chr1 19183000 19184000 Tfap2d 472.0 90000 0.00085 0.00000 0.69358 0.40000 -chr1 19184000 19185000 Tfap2d 472.0 91000 0.00042 0.00000 0.33289 0.20000 -chr1 19185000 19186000 Tfap2d 472.0 92000 0.00000 1.00000 0.00000 0.00000 -chr1 19186000 19187000 Tfap2d 472.0 93000 0.00042 0.00000 0.38776 0.20000 -chr1 19187000 19188000 Tfap2d 472.0 94000 0.00127 0.00000 1.06658 0.60000 -chr1 19188000 19189000 Tfap2d 472.0 95000 0.00169 0.00000 1.36371 0.80000 -chr1 19189000 19190000 Tfap2d 472.0 96000 0.00169 0.00000 1.32529 0.80000 -chr1 19190000 19191000 Tfap2d 472.0 97000 0.00169 0.00000 1.37366 0.80000 -chr1 19191000 19192000 Tfap2d 472.0 98000 0.00127 0.00000 1.00578 0.60000 -chr1 19192000 19193000 Tfap2d 472.0 99000 0.00127 0.00000 1.08018 0.60000 -chr1 19193000 19194000 Tfap2d 472.0 100000 0.00085 0.00000 0.80424 0.40000 -chr1 19194000 19195000 Tfap2d 472.0 101000 0.00085 0.00000 0.86063 0.40000 -chr1 19195000 19196000 Tfap2d 472.0 102000 0.00085 0.00000 0.83765 0.40000 -chr1 19196000 19197000 Tfap2d 472.0 103000 0.00085 0.00000 0.92553 0.40000 -chr1 19197000 19198000 Tfap2d 472.0 104000 0.00169 0.00000 1.76430 0.80000 -chr1 19198000 19199000 Tfap2d 472.0 105000 0.00212 0.00000 2.11293 1.00000 -chr1 19199000 19200000 Tfap2d 472.0 106000 0.00212 0.00000 2.06351 1.00000 -chr1 19200000 19201000 Tfap2d 472.0 107000 0.00212 0.00000 1.98236 1.00000 -chr1 19201000 19202000 Tfap2d 472.0 108000 0.00254 0.00000 2.32017 1.20000 -chr1 19202000 19203000 Tfap2d 472.0 109000 0.00127 0.00000 1.20293 0.60000 -chr1 19203000 19204000 Tfap2d 472.0 110000 0.00085 0.00000 0.83026 0.40000 -chr1 19204000 19205000 Tfap2d 472.0 111000 0.00127 0.00000 1.17948 0.60000 -chr1 19205000 19206000 Tfap2d 472.0 112000 0.00169 0.00000 1.61307 0.80000 -chr1 19206000 19207000 Tfap2d 472.0 113000 0.00127 0.00000 1.24173 0.60000 -chr1 19207000 19208000 Tfap2d 472.0 114000 0.00085 0.00000 0.81586 0.40000 -chr1 19208000 19209000 Tfap2d 472.0 115000 0.00085 0.00000 0.82300 0.40000 -chr1 19209000 19210000 Tfap2d 472.0 116000 0.00042 0.00000 0.47364 0.20000 -chr1 19210000 19211000 Tfap2d 472.0 117000 0.00000 1.00000 0.00000 0.00000 -chr1 19211000 19212000 Tfap2d 472.0 118000 0.00000 1.00000 0.00000 0.00000 -chr1 19212000 19213000 Tfap2d 472.0 119000 0.00000 1.00000 0.00000 0.00000 -chr1 19213000 19214000 Tfap2d 472.0 120000 0.00000 1.00000 0.00000 0.00000 -chr1 19214000 19215000 Tfap2d 472.0 121000 0.00000 1.00000 0.00000 0.00000 -chr1 19215000 19216000 Tfap2d 472.0 122000 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0.00000 2.23152 0.80000 -chr1 19229000 19230000 Tfap2d 472.0 136000 0.00212 0.00000 2.55695 1.00000 -chr1 19230000 19231000 Tfap2d 472.0 137000 0.00254 0.00000 2.86102 1.20000 -chr1 19231000 19232000 Tfap2d 472.0 138000 0.00254 0.00000 3.18370 1.20000 -chr1 19232000 19233000 Tfap2d 472.0 139000 0.00169 0.00000 1.98794 0.80000 -chr1 19233000 19234000 Tfap2d 472.0 140000 0.00127 0.00000 1.33997 0.60000 -chr1 19234000 19235000 Tfap2d 472.0 141000 0.00085 0.00000 0.96344 0.40000 -chr1 19235000 19236000 Tfap2d 472.0 142000 0.00042 0.00000 0.53872 0.20000 -chr1 19236000 19237000 Tfap2d 472.0 143000 0.00127 0.00000 1.53975 0.60000 -chr1 19237000 19238000 Tfap2d 472.0 144000 0.00127 0.00000 1.74972 0.60000 -chr1 19238000 19239000 Tfap2d 472.0 145000 0.00127 0.00000 2.11716 0.60000 -chr1 19239000 19240000 Tfap2d 472.0 146000 0.00169 0.00000 2.60173 0.80000 -chr1 19240000 19241000 Tfap2d 472.0 147000 0.00127 0.00000 1.85716 0.60000 -chr1 19241000 19242000 Tfap2d 472.0 148000 0.00042 0.00000 0.64156 0.20000 -chr1 19242000 19243000 Tfap2d 472.0 149000 0.00042 0.00000 0.65955 0.20000 -chr1 19243000 19244000 Tfap2d 472.0 150000 0.00085 0.00000 1.22734 0.40000 -chr1 19244000 19245000 Tfap2d 472.0 151000 0.00127 0.00000 1.94235 0.60000 -chr1 19245000 19246000 Tfap2d 472.0 152000 0.00127 0.00000 1.88192 0.60000 -chr1 19246000 19247000 Tfap2d 472.0 153000 0.00212 0.00000 3.16466 1.00000 -chr1 19247000 19248000 Tfap2d 472.0 154000 0.00212 0.00000 3.22246 1.00000 -chr1 19248000 19249000 Tfap2d 472.0 155000 0.00169 0.00000 2.49812 0.80000 -chr1 19249000 19250000 Tfap2d 472.0 156000 0.00085 0.00000 1.24906 0.40000 -chr1 19250000 19251000 Tfap2d 472.0 157000 0.00085 0.00000 1.17132 0.40000 -chr1 19251000 19252000 Tfap2d 472.0 158000 0.00000 1.00000 0.00000 0.00000 -chr1 19252000 19253000 Tfap2d 472.0 159000 0.00085 0.00000 1.09840 0.40000 -chr1 19253000 19254000 Tfap2d 472.0 160000 0.00085 0.00000 1.08156 0.40000 -chr1 19254000 19255000 Tfap2d 472.0 161000 0.00169 0.00000 2.03818 0.80000 -chr1 19255000 19256000 Tfap2d 472.0 162000 0.00169 0.00000 2.30439 0.80000 -chr1 19256000 19257000 Tfap2d 472.0 163000 0.00254 0.00000 3.51395 1.20000 -chr1 19257000 19258000 Tfap2d 472.0 164000 0.00212 0.00000 3.05506 1.00000 -chr1 19258000 19259000 Tfap2d 472.0 165000 0.00212 0.00000 3.25216 1.00000 -chr1 19259000 19260000 Tfap2d 472.0 166000 0.00169 0.00000 2.82288 0.80000 -chr1 19260000 19261000 Tfap2d 472.0 167000 0.00169 0.00000 2.70132 0.80000 -chr1 19261000 19262000 Tfap2d 472.0 168000 0.00085 0.00000 1.31297 0.40000 -chr1 19262000 19263000 Tfap2d 472.0 169000 0.00042 0.00000 0.59304 0.20000 -chr1 19263000 19264000 Tfap2d 472.0 170000 0.00042 0.00000 0.57376 0.20000 -chr1 19264000 19265000 Tfap2d 472.0 171000 0.00000 1.00000 0.00000 0.00000 -chr1 19265000 19266000 Tfap2d 472.0 172000 0.00000 1.00000 0.00000 0.00000 -chr1 19266000 19267000 Tfap2d 472.0 173000 0.00000 1.00000 0.00000 0.00000 -chr1 19267000 19268000 Tfap2d 472.0 174000 0.00000 1.00000 0.00000 0.00000 -chr1 19268000 19269000 Tfap2d 472.0 175000 0.00042 0.00000 0.60838 0.20000 -chr1 19269000 19270000 Tfap2d 472.0 176000 0.00042 0.00000 0.60061 0.20000 -chr1 19270000 19271000 Tfap2d 472.0 177000 0.00042 0.00000 0.64156 0.20000 -chr1 19271000 19272000 Tfap2d 472.0 178000 0.00042 0.00000 0.66577 0.20000 -chr1 19272000 19273000 Tfap2d 472.0 179000 0.00042 0.00000 0.67858 0.20000 -chr1 19273000 19274000 Tfap2d 472.0 180000 0.00000 1.00000 0.00000 0.00000 -chr1 19274000 19275000 Tfap2d 472.0 181000 0.00000 1.00000 0.00000 0.00000 -chr1 19275000 19276000 Tfap2d 472.0 182000 0.00042 0.00000 0.75884 0.20000 -chr1 19276000 19277000 Tfap2d 472.0 183000 0.00042 0.00000 0.73512 0.20000 -chr1 19277000 19278000 Tfap2d 472.0 184000 0.00042 0.00000 0.68851 0.20000 -chr1 19278000 19279000 Tfap2d 472.0 185000 0.00042 0.00000 0.67858 0.20000 -chr1 19279000 19280000 Tfap2d 472.0 186000 0.00042 0.00000 0.75077 0.20000 -chr1 19280000 19281000 Tfap2d 472.0 187000 0.00000 1.00000 0.00000 0.00000 -chr1 19281000 19282000 Tfap2d 472.0 188000 0.00000 1.00000 0.00000 0.00000 -chr1 19282000 19283000 Tfap2d 472.0 189000 0.00000 1.00000 0.00000 0.00000 -chr1 19283000 19284000 Tfap2d 472.0 190000 0.00000 1.00000 0.00000 0.00000 -chr1 19284000 19285000 Tfap2d 472.0 191000 0.00000 1.00000 0.00000 0.00000 -chr1 19285000 19286000 Tfap2d 472.0 192000 0.00000 1.00000 0.00000 0.00000 -chr1 19286000 19287000 Tfap2d 472.0 193000 0.00000 1.00000 0.00000 0.00000 -chr1 19287000 19288000 Tfap2d 472.0 194000 0.00000 1.00000 0.00000 0.00000 -chr1 19288000 19289000 Tfap2d 472.0 195000 0.00000 1.00000 0.00000 0.00000 -chr1 19289000 19290000 Tfap2d 472.0 196000 0.00000 1.00000 0.00000 0.00000 -chr1 19290000 19291000 Tfap2d 472.0 197000 0.00000 1.00000 0.00000 0.00000 -chr1 19291000 19292000 Tfap2d 472.0 198000 0.00000 1.00000 0.00000 0.00000 -chr1 19292000 19293000 Tfap2d 472.0 199000 0.00000 1.00000 0.00000 0.00000 -chr1 19293000 19294000 Tfap2d 472.0 200000 0.00000 1.00000 0.00000 0.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt deleted file mode 100644 index 47c57f05..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 4287000 4288000 Sox17 810.0 -200000 0.00000 1.00000 0.00000 0.00000 -chr1 4288000 4289000 Sox17 810.0 -199000 0.00000 1.00000 0.00000 0.00000 -chr1 4289000 4290000 Sox17 810.0 -198000 0.00000 1.00000 0.00000 0.00000 -chr1 4290000 4291000 Sox17 810.0 -197000 0.00000 1.00000 0.00000 0.00000 -chr1 4291000 4292000 Sox17 810.0 -196000 0.00000 1.00000 0.00000 0.00000 -chr1 4292000 4293000 Sox17 810.0 -195000 0.00000 1.00000 0.00000 0.00000 -chr1 4293000 4294000 Sox17 810.0 -194000 0.00000 1.00000 0.00000 0.00000 -chr1 4294000 4295000 Sox17 810.0 -193000 0.00000 1.00000 0.00000 0.00000 -chr1 4295000 4296000 Sox17 810.0 -192000 0.00000 1.00000 0.00000 0.00000 -chr1 4296000 4297000 Sox17 810.0 -191000 0.00000 1.00000 0.00000 0.00000 -chr1 4297000 4298000 Sox17 810.0 -190000 0.00000 1.00000 0.00000 0.00000 -chr1 4298000 4299000 Sox17 810.0 -189000 0.00000 1.00000 0.00000 0.00000 -chr1 4299000 4300000 Sox17 810.0 -188000 0.00000 1.00000 0.00000 0.00000 -chr1 4300000 4301000 Sox17 810.0 -187000 0.00000 1.00000 0.00000 0.00000 -chr1 4301000 4302000 Sox17 810.0 -186000 0.00000 1.00000 0.00000 0.00000 -chr1 4302000 4303000 Sox17 810.0 -185000 0.00000 1.00000 0.00000 0.00000 -chr1 4303000 4304000 Sox17 810.0 -184000 0.00000 1.00000 0.00000 0.00000 -chr1 4304000 4305000 Sox17 810.0 -183000 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0.33333 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt deleted file mode 100644 index b9a6c591..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 14100000 14101000 Eya1 832.0 -200000 0.00040 0.02837 2.42642 0.33333 -chr1 14101000 14102000 Eya1 832.0 -199000 0.00030 0.03675 1.42986 0.25000 -chr1 14102000 14103000 Eya1 832.0 -198000 0.00024 0.04285 0.93107 0.20000 -chr1 14103000 14104000 Eya1 832.0 -197000 0.00024 0.04285 0.88969 0.20000 -chr1 14104000 14105000 Eya1 832.0 -196000 0.00024 0.04285 0.97649 0.20000 -chr1 14105000 14106000 Eya1 832.0 -195000 0.00000 1.00000 0.00000 0.00000 -chr1 14106000 14107000 Eya1 832.0 -194000 0.00000 1.00000 0.00000 0.00000 -chr1 14107000 14108000 Eya1 832.0 -193000 0.00000 1.00000 0.00000 0.00000 -chr1 14108000 14109000 Eya1 832.0 -192000 0.00000 1.00000 0.00000 0.00000 -chr1 14109000 14110000 Eya1 832.0 -191000 0.00000 1.00000 0.00000 0.00000 -chr1 14110000 14111000 Eya1 832.0 -190000 0.00000 1.00000 0.00000 0.00000 -chr1 14111000 14112000 Eya1 832.0 -189000 0.00000 1.00000 0.00000 0.00000 -chr1 14112000 14113000 Eya1 832.0 -188000 0.00000 1.00000 0.00000 0.00000 -chr1 14113000 14114000 Eya1 832.0 -187000 0.00000 1.00000 0.00000 0.00000 -chr1 14114000 14115000 Eya1 832.0 -186000 0.00000 1.00000 0.00000 0.00000 -chr1 14115000 14116000 Eya1 832.0 -185000 0.00000 1.00000 0.00000 0.00000 -chr1 14116000 14117000 Eya1 832.0 -184000 0.00000 1.00000 0.00000 0.00000 -chr1 14117000 14118000 Eya1 832.0 -183000 0.00000 1.00000 0.00000 0.00000 -chr1 14118000 14119000 Eya1 832.0 -182000 0.00000 1.00000 0.00000 0.00000 -chr1 14119000 14120000 Eya1 832.0 -181000 0.00000 1.00000 0.00000 0.00000 -chr1 14120000 14121000 Eya1 832.0 -180000 0.00000 1.00000 0.00000 0.00000 -chr1 14121000 14122000 Eya1 832.0 -179000 0.00000 1.00000 0.00000 0.00000 -chr1 14122000 14123000 Eya1 832.0 -178000 0.00000 1.00000 0.00000 0.00000 -chr1 14123000 14124000 Eya1 832.0 -177000 0.00000 1.00000 0.00000 0.00000 -chr1 14124000 14125000 Eya1 832.0 -176000 0.00000 1.00000 0.00000 0.00000 -chr1 14125000 14126000 Eya1 832.0 -175000 0.00000 1.00000 0.00000 0.00000 -chr1 14126000 14127000 Eya1 832.0 -174000 0.00000 1.00000 0.00000 0.00000 -chr1 14127000 14128000 Eya1 832.0 -173000 0.00000 1.00000 0.00000 0.00000 -chr1 14128000 14129000 Eya1 832.0 -172000 0.00000 1.00000 0.00000 0.00000 -chr1 14129000 14130000 Eya1 832.0 -171000 0.00000 1.00000 0.00000 0.00000 -chr1 14130000 14131000 Eya1 832.0 -170000 0.00000 1.00000 0.00000 0.00000 -chr1 14131000 14132000 Eya1 832.0 -169000 0.00000 1.00000 0.00000 0.00000 -chr1 14132000 14133000 Eya1 832.0 -168000 0.00000 1.00000 0.00000 0.00000 -chr1 14133000 14134000 Eya1 832.0 -167000 0.00000 1.00000 0.00000 0.00000 -chr1 14134000 14135000 Eya1 832.0 -166000 0.00000 1.00000 0.00000 0.00000 -chr1 14135000 14136000 Eya1 832.0 -165000 0.00000 1.00000 0.00000 0.00000 -chr1 14136000 14137000 Eya1 832.0 -164000 0.00000 1.00000 0.00000 0.00000 -chr1 14137000 14138000 Eya1 832.0 -163000 0.00000 1.00000 0.00000 0.00000 -chr1 14138000 14139000 Eya1 832.0 -162000 0.00000 1.00000 0.00000 0.00000 -chr1 14139000 14140000 Eya1 832.0 -161000 0.00000 1.00000 0.00000 0.00000 -chr1 14140000 14141000 Eya1 832.0 -160000 0.00000 1.00000 0.00000 0.00000 -chr1 14141000 14142000 Eya1 832.0 -159000 0.00000 1.00000 0.00000 0.00000 -chr1 14142000 14143000 Eya1 832.0 -158000 0.00000 1.00000 0.00000 0.00000 -chr1 14143000 14144000 Eya1 832.0 -157000 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1.40000 -chr1 14387000 14388000 Eya1 832.0 87000 0.00096 0.00000 0.71175 0.80000 -chr1 14388000 14389000 Eya1 832.0 88000 0.00096 0.00000 0.70704 0.80000 -chr1 14389000 14390000 Eya1 832.0 89000 0.00120 0.00000 0.97649 1.00000 -chr1 14390000 14391000 Eya1 832.0 90000 0.00120 0.00000 0.98369 1.00000 -chr1 14391000 14392000 Eya1 832.0 91000 0.00072 0.00000 0.56655 0.60000 -chr1 14392000 14393000 Eya1 832.0 92000 0.00072 0.00000 0.63549 0.60000 -chr1 14393000 14394000 Eya1 832.0 93000 0.00096 0.00000 0.87991 0.80000 -chr1 14394000 14395000 Eya1 832.0 94000 0.00096 0.00000 0.80677 0.80000 -chr1 14395000 14396000 Eya1 832.0 95000 0.00072 0.00000 0.58023 0.60000 -chr1 14396000 14397000 Eya1 832.0 96000 0.00072 0.00000 0.56389 0.60000 -chr1 14397000 14398000 Eya1 832.0 97000 0.00072 0.00000 0.58447 0.60000 -chr1 14398000 14399000 Eya1 832.0 98000 0.00048 0.00000 0.38039 0.40000 -chr1 14399000 14400000 Eya1 832.0 99000 0.00024 0.00000 0.20427 0.20000 -chr1 14400000 14401000 Eya1 832.0 100000 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14414000 14415000 Eya1 832.0 114000 0.00048 0.00000 0.46284 0.40000 -chr1 14415000 14416000 Eya1 832.0 115000 0.00048 0.00000 0.46689 0.40000 -chr1 14416000 14417000 Eya1 832.0 116000 0.00024 0.00000 0.26870 0.20000 -chr1 14417000 14418000 Eya1 832.0 117000 0.00024 0.00000 0.27422 0.20000 -chr1 14418000 14419000 Eya1 832.0 118000 0.00048 0.00000 0.55606 0.40000 -chr1 14419000 14420000 Eya1 832.0 119000 0.00024 0.00000 0.27143 0.20000 -chr1 14420000 14421000 Eya1 832.0 120000 0.00048 0.00000 0.53560 0.40000 -chr1 14421000 14422000 Eya1 832.0 121000 0.00048 0.00000 0.52679 0.40000 -chr1 14422000 14423000 Eya1 832.0 122000 0.00048 0.00000 0.54103 0.40000 -chr1 14423000 14424000 Eya1 832.0 123000 0.00024 0.00000 0.27611 0.20000 -chr1 14424000 14425000 Eya1 832.0 124000 0.00048 0.00000 0.58661 0.40000 -chr1 14425000 14426000 Eya1 832.0 125000 0.00024 0.00000 0.32029 0.20000 -chr1 14426000 14427000 Eya1 832.0 126000 0.00168 0.00000 2.09143 1.40000 -chr1 14427000 14428000 Eya1 832.0 127000 0.00192 0.00000 2.44495 1.60000 -chr1 14428000 14429000 Eya1 832.0 128000 0.00192 0.00000 2.56230 1.60000 -chr1 14429000 14430000 Eya1 832.0 129000 0.00168 0.00000 2.16411 1.40000 -chr1 14430000 14431000 Eya1 832.0 130000 0.00240 0.00000 2.89069 2.00000 -chr1 14431000 14432000 Eya1 832.0 131000 0.00120 0.00000 1.57004 1.00000 -chr1 14432000 14433000 Eya1 832.0 132000 0.00096 0.00000 1.28630 0.80000 -chr1 14433000 14434000 Eya1 832.0 133000 0.00096 0.00000 1.16046 0.80000 -chr1 14434000 14435000 Eya1 832.0 134000 0.00144 0.00000 1.81295 1.20000 -chr1 14435000 14436000 Eya1 832.0 135000 0.00072 0.00000 0.94947 0.60000 -chr1 14436000 14437000 Eya1 832.0 136000 0.00048 0.00000 0.58023 0.40000 -chr1 14437000 14438000 Eya1 832.0 137000 0.00048 0.00000 0.54103 0.40000 -chr1 14438000 14439000 Eya1 832.0 138000 0.00048 0.00000 0.60205 0.40000 -chr1 14439000 14440000 Eya1 832.0 139000 0.00000 1.00000 0.00000 0.00000 -chr1 14440000 14441000 Eya1 832.0 140000 0.00000 1.00000 0.00000 0.00000 -chr1 14441000 14442000 Eya1 832.0 141000 0.00000 1.00000 0.00000 0.00000 -chr1 14442000 14443000 Eya1 832.0 142000 0.00000 1.00000 0.00000 0.00000 -chr1 14443000 14444000 Eya1 832.0 143000 0.00000 1.00000 0.00000 0.00000 -chr1 14444000 14445000 Eya1 832.0 144000 0.00024 0.00000 0.33088 0.20000 -chr1 14445000 14446000 Eya1 832.0 145000 0.00096 0.00000 1.60144 0.80000 -chr1 14446000 14447000 Eya1 832.0 146000 0.00096 0.00000 1.47598 0.80000 -chr1 14447000 14448000 Eya1 832.0 147000 0.00144 0.00000 2.10716 1.20000 -chr1 14448000 14449000 Eya1 832.0 148000 0.00168 0.00000 2.54775 1.40000 -chr1 14449000 14450000 Eya1 832.0 149000 0.00216 0.00000 3.36751 1.80000 -chr1 14450000 14451000 Eya1 832.0 150000 0.00216 0.00000 3.13325 1.80000 -chr1 14451000 14452000 Eya1 832.0 151000 0.00216 0.00000 3.30572 1.80000 -chr1 14452000 14453000 Eya1 832.0 152000 0.00216 0.00000 3.20288 1.80000 -chr1 14453000 14454000 Eya1 832.0 153000 0.00192 0.00000 2.87254 1.60000 -chr1 14454000 14455000 Eya1 832.0 154000 0.00120 0.00000 1.82813 1.00000 -chr1 14455000 14456000 Eya1 832.0 155000 0.00048 0.00000 0.70860 0.40000 -chr1 14456000 14457000 Eya1 832.0 156000 0.00072 0.00000 1.06290 0.60000 -chr1 14457000 14458000 Eya1 832.0 157000 0.00024 0.00000 0.33225 0.20000 -chr1 14458000 14459000 Eya1 832.0 158000 0.00072 0.00000 0.96086 0.60000 -chr1 14459000 14460000 Eya1 832.0 159000 0.00072 0.00000 0.93469 0.60000 -chr1 14460000 14461000 Eya1 832.0 160000 0.00168 0.00000 2.14752 1.40000 -chr1 14461000 14462000 Eya1 832.0 161000 0.00192 0.00000 2.31255 1.60000 -chr1 14462000 14463000 Eya1 832.0 162000 0.00216 0.00000 2.94142 1.80000 -chr1 14463000 14464000 Eya1 832.0 163000 0.00168 0.00000 2.32574 1.40000 -chr1 14464000 14465000 Eya1 832.0 164000 0.00168 0.00000 2.42642 1.40000 -chr1 14465000 14466000 Eya1 832.0 165000 0.00072 0.00000 1.10699 0.60000 -chr1 14466000 14467000 Eya1 832.0 166000 0.00024 0.00000 0.40036 0.20000 -chr1 14467000 14468000 Eya1 832.0 167000 0.00000 1.00000 0.00000 0.00000 -chr1 14468000 14469000 Eya1 832.0 168000 0.00000 1.00000 0.00000 0.00000 -chr1 14469000 14470000 Eya1 832.0 169000 0.00000 1.00000 0.00000 0.00000 -chr1 14470000 14471000 Eya1 832.0 170000 0.00000 1.00000 0.00000 0.00000 -chr1 14471000 14472000 Eya1 832.0 171000 0.00048 0.00000 0.65903 0.40000 -chr1 14472000 14473000 Eya1 832.0 172000 0.00048 0.00000 0.61832 0.40000 -chr1 14473000 14474000 Eya1 832.0 173000 0.00048 0.00000 0.63049 0.40000 -chr1 14474000 14475000 Eya1 832.0 174000 0.00048 0.00000 0.66727 0.40000 -chr1 14475000 14476000 Eya1 832.0 175000 0.00048 0.00000 0.69028 0.40000 -chr1 14476000 14477000 Eya1 832.0 176000 0.00024 0.00000 0.34073 0.20000 -chr1 14477000 14478000 Eya1 832.0 177000 0.00048 0.00000 0.72793 0.40000 -chr1 14478000 14479000 Eya1 832.0 178000 0.00048 0.00000 0.75540 0.40000 -chr1 14479000 14480000 Eya1 832.0 179000 0.00048 0.00000 0.76992 0.40000 -chr1 14480000 14481000 Eya1 832.0 180000 0.00048 0.00000 0.81291 0.40000 -chr1 14481000 14482000 Eya1 832.0 181000 0.00024 0.00000 0.40853 0.20000 -chr1 14482000 14483000 Eya1 832.0 182000 0.00000 1.00000 0.00000 0.00000 -chr1 14483000 14484000 Eya1 832.0 183000 0.00000 1.00000 0.00000 0.00000 -chr1 14484000 14485000 Eya1 832.0 184000 0.00024 0.00000 0.39060 0.20000 -chr1 14485000 14486000 Eya1 832.0 185000 0.00096 0.00000 1.53985 0.80000 -chr1 14486000 14487000 Eya1 832.0 186000 0.00096 0.00000 1.70366 0.80000 -chr1 14487000 14488000 Eya1 832.0 187000 0.00096 0.00000 1.73129 0.80000 -chr1 14488000 14489000 Eya1 832.0 188000 0.00120 0.00000 2.14096 1.00000 -chr1 14489000 14490000 Eya1 832.0 189000 0.00144 0.00000 2.79321 1.20000 -chr1 14490000 14491000 Eya1 832.0 190000 0.00072 0.00000 1.40477 0.60000 -chr1 14491000 14492000 Eya1 832.0 191000 0.00144 0.00000 2.66907 1.20000 -chr1 14492000 14493000 Eya1 832.0 192000 0.00240 0.00000 4.39956 2.00000 -chr1 14493000 14494000 Eya1 832.0 193000 0.00216 0.00000 4.28957 1.80000 -chr1 14494000 14495000 Eya1 832.0 194000 0.00168 0.00000 3.23991 1.40000 -chr1 14495000 14496000 Eya1 832.0 195000 0.00216 0.00000 4.42115 1.80000 -chr1 14496000 14497000 Eya1 832.0 196000 0.00168 0.00000 3.43867 1.40000 -chr1 14497000 14498000 Eya1 832.0 197000 0.00144 0.00000 2.72973 1.20000 -chr1 14498000 14499000 Eya1 832.0 198000 0.00264 0.00000 4.31761 2.20000 -chr1 14499000 14500000 Eya1 832.0 199000 0.00331 0.00000 5.76435 2.75000 -chr1 14500000 14501000 Eya1 832.0 200000 0.00361 0.00000 6.12796 3.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt deleted file mode 100644 index b462ebd9..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 18893000 18894000 Tfap2d 800.0 -200000 0.00000 1.00000 0.00000 0.00000 -chr1 18894000 18895000 Tfap2d 800.0 -199000 0.00000 1.00000 0.00000 0.00000 -chr1 18895000 18896000 Tfap2d 800.0 -198000 0.00000 1.00000 0.00000 0.00000 -chr1 18896000 18897000 Tfap2d 800.0 -197000 0.00000 1.00000 0.00000 0.00000 -chr1 18897000 18898000 Tfap2d 800.0 -196000 0.00000 1.00000 0.00000 0.00000 -chr1 18898000 18899000 Tfap2d 800.0 -195000 0.00000 1.00000 0.00000 0.00000 -chr1 18899000 18900000 Tfap2d 800.0 -194000 0.00000 1.00000 0.00000 0.00000 -chr1 18900000 18901000 Tfap2d 800.0 -193000 0.00000 1.00000 0.00000 0.00000 -chr1 18901000 18902000 Tfap2d 800.0 -192000 0.00000 1.00000 0.00000 0.00000 -chr1 18902000 18903000 Tfap2d 800.0 -191000 0.00000 1.00000 0.00000 0.00000 -chr1 18903000 18904000 Tfap2d 800.0 -190000 0.00000 1.00000 0.00000 0.00000 -chr1 18904000 18905000 Tfap2d 800.0 -189000 0.00000 1.00000 0.00000 0.00000 -chr1 18905000 18906000 Tfap2d 800.0 -188000 0.00000 1.00000 0.00000 0.00000 -chr1 18906000 18907000 Tfap2d 800.0 -187000 0.00000 1.00000 0.00000 0.00000 -chr1 18907000 18908000 Tfap2d 800.0 -186000 0.00000 1.00000 0.00000 0.00000 -chr1 18908000 18909000 Tfap2d 800.0 -185000 0.00000 1.00000 0.00000 0.00000 -chr1 18909000 18910000 Tfap2d 800.0 -184000 0.00000 1.00000 0.00000 0.00000 -chr1 18910000 18911000 Tfap2d 800.0 -183000 0.00000 1.00000 0.00000 0.00000 -chr1 18911000 18912000 Tfap2d 800.0 -182000 0.00000 1.00000 0.00000 0.00000 -chr1 18912000 18913000 Tfap2d 800.0 -181000 0.00000 1.00000 0.00000 0.00000 -chr1 18913000 18914000 Tfap2d 800.0 -180000 0.00000 1.00000 0.00000 0.00000 -chr1 18914000 18915000 Tfap2d 800.0 -179000 0.00000 1.00000 0.00000 0.00000 -chr1 18915000 18916000 Tfap2d 800.0 -178000 0.00000 1.00000 0.00000 0.00000 -chr1 18916000 18917000 Tfap2d 800.0 -177000 0.00000 1.00000 0.00000 0.00000 -chr1 18917000 18918000 Tfap2d 800.0 -176000 0.00000 1.00000 0.00000 0.00000 -chr1 18918000 18919000 Tfap2d 800.0 -175000 0.00000 1.00000 0.00000 0.00000 -chr1 18919000 18920000 Tfap2d 800.0 -174000 0.00000 1.00000 0.00000 0.00000 -chr1 18920000 18921000 Tfap2d 800.0 -173000 0.00000 1.00000 0.00000 0.00000 -chr1 18921000 18922000 Tfap2d 800.0 -172000 0.00000 1.00000 0.00000 0.00000 -chr1 18922000 18923000 Tfap2d 800.0 -171000 0.00000 1.00000 0.00000 0.00000 -chr1 18923000 18924000 Tfap2d 800.0 -170000 0.00000 1.00000 0.00000 0.00000 -chr1 18924000 18925000 Tfap2d 800.0 -169000 0.00000 1.00000 0.00000 0.00000 -chr1 18925000 18926000 Tfap2d 800.0 -168000 0.00000 1.00000 0.00000 0.00000 -chr1 18926000 18927000 Tfap2d 800.0 -167000 0.00000 1.00000 0.00000 0.00000 -chr1 18927000 18928000 Tfap2d 800.0 -166000 0.00000 1.00000 0.00000 0.00000 -chr1 18928000 18929000 Tfap2d 800.0 -165000 0.00000 1.00000 0.00000 0.00000 -chr1 18929000 18930000 Tfap2d 800.0 -164000 0.00000 1.00000 0.00000 0.00000 -chr1 18930000 18931000 Tfap2d 800.0 -163000 0.00000 1.00000 0.00000 0.00000 -chr1 18931000 18932000 Tfap2d 800.0 -162000 0.00000 1.00000 0.00000 0.00000 -chr1 18932000 18933000 Tfap2d 800.0 -161000 0.00000 1.00000 0.00000 0.00000 -chr1 18933000 18934000 Tfap2d 800.0 -160000 0.00000 1.00000 0.00000 0.00000 -chr1 18934000 18935000 Tfap2d 800.0 -159000 0.00000 1.00000 0.00000 0.00000 -chr1 18935000 18936000 Tfap2d 800.0 -158000 0.00000 1.00000 0.00000 0.00000 -chr1 18936000 18937000 Tfap2d 800.0 -157000 0.00000 1.00000 0.00000 0.00000 -chr1 18937000 18938000 Tfap2d 800.0 -156000 0.00000 1.00000 0.00000 0.00000 -chr1 18938000 18939000 Tfap2d 800.0 -155000 0.00000 1.00000 0.00000 0.00000 -chr1 18939000 18940000 Tfap2d 800.0 -154000 0.00000 1.00000 0.00000 0.00000 -chr1 18940000 18941000 Tfap2d 800.0 -153000 0.00000 1.00000 0.00000 0.00000 -chr1 18941000 18942000 Tfap2d 800.0 -152000 0.00000 1.00000 0.00000 0.00000 -chr1 18942000 18943000 Tfap2d 800.0 -151000 0.00000 1.00000 0.00000 0.00000 -chr1 18943000 18944000 Tfap2d 800.0 -150000 0.00000 1.00000 0.00000 0.00000 -chr1 18944000 18945000 Tfap2d 800.0 -149000 0.00000 1.00000 0.00000 0.00000 -chr1 18945000 18946000 Tfap2d 800.0 -148000 0.00000 1.00000 0.00000 0.00000 -chr1 18946000 18947000 Tfap2d 800.0 -147000 0.00000 1.00000 0.00000 0.00000 -chr1 18947000 18948000 Tfap2d 800.0 -146000 0.00000 1.00000 0.00000 0.00000 -chr1 18948000 18949000 Tfap2d 800.0 -145000 0.00000 1.00000 0.00000 0.00000 -chr1 18949000 18950000 Tfap2d 800.0 -144000 0.00000 1.00000 0.00000 0.00000 -chr1 18950000 18951000 Tfap2d 800.0 -143000 0.00000 1.00000 0.00000 0.00000 -chr1 18951000 18952000 Tfap2d 800.0 -142000 0.00000 1.00000 0.00000 0.00000 -chr1 18952000 18953000 Tfap2d 800.0 -141000 0.00000 1.00000 0.00000 0.00000 -chr1 18953000 18954000 Tfap2d 800.0 -140000 0.00000 1.00000 0.00000 0.00000 -chr1 18954000 18955000 Tfap2d 800.0 -139000 0.00000 1.00000 0.00000 0.00000 -chr1 18955000 18956000 Tfap2d 800.0 -138000 0.00000 1.00000 0.00000 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19194000 Tfap2d 800.0 100000 0.00225 0.00000 2.13525 1.80000 -chr1 19194000 19195000 Tfap2d 800.0 101000 0.00225 0.00000 2.28498 1.80000 -chr1 19195000 19196000 Tfap2d 800.0 102000 0.00400 0.00000 3.95370 3.20000 -chr1 19196000 19197000 Tfap2d 800.0 103000 0.00350 0.00000 3.82245 2.80000 -chr1 19197000 19198000 Tfap2d 800.0 104000 0.00425 0.00000 4.42398 3.40000 -chr1 19198000 19199000 Tfap2d 800.0 105000 0.00525 0.00000 5.23585 4.20000 -chr1 19199000 19200000 Tfap2d 800.0 106000 0.00475 0.00000 4.62638 3.80000 -chr1 19200000 19201000 Tfap2d 800.0 107000 0.00300 0.00000 2.80702 2.40000 -chr1 19201000 19202000 Tfap2d 800.0 108000 0.00375 0.00000 3.42226 3.00000 -chr1 19202000 19203000 Tfap2d 800.0 109000 0.00325 0.00000 3.07549 2.60000 -chr1 19203000 19204000 Tfap2d 800.0 110000 0.00275 0.00000 2.69419 2.20000 -chr1 19204000 19205000 Tfap2d 800.0 111000 0.00375 0.00000 3.47945 3.00000 -chr1 19205000 19206000 Tfap2d 800.0 112000 0.00375 0.00000 3.56892 3.00000 -chr1 19206000 19207000 Tfap2d 800.0 113000 0.00400 0.00000 3.90733 3.20000 -chr1 19207000 19208000 Tfap2d 800.0 114000 0.00300 0.00000 2.88815 2.40000 -chr1 19208000 19209000 Tfap2d 800.0 115000 0.00225 0.00000 2.18506 1.80000 -chr1 19209000 19210000 Tfap2d 800.0 116000 0.00200 0.00000 2.23557 1.60000 -chr1 19210000 19211000 Tfap2d 800.0 117000 0.00325 0.00000 3.70744 2.60000 -chr1 19211000 19212000 Tfap2d 800.0 118000 0.00275 0.00000 3.18064 2.20000 -chr1 19212000 19213000 Tfap2d 800.0 119000 0.00300 0.00000 3.38745 2.40000 -chr1 19213000 19214000 Tfap2d 800.0 120000 0.00325 0.00000 3.62065 2.60000 -chr1 19214000 19215000 Tfap2d 800.0 121000 0.00325 0.00000 3.56110 2.60000 -chr1 19215000 19216000 Tfap2d 800.0 122000 0.00400 0.00000 4.50134 3.20000 -chr1 19216000 19217000 Tfap2d 800.0 123000 0.00375 0.00000 4.30732 3.00000 -chr1 19217000 19218000 Tfap2d 800.0 124000 0.00450 0.00000 5.49065 3.60000 -chr1 19218000 19219000 Tfap2d 800.0 125000 0.00425 0.00000 5.66269 3.40000 -chr1 19219000 19220000 Tfap2d 800.0 126000 0.00425 0.00000 5.28236 3.40000 -chr1 19220000 19221000 Tfap2d 800.0 127000 0.00350 0.00000 4.44980 2.80000 -chr1 19221000 19222000 Tfap2d 800.0 128000 0.00325 0.00000 4.33029 2.60000 -chr1 19222000 19223000 Tfap2d 800.0 129000 0.00250 0.00000 3.21525 2.00000 -chr1 19223000 19224000 Tfap2d 800.0 130000 0.00450 0.00000 5.41136 3.60000 -chr1 19224000 19225000 Tfap2d 800.0 131000 0.00375 0.00000 4.89852 3.00000 -chr1 19225000 19226000 Tfap2d 800.0 132000 0.00275 0.00000 3.67881 2.20000 -chr1 19226000 19227000 Tfap2d 800.0 133000 0.00300 0.00000 3.62065 2.40000 -chr1 19227000 19228000 Tfap2d 800.0 134000 0.00325 0.00000 4.08518 2.60000 -chr1 19228000 19229000 Tfap2d 800.0 135000 0.00200 0.00000 2.63320 1.60000 -chr1 19229000 19230000 Tfap2d 800.0 136000 0.00325 0.00000 3.92237 2.60000 -chr1 19230000 19231000 Tfap2d 800.0 137000 0.00325 0.00000 3.65734 2.60000 -chr1 19231000 19232000 Tfap2d 800.0 138000 0.00350 0.00000 4.38289 2.80000 -chr1 19232000 19233000 Tfap2d 800.0 139000 0.00375 0.00000 4.39832 3.00000 -chr1 19233000 19234000 Tfap2d 800.0 140000 0.00350 0.00000 3.68939 2.80000 -chr1 19234000 19235000 Tfap2d 800.0 141000 0.00275 0.00000 3.12636 2.20000 -chr1 19235000 19236000 Tfap2d 800.0 142000 0.00250 0.00000 3.17843 2.00000 -chr1 19236000 19237000 Tfap2d 800.0 143000 0.00225 0.00000 2.72536 1.80000 -chr1 19237000 19238000 Tfap2d 800.0 144000 0.00125 0.00000 1.72056 1.00000 -chr1 19238000 19239000 Tfap2d 800.0 145000 0.00075 0.00000 1.24912 0.60000 -chr1 19239000 19240000 Tfap2d 800.0 146000 0.00050 0.00000 0.76751 0.40000 -chr1 19240000 19241000 Tfap2d 800.0 147000 0.00050 0.00000 0.73048 0.40000 -chr1 19241000 19242000 Tfap2d 800.0 148000 0.00075 0.00000 1.13557 0.60000 -chr1 19242000 19243000 Tfap2d 800.0 149000 0.00100 0.00000 1.55654 0.80000 -chr1 19243000 19244000 Tfap2d 800.0 150000 0.00100 0.00000 1.44826 0.80000 -chr1 19244000 19245000 Tfap2d 800.0 151000 0.00125 0.00000 1.90997 1.00000 -chr1 19245000 19246000 Tfap2d 800.0 152000 0.00125 0.00000 1.85055 1.00000 -chr1 19246000 19247000 Tfap2d 800.0 153000 0.00075 0.00000 1.12029 0.60000 -chr1 19247000 19248000 Tfap2d 800.0 154000 0.00050 0.00000 0.76050 0.40000 -chr1 19248000 19249000 Tfap2d 800.0 155000 0.00050 0.00000 0.73695 0.40000 -chr1 19249000 19250000 Tfap2d 800.0 156000 0.00000 1.00000 0.00000 0.00000 -chr1 19250000 19251000 Tfap2d 800.0 157000 0.00025 0.00000 0.34554 0.20000 -chr1 19251000 19252000 Tfap2d 800.0 158000 0.00025 0.00000 0.33310 0.20000 -chr1 19252000 19253000 Tfap2d 800.0 159000 0.00025 0.00000 0.32403 0.20000 -chr1 19253000 19254000 Tfap2d 800.0 160000 0.00025 0.00000 0.31906 0.20000 -chr1 19254000 19255000 Tfap2d 800.0 161000 0.00025 0.00000 0.30063 0.20000 -chr1 19255000 19256000 Tfap2d 800.0 162000 0.00000 1.00000 0.00000 0.00000 -chr1 19256000 19257000 Tfap2d 800.0 163000 0.00000 1.00000 0.00000 0.00000 -chr1 19257000 19258000 Tfap2d 800.0 164000 0.00000 1.00000 0.00000 0.00000 -chr1 19258000 19259000 Tfap2d 800.0 165000 0.00025 0.00000 0.38376 0.20000 -chr1 19259000 19260000 Tfap2d 800.0 166000 0.00050 0.00000 0.83275 0.40000 -chr1 19260000 19261000 Tfap2d 800.0 167000 0.00075 0.00000 1.19533 0.60000 -chr1 19261000 19262000 Tfap2d 800.0 168000 0.00075 0.00000 1.16198 0.60000 -chr1 19262000 19263000 Tfap2d 800.0 169000 0.00100 0.00000 1.39958 0.80000 -chr1 19263000 19264000 Tfap2d 800.0 170000 0.00075 0.00000 1.01555 0.60000 -chr1 19264000 19265000 Tfap2d 800.0 171000 0.00075 0.00000 1.02808 0.60000 -chr1 19265000 19266000 Tfap2d 800.0 172000 0.00050 0.00000 0.64305 0.40000 -chr1 19266000 19267000 Tfap2d 800.0 173000 0.00075 0.00000 0.98356 0.60000 -chr1 19267000 19268000 Tfap2d 800.0 174000 0.00050 0.00000 0.69396 0.40000 -chr1 19268000 19269000 Tfap2d 800.0 175000 0.00075 0.00000 1.07683 0.60000 -chr1 19269000 19270000 Tfap2d 800.0 176000 0.00075 0.00000 1.06308 0.60000 -chr1 19270000 19271000 Tfap2d 800.0 177000 0.00075 0.00000 1.13557 0.60000 -chr1 19271000 19272000 Tfap2d 800.0 178000 0.00050 0.00000 0.78561 0.40000 -chr1 19272000 19273000 Tfap2d 800.0 179000 0.00050 0.00000 0.80072 0.40000 -chr1 19273000 19274000 Tfap2d 800.0 180000 0.00025 0.00000 0.42272 0.20000 -chr1 19274000 19275000 Tfap2d 800.0 181000 0.00000 1.00000 0.00000 0.00000 -chr1 19275000 19276000 Tfap2d 800.0 182000 0.00025 0.00000 0.44771 0.20000 -chr1 19276000 19277000 Tfap2d 800.0 183000 0.00025 0.00000 0.43372 0.20000 -chr1 19277000 19278000 Tfap2d 800.0 184000 0.00075 0.00000 1.21866 0.60000 -chr1 19278000 19279000 Tfap2d 800.0 185000 0.00075 0.00000 1.20108 0.60000 -chr1 19279000 19280000 Tfap2d 800.0 186000 0.00075 0.00000 1.32885 0.60000 -chr1 19280000 19281000 Tfap2d 800.0 187000 0.00050 0.00000 0.90027 0.40000 -chr1 19281000 19282000 Tfap2d 800.0 188000 0.00050 0.00000 0.89064 0.40000 -chr1 19282000 19283000 Tfap2d 800.0 189000 0.00000 1.00000 0.00000 0.00000 -chr1 19283000 19284000 Tfap2d 800.0 190000 0.00025 0.00000 0.48699 0.20000 -chr1 19284000 19285000 Tfap2d 800.0 191000 0.00025 0.00000 0.46264 0.20000 -chr1 19285000 19286000 Tfap2d 800.0 192000 0.00025 0.00000 0.45755 0.20000 -chr1 19286000 19287000 Tfap2d 800.0 193000 0.00050 0.00000 0.99137 0.40000 -chr1 19287000 19288000 Tfap2d 800.0 194000 0.00050 0.00000 0.96272 0.40000 -chr1 19288000 19289000 Tfap2d 800.0 195000 0.00025 0.00000 0.51089 0.20000 -chr1 19289000 19290000 Tfap2d 800.0 196000 0.00025 0.00000 0.51089 0.20000 -chr1 19290000 19291000 Tfap2d 800.0 197000 0.00025 0.00000 0.47315 0.20000 -chr1 19291000 19292000 Tfap2d 800.0 198000 0.00000 1.00000 0.00000 0.00000 -chr1 19292000 19293000 Tfap2d 800.0 199000 0.00000 1.00000 0.00000 0.00000 -chr1 19293000 19294000 Tfap2d 800.0 200000 0.00000 1.00000 0.00000 0.00000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt deleted file mode 100644 index cda0fbd9..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 4287000 4288000 Sox17 978.0 -200000 0.00000 1.00000 0.00000 0.00000 -chr1 4288000 4289000 Sox17 978.0 -199000 0.00000 1.00000 0.00000 0.00000 -chr1 4289000 4290000 Sox17 978.0 -198000 0.00000 1.00000 0.00000 0.00000 -chr1 4290000 4291000 Sox17 978.0 -197000 0.00000 1.00000 0.00000 0.00000 -chr1 4291000 4292000 Sox17 978.0 -196000 0.00000 1.00000 0.00000 0.00000 -chr1 4292000 4293000 Sox17 978.0 -195000 0.00000 1.00000 0.00000 0.00000 -chr1 4293000 4294000 Sox17 978.0 -194000 0.00000 1.00000 0.00000 0.00000 -chr1 4294000 4295000 Sox17 978.0 -193000 0.00000 1.00000 0.00000 0.00000 -chr1 4295000 4296000 Sox17 978.0 -192000 0.00000 1.00000 0.00000 0.00000 -chr1 4296000 4297000 Sox17 978.0 -191000 0.00000 1.00000 0.00000 0.00000 -chr1 4297000 4298000 Sox17 978.0 -190000 0.00000 1.00000 0.00000 0.00000 -chr1 4298000 4299000 Sox17 978.0 -189000 0.00000 1.00000 0.00000 0.00000 -chr1 4299000 4300000 Sox17 978.0 -188000 0.00000 1.00000 0.00000 0.00000 -chr1 4300000 4301000 Sox17 978.0 -187000 0.00000 1.00000 0.00000 0.00000 -chr1 4301000 4302000 Sox17 978.0 -186000 0.00000 1.00000 0.00000 0.00000 -chr1 4302000 4303000 Sox17 978.0 -185000 0.00000 1.00000 0.00000 0.00000 -chr1 4303000 4304000 Sox17 978.0 -184000 0.00000 1.00000 0.00000 0.00000 -chr1 4304000 4305000 Sox17 978.0 -183000 0.00000 1.00000 0.00000 0.00000 -chr1 4305000 4306000 Sox17 978.0 -182000 0.00000 1.00000 0.00000 0.00000 -chr1 4306000 4307000 Sox17 978.0 -181000 0.00000 1.00000 0.00000 0.00000 -chr1 4307000 4308000 Sox17 978.0 -180000 0.00000 1.00000 0.00000 0.00000 -chr1 4308000 4309000 Sox17 978.0 -179000 0.00000 1.00000 0.00000 0.00000 -chr1 4309000 4310000 Sox17 978.0 -178000 0.00000 1.00000 0.00000 0.00000 -chr1 4310000 4311000 Sox17 978.0 -177000 0.00000 1.00000 0.00000 0.00000 -chr1 4311000 4312000 Sox17 978.0 -176000 0.00000 1.00000 0.00000 0.00000 -chr1 4312000 4313000 Sox17 978.0 -175000 0.00000 1.00000 0.00000 0.00000 -chr1 4313000 4314000 Sox17 978.0 -174000 0.00000 1.00000 0.00000 0.00000 -chr1 4314000 4315000 Sox17 978.0 -173000 0.00000 1.00000 0.00000 0.00000 -chr1 4315000 4316000 Sox17 978.0 -172000 0.00000 1.00000 0.00000 0.00000 -chr1 4316000 4317000 Sox17 978.0 -171000 0.00000 1.00000 0.00000 0.00000 -chr1 4317000 4318000 Sox17 978.0 -170000 0.00000 1.00000 0.00000 0.00000 -chr1 4318000 4319000 Sox17 978.0 -169000 0.00000 1.00000 0.00000 0.00000 -chr1 4319000 4320000 Sox17 978.0 -168000 0.00000 1.00000 0.00000 0.00000 -chr1 4320000 4321000 Sox17 978.0 -167000 0.00000 1.00000 0.00000 0.00000 -chr1 4321000 4322000 Sox17 978.0 -166000 0.00000 1.00000 0.00000 0.00000 -chr1 4322000 4323000 Sox17 978.0 -165000 0.00000 1.00000 0.00000 0.00000 -chr1 4323000 4324000 Sox17 978.0 -164000 0.00000 1.00000 0.00000 0.00000 -chr1 4324000 4325000 Sox17 978.0 -163000 0.00000 1.00000 0.00000 0.00000 -chr1 4325000 4326000 Sox17 978.0 -162000 0.00000 1.00000 0.00000 0.00000 -chr1 4326000 4327000 Sox17 978.0 -161000 0.00000 1.00000 0.00000 0.00000 -chr1 4327000 4328000 Sox17 978.0 -160000 0.00000 1.00000 0.00000 0.00000 -chr1 4328000 4329000 Sox17 978.0 -159000 0.00000 1.00000 0.00000 0.00000 -chr1 4329000 4330000 Sox17 978.0 -158000 0.00000 1.00000 0.00000 0.00000 -chr1 4330000 4331000 Sox17 978.0 -157000 0.00000 1.00000 0.00000 0.00000 -chr1 4331000 4332000 Sox17 978.0 -156000 0.00000 1.00000 0.00000 0.00000 -chr1 4332000 4333000 Sox17 978.0 -155000 0.00000 1.00000 0.00000 0.00000 -chr1 4333000 4334000 Sox17 978.0 -154000 0.00000 1.00000 0.00000 0.00000 -chr1 4334000 4335000 Sox17 978.0 -153000 0.00000 1.00000 0.00000 0.00000 -chr1 4335000 4336000 Sox17 978.0 -152000 0.00000 1.00000 0.00000 0.00000 -chr1 4336000 4337000 Sox17 978.0 -151000 0.00000 1.00000 0.00000 0.00000 -chr1 4337000 4338000 Sox17 978.0 -150000 0.00000 1.00000 0.00000 0.00000 -chr1 4338000 4339000 Sox17 978.0 -149000 0.00000 1.00000 0.00000 0.00000 -chr1 4339000 4340000 Sox17 978.0 -148000 0.00000 1.00000 0.00000 0.00000 -chr1 4340000 4341000 Sox17 978.0 -147000 0.00000 1.00000 0.00000 0.00000 -chr1 4341000 4342000 Sox17 978.0 -146000 0.00000 1.00000 0.00000 0.00000 -chr1 4342000 4343000 Sox17 978.0 -145000 0.00000 1.00000 0.00000 0.00000 -chr1 4343000 4344000 Sox17 978.0 -144000 0.00000 1.00000 0.00000 0.00000 -chr1 4344000 4345000 Sox17 978.0 -143000 0.00000 1.00000 0.00000 0.00000 -chr1 4345000 4346000 Sox17 978.0 -142000 0.00000 1.00000 0.00000 0.00000 -chr1 4346000 4347000 Sox17 978.0 -141000 0.00000 1.00000 0.00000 0.00000 -chr1 4347000 4348000 Sox17 978.0 -140000 0.00000 1.00000 0.00000 0.00000 -chr1 4348000 4349000 Sox17 978.0 -139000 0.00000 1.00000 0.00000 0.00000 -chr1 4349000 4350000 Sox17 978.0 -138000 0.00000 1.00000 0.00000 0.00000 -chr1 4350000 4351000 Sox17 978.0 -137000 0.00000 1.00000 0.00000 0.00000 -chr1 4351000 4352000 Sox17 978.0 -136000 0.00000 1.00000 0.00000 0.00000 -chr1 4352000 4353000 Sox17 978.0 -135000 0.00000 1.00000 0.00000 0.00000 -chr1 4353000 4354000 Sox17 978.0 -134000 0.00000 1.00000 0.00000 0.00000 -chr1 4354000 4355000 Sox17 978.0 -133000 0.00000 1.00000 0.00000 0.00000 -chr1 4355000 4356000 Sox17 978.0 -132000 0.00000 1.00000 0.00000 0.00000 -chr1 4356000 4357000 Sox17 978.0 -131000 0.00000 1.00000 0.00000 0.00000 -chr1 4357000 4358000 Sox17 978.0 -130000 0.00000 1.00000 0.00000 0.00000 -chr1 4358000 4359000 Sox17 978.0 -129000 0.00000 1.00000 0.00000 0.00000 -chr1 4359000 4360000 Sox17 978.0 -128000 0.00000 1.00000 0.00000 0.00000 -chr1 4360000 4361000 Sox17 978.0 -127000 0.00000 1.00000 0.00000 0.00000 -chr1 4361000 4362000 Sox17 978.0 -126000 0.00000 1.00000 0.00000 0.00000 -chr1 4362000 4363000 Sox17 978.0 -125000 0.00000 1.00000 0.00000 0.00000 -chr1 4363000 4364000 Sox17 978.0 -124000 0.00000 1.00000 0.00000 0.00000 -chr1 4364000 4365000 Sox17 978.0 -123000 0.00000 1.00000 0.00000 0.00000 -chr1 4365000 4366000 Sox17 978.0 -122000 0.00000 1.00000 0.00000 0.00000 -chr1 4366000 4367000 Sox17 978.0 -121000 0.00000 1.00000 0.00000 0.00000 -chr1 4367000 4368000 Sox17 978.0 -120000 0.00000 1.00000 0.00000 0.00000 -chr1 4368000 4369000 Sox17 978.0 -119000 0.00000 1.00000 0.00000 0.00000 -chr1 4369000 4370000 Sox17 978.0 -118000 0.00000 1.00000 0.00000 0.00000 -chr1 4370000 4371000 Sox17 978.0 -117000 0.00000 1.00000 0.00000 0.00000 -chr1 4371000 4372000 Sox17 978.0 -116000 0.00000 1.00000 0.00000 0.00000 -chr1 4372000 4373000 Sox17 978.0 -115000 0.00000 1.00000 0.00000 0.00000 -chr1 4373000 4374000 Sox17 978.0 -114000 0.00000 1.00000 0.00000 0.00000 -chr1 4374000 4375000 Sox17 978.0 -113000 0.00000 1.00000 0.00000 0.00000 -chr1 4375000 4376000 Sox17 978.0 -112000 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4651000 Sox17 978.0 163000 0.00020 0.00000 0.28265 0.20000 -chr1 4651000 4652000 Sox17 978.0 164000 0.00020 0.00000 0.29489 0.20000 -chr1 4652000 4653000 Sox17 978.0 165000 0.00020 0.00000 0.31391 0.20000 -chr1 4653000 4654000 Sox17 978.0 166000 0.00082 0.00000 1.36237 0.80000 -chr1 4654000 4655000 Sox17 978.0 167000 0.00082 0.00000 1.30370 0.80000 -chr1 4655000 4656000 Sox17 978.0 168000 0.00082 0.00000 1.26732 0.80000 -chr1 4656000 4657000 Sox17 978.0 169000 0.00123 0.00000 1.71727 1.20000 -chr1 4657000 4658000 Sox17 978.0 170000 0.00123 0.00000 1.66143 1.20000 -chr1 4658000 4659000 Sox17 978.0 171000 0.00061 0.00000 0.84097 0.60000 -chr1 4659000 4660000 Sox17 978.0 172000 0.00061 0.00000 0.78902 0.60000 -chr1 4660000 4661000 Sox17 978.0 173000 0.00061 0.00000 0.80455 0.60000 -chr1 4661000 4662000 Sox17 978.0 174000 0.00020 0.00000 0.28383 0.20000 -chr1 4662000 4663000 Sox17 978.0 175000 0.00000 1.00000 0.00000 0.00000 -chr1 4663000 4664000 Sox17 978.0 176000 0.00041 0.00000 0.57973 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0.00102 0.00000 1.99177 1.00000 -chr1 4678000 4679000 Sox17 978.0 191000 0.00123 0.00000 2.27062 1.20000 -chr1 4679000 4680000 Sox17 978.0 192000 0.00082 0.00000 1.49711 0.80000 -chr1 4680000 4681000 Sox17 978.0 193000 0.00102 0.00000 2.02734 1.00000 -chr1 4681000 4682000 Sox17 978.0 194000 0.00082 0.00000 1.57499 0.80000 -chr1 4682000 4683000 Sox17 978.0 195000 0.00061 0.00000 1.25371 0.60000 -chr1 4683000 4684000 Sox17 978.0 196000 0.00020 0.00000 0.41790 0.20000 -chr1 4684000 4685000 Sox17 978.0 197000 0.00102 0.00000 1.93518 1.00000 -chr1 4685000 4686000 Sox17 978.0 198000 0.00082 0.00000 1.33566 0.80000 -chr1 4686000 4687000 Sox17 978.0 199000 0.00102 0.00000 1.78321 1.00000 -chr1 4687000 4688000 Sox17 978.0 200000 0.00136 0.00000 2.31696 1.33333 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt deleted file mode 100644 index f6af4efe..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 14100000 14101000 Eya1 673.0 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14101000 14102000 Eya1 673.0 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14102000 14103000 Eya1 673.0 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14103000 14104000 Eya1 673.0 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14104000 14105000 Eya1 673.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14105000 14106000 Eya1 673.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14106000 14107000 Eya1 673.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14107000 14108000 Eya1 673.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14108000 14109000 Eya1 673.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14109000 14110000 Eya1 673.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14110000 14111000 Eya1 673.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14111000 14112000 Eya1 673.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14112000 14113000 Eya1 673.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14113000 14114000 Eya1 673.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14114000 14115000 Eya1 673.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14115000 14116000 Eya1 673.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14116000 14117000 Eya1 673.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14117000 14118000 Eya1 673.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14118000 14119000 Eya1 673.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14119000 14120000 Eya1 673.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14120000 14121000 Eya1 673.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14121000 14122000 Eya1 673.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14122000 14123000 Eya1 673.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14123000 14124000 Eya1 673.0 -177000 0.000000000000 1.000000000000 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14143000 14144000 Eya1 673.0 -157000 0.000891530461 0.012107544045 4.367181637306 0.600000000000 -chr1 14144000 14145000 Eya1 673.0 -156000 0.000891530461 0.012107544045 5.120143967809 0.600000000000 -chr1 14145000 14146000 Eya1 673.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14146000 14147000 Eya1 673.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14147000 14148000 Eya1 673.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14148000 14149000 Eya1 673.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14149000 14150000 Eya1 673.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14150000 14151000 Eya1 673.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14151000 14152000 Eya1 673.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14152000 14153000 Eya1 673.0 -148000 0.000000000000 1.000000000000 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14172000 14173000 Eya1 673.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14173000 14174000 Eya1 673.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14174000 14175000 Eya1 673.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14175000 14176000 Eya1 673.0 -125000 0.000297176820 0.042850447268 0.916568982282 0.200000000000 -chr1 14176000 14177000 Eya1 673.0 -124000 0.000297176820 0.042850447268 0.908160092485 0.200000000000 -chr1 14177000 14178000 Eya1 673.0 -123000 0.000297176820 0.042850447268 0.798302018335 0.200000000000 -chr1 14178000 14179000 Eya1 673.0 -122000 0.000297176820 0.042850447268 0.925135047590 0.200000000000 -chr1 14179000 14180000 Eya1 673.0 -121000 0.000297176820 0.042850447268 0.883834378206 0.200000000000 -chr1 14180000 14181000 Eya1 673.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14181000 14182000 Eya1 673.0 -119000 0.000000000000 1.000000000000 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136000 0.000297176820 0.000000000000 0.358657428234 0.200000000000 -chr1 14437000 14438000 Eya1 673.0 137000 0.000297176820 0.000000000000 0.334423818431 0.200000000000 -chr1 14438000 14439000 Eya1 673.0 138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14439000 14440000 Eya1 673.0 139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14440000 14441000 Eya1 673.0 140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14441000 14442000 Eya1 673.0 141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14442000 14443000 Eya1 673.0 142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14443000 14444000 Eya1 673.0 143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14444000 14445000 Eya1 673.0 144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14445000 14446000 Eya1 673.0 145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14446000 14447000 Eya1 673.0 146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14447000 14448000 Eya1 673.0 147000 0.000594353640 0.000000000000 0.868328510517 0.400000000000 -chr1 14448000 14449000 Eya1 673.0 148000 0.000594353640 0.000000000000 0.899904092956 0.400000000000 -chr1 14449000 14450000 Eya1 673.0 149000 0.000891530461 0.000000000000 1.387702573545 0.600000000000 -chr1 14450000 14451000 Eya1 673.0 150000 0.001188707281 0.000000000000 1.721555655524 0.800000000000 -chr1 14451000 14452000 Eya1 673.0 151000 0.001188707281 0.000000000000 1.816320187745 0.800000000000 -chr1 14452000 14453000 Eya1 673.0 152000 0.000594353640 0.000000000000 0.879906224076 0.400000000000 -chr1 14453000 14454000 Eya1 673.0 153000 0.000594353640 0.000000000000 0.887797759777 0.400000000000 -chr1 14454000 14455000 Eya1 673.0 154000 0.000891530461 0.000000000000 1.356019866146 0.600000000000 -chr1 14455000 14456000 Eya1 673.0 155000 0.000594353640 0.000000000000 0.876012833675 0.400000000000 -chr1 14456000 14457000 Eya1 673.0 156000 0.000594353640 0.000000000000 0.876012833675 0.400000000000 -chr1 14457000 14458000 Eya1 673.0 157000 0.000594353640 0.000000000000 0.821489212945 0.400000000000 -chr1 14458000 14459000 Eya1 673.0 158000 0.001188707281 0.000000000000 1.583831204275 0.800000000000 -chr1 14459000 14460000 Eya1 673.0 159000 0.000594353640 0.000000000000 0.770345916308 0.400000000000 -chr1 14460000 14461000 Eya1 673.0 160000 0.001188707281 0.000000000000 1.517079697070 0.800000000000 -chr1 14461000 14462000 Eya1 673.0 161000 0.001188707281 0.000000000000 1.429450544260 0.800000000000 -chr1 14462000 14463000 Eya1 673.0 162000 0.001188707281 0.000000000000 1.616154290340 0.800000000000 -chr1 14463000 14464000 Eya1 673.0 163000 0.000594353640 0.000000000000 0.821489212945 0.400000000000 -chr1 14464000 14465000 Eya1 673.0 164000 0.000594353640 0.000000000000 0.857051516792 0.400000000000 -chr1 14465000 14466000 Eya1 673.0 165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14466000 14467000 Eya1 673.0 166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14467000 14468000 Eya1 673.0 167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14468000 14469000 Eya1 673.0 168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14469000 14470000 Eya1 673.0 169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14470000 14471000 Eya1 673.0 170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14471000 14472000 Eya1 673.0 171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14472000 14473000 Eya1 673.0 172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14473000 14474000 Eya1 673.0 173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14474000 14475000 Eya1 673.0 174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14475000 14476000 Eya1 673.0 175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 14476000 14477000 Eya1 673.0 176000 0.000297176820 0.000000000000 0.421231702882 0.200000000000 -chr1 14477000 14478000 Eya1 673.0 177000 0.000297176820 0.000000000000 0.449952046478 0.200000000000 -chr1 14478000 14479000 Eya1 673.0 178000 0.000594353640 0.000000000000 0.933862738240 0.400000000000 -chr1 14479000 14480000 Eya1 673.0 179000 0.000594353640 0.000000000000 0.951821637197 0.400000000000 -chr1 14480000 14481000 Eya1 673.0 180000 0.001485884101 0.000000000000 2.512422592521 1.000000000000 -chr1 14481000 14482000 Eya1 673.0 181000 0.001188707281 0.000000000000 2.020192860178 0.800000000000 -chr1 14482000 14483000 Eya1 673.0 182000 0.001188707281 0.000000000000 2.128805380321 0.800000000000 -chr1 14483000 14484000 Eya1 673.0 183000 0.001783060921 0.000000000000 3.093420317586 1.200000000000 -chr1 14484000 14485000 Eya1 673.0 184000 0.002080237741 0.000000000000 3.380127570538 1.400000000000 -chr1 14485000 14486000 Eya1 673.0 185000 0.001188707281 0.000000000000 1.903643274393 0.800000000000 -chr1 14486000 14487000 Eya1 673.0 186000 0.001188707281 0.000000000000 2.106158514412 0.800000000000 -chr1 14487000 14488000 Eya1 673.0 187000 0.001188707281 0.000000000000 2.140312436513 0.800000000000 -chr1 14488000 14489000 Eya1 673.0 188000 0.000594353640 0.000000000000 1.058710697124 0.400000000000 -chr1 14489000 14490000 Eya1 673.0 189000 0.000297176820 0.000000000000 0.575520059550 0.200000000000 -chr1 14490000 14491000 Eya1 673.0 190000 0.000297176820 0.000000000000 0.578885673960 0.200000000000 -chr1 14491000 14492000 Eya1 673.0 191000 0.002080237741 0.000000000000 3.849589730333 1.400000000000 -chr1 14492000 14493000 Eya1 673.0 192000 0.003268945022 0.000000000000 5.982878858272 2.200000000000 -chr1 14493000 14494000 Eya1 673.0 193000 0.002971768202 0.000000000000 5.892229182196 2.000000000000 -chr1 14494000 14495000 Eya1 673.0 194000 0.003268945022 0.000000000000 6.294126893758 2.200000000000 -chr1 14495000 14496000 Eya1 673.0 195000 0.003268945022 0.000000000000 6.680269651133 2.200000000000 -chr1 14496000 14497000 Eya1 673.0 196000 0.002971768202 0.000000000000 6.072972410121 2.000000000000 -chr1 14497000 14498000 Eya1 673.0 197000 0.002080237741 0.000000000000 3.937080406684 1.400000000000 -chr1 14498000 14499000 Eya1 673.0 198000 0.002971768202 0.000000000000 4.852424033528 2.000000000000 -chr1 14499000 14500000 Eya1 673.0 199000 0.003343239227 0.000000000000 5.830530441735 2.250000000000 -chr1 14500000 14501000 Eya1 673.0 200000 0.004457652303 0.000000000000 7.575723225668 3.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt deleted file mode 100644 index fbac2858..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 18893000 18894000 Tfap2d 472.0 -200000 0.001412429379 0.009736859396 8.554173074049 0.666666666667 -chr1 18894000 18895000 Tfap2d 472.0 -199000 0.001059322034 0.016726462474 5.040852007510 0.500000000000 -chr1 18895000 18896000 Tfap2d 472.0 -198000 0.000847457627 0.023000625561 3.282415254892 0.400000000000 -chr1 18896000 18897000 Tfap2d 472.0 -197000 0.000847457627 0.023000625561 3.136530131373 0.400000000000 -chr1 18897000 18898000 Tfap2d 472.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18898000 18899000 Tfap2d 472.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18899000 18900000 Tfap2d 472.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18900000 18901000 Tfap2d 472.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18901000 18902000 Tfap2d 472.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18902000 18903000 Tfap2d 472.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18903000 18904000 Tfap2d 472.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18904000 18905000 Tfap2d 472.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18905000 18906000 Tfap2d 472.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18906000 18907000 Tfap2d 472.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18907000 18908000 Tfap2d 472.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18908000 18909000 Tfap2d 472.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18909000 18910000 Tfap2d 472.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18910000 18911000 Tfap2d 472.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18911000 18912000 Tfap2d 472.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18912000 18913000 Tfap2d 472.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18913000 18914000 Tfap2d 472.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18914000 18915000 Tfap2d 472.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18915000 18916000 Tfap2d 472.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18916000 18917000 Tfap2d 472.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18917000 18918000 Tfap2d 472.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18918000 18919000 Tfap2d 472.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18919000 18920000 Tfap2d 472.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18920000 18921000 Tfap2d 472.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18921000 18922000 Tfap2d 472.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18922000 18923000 Tfap2d 472.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18923000 18924000 Tfap2d 472.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18924000 18925000 Tfap2d 472.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18925000 18926000 Tfap2d 472.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18926000 18927000 Tfap2d 472.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18927000 18928000 Tfap2d 472.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18928000 18929000 Tfap2d 472.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18929000 18930000 Tfap2d 472.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18930000 18931000 Tfap2d 472.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18931000 18932000 Tfap2d 472.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18932000 18933000 Tfap2d 472.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18933000 18934000 Tfap2d 472.0 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18934000 18935000 Tfap2d 472.0 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18935000 18936000 Tfap2d 472.0 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18936000 18937000 Tfap2d 472.0 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18937000 18938000 Tfap2d 472.0 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18938000 18939000 Tfap2d 472.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18939000 18940000 Tfap2d 472.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18940000 18941000 Tfap2d 472.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18941000 18942000 Tfap2d 472.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18942000 18943000 Tfap2d 472.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18943000 18944000 Tfap2d 472.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18944000 18945000 Tfap2d 472.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18945000 18946000 Tfap2d 472.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18946000 18947000 Tfap2d 472.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18947000 18948000 Tfap2d 472.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18948000 18949000 Tfap2d 472.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18949000 18950000 Tfap2d 472.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18950000 18951000 Tfap2d 472.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18951000 18952000 Tfap2d 472.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18952000 18953000 Tfap2d 472.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18953000 18954000 Tfap2d 472.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18954000 18955000 Tfap2d 472.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18955000 18956000 Tfap2d 472.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18956000 18957000 Tfap2d 472.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18957000 18958000 Tfap2d 472.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18958000 18959000 Tfap2d 472.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18959000 18960000 Tfap2d 472.0 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18960000 18961000 Tfap2d 472.0 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18961000 18962000 Tfap2d 472.0 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18962000 18963000 Tfap2d 472.0 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18963000 18964000 Tfap2d 472.0 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18964000 18965000 Tfap2d 472.0 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18965000 18966000 Tfap2d 472.0 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18966000 18967000 Tfap2d 472.0 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18967000 18968000 Tfap2d 472.0 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18968000 18969000 Tfap2d 472.0 -125000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18969000 18970000 Tfap2d 472.0 -124000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18970000 18971000 Tfap2d 472.0 -123000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18971000 18972000 Tfap2d 472.0 -122000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18972000 18973000 Tfap2d 472.0 -121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18973000 18974000 Tfap2d 472.0 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18974000 18975000 Tfap2d 472.0 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18975000 18976000 Tfap2d 472.0 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18976000 18977000 Tfap2d 472.0 -117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18977000 18978000 Tfap2d 472.0 -116000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18978000 18979000 Tfap2d 472.0 -115000 0.001271186441 0.012107544045 3.257165906583 0.600000000000 -chr1 18979000 18980000 Tfap2d 472.0 -114000 0.001271186441 0.012107544045 3.470750557945 0.600000000000 -chr1 18980000 18981000 Tfap2d 472.0 -113000 0.001271186441 0.012107544045 3.814698814531 0.600000000000 -chr1 18981000 18982000 Tfap2d 472.0 -112000 0.001271186441 0.012107544045 4.602517039860 0.600000000000 -chr1 18982000 18983000 Tfap2d 472.0 -111000 0.001271186441 0.012107544045 4.553027608970 0.600000000000 -chr1 18983000 18984000 Tfap2d 472.0 -110000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18984000 18985000 Tfap2d 472.0 -109000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18985000 18986000 Tfap2d 472.0 -108000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18986000 18987000 Tfap2d 472.0 -107000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18987000 18988000 Tfap2d 472.0 -106000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18988000 18989000 Tfap2d 472.0 -105000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18989000 18990000 Tfap2d 472.0 -104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18990000 18991000 Tfap2d 472.0 -103000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18991000 18992000 Tfap2d 472.0 -102000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18992000 18993000 Tfap2d 472.0 -101000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18993000 18994000 Tfap2d 472.0 -100000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18994000 18995000 Tfap2d 472.0 -99000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18995000 18996000 Tfap2d 472.0 -98000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18996000 18997000 Tfap2d 472.0 -97000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18997000 18998000 Tfap2d 472.0 -96000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18998000 18999000 Tfap2d 472.0 -95000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 18999000 19000000 Tfap2d 472.0 -94000 0.000423728814 0.042850447268 1.102686374757 0.200000000000 -chr1 19000000 19001000 Tfap2d 472.0 -93000 0.000423728814 0.042850447268 1.061231999455 0.200000000000 -chr1 19001000 19002000 Tfap2d 472.0 -92000 0.000423728814 0.042850447268 0.779800308873 0.200000000000 -chr1 19002000 19003000 Tfap2d 472.0 -91000 0.000423728814 0.042850447268 0.735124249200 0.200000000000 -chr1 19003000 19004000 Tfap2d 472.0 -90000 0.000423728814 0.042850447268 0.727545648641 0.200000000000 -chr1 19004000 19005000 Tfap2d 472.0 -89000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19005000 19006000 Tfap2d 472.0 -88000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19006000 19007000 Tfap2d 472.0 -87000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19007000 19008000 Tfap2d 472.0 -86000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19008000 19009000 Tfap2d 472.0 -85000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19009000 19010000 Tfap2d 472.0 -84000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19010000 19011000 Tfap2d 472.0 -83000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19011000 19012000 Tfap2d 472.0 -82000 0.000000000000 1.000000000000 0.000000000000 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1.000000000000 0.000000000000 0.000000000000 -chr1 19041000 19042000 Tfap2d 472.0 -52000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19042000 19043000 Tfap2d 472.0 -51000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19043000 19044000 Tfap2d 472.0 -50000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19044000 19045000 Tfap2d 472.0 -49000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19045000 19046000 Tfap2d 472.0 -48000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19046000 19047000 Tfap2d 472.0 -47000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19047000 19048000 Tfap2d 472.0 -46000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19048000 19049000 Tfap2d 472.0 -45000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19049000 19050000 Tfap2d 472.0 -44000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19050000 19051000 Tfap2d 472.0 -43000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19051000 19052000 Tfap2d 472.0 -42000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19052000 19053000 Tfap2d 472.0 -41000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19053000 19054000 Tfap2d 472.0 -40000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19054000 19055000 Tfap2d 472.0 -39000 0.000423728814 0.042850447268 0.571432615421 0.200000000000 -chr1 19055000 19056000 Tfap2d 472.0 -38000 0.000423728814 0.042850447268 0.624530335872 0.200000000000 -chr1 19056000 19057000 Tfap2d 472.0 -37000 0.000423728814 0.042850447268 0.551343187379 0.200000000000 -chr1 19057000 19058000 Tfap2d 472.0 -36000 0.000423728814 0.042850447268 0.566842795180 0.200000000000 -chr1 19058000 19059000 Tfap2d 472.0 -35000 0.000423728814 0.042850447268 0.593041411154 0.200000000000 -chr1 19059000 19060000 Tfap2d 472.0 -34000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19060000 19061000 Tfap2d 472.0 -33000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19061000 19062000 Tfap2d 472.0 -32000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19062000 19063000 Tfap2d 472.0 -31000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19063000 19064000 Tfap2d 472.0 -30000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19064000 19065000 Tfap2d 472.0 -29000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19065000 19066000 Tfap2d 472.0 -28000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19066000 19067000 Tfap2d 472.0 -27000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19067000 19068000 Tfap2d 472.0 -26000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19068000 19069000 Tfap2d 472.0 -25000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19069000 19070000 Tfap2d 472.0 -24000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19070000 19071000 Tfap2d 472.0 -23000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19071000 19072000 Tfap2d 472.0 -22000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19072000 19073000 Tfap2d 472.0 -21000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19073000 19074000 Tfap2d 472.0 -20000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19074000 19075000 Tfap2d 472.0 -19000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19075000 19076000 Tfap2d 472.0 -18000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19076000 19077000 Tfap2d 472.0 -17000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19077000 19078000 Tfap2d 472.0 -16000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19078000 19079000 Tfap2d 472.0 -15000 0.000000000000 1.000000000000 0.000000000000 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0.008474576271 0.000000032703 1.449115563952 4.000000000000 -chr1 19089000 19090000 Tfap2d 472.0 -4000 0.022881355932 0.000000000000 2.298482575464 10.800000000000 -chr1 19090000 19091000 Tfap2d 472.0 -3000 0.038135593220 0.000000000000 1.769705633062 18.000000000000 -chr1 19091000 19092000 Tfap2d 472.0 -2000 0.089830508475 0.000000000000 1.342839718965 42.400000000000 -chr1 19092000 19093000 Tfap2d 472.0 -1000 0.096186440678 0.000000000000 1.258183989657 45.400000000000 -chr1 19093000 19094000 Tfap2d 472.0 0 0.097033898305 0.573211350056 1.219741990578 45.800000000000 -chr1 19094000 19095000 Tfap2d 472.0 1000 0.088559322034 0.000000000000 1.131750082102 41.800000000000 -chr1 19095000 19096000 Tfap2d 472.0 2000 0.079237288136 0.000000000000 1.158236837774 37.400000000000 -chr1 19096000 19097000 Tfap2d 472.0 3000 0.030084745763 0.000000000000 1.213515835692 14.200000000000 -chr1 19097000 19098000 Tfap2d 472.0 4000 0.025423728814 0.000000000000 1.625145146017 12.000000000000 -chr1 19098000 19099000 Tfap2d 472.0 5000 0.017796610169 0.000000000000 1.469519570887 8.400000000000 -chr1 19099000 19100000 Tfap2d 472.0 6000 0.012288135593 0.000000000000 1.174511283228 5.800000000000 -chr1 19100000 19101000 Tfap2d 472.0 7000 0.009745762712 0.000000000000 1.020530866525 4.600000000000 -chr1 19101000 19102000 Tfap2d 472.0 8000 0.010169491525 0.000000000000 1.167282061499 4.800000000000 -chr1 19102000 19103000 Tfap2d 472.0 9000 0.011440677966 0.000000000000 1.429438900967 5.400000000000 -chr1 19103000 19104000 Tfap2d 472.0 10000 0.010593220339 0.000000000000 1.461721788921 5.000000000000 -chr1 19104000 19105000 Tfap2d 472.0 11000 0.012288135593 0.000000000000 1.918974131188 5.800000000000 -chr1 19105000 19106000 Tfap2d 472.0 12000 0.010169491525 0.000000000000 1.708246365312 4.800000000000 -chr1 19106000 19107000 Tfap2d 472.0 13000 0.007203389831 0.000000000000 1.341221660736 3.400000000000 -chr1 19107000 19108000 Tfap2d 472.0 14000 0.007203389831 0.000000000000 1.483887168230 3.400000000000 -chr1 19108000 19109000 Tfap2d 472.0 15000 0.006355932203 0.000000000000 1.367673022577 3.000000000000 -chr1 19109000 19110000 Tfap2d 472.0 16000 0.008050847458 0.000000000000 1.767787252797 3.800000000000 -chr1 19110000 19111000 Tfap2d 472.0 17000 0.006779661017 0.000000000000 1.614225657668 3.200000000000 -chr1 19111000 19112000 Tfap2d 472.0 18000 0.009745762712 0.000000000000 2.388748113765 4.600000000000 -chr1 19112000 19113000 Tfap2d 472.0 19000 0.007203389831 0.000000000000 1.810902302517 3.400000000000 -chr1 19113000 19114000 Tfap2d 472.0 20000 0.007627118644 0.000000000000 2.035728691180 3.600000000000 -chr1 19114000 19115000 Tfap2d 472.0 21000 0.003813559322 0.000000000000 1.046371254994 1.800000000000 -chr1 19115000 19116000 Tfap2d 472.0 22000 0.003813559322 0.000000000000 1.090381719525 1.800000000000 -chr1 19116000 19117000 Tfap2d 472.0 23000 0.000847457627 0.000000000000 0.270649771714 0.400000000000 -chr1 19117000 19118000 Tfap2d 472.0 24000 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19127000 19128000 Tfap2d 472.0 34000 0.004237288136 0.000000000000 1.884430653326 2.000000000000 -chr1 19128000 19129000 Tfap2d 472.0 35000 0.004237288136 0.000000000000 1.993557287139 2.000000000000 -chr1 19129000 19130000 Tfap2d 472.0 36000 0.002118644068 0.000000000000 1.024266008409 1.000000000000 -chr1 19130000 19131000 Tfap2d 472.0 37000 0.000847457627 0.000000000000 0.420070999751 0.400000000000 -chr1 19131000 19132000 Tfap2d 472.0 38000 0.000847457627 0.000000000000 0.430316633970 0.400000000000 -chr1 19132000 19133000 Tfap2d 472.0 39000 0.001694915254 0.000000000000 0.865913226679 0.800000000000 -chr1 19133000 19134000 Tfap2d 472.0 40000 0.003389830508 0.000000000000 1.629366302482 1.600000000000 -chr1 19134000 19135000 Tfap2d 472.0 41000 0.004237288136 0.000000000000 2.072597002974 2.000000000000 -chr1 19135000 19136000 Tfap2d 472.0 42000 0.004237288136 0.000000000000 2.045563129814 2.000000000000 -chr1 19136000 19137000 Tfap2d 472.0 43000 0.004237288136 0.000000000000 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19156000 19157000 Tfap2d 472.0 63000 0.001694915254 0.000000000000 1.246303363398 0.800000000000 -chr1 19157000 19158000 Tfap2d 472.0 64000 0.002118644068 0.000000000000 1.564787759528 1.000000000000 -chr1 19158000 19159000 Tfap2d 472.0 65000 0.002966101695 0.000000000000 2.313833704394 1.400000000000 -chr1 19159000 19160000 Tfap2d 472.0 66000 0.001694915254 0.000000000000 1.447629291815 0.800000000000 -chr1 19160000 19161000 Tfap2d 472.0 67000 0.002118644068 0.000000000000 1.729704116472 1.000000000000 -chr1 19161000 19162000 Tfap2d 472.0 68000 0.002118644068 0.000000000000 1.759898452895 1.000000000000 -chr1 19162000 19163000 Tfap2d 472.0 69000 0.001694915254 0.000000000000 1.394013391721 0.800000000000 -chr1 19163000 19164000 Tfap2d 472.0 70000 0.000423728814 0.000000000000 0.341752677703 0.200000000000 -chr1 19164000 19165000 Tfap2d 472.0 71000 0.000847457627 0.000000000000 0.661095344113 0.400000000000 -chr1 19165000 19166000 Tfap2d 472.0 72000 0.000423728814 0.000000000000 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0.000423728814 0.000000000000 0.364712806099 0.200000000000 -chr1 19176000 19177000 Tfap2d 472.0 83000 0.000423728814 0.000000000000 0.319329990793 0.200000000000 -chr1 19177000 19178000 Tfap2d 472.0 84000 0.000423728814 0.000000000000 0.300306076526 0.200000000000 -chr1 19178000 19179000 Tfap2d 472.0 85000 0.000423728814 0.000000000000 0.299668484002 0.200000000000 -chr1 19179000 19180000 Tfap2d 472.0 86000 0.000423728814 0.000000000000 0.329006657256 0.200000000000 -chr1 19180000 19181000 Tfap2d 472.0 87000 0.000847457627 0.000000000000 0.627306026275 0.400000000000 -chr1 19181000 19182000 Tfap2d 472.0 88000 0.000847457627 0.000000000000 0.623151681699 0.400000000000 -chr1 19182000 19183000 Tfap2d 472.0 89000 0.000847457627 0.000000000000 0.688506614142 0.400000000000 -chr1 19183000 19184000 Tfap2d 472.0 90000 0.000847457627 0.000000000000 0.693581601507 0.400000000000 -chr1 19184000 19185000 Tfap2d 472.0 91000 0.000423728814 0.000000000000 0.332886452773 0.200000000000 -chr1 19185000 19186000 Tfap2d 472.0 92000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19186000 19187000 Tfap2d 472.0 93000 0.000423728814 0.000000000000 0.387757845880 0.200000000000 -chr1 19187000 19188000 Tfap2d 472.0 94000 0.001271186441 0.000000000000 1.066578256419 0.600000000000 -chr1 19188000 19189000 Tfap2d 472.0 95000 0.001694915254 0.000000000000 1.363708752551 0.800000000000 -chr1 19189000 19190000 Tfap2d 472.0 96000 0.001694915254 0.000000000000 1.325294422259 0.800000000000 -chr1 19190000 19191000 Tfap2d 472.0 97000 0.001694915254 0.000000000000 1.373662831110 0.800000000000 -chr1 19191000 19192000 Tfap2d 472.0 98000 0.001271186441 0.000000000000 1.005775695846 0.600000000000 -chr1 19192000 19193000 Tfap2d 472.0 99000 0.001271186441 0.000000000000 1.080182571018 0.600000000000 -chr1 19193000 19194000 Tfap2d 472.0 100000 0.000847457627 0.000000000000 0.804238495376 0.400000000000 -chr1 19194000 19195000 Tfap2d 472.0 101000 0.000847457627 0.000000000000 0.860633267502 0.400000000000 -chr1 19195000 19196000 Tfap2d 472.0 102000 0.000847457627 0.000000000000 0.837648996932 0.400000000000 -chr1 19196000 19197000 Tfap2d 472.0 103000 0.000847457627 0.000000000000 0.925533481613 0.400000000000 -chr1 19197000 19198000 Tfap2d 472.0 104000 0.001694915254 0.000000000000 1.764298198693 0.800000000000 -chr1 19198000 19199000 Tfap2d 472.0 105000 0.002118644068 0.000000000000 2.112931975945 1.000000000000 -chr1 19199000 19200000 Tfap2d 472.0 106000 0.002118644068 0.000000000000 2.063506666181 1.000000000000 -chr1 19200000 19201000 Tfap2d 472.0 107000 0.002118644068 0.000000000000 1.982357527016 1.000000000000 -chr1 19201000 19202000 Tfap2d 472.0 108000 0.002542372881 0.000000000000 2.320172973657 1.200000000000 -chr1 19202000 19203000 Tfap2d 472.0 109000 0.001271186441 0.000000000000 1.202930590359 0.600000000000 -chr1 19203000 19204000 Tfap2d 472.0 110000 0.000847457627 0.000000000000 0.830257976313 0.400000000000 -chr1 19204000 19205000 Tfap2d 472.0 111000 0.001271186441 0.000000000000 1.179475119064 0.600000000000 -chr1 19205000 19206000 Tfap2d 472.0 112000 0.001694915254 0.000000000000 1.613072639333 0.800000000000 -chr1 19206000 19207000 Tfap2d 472.0 113000 0.001271186441 0.000000000000 1.241734803255 0.600000000000 -chr1 19207000 19208000 Tfap2d 472.0 114000 0.000847457627 0.000000000000 0.815860439041 0.400000000000 -chr1 19208000 19209000 Tfap2d 472.0 115000 0.000847457627 0.000000000000 0.822996244685 0.400000000000 -chr1 19209000 19210000 Tfap2d 472.0 116000 0.000423728814 0.000000000000 0.473637100575 0.200000000000 -chr1 19210000 19211000 Tfap2d 472.0 117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19211000 19212000 Tfap2d 472.0 118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19212000 19213000 Tfap2d 472.0 119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19213000 19214000 Tfap2d 472.0 120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19214000 19215000 Tfap2d 472.0 121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19215000 19216000 Tfap2d 472.0 122000 0.000847457627 0.000000000000 0.953674702560 0.400000000000 -chr1 19216000 19217000 Tfap2d 472.0 123000 0.000847457627 0.000000000000 0.973405903461 0.400000000000 -chr1 19217000 19218000 Tfap2d 472.0 124000 0.000847457627 0.000000000000 1.034020922346 0.400000000000 -chr1 19218000 19219000 Tfap2d 472.0 125000 0.000847457627 0.000000000000 1.129150847963 0.400000000000 -chr1 19219000 19220000 Tfap2d 472.0 126000 0.001271186441 0.000000000000 1.579968536413 0.600000000000 -chr1 19220000 19221000 Tfap2d 472.0 127000 0.000847457627 0.000000000000 1.077434014837 0.400000000000 -chr1 19221000 19222000 Tfap2d 472.0 128000 0.000847457627 0.000000000000 1.129150847963 0.400000000000 -chr1 19222000 19223000 Tfap2d 472.0 129000 0.000847457627 0.000000000000 1.089913945607 0.400000000000 -chr1 19223000 19224000 Tfap2d 472.0 130000 0.000847457627 0.000000000000 1.019089212169 0.400000000000 -chr1 19224000 19225000 Tfap2d 472.0 131000 0.000423728814 0.000000000000 0.553505317542 0.200000000000 -chr1 19225000 19226000 Tfap2d 472.0 132000 0.000423728814 0.000000000000 0.566842795180 0.200000000000 -chr1 19226000 19227000 Tfap2d 472.0 133000 0.000423728814 0.000000000000 0.511390782207 0.200000000000 -chr1 19227000 19228000 Tfap2d 472.0 134000 0.001271186441 0.000000000000 1.597854972809 0.600000000000 -chr1 19228000 19229000 Tfap2d 472.0 135000 0.001694915254 0.000000000000 2.231523414735 0.800000000000 -chr1 19229000 19230000 Tfap2d 472.0 136000 0.002118644068 0.000000000000 2.556953911034 1.000000000000 -chr1 19230000 19231000 Tfap2d 472.0 137000 0.002542372881 0.000000000000 2.861024107679 1.200000000000 -chr1 19231000 19232000 Tfap2d 472.0 138000 0.002542372881 0.000000000000 3.183695998364 1.200000000000 -chr1 19232000 19233000 Tfap2d 472.0 139000 0.001694915254 0.000000000000 1.987941631835 0.800000000000 -chr1 19233000 19234000 Tfap2d 472.0 140000 0.001271186441 0.000000000000 1.339973315587 0.600000000000 -chr1 19234000 19235000 Tfap2d 472.0 141000 0.000847457627 0.000000000000 0.963439290036 0.400000000000 -chr1 19235000 19236000 Tfap2d 472.0 142000 0.000423728814 0.000000000000 0.538717007419 0.200000000000 -chr1 19236000 19237000 Tfap2d 472.0 143000 0.001271186441 0.000000000000 1.539751155194 0.600000000000 -chr1 19237000 19238000 Tfap2d 472.0 144000 0.001271186441 0.000000000000 1.749717221137 0.600000000000 -chr1 19238000 19239000 Tfap2d 472.0 145000 0.001271186441 0.000000000000 2.117157840635 0.600000000000 -chr1 19239000 19240000 Tfap2d 472.0 146000 0.001694915254 0.000000000000 2.601730063600 0.800000000000 -chr1 19240000 19241000 Tfap2d 472.0 147000 0.001271186441 0.000000000000 1.857155998658 0.600000000000 -chr1 19241000 19242000 Tfap2d 472.0 148000 0.000423728814 0.000000000000 0.641562981525 0.200000000000 -chr1 19242000 19243000 Tfap2d 472.0 149000 0.000423728814 0.000000000000 0.659550728811 0.200000000000 -chr1 19243000 19244000 Tfap2d 472.0 150000 0.000847457627 0.000000000000 1.227337877296 0.400000000000 -chr1 19244000 19245000 Tfap2d 472.0 151000 0.001271186441 0.000000000000 1.942346641449 0.600000000000 -chr1 19245000 19246000 Tfap2d 472.0 152000 0.001271186441 0.000000000000 1.881918078824 0.600000000000 -chr1 19246000 19247000 Tfap2d 472.0 153000 0.002118644068 0.000000000000 3.164660446662 1.000000000000 -chr1 19247000 19248000 Tfap2d 472.0 154000 0.002118644068 0.000000000000 3.222462464392 1.000000000000 -chr1 19248000 19249000 Tfap2d 472.0 155000 0.001694915254 0.000000000000 2.498121343489 0.800000000000 -chr1 19249000 19250000 Tfap2d 472.0 156000 0.000847457627 0.000000000000 1.249060671745 0.400000000000 -chr1 19250000 19251000 Tfap2d 472.0 157000 0.000847457627 0.000000000000 1.171318305746 0.400000000000 -chr1 19251000 19252000 Tfap2d 472.0 158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19252000 19253000 Tfap2d 472.0 159000 0.000847457627 0.000000000000 1.098395766262 0.400000000000 -chr1 19253000 19254000 Tfap2d 472.0 160000 0.000847457627 0.000000000000 1.081562114542 0.400000000000 -chr1 19254000 19255000 Tfap2d 472.0 161000 0.001694915254 0.000000000000 2.038178424337 0.800000000000 -chr1 19255000 19256000 Tfap2d 472.0 162000 0.001694915254 0.000000000000 2.304389486014 0.800000000000 -chr1 19256000 19257000 Tfap2d 472.0 163000 0.002542372881 0.000000000000 3.513954917238 1.200000000000 -chr1 19257000 19258000 Tfap2d 472.0 164000 0.002118644068 0.000000000000 3.055061815685 1.000000000000 -chr1 19258000 19259000 Tfap2d 472.0 165000 0.002118644068 0.000000000000 3.252162579500 1.000000000000 -chr1 19259000 19260000 Tfap2d 472.0 166000 0.001694915254 0.000000000000 2.822877120847 0.800000000000 -chr1 19260000 19261000 Tfap2d 472.0 167000 0.001694915254 0.000000000000 2.701317818024 0.800000000000 -chr1 19261000 19262000 Tfap2d 472.0 168000 0.000847457627 0.000000000000 1.312966101957 0.400000000000 -chr1 19262000 19263000 Tfap2d 472.0 169000 0.000423728814 0.000000000000 0.593041411154 0.200000000000 -chr1 19263000 19264000 Tfap2d 472.0 170000 0.000423728814 0.000000000000 0.573755512251 0.200000000000 -chr1 19264000 19265000 Tfap2d 472.0 171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19265000 19266000 Tfap2d 472.0 172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19266000 19267000 Tfap2d 472.0 173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19267000 19268000 Tfap2d 472.0 174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19268000 19269000 Tfap2d 472.0 175000 0.000423728814 0.000000000000 0.608378689139 0.200000000000 -chr1 19269000 19270000 Tfap2d 472.0 176000 0.000423728814 0.000000000000 0.600612152627 0.200000000000 -chr1 19270000 19271000 Tfap2d 472.0 177000 0.000423728814 0.000000000000 0.641562981525 0.200000000000 -chr1 19271000 19272000 Tfap2d 472.0 178000 0.000423728814 0.000000000000 0.665772905546 0.200000000000 -chr1 19272000 19273000 Tfap2d 472.0 179000 0.000423728814 0.000000000000 0.678576230756 0.200000000000 -chr1 19273000 19274000 Tfap2d 472.0 180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19274000 19275000 Tfap2d 472.0 181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19275000 19276000 Tfap2d 472.0 182000 0.000423728814 0.000000000000 0.758837934828 0.200000000000 -chr1 19276000 19277000 Tfap2d 472.0 183000 0.000423728814 0.000000000000 0.735124249200 0.200000000000 -chr1 19277000 19278000 Tfap2d 472.0 184000 0.000423728814 0.000000000000 0.688506614701 0.200000000000 -chr1 19278000 19279000 Tfap2d 472.0 185000 0.000423728814 0.000000000000 0.678576230756 0.200000000000 -chr1 19279000 19280000 Tfap2d 472.0 186000 0.000423728814 0.000000000000 0.750765190784 0.200000000000 -chr1 19280000 19281000 Tfap2d 472.0 187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19281000 19282000 Tfap2d 472.0 188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19282000 19283000 Tfap2d 472.0 189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19283000 19284000 Tfap2d 472.0 190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19284000 19285000 Tfap2d 472.0 191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19285000 19286000 Tfap2d 472.0 192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19286000 19287000 Tfap2d 472.0 193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19287000 19288000 Tfap2d 472.0 194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19288000 19289000 Tfap2d 472.0 195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19289000 19290000 Tfap2d 472.0 196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19290000 19291000 Tfap2d 472.0 197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19291000 19292000 Tfap2d 472.0 198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19292000 19293000 Tfap2d 472.0 199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 19293000 19294000 Tfap2d 472.0 200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 diff --git a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt b/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt deleted file mode 100644 index cdb1a506..00000000 --- a/hicexplorer/test/test_data/cHi-C/chicViewpoint/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt +++ /dev/null @@ -1,405 +0,0 @@ -# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3-dev -# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0 -# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw -# -chr1 4287000 4288000 Sox17 810.0 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4288000 4289000 Sox17 810.0 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4289000 4290000 Sox17 810.0 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4290000 4291000 Sox17 810.0 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4291000 4292000 Sox17 810.0 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4292000 4293000 Sox17 810.0 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4293000 4294000 Sox17 810.0 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4294000 4295000 Sox17 810.0 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4295000 4296000 Sox17 810.0 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4296000 4297000 Sox17 810.0 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4297000 4298000 Sox17 810.0 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4298000 4299000 Sox17 810.0 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4299000 4300000 Sox17 810.0 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4300000 4301000 Sox17 810.0 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4301000 4302000 Sox17 810.0 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4302000 4303000 Sox17 810.0 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4303000 4304000 Sox17 810.0 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4304000 4305000 Sox17 810.0 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4305000 4306000 Sox17 810.0 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4306000 4307000 Sox17 810.0 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4307000 4308000 Sox17 810.0 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4308000 4309000 Sox17 810.0 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4309000 4310000 Sox17 810.0 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4310000 4311000 Sox17 810.0 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4311000 4312000 Sox17 810.0 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4312000 4313000 Sox17 810.0 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4313000 4314000 Sox17 810.0 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4314000 4315000 Sox17 810.0 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4315000 4316000 Sox17 810.0 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4316000 4317000 Sox17 810.0 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4317000 4318000 Sox17 810.0 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4318000 4319000 Sox17 810.0 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4319000 4320000 Sox17 810.0 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4320000 4321000 Sox17 810.0 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4321000 4322000 Sox17 810.0 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4322000 4323000 Sox17 810.0 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4323000 4324000 Sox17 810.0 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4324000 4325000 Sox17 810.0 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4325000 4326000 Sox17 810.0 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4326000 4327000 Sox17 810.0 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4327000 4328000 Sox17 810.0 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4328000 4329000 Sox17 810.0 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4329000 4330000 Sox17 810.0 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4330000 4331000 Sox17 810.0 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4331000 4332000 Sox17 810.0 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4332000 4333000 Sox17 810.0 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4333000 4334000 Sox17 810.0 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4334000 4335000 Sox17 810.0 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4335000 4336000 Sox17 810.0 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4336000 4337000 Sox17 810.0 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4337000 4338000 Sox17 810.0 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4338000 4339000 Sox17 810.0 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4339000 4340000 Sox17 810.0 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4340000 4341000 Sox17 810.0 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4341000 4342000 Sox17 810.0 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4342000 4343000 Sox17 810.0 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4343000 4344000 Sox17 810.0 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4344000 4345000 Sox17 810.0 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4345000 4346000 Sox17 810.0 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4346000 4347000 Sox17 810.0 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4347000 4348000 Sox17 810.0 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4348000 4349000 Sox17 810.0 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4349000 4350000 Sox17 810.0 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4350000 4351000 Sox17 810.0 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4351000 4352000 Sox17 810.0 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4352000 4353000 Sox17 810.0 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 -chr1 4353000 4354000 Sox17 810.0 -134000 0.000000000000 1.000000000000 0.000000000000 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2.28363584748403 +chr17 55935737 55936099 chr17 56072822 56073114 2.95734118880821 +chr17 55935737 55936099 chr17 56076925 56077120 2.9214419425273 +chr12 64943314 64943798 chr12 65090199 65090423 3.23555574413297 +chr22 42092980 42093866 chr22 42159132 42159429 2.10400066069958 +chr17 55935737 55936099 chr17 56190365 56190770 2.88126072360434 +chr12 127593244 127593484 chr12 128162137 128162347 3.7481808942314 +chr16 33963114 33963487 chr2 133012624 133012990 2.13583221262673 +chr1 121484228 121485221 chr10 42529551 42529721 -1.84581207064953 +chr1 121485244 121485510 chr12 34846267 34846471 -0.053284227252058 +chr6 58778098 58778474 chr10 103539709 103539949 -0.949127868852785 +chr6 58778098 58778474 chr10 103540905 103541164 -0.987874581868838 +chr19 27739073 27739440 chr10 42529793 42529937 -0.946696465553499 +chr2 133012624 133012990 chr21 9825501 9826596 1.5886518541928 +chr1 121484228 121485221 chr12 34846267 34846471 -0.181494465044725 +chr1 91852718 91853144 chr12 34372527 34372768 2.76052969833544 +chr16 33964837 33964977 chr21 9826742 9827563 1.3483824850377 +chr1 121485244 121485510 chr10 42529793 42529937 -1.33390778053503 +chr20 26189870 26190303 chr21 9825501 9826596 1.68049013972561 +chr20 26188844 26189203 chr21 9826742 9827563 1.46477612725631 +chr20 26189870 26190303 chr21 9826742 9827563 1.58116976947492 +chr16 33964837 33964977 chr21 9825501 9826596 1.44770285528839 +chr20 26188844 26189203 chr21 9825501 9826596 1.564096497507 +chr1 91852718 91853144 chr12 34371447 34371686 2.81678518546069 +chr2 133012624 133012990 chr21 9826742 9827563 1.48933148394211 +chr16 33963114 33963487 chr21 9826742 9827563 1.51813092113023 +chr16 33963114 33963487 chr21 9825501 9826596 1.61745129138092 +chr19 27739073 27739440 chr10 42529551 42529721 -0.856324383087355 +chr1 121485244 121485510 chr10 42529551 42529721 -1.24353569806889 +chr2 91815114 91815304 chr4 9764754 9765075 1.5316452618788 +chr19 27739073 27739440 chr1 121485244 121485510 0.665658949132087 +chr19 27739073 27739440 chr1 121484228 121485221 0.420403755247875 diff --git a/hicexplorer/test/test_data/hicConvertFormat/hg19.chrom.sizes b/hicexplorer/test/test_data/hicConvertFormat/hg19.chrom.sizes new file mode 100644 index 00000000..050d5c66 --- /dev/null +++ b/hicexplorer/test/test_data/hicConvertFormat/hg19.chrom.sizes @@ -0,0 +1,93 @@ +chr1 249250621 +chr2 243199373 +chr3 198022430 +chr4 191154276 +chr5 180915260 +chr6 171115067 +chr7 159138663 +chrX 155270560 +chr8 146364022 +chr9 141213431 +chr10 135534747 +chr11 135006516 +chr12 133851895 +chr13 115169878 +chr14 107349540 +chr15 102531392 +chr16 90354753 +chr17 81195210 +chr18 78077248 +chr20 63025520 +chrY 59373566 +chr19 59128983 +chr22 51304566 +chr21 48129895 +chr6_ssto_hap7 4928567 +chr6_mcf_hap5 4833398 +chr6_cox_hap2 4795371 +chr6_mann_hap4 4683263 +chr6_apd_hap1 4622290 +chr6_qbl_hap6 4611984 +chr6_dbb_hap3 4610396 +chr17_ctg5_hap1 1680828 +chr4_ctg9_hap1 590426 +chr1_gl000192_random 547496 +chrUn_gl000225 211173 +chr4_gl000194_random 191469 +chr4_gl000193_random 189789 +chr9_gl000200_random 187035 +chrUn_gl000222 186861 +chrUn_gl000212 186858 +chr7_gl000195_random 182896 +chrUn_gl000223 180455 +chrUn_gl000224 179693 +chrUn_gl000219 179198 +chr17_gl000205_random 174588 +chrUn_gl000215 172545 +chrUn_gl000216 172294 +chrUn_gl000217 172149 +chr9_gl000199_random 169874 +chrUn_gl000211 166566 +chrUn_gl000213 164239 +chrUn_gl000220 161802 +chrUn_gl000218 161147 +chr19_gl000209_random 159169 +chrUn_gl000221 155397 +chrUn_gl000214 137718 +chrUn_gl000228 129120 +chrUn_gl000227 128374 +chr1_gl000191_random 106433 +chr19_gl000208_random 92689 +chr9_gl000198_random 90085 +chr17_gl000204_random 81310 +chrUn_gl000233 45941 +chrUn_gl000237 45867 +chrUn_gl000230 43691 +chrUn_gl000242 43523 +chrUn_gl000243 43341 +chrUn_gl000241 42152 +chrUn_gl000236 41934 +chrUn_gl000240 41933 +chr17_gl000206_random 41001 +chrUn_gl000232 40652 +chrUn_gl000234 40531 +chr11_gl000202_random 40103 +chrUn_gl000238 39939 +chrUn_gl000244 39929 +chrUn_gl000248 39786 +chr8_gl000196_random 38914 +chrUn_gl000249 38502 +chrUn_gl000246 38154 +chr17_gl000203_random 37498 +chr8_gl000197_random 37175 +chrUn_gl000245 36651 +chrUn_gl000247 36422 +chr9_gl000201_random 36148 +chrUn_gl000235 34474 +chrUn_gl000239 33824 +chr21_gl000210_random 27682 +chrUn_gl000231 27386 +chrUn_gl000229 19913 +chrM 16571 +chrUn_gl000226 15008 +chr18_gl000207_random 4262 diff --git a/hicexplorer/test/test_data/hicCorrectMatrix/gm12878_KR.cool b/hicexplorer/test/test_data/hicCorrectMatrix/gm12878_KR.cool new file mode 100644 index 00000000..51df92eb Binary files /dev/null and b/hicexplorer/test/test_data/hicCorrectMatrix/gm12878_KR.cool differ diff --git a/hicexplorer/test/test_data/hicCorrectMatrix/gm12878_raw_values.cool b/hicexplorer/test/test_data/hicCorrectMatrix/gm12878_raw_values.cool new file mode 100644 index 00000000..287f3c7c Binary files /dev/null and b/hicexplorer/test/test_data/hicCorrectMatrix/gm12878_raw_values.cool differ diff --git a/hicexplorer/test/test_data/hicCorrectMatrix/kr_partial.cool b/hicexplorer/test/test_data/hicCorrectMatrix/kr_partial.cool index c72a0b94..9236bb6c 100644 Binary files a/hicexplorer/test/test_data/hicCorrectMatrix/kr_partial.cool and b/hicexplorer/test/test_data/hicCorrectMatrix/kr_partial.cool differ diff --git a/hicexplorer/test/test_data/hicCorrelate/heatmap.png b/hicexplorer/test/test_data/hicCorrelate/heatmap.png index 85512a9f..c06f3cbe 100644 Binary files a/hicexplorer/test/test_data/hicCorrelate/heatmap.png and b/hicexplorer/test/test_data/hicCorrelate/heatmap.png differ diff --git a/hicexplorer/test/test_data/hicCorrelate/scatter.png b/hicexplorer/test/test_data/hicCorrelate/scatter.png index 4c71fa62..3f7d839a 100644 Binary files a/hicexplorer/test/test_data/hicCorrelate/scatter.png and b/hicexplorer/test/test_data/hicCorrelate/scatter.png differ diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_accepted.diff_tad new file mode 100644 index 00000000..c4e26858 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_accepted.diff_tad @@ -0,0 +1,133 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. +# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 nan -0.7930969487289069 3.7263815455490827 +chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -0.9386590778150411 -0.45126112355691883 2.5371900826446283 +chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -0.30289374467773583 0.07414294720451348 4.5791565418309395 +chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -0.16282276617118813 1.6051606385162123 1.6442942874387492 +chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.2022260523997077 0.006197912102328514 1.627875146104104 -1.2752350682626996 2.737122965561303 +chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -0.8494330724907115 -1.9655771567720404 5.023672092995246 +chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.5322636852613494 1.8146100883843892e-06 -1.774031958289595 0.624554202910739 4.773045240138744 +chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.692745144471043 0.002562121461829293 0.67718850743882 -0.39513244622709864 3.0159066257881317 +chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.011911117420279341 0.00020602838341698515 -0.2226922466874271 -2.514766701978045 3.7115077195445525 +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.07553560212368073 0.03561337274424189 -2.692614553612967 1.7771984030211898 2.10131444292845 +chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.6730908477968309 0.012760792164069699 -2.5244662175837944 -0.42190981210011114 2.4903762617335548 +chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.15658860942159403 1.5995491571971796e-05 -0.2856207321579987 -1.416638625821259 4.314513284521457 +chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0005012323510345417 0.06748479713761105 -1.3364107145509396 -3.4800969585043267 1.8284316353792964 +chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.27686582704511986 0.05430086444564102 -3.14911317809443 -1.0873869704262455 1.9244287435607725 +chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6700147806330939 0.6148221863583603 -1.1220832111082402 -0.4261277223514882 0.5032021030649116 +chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.13322270222894567 0.4437394229186403 -0.4019090951745341 -1.501513869069336 0.7658939216443722 +chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 0.0751792941984631 0.011491613276272431 -1.41560597278901 -1.7793689460462792 2.527382919088952 +chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.06092217809404407 0.7553056597956419 0.0029466965398313415 -1.8740598377871773 0.3116511459654997 2.9732444649577383 +chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.0032786219354516257 0.03802402407151029 0.4820422473187418 -2.9403306275639056 2.074595666547732 +chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.004589686716285295 0.6973127707358744 2.176332048622399e-05 -2.834504112745991 0.3889504909464499 4.245987045730281 +chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.056864972978018666 0.08020149262448194 0.2007968317101773 -1.9043472603872424 1.7495181593666547 +chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.2104763476986481 0.1747211852405891 -1.741541630525145 -1.2522566823724743 1.3571889362732306 +chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.602727841142918 0.8201583130184009 -1.4741429475701973 0.5204817549965299 0.22734136168220886 +chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 5.1315106976375586e-05 0.012025540121556799 0.5835697449332469 4.049555046000217 2.511393982268917 +chr1 49100000 50200000 ID_0.01_30 0.046019 . 2.942555439185868e-05 0.002614171734234889 0.29644970367180923 4.1778670647745235 3.0098030142733485 1.044077134986226 +chr1 50200000 51500000 ID_0.01_31 0.1636485 . 0.0008092768618695985 0.8509905551285051 0.024559156167662435 3.349602227967295 -0.18785469932274496 2.2482672114800883 +chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.13176628976737523 0.22846083076168777 -0.32220269785311184 -1.5071731142971523 1.204333170795542 +chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 0.1852701563028485 0.9645664795137245 0.020176549895482607 -1.3247015577674193 -0.04442393950935331 2.323048448493291 +chr1 53100000 54700000 ID_0.01_34 -0.3917385 . 0.9977418713186132 0.05733282574350129 0.01347363335675291 0.0028301483783805185 -1.90076480636879 2.4709986335641756 +chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.07324790085975154 0.5587485506872516 0.07965863199293258 -1.7912829494553992 -0.58470134327905 1.7526702100869194 +chr1 57400000 58500000 ID_0.01_36 -0.8692615 . 0.4613597757566176 0.602568507215703 0.0022224806797976654 -0.7366096320849878 0.5207104304286511 3.0587695133149677 +chr1 58500000 59800000 ID_0.01_37 -0.793426 . 0.7255531686935289 0.002317254091988157 0.1865328113880741 0.35104689304844006 -3.0462366030597323 1.3209056927066725 +chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 8.981513689059817e-07 0.7034477559259763 0.0006863754125470629 -4.912733900814666 -0.380670507157995 3.394964334454319 +chr1 64600000 65300000 ID_0.01_41 -0.6812605 . 0.6251410835835239 0.19160573772369172 0.037684124607603085 -0.48857716389553185 -1.3058436350822609 2.078274055797617 +chr1 65300000 67100000 ID_0.01_42 -1.5001585 . 0.2769473036693756 0.1102978772132991 0.0001487713535869077 -1.0872025510356067 -1.596855697089364 3.7931114324442627 +chr1 67100000 69200000 ID_0.01_43 -1.2359205 . 0.21018617334750922 0.5842300956584897 5.323176929219475e-06 -1.2530536752875465 0.5472163632097017 4.551630476787783 +chr1 69200000 72300000 ID_0.01_44 -0.879535 . 0.5736042769931946 0.09203088161416222 3.81637198003483e-06 0.5627512551652414 1.6847807428437485 4.621139956276993 +chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.06678381915279902 0.5145237050757046 0.060089867957957795 1.8331261092037683 -0.651810069314388 1.8801336314860881 +chr1 73900000 74500000 ID_0.01_46 -1.0827955 . 0.12223509534990191 0.8956044627394589 0.04150250991588339 -1.5454597586856647 -0.1312159702703695 2.038474424838449 +chr1 74500000 75600000 ID_0.01_47 -0.513854 . 0.8555467191654857 3.91456713401117e-05 0.3465867566931127 -0.1820458815715487 -4.112465069905653 0.9412304866850322 +chr1 75600000 77900000 ID_0.01_48 -1.3889375 . 3.797132100093945e-05 0.42733505304910036 9.692510228743163e-10 -4.119489206445728 0.7937601890797391 6.114393122590527 +chr1 77900000 78500000 ID_0.01_49 -0.809386 . 0.32099041607424383 0.030960123115897433 0.02158985927361434 0.9924246566162215 -2.157584856684229 2.297507086558252 +chr1 78500000 79800000 ID_0.01_50 -0.9250035 . 0.04049346006516931 0.43476248017776276 6.812065470133609e-05 -2.0486795511046525 0.7810680362784915 3.982756102535289 +chr1 79800000 81300000 ID_0.01_51 -0.4445345 . 0.36159988539911325 0.9067590498240921 0.01642702919823067 0.9123207669109652 0.1171274596754559 2.399287102244771 +chr1 81300000 82500000 ID_0.01_52 -0.548837 . 0.5657569719808291 0.843855131941061 0.00024054901022731013 0.5743115835623119 -0.19696473833171133 3.6721175209487225 +chr1 82500000 87500000 ID_0.01_53 -0.8209955 . 0.8764781973172943 0.9108556321417692 0.7914181971243179 -0.1554352488000241 0.11195935721526085 0.2644694568022624 +chr1 87500000 88300000 ID_0.01_54 -1.9215335 . 0.9275875256501712 0.2492381416564282 0.5261968745640497 -0.09088052411227253 -1.1522018402734988 0.6338221829448881 +chr1 88300000 89100000 ID_0.01_55 -0.899375 . 0.17591995531921567 0.43251092514368816 0.12028482748081724 -1.3534248117018666 -0.7849021777084254 1.5535791852634102 +chr1 89100000 90200000 ID_0.01_56 -0.4054365 . 0.5441416438186202 0.42374428509921525 0.025472561795012016 -0.6065619716152021 -0.7999422020457385 2.234159779614325 +chr1 90200000 91200000 ID_0.01_57 -0.78976 . 0.4111181440863949 0.11354652971924255 0.03434695290132837 -0.8219275290100351 -1.5824515270326678 2.1159747762512064 +chr1 91200000 92500000 ID_0.01_58 -0.2421285 . 0.10529359211850775 0.8142018243105789 0.2526674709156823 -1.6197146295549456 -0.23500890147331419 1.1438943103717707 +chr1 92500000 93400000 ID_0.01_59 -0.291361 . 0.8400491187457132 0.5095291832844049 0.05686718419251078 -0.2018306508017106 0.6595709784572648 1.9043302710431667 +chr1 93400000 94800000 ID_0.01_60 -0.2776395 . 0.36508722454503795 0.5449971536535985 0.009330112076071657 0.9057140488754497 -0.6052736994437801 2.5997153359424354 +chr1 94800000 96000000 ID_0.01_61 -0.832662 . 0.6069467678774632 0.0005039011291777808 0.08607331261640087 -0.5144366114015662 -3.478674029270414 1.7164849914877844 +chr1 97800000 98900000 ID_0.01_63 -0.276687 . 0.00010213250271617032 0.8352588327918076 0.008702945093227717 3.88546905456647 -0.20796175085230958 2.6235078053259873 +chr1 98900000 100200000 ID_0.01_64 -0.196956 . 0.8846023001054634 0.23907870581962454 0.2138766210891413 -0.14513751382654447 -1.1772926843972238 1.2429761533139483 +chr1 100200000 101600000 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ID_0.01_139 -0.7580275 . 0.04421986858246246 0.7132136329381122 0.044593831085039316 -2.012000648941653 0.3675435235484022 2.008465665217658 +chr1 193700000 195200000 ID_0.01_140 -0.457743 . 0.9185395091955513 nan 0.047431185522004114 0.10227360045452025 nan 1.9824295455773762 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_h5_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_h5_accepted.diff_tad new file mode 100644 index 00000000..ed5d3926 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_h5_accepted.diff_tad @@ -0,0 +1,133 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. +# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD 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-0.31503614485233666 2.4947000537557527 +chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.7002651772916688 0.6532815227685426 -0.31503614485233666 -0.3849625294154097 0.449208130642345 +chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10175226570984419 0.09421071964878189 -0.3849625294154097 -1.6364173727117624 1.6735924688116193 +chr1 186600000 187300000 ID_0.01_133 -0.640236 . 0.10175226570984419 0.49143870397462885 0.027372249868613835 -1.6364173727117624 -0.6880223548042432 2.206167843846701 +chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.05908440312646483 7.763551868301071e-05 -0.6880223548042432 -1.8875647720051942 3.9515842867781994 +chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.005209894937738622 0.00010479145543859941 -1.8875647720051942 2.7937611137289413 3.8792211430563843 +chr1 189900000 190800000 ID_0.01_136 0.306214 . 0.005209894937738622 0.4221899834667334 0.004870730457159574 2.7937611137289413 -0.8026276473397439 2.8154610251746375 +chr1 190800000 191500000 ID_0.01_137 -0.191605 . 0.4221899834667334 0.9216624111662307 0.0015871064433715795 -0.8026276473397439 0.09833988101581538 3.158266043767661 +chr1 191500000 192700000 ID_0.01_138 -0.313625 . 0.9216624111662307 0.04421986858246246 0.003524165806862319 0.09833988101581538 -2.012000648941653 2.9178829781103146 +chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.04421986858246246 0.7282747240054768 0.044593831085039316 -2.012000648941653 0.34742144598393476 2.008465665217658 +chr1 193700000 195200000 ID_0.01_140 -0.457743 . nan nan 0.047431185522004114 nan nan 1.9824295455773762 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_h5_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_h5_rejected.diff_tad new file mode 100644 index 00000000..b70e95e1 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_h5_rejected.diff_tad @@ -0,0 +1,15 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.030230438882868516 0.03561337274424189 -2.692614553612967 2.167057908282934 2.10131444292845 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.011587414142526327 6.125855825029621e-06 2.167057908282934 -2.5244662175837944 4.521998277761523 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 5.081008401228345e-05 0.002710122418266765 -3.4245266094056284 4.05186913357941 2.99883701418205 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004986133195426291 4.483351940271164e-11 4.05186913357941 2.807928267339102 6.587154663693872 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0016376675728931981 2.9941210791658745e-07 2.807928267339102 -3.14911317809443 5.123816675539011 +chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.008928314591401266 0.00022924443696242214 -2.9462932286120593 -2.614786881491451 3.684397294574574 +chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 8.981513689059817e-07 6.115423785857918e-07 -2.614786881491451 -4.912733900814666 4.987535965432151 +chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00010213250271617032 0.000289635147178882 -3.421967604643488 3.88546905456647 3.624398133501732 +chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.047852690134436014 7.963547815901498e-06 -3.8073606560359816 1.9786742837141795 4.466161567031553 +chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0011513494284931425 0.005179707699348202 -2.5209450069288897 3.250666219136754 2.7956399072164286 +chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.004803857809584436 2.0311415510577494e-07 2.573259593232858 2.819900262147225 5.19646469403844 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_cool_multi_chromosomes_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_cool_multi_chromosomes_accepted.diff_tad deleted file mode 100644 index ecd318a1..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_cool_multi_chromosomes_accepted.diff_tad +++ /dev/null @@ -1,209 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5.2 -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.8268172476121132 1.1058975157219717e-05 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.7240996969343069 0.8243359234081221 0.0024356665657895523 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7008731541371999 0.650310296312886 8.408429587003463e-08 -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.775381473841675 0.04169142522984199 0.03824108000678763 -chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.03886635487751637 0.554164823075991 0.0011349170069066487 -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.8775507172147219 0.14300670825076836 3.723342500468501e-08 -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.10043295080776385 0.15901049598704675 0.0005125545788190994 -chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.22216806375823106 0.21229731104314642 1.083164714961291e-07 -chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.19688386332905916 0.8248789609562149 0.0002659845110845362 -chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.6773060416506496 0.03474017021549905 3.5997957192554745e-05 -chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.004933893894531303 0.09589931523564295 3.077331912182654e-07 -chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.04751915245141374 0.904050911399648 0.005175536195069642 -chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.3945187634973626 1.476608408563463e-06 -chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.4517230355955235 0.006600245133619858 0.01847468692656644 -chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.013383537582534024 0.6029863369698101 0.020907568598504074 -chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.6067051125745504 0.7634577197763519 0.2396121095619237 -chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.7234142195281222 0.3494027566512913 0.17408908021704805 -chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.4174483708095371 0.15435903209148993 0.0037812717498604915 -chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.14703280928528345 0.5148715751262816 0.0011347156298055663 -chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.40888817047264736 0.020033161970560896 0.01046765700832177 -chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.029768372427647013 0.3232299806965241 5.661896787269534e-07 -chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.4238932930845717 0.31855216824530097 0.027231089546047107 -chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.2593674551155798 0.8153952319211535 1.9632202705034285e-11 -chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.8624378083654324 0.6022635464423499 0.8654886280422122 -chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5435679928715043 2.874689743232649e-06 0.0014020864555605958 -chr1 49100000 50200000 ID_0.01_30 0.046019 . 1.462991983438978e-06 0.0003647343839865502 0.10118859177318387 -chr1 50200000 51500000 ID_0.01_31 0.1636485 . 9.279280726368033e-05 0.8454371355833938 0.0046151086387062525 -chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.9271311292713041 0.258929458622544 0.09999946543494605 -chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 0.35517009321681603 0.6540548808159248 0.007112713863390754 -chr1 53100000 54700000 ID_0.01_34 -0.3917385 . 0.6274135919991417 0.2576928729588498 0.002042590170183633 -chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.3204559662272003 0.8607571669174674 0.013227891559998137 -chr1 57400000 58500000 ID_0.01_36 -0.8692615 . 0.9643398880083548 0.3531102128603071 0.0003919365784997684 -chr1 58500000 59800000 ID_0.01_37 -0.793426 . 0.4311797824095879 0.011724455692841874 0.08194708998218529 -chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.06195469652396533 2.320703146298079e-05 9.54955812467016e-09 -chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 3.1998179426018816e-05 0.9090783386043256 0.0001402398162148534 -chr1 64600000 65300000 ID_0.01_41 -0.6812605 . 0.9799078880701289 0.4395451557789324 0.014375335496283982 -chr1 65300000 67100000 ID_0.01_42 -1.5001585 . 0.6052887178857895 0.5219186024777596 8.674627087508455e-06 -chr1 67100000 69200000 ID_0.01_43 -1.2359205 . 0.7906503578668709 0.11399561731585331 1.2129521659938234e-07 -chr1 69200000 72300000 ID_0.01_44 -0.879535 . 0.112216850948871 0.010067587160355804 4.0304504067763294e-08 -chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.005951077057798234 0.8941205362134248 0.01379204254338282 -chr1 73900000 74500000 ID_0.01_46 -1.0827955 . 0.3313332753869537 0.8707485028548523 0.018581679780480545 -chr1 74500000 75600000 ID_0.01_47 -0.513854 . 0.9238588458891327 0.00031550435807928685 0.21680145643800885 -chr1 75600000 77900000 ID_0.01_48 -1.3889375 . 0.0003247535612809871 0.18454259326370037 3.237860112254183e-12 -chr1 77900000 78500000 ID_0.01_49 -0.809386 . 0.118872299825002 0.09332337155183495 0.007352875386775665 -chr1 78500000 79800000 ID_0.01_50 -0.9250035 . 0.1239797088446756 0.1533952338122478 7.2966959465800866e-06 -chr1 79800000 81300000 ID_0.01_51 -0.4445345 . 0.11028839209007249 0.42422034349259397 0.003437760032436051 -chr1 81300000 82500000 ID_0.01_52 -0.548837 . 0.18859797704634573 0.9047287273528857 1.6939667078897195e-05 -chr1 82500000 87500000 ID_0.01_53 -0.8209955 . 0.9489914469569004 0.8038218522559868 0.8172820464028451 -chr1 87500000 88300000 ID_0.01_54 -1.9215335 . 0.9641222386067881 0.4287039800894066 0.34053126754285534 -chr1 88300000 89100000 ID_0.01_55 -0.899375 . 0.33572458949349204 0.7535507575266267 0.0624141777690027 -chr1 89100000 90200000 ID_0.01_56 -0.4054365 . 0.42889361357359657 0.3261877972807914 0.01071426573857872 -chr1 90200000 91200000 ID_0.01_57 -0.78976 . 0.7765164687723072 0.28329667131638947 0.007516113808133743 -chr1 91200000 92500000 ID_0.01_58 -0.2421285 . 0.27851630360875024 0.8213625258210666 0.12404980703247502 -chr1 92500000 93400000 ID_0.01_59 -0.291361 . 0.7935497657534414 0.23605299808554248 0.018950835732016932 -chr1 93400000 94800000 ID_0.01_60 -0.2776395 . 0.1455682568337237 0.5526747441544666 0.0009869490050939936 -chr1 94800000 96000000 ID_0.01_61 -0.832662 . 0.633098517669112 0.0012967279545514894 0.07208842123163033 -chr1 97800000 98900000 ID_0.01_63 -0.276687 . 3.7654117073312066e-06 0.9922824705634153 0.001588865850306781 -chr1 98900000 100200000 ID_0.01_64 -0.196956 . 0.9265151101812986 0.3615938420733621 0.12377783395873031 -chr1 100200000 101600000 ID_0.01_65 -0.480589 . 0.3970947826174175 0.011454692746884909 0.008627778289469519 -chr1 101600000 102400000 ID_0.01_66 -0.1597755 . 0.004209665959456069 0.24298139557782739 0.027686640387440266 -chr1 102400000 103300000 ID_0.01_67 -0.2325575 . 0.21401193102148075 0.0027323506564958682 0.021093890705597605 -chr1 103300000 104300000 ID_0.01_68 -0.3313575 . 0.0009137137858619813 0.21362820654646963 0.023964910037271563 -chr1 104300000 105700000 ID_0.01_69 -0.3473065 . 0.11390548385818876 0.1835358511509746 0.0028453763083392744 -chr1 105700000 106800000 ID_0.01_70 -0.5329025 . 0.10440273752761838 0.2543852147322475 0.0011549820430741976 -chr1 106800000 107800000 ID_0.01_71 -0.404506 . 0.22320014537589428 0.7329064904578018 0.0008827521132867005 -chr1 107800000 108700000 ID_0.01_72 -0.679396 . 0.7791919868195498 0.9705912506478017 0.16601585958317122 -chr1 108700000 109400000 ID_0.01_73 -0.80483 . 0.9435980524890623 0.9607240867340539 0.22301746994661498 -chr1 109400000 110800000 ID_0.01_74 -0.327192 . 0.8031090388611654 2.8212837060809916e-06 0.0008495555482788019 -chr1 110800000 112200000 ID_0.01_75 -0.168549 . 1.3876581751402857e-06 0.0002698817440942586 0.058039047167262416 -chr1 112200000 113500000 ID_0.01_76 -0.174322 . 4.032868585238236e-05 0.238138443151794 0.0003808205161931987 -chr1 113500000 114400000 ID_0.01_77 -0.6967465 . 0.259755894535457 0.547653972517973 0.00046150440242876827 -chr1 114400000 115400000 ID_0.01_78 -0.4525885 . 0.6553757038732764 0.008756886413554082 0.014257118337478758 -chr1 116200000 117100000 ID_0.01_80 -0.0989215 . 0.0008132301221824033 0.015746885059058437 0.06277474512351948 -chr1 117100000 118400000 ID_0.01_81 -0.1478965 . 0.0062591348613949315 0.7176775360429644 0.003345733707027353 -chr1 118400000 120200000 ID_0.01_82 -0.13017 . 0.6245287018950698 0.006935416844526041 0.2552183912523175 -chr1 120200000 123500000 ID_0.01_83 -0.6265325 . 0.004840082169336795 0.0015813471656511095 0.600799217922401 -chr1 126000000 127300000 ID_0.01_85 -0.1791345 . 0.006249700345752678 0.22181783152836143 0.09570898798205833 -chr1 127300000 129400000 ID_0.01_86 -0.702347 . 0.24222163567255006 0.06191083067762089 0.0025631580408357526 -chr1 129400000 130700000 ID_0.01_87 -0.642071 . 0.12934762897339674 0.24302258345387828 0.000419622722889291 -chr1 130700000 132300000 ID_0.01_88 -0.7337655 . 0.13429449059375498 0.07478544377402001 1.443335880184218e-06 -chr1 132300000 137700000 ID_0.01_89 -0.9940975 . 0.08524190522412639 0.001583290562072246 0.9047270035099604 -chr1 137700000 138400000 ID_0.01_90 -0.501823 . 0.000698654993761795 0.3904387914821358 0.014094330381635453 -chr1 138400000 139100000 ID_0.01_91 -0.588051 . 0.5248309551228452 0.28691492953866493 0.03049993330528615 -chr1 139100000 140000000 ID_0.01_92 -0.5246415 . 0.42501648055627117 0.5178351945603963 5.3881725231507235e-05 -chr1 140000000 141300000 ID_0.01_93 -0.509084 . 0.5448521702574729 0.24258906453716045 2.4930112098844777e-05 -chr1 141300000 142600000 ID_0.01_94 -0.7975355 . 0.1865328113880741 0.46278594901472325 0.0010288969847182406 -chr1 142600000 143800000 ID_0.01_95 -0.560399 . 0.35363997512644385 0.00527699695526016 0.0019980498261275735 -chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.05083946313912518 0.00043943253484140377 0.0005520490180596102 -chr1 147800000 148600000 ID_0.01_99 -0.101212 . 0.00016102955971323413 0.00499876925806227 0.05359940008122595 -chr1 151600000 152200000 ID_0.01_101 -0.3447745 . 0.0009224151870446465 0.32717537352572434 0.00760406183601162 -chr1 152200000 152900000 ID_0.01_102 -0.8149895 . 0.3339568102004268 0.2952429592421498 0.020736608272804644 -chr1 152900000 153600000 ID_0.01_103 -0.702321 . 0.32508028650354415 0.5965708756740098 0.006860672291893038 -chr1 153600000 154400000 ID_0.01_104 -0.725986 . 0.6004676618671748 0.1884090413257843 0.003178827442935124 -chr1 154400000 155300000 ID_0.01_105 -0.4089925 . 0.17431162936238864 0.011447285855752045 0.01193758707917701 -chr1 155300000 156800000 ID_0.01_106 -0.8541315 . 0.005255935171740207 0.5716055223533391 0.37860168698671826 -chr1 156800000 157400000 ID_0.01_107 -0.2000635 . 0.42974997057899345 0.4554329969755122 0.018026136448103032 -chr1 157400000 158600000 ID_0.01_108 -0.461399 . 0.5786359155291383 0.09035801347356912 0.07141892054126378 -chr1 158600000 159500000 ID_0.01_109 -0.3391315 . 0.0677248108258426 0.7605697898547499 0.0024740692372391196 -chr1 159500000 161100000 ID_0.01_110 -0.766471 . 0.8518254500959679 0.7739132016092966 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0.10913756920793073 0.0010618782692566118 -chr2 51500000 52200000 ID_0.01_32 -0.692286 . 0.24118505156876602 0.6208598367844064 0.672470358702386 -chr2 52200000 53100000 ID_0.01_33 -0.7849475 . 0.39725134284435715 0.15447421559355445 0.5701831064617965 -chr2 53100000 54700000 ID_0.01_34 -0.3917385 . 0.1521280588110987 0.3799632165194018 0.002967803257668766 -chr2 54700000 57400000 ID_0.01_35 -0.5543145 . 0.346755759830367 0.0014312329071657585 0.47352499353758404 -chr2 57400000 58500000 ID_0.01_36 -0.8692615 . 0.0024233876609619552 0.20626894756799574 0.7822405746331198 -chr2 58500000 59800000 ID_0.01_37 -0.793426 . 0.18239853130591577 0.6218204561761443 0.13736616371185872 -chr2 59800000 61100000 ID_0.01_38 -1.1246435 . 0.5827287423546319 0.1054007296071133 0.21759194136983662 -chr2 61100000 63200000 ID_0.01_39 -1.068387 . 0.10274298887110098 0.34115174774935353 0.07048470925924007 -chr2 63200000 64600000 ID_0.01_40 -1.4349735 . 0.48417731843647505 0.00033753405819330907 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. 0.05863270833799688 0.5874252605886783 0.4952237214341225 -chr2 94800000 96000000 ID_0.01_61 -0.832662 . 0.6950543784533142 0.0032772769467099175 0.011218663998675783 -chr2 97800000 98900000 ID_0.01_63 -0.276687 . 0.01182135449288108 0.9781360625835592 0.11444794246631047 -chr2 98900000 100200000 ID_0.01_64 -0.196956 . 0.9231075732967555 0.006380970470955413 0.8546925510997803 -chr2 100200000 101600000 ID_0.01_65 -0.480589 . 0.019713998589890258 0.01605654685424601 0.8441535520280872 -chr2 101600000 102400000 ID_0.01_66 -0.1597755 . 0.015843566166002136 0.11038403054109522 0.010933411544174087 -chr2 102400000 103300000 ID_0.01_67 -0.2325575 . 0.07739196334618564 0.8920863632839254 0.004479508580355494 -chr2 103300000 104300000 ID_0.01_68 -0.3313575 . 0.7682407326952878 0.07116112497945337 0.12194400706680208 -chr2 104300000 105700000 ID_0.01_69 -0.3473065 . 0.06228140735132291 0.7066195504607469 0.6295784282194834 -chr2 105700000 106800000 ID_0.01_70 -0.5329025 . 0.6700182786304059 0.42087560865213913 0.4939032667187476 -chr2 106800000 107800000 ID_0.01_71 -0.404506 . 0.7314661136592258 0.8324328988453884 3.960360576478446e-05 -chr2 107800000 108700000 ID_0.01_72 -0.679396 . 0.8412726808275693 0.14875367516572954 0.010142593994358249 -chr2 108700000 109400000 ID_0.01_73 -0.80483 . 0.046781600773732696 0.1109070316615554 0.00202042128660821 -chr2 109400000 110800000 ID_0.01_74 -0.327192 . 0.0915352797518888 0.4400541989813883 0.1879067363032434 -chr2 110800000 112200000 ID_0.01_75 -0.168549 . 0.3847123825595731 0.6768860622762672 0.026973732909941883 -chr2 112200000 113500000 ID_0.01_76 -0.174322 . 0.7461011302024421 0.9632463458767686 0.0062423840221954045 -chr2 113500000 114400000 ID_0.01_77 -0.6967465 . 0.7935497657534414 0.008592001054516171 0.006971136756122058 -chr2 115400000 116200000 ID_0.01_79 0.0065005 . 0.002794769727443374 0.7712804658813557 0.41512140421829624 -chr2 116200000 117100000 ID_0.01_80 -0.0989215 . 0.8604485472741461 0.22271495241320893 0.6840123446798727 -chr2 117100000 118400000 ID_0.01_81 -0.1478965 . 0.2315021025397601 0.033704773718936 0.1281855894415085 -chr2 118400000 120200000 ID_0.01_82 -0.13017 . 0.0343724402430932 0.8055360874068784 0.25821047039345024 -chr2 120200000 123500000 ID_0.01_83 -0.6265325 . 0.8263054157245454 0.846247992608086 0.6848118044173057 -chr2 123500000 126000000 ID_0.01_84 -0.878022 . 0.5546805518960432 0.7586273282794862 0.04195680648346834 -chr2 126000000 127300000 ID_0.01_85 -0.1791345 . 0.9044013891860989 nan 0.4078273699642819 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_cool_multi_chromosomes_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_cool_multi_chromosomes_rejected.diff_tad deleted file mode 100644 index 9ade9a50..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_cool_multi_chromosomes_rejected.diff_tad +++ /dev/null @@ -1,21 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5.2 -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.023812890829327776 0.016456650095058242 0.013780451222869307 -chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0089215993395334 1.285472801127568e-06 0.00027371449872326916 -chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.62488175706287e-07 1.4504561507903456e-05 1.3778440238424469e-14 -chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 1.5786397432173645e-05 0.022701527679266198 1.9076805322791016e-09 -chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.01586879590979828 0.03659340267092997 3.124179401591242e-05 -chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.0017124997724517516 4.9680693940233185e-06 1.922983338658536e-05 -chr1 115400000 116200000 ID_0.01_79 0.0065005 . 0.002826148476629719 0.0011343574929371728 0.023595609786263398 -chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.003332413744234827 0.005556795523194584 2.24757528005326e-07 -chr1 143800000 144700000 ID_0.01_96 0.08656 . 0.0009197364332563303 0.022759326510606574 0.002340427025911093 -chr1 144700000 145600000 ID_0.01_97 -0.021447 . 0.024067278280406255 0.027757272426992927 0.005130682934469564 -chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.002139568756318835 0.00348013763924427 1.4947314536052858e-09 -chr2 40900000 42900000 ID_0.01_25 -0.7016145 . 2.0772087272910948e-05 0.0008763900376773169 4.5966555611854654e-05 -chr2 45900000 47300000 ID_0.01_28 -0.656308 . 1.9510796109536805e-06 0.016393108655039807 0.0003837953285890675 -chr2 47300000 49100000 ID_0.01_29 -0.0033885 . 0.027525391564099017 0.00017069331965971062 2.57653091365844e-07 -chr2 77900000 78500000 ID_0.01_49 -0.809386 . 0.01855417571756637 0.0002025292493976715 0.03930313509400304 -chr2 96000000 97800000 ID_0.01_62 -1.285079 . 0.005308851713796463 0.02315236266375798 0.03434048057916755 -chr2 114400000 115400000 ID_0.01_78 -0.4525885 . 0.004262135097073559 0.0021003189556864257 0.014354178641596564 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_h5_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_h5_accepted.diff_tad deleted file mode 100644 index a9053fd2..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_h5_accepted.diff_tad +++ /dev/null @@ -1,133 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.3479058102348157 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.7619708385959597 0.011174626122333891 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.8706579826550646 4.668547072331386e-06 -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10355136240139871 0.10011542876256041 -chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.39564035674322084 0.006197912102328514 -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.030328896271663634 5.069275897797787e-07 -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.07605786424686575 0.0023999817017426378 -chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.4982863585572014 1.8146100883843892e-06 -chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.8237750360973404 0.002562121461829293 -chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.007089417650089524 0.00020602838341698515 -chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.775168622700411 0.012760792164069699 -chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.18141506612462333 1.5995491571971796e-05 -chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0006158715296021736 0.06748479713761105 -chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.2618270615259555 0.05430086444564102 -chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6877509288862875 0.6148221863583603 -chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.15689090160302394 0.4437394229186403 -chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 0.06092217809404407 0.011491613276272431 -chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.06092217809404407 0.629775934868511 0.0029466965398313415 -chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.004589686716285295 0.03802402407151029 -chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.004589686716285295 0.840857440405701 2.176332048622399e-05 -chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.08158868260078066 0.08020149262448194 -chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.1404431071415064 0.1747211852405891 -chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.5595098204829343 0.8201583130184009 -chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 2.942555439185868e-05 0.012025540121556799 -chr1 49100000 50200000 ID_0.01_30 0.046019 . 2.942555439185868e-05 0.0008092768618695985 0.29644970367180923 -chr1 50200000 51500000 ID_0.01_31 0.1636485 . 0.0008092768618695985 0.7472991407953615 0.024559156167662435 -chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.1852701563028485 0.22846083076168777 -chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 0.1852701563028485 0.9977418713186132 0.020176549895482607 -chr1 53100000 54700000 ID_0.01_34 -0.3917385 . 0.9977418713186132 0.07324790085975154 0.01347363335675291 -chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.07324790085975154 0.4613597757566176 0.07965863199293258 -chr1 57400000 58500000 ID_0.01_36 -0.8692615 . 0.4613597757566176 0.7255531686935289 0.0022224806797976654 -chr1 58500000 59800000 ID_0.01_37 -0.793426 . 0.7255531686935289 0.003216073606046391 0.1865328113880741 -chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 8.981513689059817e-07 0.6251410835835239 0.0006863754125470629 -chr1 64600000 65300000 ID_0.01_41 -0.6812605 . 0.6251410835835239 0.2769473036693756 0.037684124607603085 -chr1 65300000 67100000 ID_0.01_42 -1.5001585 . 0.2769473036693756 0.21018617334750922 0.0001487713535869077 -chr1 67100000 69200000 ID_0.01_43 -1.2359205 . 0.21018617334750922 0.5736042769931946 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. 0.0012227567577424718 0.22500121196367384 0.1900077841533132 -chr1 182800000 183800000 ID_0.01_130 -0.756317 . 0.22500121196367384 0.7527342104844837 0.012606364228184988 -chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.7002651772916688 0.6532815227685426 -chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10175226570984419 0.09421071964878189 -chr1 186600000 187300000 ID_0.01_133 -0.640236 . 0.10175226570984419 0.49143870397462885 0.027372249868613835 -chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.05908440312646483 7.763551868301071e-05 -chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.005209894937738622 0.00010479145543859941 -chr1 189900000 190800000 ID_0.01_136 0.306214 . 0.005209894937738622 0.4221899834667334 0.004870730457159574 -chr1 190800000 191500000 ID_0.01_137 -0.191605 . 0.4221899834667334 0.9216624111662307 0.0015871064433715795 -chr1 191500000 192700000 ID_0.01_138 -0.313625 . 0.9216624111662307 0.04421986858246246 0.003524165806862319 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.04421986858246246 0.7282747240054768 0.044593831085039316 -chr1 193700000 195200000 ID_0.01_140 -0.457743 . nan nan 0.047431185522004114 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_h5_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_h5_rejected.diff_tad deleted file mode 100644 index 6e6fa316..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all__t4_h5_rejected.diff_tad +++ /dev/null @@ -1,15 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.030230438882868516 0.03561337274424189 -chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.011587414142526327 6.125855825029621e-06 -chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 5.081008401228345e-05 0.002710122418266765 -chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004986133195426291 4.483351940271164e-11 -chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0016376675728931981 2.9941210791658745e-07 -chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.008928314591401266 0.00022924443696242214 -chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 8.981513689059817e-07 6.115423785857918e-07 -chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00010213250271617032 0.000289635147178882 -chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.047852690134436014 7.963547815901498e-06 -chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0011513494284931425 0.005179707699348202 -chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.004803857809584436 2.0311415510577494e-07 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all_accepted.diff_tad deleted file mode 100644 index 1e737c01..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all_accepted.diff_tad +++ /dev/null @@ -1,133 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.2022260523997077 0.006197912102328514 -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.5322636852613494 1.8146100883843892e-06 -chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.692745144471043 0.002562121461829293 -chr1 17100000 18100000 ID_0.01_10 -0.230354 . 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0.05479964256414248 0.003524165806862319 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 193700000 195200000 ID_0.01_140 -0.457743 . 0.9088908933305142 nan 0.047431185522004114 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all_rejected.diff_tad deleted file mode 100644 index 3126b5d4..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_all_rejected.diff_tad +++ /dev/null @@ -1,15 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 -chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 -chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 -chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00012207984276411976 0.000289635147178882 -chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.0396948681031242 7.963547815901498e-06 -chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0024232283144502514 0.005179707699348202 -chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.013340569405590395 2.0311415510577494e-07 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_intra-TAD_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_intra-TAD_accepted.diff_tad deleted file mode 100644 index 723e9ab2..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_intra-TAD_accepted.diff_tad +++ /dev/null @@ -1,144 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: intra-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 193700000 195200000 ID_0.01_140 -0.457743 . 0.9088908933305142 nan 0.047431185522004114 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 192700000 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b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_intra-TAD_rejected.diff_tad deleted file mode 100644 index 3e6590bb..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_intra-TAD_rejected.diff_tad +++ /dev/null @@ -1,144 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: intra-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 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0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_left_inter-TAD_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_left_inter-TAD_accepted.diff_tad deleted file mode 100644 index 5f7482a0..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_left_inter-TAD_accepted.diff_tad +++ /dev/null @@ -1,114 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: left-inter-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.2022260523997077 0.006197912102328514 -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.5322636852613494 1.8146100883843892e-06 -chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.692745144471043 0.002562121461829293 -chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.011911117420279341 0.00020602838341698515 -chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.15658860942159403 1.5995491571971796e-05 -chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0005012323510345417 0.06748479713761105 -chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.27686582704511986 0.05430086444564102 -chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6700147806330939 0.6148221863583603 -chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.13322270222894567 0.4437394229186403 -chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 0.0751792941984631 0.011491613276272431 -chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.06092217809404407 0.7553056597956419 0.0029466965398313415 -chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.0032786219354516257 0.03802402407151029 -chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.056864972978018666 0.08020149262448194 -chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.2104763476986481 0.1747211852405891 -chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.602727841142918 0.8201583130184009 -chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 5.1315106976375586e-05 0.012025540121556799 -chr1 49100000 50200000 ID_0.01_30 0.046019 . 2.942555439185868e-05 0.002614171734234889 0.29644970367180923 -chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.13176628976737523 0.22846083076168777 -chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 0.1852701563028485 0.9645664795137245 0.020176549895482607 -chr1 53100000 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ID_0.01_105 -0.4089925 . 0.08290762581038606 0.004488898188060745 0.04717516917172698 -chr1 155300000 156800000 ID_0.01_106 -0.8541315 . 0.0018192914932849032 0.36203645571210885 0.7113102073721501 -chr1 156800000 157400000 ID_0.01_107 -0.2000635 . 0.23398695027019234 0.6166342379605749 0.03328962570206317 -chr1 157400000 158600000 ID_0.01_108 -0.461399 . 0.7705362661241195 0.045499535397448665 0.11477247492915878 -chr1 159500000 161100000 ID_0.01_110 -0.766471 . 0.4670127190331427 0.2783883747191276 0.000808617036215606 -chr1 161100000 162100000 ID_0.01_111 -0.601909 . 0.39963730606682835 0.00048013180818610735 0.0008523015251096703 -chr1 163200000 164700000 ID_0.01_113 -0.4903745 . 0.31959284973395574 0.30724523933881387 0.1316634847801889 -chr1 164700000 166200000 ID_0.01_114 -0.773071 . 0.38729882591747644 0.3740833969491387 0.001137817310359038 -chr1 166200000 167100000 ID_0.01_115 -1.0252675 . 0.4417534695877726 0.70993045249208 0.000280363510298871 -chr1 167100000 167500000 ID_0.01_116 -0.7404205 . 0.620218468763515 0.7431107046158174 0.14159756069322943 -chr1 167500000 168300000 ID_0.01_117 -0.620643 . 0.727009731456113 0.6208598367844064 0.02330384925311846 -chr1 168300000 169100000 ID_0.01_118 -0.381752 . 0.5138307395323829 0.3655258965522935 0.1813057960560731 -chr1 169100000 169900000 ID_0.01_119 -0.2253555 . 0.38315317206763244 0.15595331814640168 0.04904679309334625 -chr1 169900000 171500000 ID_0.01_120 -0.5875475 . 0.22418438342946512 0.8385096247923436 1.3379176305445405e-07 -chr1 171500000 173400000 ID_0.01_121 -0.2808725 . 0.9572831895796499 0.0341793304958039 0.7959787354532785 -chr1 173400000 174300000 ID_0.01_122 -1.752554 . 0.03547655243943487 0.004662514812705979 0.30456317597982274 -chr1 175400000 176400000 ID_0.01_124 0.1718505 . 0.7627529090665852 0.5766236917735681 0.45244680893218303 -chr1 176400000 177800000 ID_0.01_125 0.0112955 . 0.6356274376221928 0.021734997211659477 6.325784122034014e-05 -chr1 178700000 179700000 ID_0.01_127 -0.2865335 . 0.3923180055901787 0.04550716311782837 2.6383293815311617e-05 -chr1 179700000 181400000 ID_0.01_128 -1.300036 . 0.04567304175680046 0.0017016130383748175 0.07029573025202325 -chr1 181400000 182800000 ID_0.01_129 -0.9773875 . 0.0012227567577424718 0.1837862101652874 0.1900077841533132 -chr1 182800000 183800000 ID_0.01_130 -0.756317 . 0.22500121196367384 0.7224634953522755 0.012606364228184988 -chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.6381872465439603 0.6532815227685426 -chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10662063212498882 0.09421071964878189 -chr1 186600000 187300000 ID_0.01_133 -0.640236 . 0.10175226570984419 0.3130816687642489 0.027372249868613835 -chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.022646678654874207 7.763551868301071e-05 -chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.01171597151998054 0.00010479145543859941 -chr1 190800000 191500000 ID_0.01_137 -0.191605 . 0.4221899834667334 0.920842420803457 0.0015871064433715795 -chr1 191500000 192700000 ID_0.01_138 -0.313625 . 0.9216624111662307 0.05479964256414248 0.003524165806862319 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 193700000 195200000 ID_0.01_140 -0.457743 . 0.9088908933305142 nan 0.047431185522004114 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_left_inter-TAD_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_left_inter-TAD_rejected.diff_tad deleted file mode 100644 index 5119718c..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_left_inter-TAD_rejected.diff_tad +++ /dev/null @@ -1,34 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: left-inter-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.07553560212368073 0.03561337274424189 -chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 -chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.6730908477968309 0.012760792164069699 -chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 -chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 -chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.004589686716285295 0.6973127707358744 2.176332048622399e-05 -chr1 50200000 51500000 ID_0.01_31 0.1636485 . 0.0008092768618695985 0.8509905551285051 0.024559156167662435 -chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 8.981513689059817e-07 0.7034477559259763 0.0006863754125470629 -chr1 75600000 77900000 ID_0.01_48 -1.3889375 . 3.797132100093945e-05 0.42733505304910036 9.692510228743163e-10 -chr1 78500000 79800000 ID_0.01_50 -0.9250035 . 0.04049346006516931 0.43476248017776276 6.812065470133609e-05 -chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00012207984276411976 0.000289635147178882 -chr1 97800000 98900000 ID_0.01_63 -0.276687 . 0.00010213250271617032 0.8352588327918076 0.008702945093227717 -chr1 112200000 113500000 ID_0.01_76 -0.174322 . 0.0002992751986200488 0.09080959225979315 0.0025389833435517767 -chr1 117100000 118400000 ID_0.01_81 -0.1478965 . 0.031660125091572386 0.30530880216132816 0.017173407823036953 -chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.0396948681031242 7.963547815901498e-06 -chr1 129400000 130700000 ID_0.01_87 -0.642071 . 0.03017913679184316 0.5041609424790332 0.0019284287143192423 -chr1 137700000 138400000 ID_0.01_90 -0.501823 . 0.005584317239180269 0.22373195320470718 0.018503908737416766 -chr1 143800000 144700000 ID_0.01_96 0.08656 . 0.005958644680235337 0.0660708557024396 0.00623675545221349 -chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0024232283144502514 0.005179707699348202 -chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.013340569405590395 2.0311415510577494e-07 -chr1 151600000 152200000 ID_0.01_101 -0.3447745 . 0.004803857809584436 0.6768944039554314 0.024293348557061004 -chr1 158600000 159500000 ID_0.01_109 -0.3391315 . 0.03668887396610668 0.41094454833779814 0.00690130176232161 -chr1 162100000 163200000 ID_0.01_112 -1.180553 . 0.0005289450998701394 0.3108302076215622 0.0007692282402994766 -chr1 174300000 175400000 ID_0.01_123 -0.8041275 . 0.004527435624232897 0.9367350609061894 0.0012318328197052071 -chr1 177800000 178700000 ID_0.01_126 -0.2328815 . 0.018912494527358454 0.733857160443065 0.02427783153155655 -chr1 189900000 190800000 ID_0.01_136 0.306214 . 0.005209894937738622 0.2767853552349526 0.004870730457159574 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_accepted.diff_tad deleted file mode 100644 index dba35fb9..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_accepted.diff_tad +++ /dev/null @@ -1,117 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.2022260523997077 0.006197912102328514 -chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.5322636852613494 1.8146100883843892e-06 -chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.692745144471043 0.002562121461829293 -chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.07553560212368073 0.03561337274424189 -chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.6730908477968309 0.012760792164069699 -chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.15658860942159403 1.5995491571971796e-05 -chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0005012323510345417 0.06748479713761105 -chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.27686582704511986 0.05430086444564102 -chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6700147806330939 0.6148221863583603 -chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.13322270222894567 0.4437394229186403 -chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 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deleted file mode 100644 index e541b754..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_rejected.diff_tad +++ /dev/null @@ -1,31 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.011911117420279341 0.00020602838341698515 -chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 -chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 -chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 -chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.0032786219354516257 0.03802402407151029 -chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 5.1315106976375586e-05 0.012025540121556799 -chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -chr1 77900000 78500000 ID_0.01_49 -0.809386 . 0.32099041607424383 0.030960123115897433 0.02158985927361434 -chr1 96000000 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151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.013340569405590395 2.0311415510577494e-07 -chr1 161100000 162100000 ID_0.01_111 -0.601909 . 0.39963730606682835 0.00048013180818610735 0.0008523015251096703 -chr1 176400000 177800000 ID_0.01_125 0.0112955 . 0.6356274376221928 0.021734997211659477 6.325784122034014e-05 -chr1 178700000 179700000 ID_0.01_127 -0.2865335 . 0.3923180055901787 0.04550716311782837 2.6383293815311617e-05 -chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.022646678654874207 7.763551868301071e-05 -chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.01171597151998054 0.00010479145543859941 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_t1_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_t1_accepted.diff_tad deleted file mode 100644 index c0693dc6..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_t1_accepted.diff_tad +++ /dev/null @@ -1,116 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -chr1 10100000 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0.0011513494284931425 0.020776289543401466 0.12490254773012759 -chr1 151600000 152200000 ID_0.01_101 -0.3447745 . 0.004803857809584436 0.6768944039554314 0.024293348557061004 -chr1 152200000 152900000 ID_0.01_102 -0.8149895 . 0.6546562542419797 0.1682979574732668 0.04178623740063356 -chr1 152900000 153600000 ID_0.01_103 -0.702321 . 0.17362501794492147 0.3012258747984379 0.02235242837446713 -chr1 153600000 154400000 ID_0.01_104 -0.725986 . 0.31406847823776596 0.10723070176672636 0.012859638579802452 -chr1 155300000 156800000 ID_0.01_106 -0.8541315 . 0.0018192914932849032 0.36203645571210885 0.7113102073721501 -chr1 156800000 157400000 ID_0.01_107 -0.2000635 . 0.23398695027019234 0.6166342379605749 0.03328962570206317 -chr1 157400000 158600000 ID_0.01_108 -0.461399 . 0.7705362661241195 0.045499535397448665 0.11477247492915878 -chr1 158600000 159500000 ID_0.01_109 -0.3391315 . 0.03668887396610668 0.41094454833779814 0.00690130176232161 -chr1 159500000 161100000 ID_0.01_110 -0.766471 . 0.4670127190331427 0.2783883747191276 0.000808617036215606 -chr1 162100000 163200000 ID_0.01_112 -1.180553 . 0.0005289450998701394 0.3108302076215622 0.0007692282402994766 -chr1 163200000 164700000 ID_0.01_113 -0.4903745 . 0.31959284973395574 0.30724523933881387 0.1316634847801889 -chr1 164700000 166200000 ID_0.01_114 -0.773071 . 0.38729882591747644 0.3740833969491387 0.001137817310359038 -chr1 166200000 167100000 ID_0.01_115 -1.0252675 . 0.4417534695877726 0.70993045249208 0.000280363510298871 -chr1 167100000 167500000 ID_0.01_116 -0.7404205 . 0.620218468763515 0.7431107046158174 0.14159756069322943 -chr1 167500000 168300000 ID_0.01_117 -0.620643 . 0.727009731456113 0.6208598367844064 0.02330384925311846 -chr1 168300000 169100000 ID_0.01_118 -0.381752 . 0.5138307395323829 0.3655258965522935 0.1813057960560731 -chr1 169100000 169900000 ID_0.01_119 -0.2253555 . 0.38315317206763244 0.15595331814640168 0.04904679309334625 -chr1 169900000 171500000 ID_0.01_120 -0.5875475 . 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0.7527342104844837 0.6381872465439603 0.6532815227685426 -chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10662063212498882 0.09421071964878189 -chr1 186600000 187300000 ID_0.01_133 -0.640236 . 0.10175226570984419 0.3130816687642489 0.027372249868613835 -chr1 189900000 190800000 ID_0.01_136 0.306214 . 0.005209894937738622 0.2767853552349526 0.004870730457159574 -chr1 190800000 191500000 ID_0.01_137 -0.191605 . 0.4221899834667334 0.920842420803457 0.0015871064433715795 -chr1 191500000 192700000 ID_0.01_138 -0.313625 . 0.9216624111662307 0.05479964256414248 0.003524165806862319 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 193700000 195200000 ID_0.01_140 -0.457743 . 0.9088908933305142 nan 0.047431185522004114 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_t1_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_t1_rejected.diff_tad deleted file mode 100644 index 551412af..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_reject_right_inter-TAD_t1_rejected.diff_tad +++ /dev/null @@ -1,32 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: all -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.011911117420279341 0.00020602838341698515 -chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 -chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 -chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 -chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.0032786219354516257 0.03802402407151029 -chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 5.1315106976375586e-05 0.012025540121556799 -chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -chr1 77900000 78500000 ID_0.01_49 -0.809386 . 0.32099041607424383 0.030960123115897433 0.02158985927361434 -chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00012207984276411976 0.000289635147178882 -chr1 100200000 101600000 ID_0.01_65 -0.480589 . 0.2696554530687709 0.03750438635138998 0.04217312747454267 -chr1 109400000 110800000 ID_0.01_74 -0.327192 . 0.8719515577799544 4.067775971974873e-05 0.007150334840595598 -chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.0396948681031242 7.963547815901498e-06 -chr1 127300000 129400000 ID_0.01_86 -0.702347 . 0.6151989343062929 0.013030884814290544 0.02644757894272022 -chr1 130700000 132300000 ID_0.01_88 -0.7337655 . 0.3313792760154809 0.013463601572888518 2.3322425005292974e-05 -chr1 142600000 143800000 ID_0.01_95 -0.560399 . 0.11405480060793942 0.02498943527646134 0.007235404471539694 -chr1 144700000 145600000 ID_0.01_97 -0.021447 . 0.06420778059889237 0.005915933786202155 0.01747092284081774 -chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0024232283144502514 0.005179707699348202 -chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.013340569405590395 2.0311415510577494e-07 -chr1 154400000 155300000 ID_0.01_105 -0.4089925 . 0.08290762581038606 0.004488898188060745 0.04717516917172698 -chr1 161100000 162100000 ID_0.01_111 -0.601909 . 0.39963730606682835 0.00048013180818610735 0.0008523015251096703 -chr1 176400000 177800000 ID_0.01_125 0.0112955 . 0.6356274376221928 0.021734997211659477 6.325784122034014e-05 -chr1 178700000 179700000 ID_0.01_127 -0.2865335 . 0.3923180055901787 0.04550716311782837 2.6383293815311617e-05 -chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.022646678654874207 7.763551868301071e-05 -chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.01171597151998054 0.00010479145543859941 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_rejected.diff_tad new file mode 100644 index 00000000..39611c13 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_all_rejected.diff_tad @@ -0,0 +1,15 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -2.1657683076952483 -1.9765043757997804 3.0356746656834117 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 2.167057908282934 -2.1628710201312877 4.521998277761523 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -3.4245266094056284 3.902499692881189 2.99883701418205 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 4.05186913357941 2.818330247918638 6.587154663693872 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 2.807928267339102 -2.93193644190598 5.123816675539011 +chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -2.9462932286120593 -2.7743818055769554 3.684397294574574 +chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -2.614786881491451 -4.957488355561393 4.987535965432151 +chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00012207984276411976 0.000289635147178882 -3.421967604643488 3.841911528133773 3.624398133501732 +chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.0396948681031242 7.963547815901498e-06 -3.8073606560359816 2.0569101641013843 4.466161567031553 +chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0024232283144502514 0.005179707699348202 -2.5209450069288897 3.0327667392849023 2.7956399072164286 +chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.013340569405590395 2.0311415510577494e-07 2.573259593232858 2.4745458547284858 5.19646469403844 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_intra-TAD_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_intra-TAD_accepted.diff_tad new file mode 100644 index 00000000..8a2107d6 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_intra-TAD_accepted.diff_tad @@ -0,0 +1,53 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. +# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: intra-TAD and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -0.16282276617118813 1.6051606385162123 1.6442942874387492 +chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0005012323510345417 0.06748479713761105 -1.3364107145509396 -3.4800969585043267 1.8284316353792964 +chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.27686582704511986 0.05430086444564102 -3.14911317809443 -1.0873869704262455 1.9244287435607725 +chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6700147806330939 0.6148221863583603 -1.1220832111082402 -0.4261277223514882 0.5032021030649116 +chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.13322270222894567 0.4437394229186403 -0.4019090951745341 -1.501513869069336 0.7658939216443722 +chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.056864972978018666 0.08020149262448194 0.2007968317101773 -1.9043472603872424 1.7495181593666547 +chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.2104763476986481 0.1747211852405891 -1.741541630525145 -1.2522566823724743 1.3571889362732306 +chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.602727841142918 0.8201583130184009 -1.4741429475701973 0.5204817549965299 0.22734136168220886 +chr1 49100000 50200000 ID_0.01_30 0.046019 . 2.942555439185868e-05 0.002614171734234889 0.29644970367180923 4.1778670647745235 3.0098030142733485 1.044077134986226 +chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.13176628976737523 0.22846083076168777 -0.32220269785311184 -1.5071731142971523 1.204333170795542 +chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.07324790085975154 0.5587485506872516 0.07965863199293258 -1.7912829494553992 -0.58470134327905 1.7526702100869194 +chr1 58500000 59800000 ID_0.01_37 -0.793426 . 0.7255531686935289 0.002317254091988157 0.1865328113880741 0.35104689304844006 -3.0462366030597323 1.3209056927066725 +chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.06678381915279902 0.5145237050757046 0.060089867957957795 1.8331261092037683 -0.651810069314388 1.8801336314860881 +chr1 74500000 75600000 ID_0.01_47 -0.513854 . 0.8555467191654857 3.91456713401117e-05 0.3465867566931127 -0.1820458815715487 -4.112465069905653 0.9412304866850322 +chr1 82500000 87500000 ID_0.01_53 -0.8209955 . 0.8764781973172943 0.9108556321417692 0.7914181971243179 -0.1554352488000241 0.11195935721526085 0.2644694568022624 +chr1 87500000 88300000 ID_0.01_54 -1.9215335 . 0.9275875256501712 0.2492381416564282 0.5261968745640497 -0.09088052411227253 -1.1522018402734988 0.6338221829448881 +chr1 88300000 89100000 ID_0.01_55 -0.899375 . 0.17591995531921567 0.43251092514368816 0.12028482748081724 -1.3534248117018666 -0.7849021777084254 1.5535791852634102 +chr1 91200000 92500000 ID_0.01_58 -0.2421285 . 0.10529359211850775 0.8142018243105789 0.2526674709156823 -1.6197146295549456 -0.23500890147331419 1.1438943103717707 +chr1 92500000 93400000 ID_0.01_59 -0.291361 . 0.8400491187457132 0.5095291832844049 0.05686718419251078 -0.2018306508017106 0.6595709784572648 1.9043302710431667 +chr1 94800000 96000000 ID_0.01_61 -0.832662 . 0.6069467678774632 0.0005039011291777808 0.08607331261640087 -0.5144366114015662 -3.478674029270414 1.7164849914877844 +chr1 98900000 100200000 ID_0.01_64 -0.196956 . 0.8846023001054634 0.23907870581962454 0.2138766210891413 -0.14513751382654447 -1.1772926843972238 1.2429761533139483 +chr1 101600000 102400000 ID_0.01_66 -0.1597755 . 0.01843186740506446 0.5481976319769135 0.08450223158802864 2.356826277441937 0.6004631206846309 1.7251400768875904 +chr1 102400000 103300000 ID_0.01_67 -0.2325575 . 0.5071656079618452 0.013368937907233164 0.09494942262429858 0.6632575670547814 2.473786992375336 1.669848091671097 +chr1 103300000 104300000 ID_0.01_68 -0.3313575 . 0.0059711068230264164 0.5041281160378562 0.09087020993163282 2.7493638232092166 0.6680085793989338 1.6908251098912643 +chr1 107800000 108700000 ID_0.01_72 -0.679396 . 0.7791919868195498 0.9094974273085202 0.3321704734253206 -0.28037216927627806 -0.11367248196414026 0.9697512989744885 +chr1 108700000 109400000 ID_0.01_73 -0.80483 . 0.8951913091086809 0.7419760360373884 0.3338897735741172 -0.13173827646305827 -0.3292376912560182 0.9663086208153022 +chr1 110800000 112200000 ID_0.01_75 -0.168549 . 2.2427004709106132e-05 0.0014735269622088004 0.1404404786989442 4.2392477443094245 3.179847263925401 1.474152711927578 +chr1 114400000 115400000 ID_0.01_78 -0.4525885 . 0.3614318988630364 0.026899003883349634 0.054180530313661726 -0.9126400203993132 2.212980299582343 1.9253904430553703 +chr1 115400000 116200000 ID_0.01_79 0.0065005 . 0.01144695116513853 0.005151640525496448 0.0624141777690027 2.52875005948671 2.797395649538717 1.8633419062515133 +chr1 116200000 117100000 ID_0.01_80 -0.0989215 . 0.0037226721775892673 0.06295709440414389 0.1609545309684186 2.9007529739865743 1.859494385071822 1.4018684581030172 +chr1 118400000 120200000 ID_0.01_82 -0.13017 . 0.28717850735668105 0.06981354638050603 0.43207256966425345 1.0643316006880144 -1.8131185001213783 0.7856499891055168 +chr1 120200000 123500000 ID_0.01_83 -0.6265325 . 0.06430179613534404 6.0213881108940645e-05 0.19307511054649118 -1.85008155389624 -4.011971067650065 -1.3015358239132966 +chr1 126000000 127300000 ID_0.01_85 -0.1791345 . 0.047852690134436014 0.5860265670331393 0.2535921500196371 1.9786742837141795 0.5446030348418471 1.141667752103407 +chr1 132300000 137700000 ID_0.01_89 -0.9940975 . 0.01568514365125829 0.00964799804723899 0.3825876272232871 -2.416160548488812 2.5881963049218597 -0.8731384339136451 +chr1 138400000 139100000 ID_0.01_91 -0.588051 . 0.3012258747984379 0.14572455419105776 0.069465337533249 -1.03380812006343 -1.4548003033756296 1.8153812692522773 +chr1 141300000 142600000 ID_0.01_94 -0.7975355 . 0.16353851067801284 0.10023814088277018 0.4276546765554601 -1.3932688364284875 -1.6437002181636735 -0.7932113831045124 +chr1 147800000 148600000 ID_0.01_99 -0.101212 . 0.0011513494284931425 0.020776289543401466 0.12490254773012759 3.250666219136754 2.3120252924184856 1.5345168639718345 +chr1 155300000 156800000 ID_0.01_106 -0.8541315 . 0.0018192914932849032 0.36203645571210885 0.7113102073721501 -3.1182488066126774 -0.9114915123257828 0.3700970133542697 +chr1 157400000 158600000 ID_0.01_108 -0.461399 . 0.7705362661241195 0.045499535397448665 0.11477247492915878 0.2916735084036087 -2.0000067465343894 1.5771001838525438 +chr1 163200000 164700000 ID_0.01_113 -0.4903745 . 0.31959284973395574 0.30724523933881387 0.1316634847801889 0.9952949159613864 -1.0210194171597968 1.5075744158084308 +chr1 167100000 167500000 ID_0.01_116 -0.7404205 . 0.620218468763515 0.7431107046158174 0.14159756069322943 -0.495540744159623 -0.32773676267223106 1.4698678048165976 +chr1 168300000 169100000 ID_0.01_118 -0.381752 . 0.5138307395323829 0.3655258965522935 0.1813057960560731 -0.6528845042364637 -0.9048857886996416 1.336745280571738 +chr1 171500000 173400000 ID_0.01_121 -0.2808725 . 0.9572831895796499 0.0341793304958039 0.7959787354532785 0.05356318364201131 -2.1179496686141954 -0.25855483425340825 +chr1 173400000 174300000 ID_0.01_122 -1.752554 . 0.03547655243943487 0.004662514812705979 0.30456317597982274 -2.102876661547345 -2.829470157288153 1.0266969711077054 +chr1 175400000 176400000 ID_0.01_124 0.1718505 . 0.7627529090665852 0.5766236917735681 0.45244680893218303 0.3018677136183763 -0.5583232200655286 0.7513420827912771 +chr1 179700000 181400000 ID_0.01_128 -1.300036 . 0.04567304175680046 0.0017016130383748175 0.07029573025202325 -1.9984024913992735 -3.1379027839288853 1.8100003670210254 +chr1 181400000 182800000 ID_0.01_129 -0.9773875 . 0.0012227567577424718 0.1837862101652874 0.1900077841533132 -3.2335178940373406 -1.3291872205824826 1.310556084991557 +chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.6381872465439603 0.6532815227685426 -0.31503614485233666 -0.47023483816766326 0.449208130642345 +chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10662063212498882 0.09421071964878189 -0.3849625294154097 -1.6135704435900085 1.6735924688116193 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_intra-TAD_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_intra-TAD_rejected.diff_tad new file mode 100644 index 00000000..55263ff8 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_intra-TAD_rejected.diff_tad @@ -0,0 +1,95 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: intra-TAD and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 nan -0.7930969487289069 3.7263815455490827 +chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -0.9386590778150411 -0.45126112355691883 2.5371900826446283 +chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -0.30289374467773583 0.07414294720451348 4.5791565418309395 +chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.2022260523997077 0.006197912102328514 1.627875146104104 -1.2752350682626996 2.737122965561303 +chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -0.8494330724907115 -1.9655771567720404 5.023672092995246 +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -2.1657683076952483 -1.9765043757997804 3.0356746656834117 +chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.5322636852613494 1.8146100883843892e-06 -1.774031958289595 0.624554202910739 4.773045240138744 +chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.692745144471043 0.002562121461829293 0.67718850743882 -0.39513244622709864 3.0159066257881317 +chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.011911117420279341 0.00020602838341698515 -0.2226922466874271 -2.514766701978045 3.7115077195445525 +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.07553560212368073 0.03561337274424189 -2.692614553612967 1.7771984030211898 2.10131444292845 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 2.167057908282934 -2.1628710201312877 4.521998277761523 +chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.6730908477968309 0.012760792164069699 -2.5244662175837944 -0.42190981210011114 2.4903762617335548 +chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.15658860942159403 1.5995491571971796e-05 -0.2856207321579987 -1.416638625821259 4.314513284521457 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -3.4245266094056284 3.902499692881189 2.99883701418205 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 4.05186913357941 2.818330247918638 6.587154663693872 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 2.807928267339102 -2.93193644190598 5.123816675539011 +chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 0.0751792941984631 0.011491613276272431 -1.41560597278901 -1.7793689460462792 2.527382919088952 +chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.06092217809404407 0.7553056597956419 0.0029466965398313415 -1.8740598377871773 0.3116511459654997 2.9732444649577383 +chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.0032786219354516257 0.03802402407151029 0.4820422473187418 -2.9403306275639056 2.074595666547732 +chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.004589686716285295 0.6973127707358744 2.176332048622399e-05 -2.834504112745991 0.3889504909464499 4.245987045730281 +chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 5.1315106976375586e-05 0.012025540121556799 0.5835697449332469 4.049555046000217 2.511393982268917 +chr1 50200000 51500000 ID_0.01_31 0.1636485 . 0.0008092768618695985 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b/hicexplorer/test/test_data/hicDifferentialTAD/mode_left_inter-TAD_accepted.diff_tad @@ -0,0 +1,113 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. +# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: left-inter-TAD and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 nan -0.7930969487289069 3.7263815455490827 +chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -0.9386590778150411 -0.45126112355691883 2.5371900826446283 +chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 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+chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.022646678654874207 7.763551868301071e-05 -0.6880223548042432 -2.279343086591048 3.9515842867781994 +chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.01171597151998054 0.00010479145543859941 -1.8875647720051942 2.5205856687431933 3.8792211430563843 +chr1 190800000 191500000 ID_0.01_137 -0.191605 . 0.4221899834667334 0.920842420803457 0.0015871064433715795 -0.8026276473397439 0.09937262052003606 3.158266043767661 +chr1 191500000 192700000 ID_0.01_138 -0.313625 . 0.9216624111662307 0.05479964256414248 0.003524165806862319 0.09833988101581538 -1.9204614140905703 2.9178829781103146 +chr1 193700000 195200000 ID_0.01_140 -0.457743 . 0.9185395091955513 nan 0.047431185522004114 0.10227360045452025 nan 1.9824295455773762 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_left_inter-TAD_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_left_inter-TAD_rejected.diff_tad new file mode 100644 index 00000000..4869b907 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_left_inter-TAD_rejected.diff_tad @@ -0,0 +1,35 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: left-inter-TAD and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -2.1657683076952483 -1.9765043757997804 3.0356746656834117 +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.07553560212368073 0.03561337274424189 -2.692614553612967 1.7771984030211898 2.10131444292845 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 2.167057908282934 -2.1628710201312877 4.521998277761523 +chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.6730908477968309 0.012760792164069699 -2.5244662175837944 -0.42190981210011114 2.4903762617335548 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -3.4245266094056284 3.902499692881189 2.99883701418205 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 4.05186913357941 2.818330247918638 6.587154663693872 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 2.807928267339102 -2.93193644190598 5.123816675539011 +chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.004589686716285295 0.6973127707358744 2.176332048622399e-05 -2.834504112745991 0.3889504909464499 4.245987045730281 +chr1 50200000 51500000 ID_0.01_31 0.1636485 . 0.0008092768618695985 0.8509905551285051 0.024559156167662435 3.349602227967295 -0.18785469932274496 2.2482672114800883 +chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -2.9462932286120593 -2.7743818055769554 3.684397294574574 +chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -2.614786881491451 -4.957488355561393 4.987535965432151 +chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 8.981513689059817e-07 0.7034477559259763 0.0006863754125470629 -4.912733900814666 -0.380670507157995 3.394964334454319 +chr1 75600000 77900000 ID_0.01_48 -1.3889375 . 3.797132100093945e-05 0.42733505304910036 9.692510228743163e-10 -4.119489206445728 0.7937601890797391 6.114393122590527 +chr1 78500000 79800000 ID_0.01_50 -0.9250035 . 0.04049346006516931 0.43476248017776276 6.812065470133609e-05 -2.0486795511046525 0.7810680362784915 3.982756102535289 +chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00012207984276411976 0.000289635147178882 -3.421967604643488 3.841911528133773 3.624398133501732 +chr1 97800000 98900000 ID_0.01_63 -0.276687 . 0.00010213250271617032 0.8352588327918076 0.008702945093227717 3.88546905456647 -0.20796175085230958 2.6235078053259873 +chr1 112200000 113500000 ID_0.01_76 -0.174322 . 0.0002992751986200488 0.09080959225979315 0.0025389833435517767 3.6159265786642667 -1.6911424870726728 3.0186563723338744 +chr1 117100000 118400000 ID_0.01_81 -0.1478965 . 0.031660125091572386 0.30530880216132816 0.017173407823036953 2.148675588678498 1.0251152680854658 2.382973986716083 +chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.0396948681031242 7.963547815901498e-06 -3.8073606560359816 2.0569101641013843 4.466161567031553 +chr1 129400000 130700000 ID_0.01_87 -0.642071 . 0.03017913679184316 0.5041609424790332 0.0019284287143192423 -2.167731296814834 0.667957154306551 3.1010390282633256 +chr1 137700000 138400000 ID_0.01_90 -0.501823 . 0.005584317239180269 0.22373195320470718 0.018503908737416766 2.7712404514599647 -1.2166643369654333 2.3553772632372993 +chr1 143800000 144700000 ID_0.01_96 0.08656 . 0.005958644680235337 0.0660708557024396 0.00623675545221349 2.7500484875242517 1.8379426556939726 2.735067135104214 +chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0024232283144502514 0.005179707699348202 -2.5209450069288897 3.0327667392849023 2.7956399072164286 +chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.013340569405590395 2.0311415510577494e-07 2.573259593232858 2.4745458547284858 5.19646469403844 +chr1 151600000 152200000 ID_0.01_101 -0.3447745 . 0.004803857809584436 0.6768944039554314 0.024293348557061004 2.819900262147225 0.416704716679683 2.2524579279982864 +chr1 158600000 159500000 ID_0.01_109 -0.3391315 . 0.03668887396610668 0.41094454833779814 0.00690130176232161 -2.089209440838891 -0.8222325646029429 2.7015696809082037 +chr1 162100000 163200000 ID_0.01_112 -1.180553 . 0.0005289450998701394 0.3108302076215622 0.0007692282402994766 -3.4656531893309728 1.0134815432547015 3.3636363636363638 +chr1 174300000 175400000 ID_0.01_123 -0.8041275 . 0.004527435624232897 0.9367350609061894 0.0012318328197052071 -2.838864651911156 0.07937410997042987 3.231404958677686 +chr1 177800000 178700000 ID_0.01_126 -0.2328815 . 0.018912494527358454 0.733857160443065 0.02427783153155655 2.347251294604696 0.33999916008950115 2.25270379468167 +chr1 189900000 190800000 ID_0.01_136 0.306214 . 0.005209894937738622 0.2767853552349526 0.004870730457159574 2.7937611137289413 -1.0875691517650177 2.8154610251746375 +chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.04421986858246246 0.7132136329381122 0.044593831085039316 -2.012000648941653 0.3675435235484022 2.008465665217658 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_h5_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_h5_accepted.diff_tad new file mode 100644 index 00000000..43546424 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_h5_accepted.diff_tad @@ -0,0 +1,30 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. +# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: one +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10355136240139871 0.10011542876256041 -0.16282276617118813 1.627875146104104 1.6442942874387492 +chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6877509288862875 0.6148221863583603 -1.1220832111082402 -0.4019090951745341 0.5032021030649116 +chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.15689090160302394 0.4437394229186403 -0.4019090951745341 -1.41560597278901 0.7658939216443722 +chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.08158868260078066 0.08020149262448194 0.2007968317101773 -1.741541630525145 1.7495181593666547 +chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.1404431071415064 0.1747211852405891 -1.741541630525145 -1.4741429475701973 1.3571889362732306 +chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.5595098204829343 0.8201583130184009 -1.4741429475701973 0.5835697449332469 0.22734136168220886 +chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.1852701563028485 0.22846083076168777 -0.32220269785311184 -1.3247015577674193 1.204333170795542 +chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.07324790085975154 0.4613597757566176 0.07965863199293258 -1.7912829494553992 -0.7366096320849878 1.7526702100869194 +chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.06678381915279902 0.12223509534990191 0.060089867957957795 1.8331261092037683 -1.5454597586856647 1.8801336314860881 +chr1 82500000 87500000 ID_0.01_53 -0.8209955 . 0.8764781973172943 0.9275875256501712 0.7914181971243179 -0.1554352488000241 -0.09088052411227253 0.2644694568022624 +chr1 87500000 88300000 ID_0.01_54 -1.9215335 . 0.9275875256501712 0.17591995531921567 0.5261968745640497 -0.09088052411227253 -1.3534248117018666 0.6338221829448881 +chr1 88300000 89100000 ID_0.01_55 -0.899375 . 0.17591995531921567 0.5441416438186202 0.12028482748081724 -1.3534248117018666 -0.6065619716152021 1.5535791852634102 +chr1 91200000 92500000 ID_0.01_58 -0.2421285 . 0.10529359211850775 0.8400491187457132 0.2526674709156823 -1.6197146295549456 -0.2018306508017106 1.1438943103717707 +chr1 92500000 93400000 ID_0.01_59 -0.291361 . 0.8400491187457132 0.36508722454503795 0.05686718419251078 -0.2018306508017106 0.9057140488754497 1.9043302710431667 +chr1 98900000 100200000 ID_0.01_64 -0.196956 . 0.8846023001054634 0.2696554530687709 0.2138766210891413 -0.14513751382654447 -1.1038563573935825 1.2429761533139483 +chr1 107800000 108700000 ID_0.01_72 -0.679396 . 0.7791919868195498 0.8951913091086809 0.3321704734253206 -0.28037216927627806 -0.13173827646305827 0.9697512989744885 +chr1 108700000 109400000 ID_0.01_73 -0.80483 . 0.8951913091086809 0.8719515577799544 0.3338897735741172 -0.13173827646305827 -0.16118009530574245 0.9663086208153022 +chr1 118400000 120200000 ID_0.01_82 -0.13017 . 0.28717850735668105 0.06430179613534404 0.43207256966425345 1.0643316006880144 -1.85008155389624 0.7856499891055168 +chr1 138400000 139100000 ID_0.01_91 -0.588051 . 0.3012258747984379 0.2125315709396568 0.069465337533249 -1.03380812006343 -1.2466344309744959 1.8153812692522773 +chr1 141300000 142600000 ID_0.01_94 -0.7975355 . 0.16353851067801284 0.11405480060793942 0.4276546765554601 -1.3932688364284875 -1.5802273931817894 -0.7932113831045124 +chr1 163200000 164700000 ID_0.01_113 -0.4903745 . 0.31959284973395574 0.38729882591747644 0.1316634847801889 0.9952949159613864 -0.8645263240449885 1.5075744158084308 +chr1 167100000 167500000 ID_0.01_116 -0.7404205 . 0.620218468763515 0.727009731456113 0.14159756069322943 -0.495540744159623 -0.3491060010942235 1.4698678048165976 +chr1 168300000 169100000 ID_0.01_118 -0.381752 . 0.5138307395323829 0.38315317206763244 0.1813057960560731 -0.6528845042364637 -0.872101199089583 1.336745280571738 +chr1 175400000 176400000 ID_0.01_124 0.1718505 . 0.7627529090665852 0.6356274376221928 0.45244680893218303 0.3018677136183763 -0.4738211689117956 0.7513420827912771 +chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.7002651772916688 0.6532815227685426 -0.31503614485233666 -0.3849625294154097 0.449208130642345 +chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10175226570984419 0.09421071964878189 -0.3849625294154097 -1.6364173727117624 1.6735924688116193 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_h5_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_h5_rejected.diff_tad new file mode 100644 index 00000000..4413ec49 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_h5_rejected.diff_tad @@ -0,0 +1,118 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: one +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.3479058102348157 0.0001942482956610518 nan -0.9386590778150411 3.7263815455490827 +chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.7619708385959597 0.011174626122333891 -0.9386590778150411 -0.30289374467773583 2.5371900826446283 +chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.8706579826550646 4.668547072331386e-06 -0.30289374467773583 -0.16282276617118813 4.5791565418309395 +chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.39564035674322084 0.006197912102328514 1.627875146104104 -0.8494330724907115 2.737122965561303 +chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.030328896271663634 5.069275897797787e-07 -0.8494330724907115 -2.1657683076952483 5.023672092995246 +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.07605786424686575 0.0023999817017426378 -2.1657683076952483 -1.774031958289595 3.0356746656834117 +chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.4982863585572014 1.8146100883843892e-06 -1.774031958289595 0.67718850743882 4.773045240138744 +chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.8237750360973404 0.002562121461829293 0.67718850743882 -0.2226922466874271 3.0159066257881317 +chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.007089417650089524 0.00020602838341698515 -0.2226922466874271 -2.692614553612967 3.7115077195445525 +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.030230438882868516 0.03561337274424189 -2.692614553612967 2.167057908282934 2.10131444292845 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.011587414142526327 6.125855825029621e-06 2.167057908282934 -2.5244662175837944 4.521998277761523 +chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.775168622700411 0.012760792164069699 -2.5244662175837944 -0.2856207321579987 2.4903762617335548 +chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.18141506612462333 1.5995491571971796e-05 -0.2856207321579987 -1.3364107145509396 4.314513284521457 +chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0006158715296021736 0.06748479713761105 -1.3364107145509396 -3.4245266094056284 1.8284316353792964 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 5.081008401228345e-05 0.002710122418266765 -3.4245266094056284 4.05186913357941 2.99883701418205 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004986133195426291 4.483351940271164e-11 4.05186913357941 2.807928267339102 6.587154663693872 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0016376675728931981 2.9941210791658745e-07 2.807928267339102 -3.14911317809443 5.123816675539011 +chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.2618270615259555 0.05430086444564102 -3.14911317809443 -1.1220832111082402 1.9244287435607725 +chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 0.06092217809404407 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1.9824295455773762 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_all_h5_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_all_h5_accepted.diff_tad deleted file mode 100644 index d79fe1de..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_all_h5_accepted.diff_tad +++ /dev/null @@ -1,30 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: one -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10355136240139871 0.10011542876256041 -chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6877509288862875 0.6148221863583603 -chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.15689090160302394 0.4437394229186403 -chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.08158868260078066 0.08020149262448194 -chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.1404431071415064 0.1747211852405891 -chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.5595098204829343 0.8201583130184009 -chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.1852701563028485 0.22846083076168777 -chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.07324790085975154 0.4613597757566176 0.07965863199293258 -chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.06678381915279902 0.12223509534990191 0.060089867957957795 -chr1 82500000 87500000 ID_0.01_53 -0.8209955 . 0.8764781973172943 0.9275875256501712 0.7914181971243179 -chr1 87500000 88300000 ID_0.01_54 -1.9215335 . 0.9275875256501712 0.17591995531921567 0.5261968745640497 -chr1 88300000 89100000 ID_0.01_55 -0.899375 . 0.17591995531921567 0.5441416438186202 0.12028482748081724 -chr1 91200000 92500000 ID_0.01_58 -0.2421285 . 0.10529359211850775 0.8400491187457132 0.2526674709156823 -chr1 92500000 93400000 ID_0.01_59 -0.291361 . 0.8400491187457132 0.36508722454503795 0.05686718419251078 -chr1 98900000 100200000 ID_0.01_64 -0.196956 . 0.8846023001054634 0.2696554530687709 0.2138766210891413 -chr1 107800000 108700000 ID_0.01_72 -0.679396 . 0.7791919868195498 0.8951913091086809 0.3321704734253206 -chr1 108700000 109400000 ID_0.01_73 -0.80483 . 0.8951913091086809 0.8719515577799544 0.3338897735741172 -chr1 118400000 120200000 ID_0.01_82 -0.13017 . 0.28717850735668105 0.06430179613534404 0.43207256966425345 -chr1 138400000 139100000 ID_0.01_91 -0.588051 . 0.3012258747984379 0.2125315709396568 0.069465337533249 -chr1 141300000 142600000 ID_0.01_94 -0.7975355 . 0.16353851067801284 0.11405480060793942 0.4276546765554601 -chr1 163200000 164700000 ID_0.01_113 -0.4903745 . 0.31959284973395574 0.38729882591747644 0.1316634847801889 -chr1 167100000 167500000 ID_0.01_116 -0.7404205 . 0.620218468763515 0.727009731456113 0.14159756069322943 -chr1 168300000 169100000 ID_0.01_118 -0.381752 . 0.5138307395323829 0.38315317206763244 0.1813057960560731 -chr1 175400000 176400000 ID_0.01_124 0.1718505 . 0.7627529090665852 0.6356274376221928 0.45244680893218303 -chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.7002651772916688 0.6532815227685426 -chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10175226570984419 0.09421071964878189 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_all_h5_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_all_h5_rejected.diff_tad deleted file mode 100644 index 5f45d2c9..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_all_h5_rejected.diff_tad +++ /dev/null @@ -1,118 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: one -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.3479058102348157 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.7619708385959597 0.011174626122333891 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.8706579826550646 4.668547072331386e-06 -chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.39564035674322084 0.006197912102328514 -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.030328896271663634 5.069275897797787e-07 -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.07605786424686575 0.0023999817017426378 -chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.4982863585572014 1.8146100883843892e-06 -chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.8237750360973404 0.002562121461829293 -chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.007089417650089524 0.00020602838341698515 -chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.030230438882868516 0.03561337274424189 -chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.011587414142526327 6.125855825029621e-06 -chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.775168622700411 0.012760792164069699 -chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.18141506612462333 1.5995491571971796e-05 -chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0006158715296021736 0.06748479713761105 -chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 5.081008401228345e-05 0.002710122418266765 -chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004986133195426291 4.483351940271164e-11 -chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0016376675728931981 2.9941210791658745e-07 -chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.2618270615259555 0.05430086444564102 -chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 0.06092217809404407 0.011491613276272431 -chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.06092217809404407 0.629775934868511 0.0029466965398313415 -chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.004589686716285295 0.03802402407151029 -chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.004589686716285295 0.840857440405701 2.176332048622399e-05 -chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 2.942555439185868e-05 0.012025540121556799 -chr1 49100000 50200000 ID_0.01_30 0.046019 . 2.942555439185868e-05 0.0008092768618695985 0.29644970367180923 -chr1 50200000 51500000 ID_0.01_31 0.1636485 . 0.0008092768618695985 0.7472991407953615 0.024559156167662435 -chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 0.1852701563028485 0.9977418713186132 0.020176549895482607 -chr1 53100000 54700000 ID_0.01_34 -0.3917385 . 0.9977418713186132 0.07324790085975154 0.01347363335675291 -chr1 57400000 58500000 ID_0.01_36 -0.8692615 . 0.4613597757566176 0.7255531686935289 0.0022224806797976654 -chr1 58500000 59800000 ID_0.01_37 -0.793426 . 0.7255531686935289 0.003216073606046391 0.1865328113880741 -chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.008928314591401266 0.00022924443696242214 -chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 8.981513689059817e-07 6.115423785857918e-07 -chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 8.981513689059817e-07 0.6251410835835239 0.0006863754125470629 -chr1 64600000 65300000 ID_0.01_41 -0.6812605 . 0.6251410835835239 0.2769473036693756 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ID_0.01_78 -0.4525885 . 0.3614318988630364 0.01144695116513853 0.054180530313661726 -chr1 115400000 116200000 ID_0.01_79 0.0065005 . 0.01144695116513853 0.0037226721775892673 0.0624141777690027 -chr1 116200000 117100000 ID_0.01_80 -0.0989215 . 0.0037226721775892673 0.031660125091572386 0.1609545309684186 -chr1 117100000 118400000 ID_0.01_81 -0.1478965 . 0.031660125091572386 0.28717850735668105 0.017173407823036953 -chr1 120200000 123500000 ID_0.01_83 -0.6265325 . 0.06430179613534404 0.00014045783392288526 0.19307511054649118 -chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.047852690134436014 7.963547815901498e-06 -chr1 126000000 127300000 ID_0.01_85 -0.1791345 . 0.047852690134436014 0.6151989343062929 0.2535921500196371 -chr1 127300000 129400000 ID_0.01_86 -0.702347 . 0.6151989343062929 0.03017913679184316 0.02644757894272022 -chr1 129400000 130700000 ID_0.01_87 -0.642071 . 0.03017913679184316 0.3313792760154809 0.0019284287143192423 -chr1 130700000 132300000 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a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_right_inter-TAD_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_right_inter-TAD_accepted.diff_tad deleted file mode 100644 index 81b24e3a..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_right_inter-TAD_accepted.diff_tad +++ /dev/null @@ -1,37 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. -# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: one -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.27686582704511986 0.05430086444564102 -chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6700147806330939 0.6148221863583603 -chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.13322270222894567 0.4437394229186403 -chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.056864972978018666 0.08020149262448194 -chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.2104763476986481 0.1747211852405891 -chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.602727841142918 0.8201583130184009 -chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.13176628976737523 0.22846083076168777 -chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.07324790085975154 0.5587485506872516 0.07965863199293258 -chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.06678381915279902 0.5145237050757046 0.060089867957957795 -chr1 82500000 87500000 ID_0.01_53 -0.8209955 . 0.8764781973172943 0.9108556321417692 0.7914181971243179 -chr1 87500000 88300000 ID_0.01_54 -1.9215335 . 0.9275875256501712 0.2492381416564282 0.5261968745640497 -chr1 88300000 89100000 ID_0.01_55 -0.899375 . 0.17591995531921567 0.43251092514368816 0.12028482748081724 -chr1 91200000 92500000 ID_0.01_58 -0.2421285 . 0.10529359211850775 0.8142018243105789 0.2526674709156823 -chr1 92500000 93400000 ID_0.01_59 -0.291361 . 0.8400491187457132 0.5095291832844049 0.05686718419251078 -chr1 98900000 100200000 ID_0.01_64 -0.196956 . 0.8846023001054634 0.23907870581962454 0.2138766210891413 -chr1 101600000 102400000 ID_0.01_66 -0.1597755 . 0.01843186740506446 0.5481976319769135 0.08450223158802864 -chr1 103300000 104300000 ID_0.01_68 -0.3313575 . 0.0059711068230264164 0.5041281160378562 0.09087020993163282 -chr1 107800000 108700000 ID_0.01_72 -0.679396 . 0.7791919868195498 0.9094974273085202 0.3321704734253206 -chr1 108700000 109400000 ID_0.01_73 -0.80483 . 0.8951913091086809 0.7419760360373884 0.3338897735741172 -chr1 116200000 117100000 ID_0.01_80 -0.0989215 . 0.0037226721775892673 0.06295709440414389 0.1609545309684186 -chr1 118400000 120200000 ID_0.01_82 -0.13017 . 0.28717850735668105 0.06981354638050603 0.43207256966425345 -chr1 126000000 127300000 ID_0.01_85 -0.1791345 . 0.047852690134436014 0.5860265670331393 0.2535921500196371 -chr1 138400000 139100000 ID_0.01_91 -0.588051 . 0.3012258747984379 0.14572455419105776 0.069465337533249 -chr1 141300000 142600000 ID_0.01_94 -0.7975355 . 0.16353851067801284 0.10023814088277018 0.4276546765554601 -chr1 155300000 156800000 ID_0.01_106 -0.8541315 . 0.0018192914932849032 0.36203645571210885 0.7113102073721501 -chr1 163200000 164700000 ID_0.01_113 -0.4903745 . 0.31959284973395574 0.30724523933881387 0.1316634847801889 -chr1 167100000 167500000 ID_0.01_116 -0.7404205 . 0.620218468763515 0.7431107046158174 0.14159756069322943 -chr1 168300000 169100000 ID_0.01_118 -0.381752 . 0.5138307395323829 0.3655258965522935 0.1813057960560731 -chr1 175400000 176400000 ID_0.01_124 0.1718505 . 0.7627529090665852 0.5766236917735681 0.45244680893218303 -chr1 181400000 182800000 ID_0.01_129 -0.9773875 . 0.0012227567577424718 0.1837862101652874 0.1900077841533132 -chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.6381872465439603 0.6532815227685426 -chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10662063212498882 0.09421071964878189 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_right_inter-TAD_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_right_inter-TAD_rejected.diff_tad deleted file mode 100644 index 015f0c1d..00000000 --- a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_reject_right_inter-TAD_rejected.diff_tad +++ /dev/null @@ -1,111 +0,0 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev -# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. -# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: one -# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD -chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 -chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.2022260523997077 0.006197912102328514 -chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.5322636852613494 1.8146100883843892e-06 -chr1 14900000 17100000 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0.0017016130383748175 0.07029573025202325 -chr1 182800000 183800000 ID_0.01_130 -0.756317 . 0.22500121196367384 0.7224634953522755 0.012606364228184988 -chr1 186600000 187300000 ID_0.01_133 -0.640236 . 0.10175226570984419 0.3130816687642489 0.027372249868613835 -chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.022646678654874207 7.763551868301071e-05 -chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.01171597151998054 0.00010479145543859941 -chr1 189900000 190800000 ID_0.01_136 0.306214 . 0.005209894937738622 0.2767853552349526 0.004870730457159574 -chr1 190800000 191500000 ID_0.01_137 -0.191605 . 0.4221899834667334 0.920842420803457 0.0015871064433715795 -chr1 191500000 192700000 ID_0.01_138 -0.313625 . 0.9216624111662307 0.05479964256414248 0.003524165806862319 -chr1 192700000 193700000 ID_0.01_139 -0.7580275 . 0.10501293994348296 0.3756498286712808 0.044593831085039316 -chr1 193700000 195200000 ID_0.01_140 -0.457743 . 0.9088908933305142 nan 0.047431185522004114 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_right_inter-TAD_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_right_inter-TAD_accepted.diff_tad new file mode 100644 index 00000000..cf66c403 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_right_inter-TAD_accepted.diff_tad @@ -0,0 +1,37 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. +# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: one +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.8706579826550646 0.10845845730738995 0.10011542876256041 -0.16282276617118813 1.6051606385162123 1.6442942874387492 +chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.0016376675728931981 0.27686582704511986 0.05430086444564102 -3.14911317809443 -1.0873869704262455 1.9244287435607725 +chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.2618270615259555 0.6700147806330939 0.6148221863583603 -1.1220832111082402 -0.4261277223514882 0.5032021030649116 +chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.6877509288862875 0.13322270222894567 0.4437394229186403 -0.4019090951745341 -1.501513869069336 0.7658939216443722 +chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.840857440405701 0.056864972978018666 0.08020149262448194 0.2007968317101773 -1.9043472603872424 1.7495181593666547 +chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.08158868260078066 0.2104763476986481 0.1747211852405891 -1.741541630525145 -1.2522566823724743 1.3571889362732306 +chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.1404431071415064 0.602727841142918 0.8201583130184009 -1.4741429475701973 0.5204817549965299 0.22734136168220886 +chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.7472991407953615 0.13176628976737523 0.22846083076168777 -0.32220269785311184 -1.5071731142971523 1.204333170795542 +chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.07324790085975154 0.5587485506872516 0.07965863199293258 -1.7912829494553992 -0.58470134327905 1.7526702100869194 +chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.06678381915279902 0.5145237050757046 0.060089867957957795 1.8331261092037683 -0.651810069314388 1.8801336314860881 +chr1 82500000 87500000 ID_0.01_53 -0.8209955 . 0.8764781973172943 0.9108556321417692 0.7914181971243179 -0.1554352488000241 0.11195935721526085 0.2644694568022624 +chr1 87500000 88300000 ID_0.01_54 -1.9215335 . 0.9275875256501712 0.2492381416564282 0.5261968745640497 -0.09088052411227253 -1.1522018402734988 0.6338221829448881 +chr1 88300000 89100000 ID_0.01_55 -0.899375 . 0.17591995531921567 0.43251092514368816 0.12028482748081724 -1.3534248117018666 -0.7849021777084254 1.5535791852634102 +chr1 91200000 92500000 ID_0.01_58 -0.2421285 . 0.10529359211850775 0.8142018243105789 0.2526674709156823 -1.6197146295549456 -0.23500890147331419 1.1438943103717707 +chr1 92500000 93400000 ID_0.01_59 -0.291361 . 0.8400491187457132 0.5095291832844049 0.05686718419251078 -0.2018306508017106 0.6595709784572648 1.9043302710431667 +chr1 98900000 100200000 ID_0.01_64 -0.196956 . 0.8846023001054634 0.23907870581962454 0.2138766210891413 -0.14513751382654447 -1.1772926843972238 1.2429761533139483 +chr1 101600000 102400000 ID_0.01_66 -0.1597755 . 0.01843186740506446 0.5481976319769135 0.08450223158802864 2.356826277441937 0.6004631206846309 1.7251400768875904 +chr1 103300000 104300000 ID_0.01_68 -0.3313575 . 0.0059711068230264164 0.5041281160378562 0.09087020993163282 2.7493638232092166 0.6680085793989338 1.6908251098912643 +chr1 107800000 108700000 ID_0.01_72 -0.679396 . 0.7791919868195498 0.9094974273085202 0.3321704734253206 -0.28037216927627806 -0.11367248196414026 0.9697512989744885 +chr1 108700000 109400000 ID_0.01_73 -0.80483 . 0.8951913091086809 0.7419760360373884 0.3338897735741172 -0.13173827646305827 -0.3292376912560182 0.9663086208153022 +chr1 116200000 117100000 ID_0.01_80 -0.0989215 . 0.0037226721775892673 0.06295709440414389 0.1609545309684186 2.9007529739865743 1.859494385071822 1.4018684581030172 +chr1 118400000 120200000 ID_0.01_82 -0.13017 . 0.28717850735668105 0.06981354638050603 0.43207256966425345 1.0643316006880144 -1.8131185001213783 0.7856499891055168 +chr1 126000000 127300000 ID_0.01_85 -0.1791345 . 0.047852690134436014 0.5860265670331393 0.2535921500196371 1.9786742837141795 0.5446030348418471 1.141667752103407 +chr1 138400000 139100000 ID_0.01_91 -0.588051 . 0.3012258747984379 0.14572455419105776 0.069465337533249 -1.03380812006343 -1.4548003033756296 1.8153812692522773 +chr1 141300000 142600000 ID_0.01_94 -0.7975355 . 0.16353851067801284 0.10023814088277018 0.4276546765554601 -1.3932688364284875 -1.6437002181636735 -0.7932113831045124 +chr1 155300000 156800000 ID_0.01_106 -0.8541315 . 0.0018192914932849032 0.36203645571210885 0.7113102073721501 -3.1182488066126774 -0.9114915123257828 0.3700970133542697 +chr1 163200000 164700000 ID_0.01_113 -0.4903745 . 0.31959284973395574 0.30724523933881387 0.1316634847801889 0.9952949159613864 -1.0210194171597968 1.5075744158084308 +chr1 167100000 167500000 ID_0.01_116 -0.7404205 . 0.620218468763515 0.7431107046158174 0.14159756069322943 -0.495540744159623 -0.32773676267223106 1.4698678048165976 +chr1 168300000 169100000 ID_0.01_118 -0.381752 . 0.5138307395323829 0.3655258965522935 0.1813057960560731 -0.6528845042364637 -0.9048857886996416 1.336745280571738 +chr1 175400000 176400000 ID_0.01_124 0.1718505 . 0.7627529090665852 0.5766236917735681 0.45244680893218303 0.3018677136183763 -0.5583232200655286 0.7513420827912771 +chr1 181400000 182800000 ID_0.01_129 -0.9773875 . 0.0012227567577424718 0.1837862101652874 0.1900077841533132 -3.2335178940373406 -1.3291872205824826 1.310556084991557 +chr1 183800000 185100000 ID_0.01_131 -0.2936195 . 0.7527342104844837 0.6381872465439603 0.6532815227685426 -0.31503614485233666 -0.47023483816766326 0.449208130642345 +chr1 185100000 186600000 ID_0.01_132 -0.183922 . 0.7002651772916688 0.10662063212498882 0.09421071964878189 -0.3849625294154097 -1.6135704435900085 1.6735924688116193 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_right_inter-TAD_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_right_inter-TAD_rejected.diff_tad new file mode 100644 index 00000000..b414cb42 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_one_right_inter-TAD_rejected.diff_tad @@ -0,0 +1,111 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: one +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.42772134044376386 0.0001942482956610518 nan -0.7930969487289069 3.7263815455490827 +chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.3479058102348157 0.651801360704674 0.011174626122333891 -0.9386590778150411 -0.45126112355691883 2.5371900826446283 +chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7619708385959597 0.9408966423531526 4.668547072331386e-06 -0.30289374467773583 0.07414294720451348 4.5791565418309395 +chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.10355136240139871 0.2022260523997077 0.006197912102328514 1.627875146104104 -1.2752350682626996 2.737122965561303 +chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -0.8494330724907115 -1.9655771567720404 5.023672092995246 +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -2.1657683076952483 -1.9765043757997804 3.0356746656834117 +chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.07605786424686575 0.5322636852613494 1.8146100883843892e-06 -1.774031958289595 0.624554202910739 4.773045240138744 +chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.4982863585572014 0.692745144471043 0.002562121461829293 0.67718850743882 -0.39513244622709864 3.0159066257881317 +chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.011911117420279341 0.00020602838341698515 -0.2226922466874271 -2.514766701978045 3.7115077195445525 +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.007089417650089524 0.07553560212368073 0.03561337274424189 -2.692614553612967 1.7771984030211898 2.10131444292845 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 2.167057908282934 -2.1628710201312877 4.521998277761523 +chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.011587414142526327 0.6730908477968309 0.012760792164069699 -2.5244662175837944 -0.42190981210011114 2.4903762617335548 +chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.15658860942159403 1.5995491571971796e-05 -0.2856207321579987 -1.416638625821259 4.314513284521457 +chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.18141506612462333 0.0005012323510345417 0.06748479713761105 -1.3364107145509396 -3.4800969585043267 1.8284316353792964 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -3.4245266094056284 3.902499692881189 2.99883701418205 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 4.05186913357941 2.818330247918638 6.587154663693872 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 2.807928267339102 -2.93193644190598 5.123816675539011 +chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.15689090160302394 0.0751792941984631 0.011491613276272431 -1.41560597278901 -1.7793689460462792 2.527382919088952 +chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.06092217809404407 0.7553056597956419 0.0029466965398313415 -1.8740598377871773 0.3116511459654997 2.9732444649577383 +chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.0032786219354516257 0.03802402407151029 0.4820422473187418 -2.9403306275639056 2.074595666547732 +chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.004589686716285295 0.6973127707358744 2.176332048622399e-05 -2.834504112745991 0.3889504909464499 4.245987045730281 +chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 5.1315106976375586e-05 0.012025540121556799 0.5835697449332469 4.049555046000217 2.511393982268917 +chr1 49100000 50200000 ID_0.01_30 0.046019 . 2.942555439185868e-05 0.002614171734234889 0.29644970367180923 4.1778670647745235 3.0098030142733485 1.044077134986226 +chr1 50200000 51500000 ID_0.01_31 0.1636485 . 0.0008092768618695985 0.8509905551285051 0.024559156167662435 3.349602227967295 -0.18785469932274496 2.2482672114800883 +chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 0.1852701563028485 0.9645664795137245 0.020176549895482607 -1.3247015577674193 -0.04442393950935331 2.323048448493291 +chr1 53100000 54700000 ID_0.01_34 -0.3917385 . 0.9977418713186132 0.05733282574350129 0.01347363335675291 0.0028301483783805185 -1.90076480636879 2.4709986335641756 +chr1 57400000 58500000 ID_0.01_36 -0.8692615 . 0.4613597757566176 0.602568507215703 0.0022224806797976654 -0.7366096320849878 0.5207104304286511 3.0587695133149677 +chr1 58500000 59800000 ID_0.01_37 -0.793426 . 0.7255531686935289 0.002317254091988157 0.1865328113880741 0.35104689304844006 -3.0462366030597323 1.3209056927066725 +chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -2.9462932286120593 -2.7743818055769554 3.684397294574574 +chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -2.614786881491451 -4.957488355561393 4.987535965432151 +chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 8.981513689059817e-07 0.7034477559259763 0.0006863754125470629 -4.912733900814666 -0.380670507157995 3.394964334454319 +chr1 64600000 65300000 ID_0.01_41 -0.6812605 . 0.6251410835835239 0.19160573772369172 0.037684124607603085 -0.48857716389553185 -1.3058436350822609 2.078274055797617 +chr1 65300000 67100000 ID_0.01_42 -1.5001585 . 0.2769473036693756 0.1102978772132991 0.0001487713535869077 -1.0872025510356067 -1.596855697089364 3.7931114324442627 +chr1 67100000 69200000 ID_0.01_43 -1.2359205 . 0.21018617334750922 0.5842300956584897 5.323176929219475e-06 -1.2530536752875465 0.5472163632097017 4.551630476787783 +chr1 69200000 72300000 ID_0.01_44 -0.879535 . 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file mode 100644 index 00000000..90935932 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/mode_right_inter-TAD_rejected.diff_tad @@ -0,0 +1,32 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: right-inter-TAD and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.39564035674322084 0.04934747494654432 5.069275897797787e-07 -0.8494330724907115 -1.9655771567720404 5.023672092995246 +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.030328896271663634 0.048097680638217614 0.0023999817017426378 -2.1657683076952483 -1.9765043757997804 3.0356746656834117 +chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.8237750360973404 0.011911117420279341 0.00020602838341698515 -0.2226922466874271 -2.514766701978045 3.7115077195445525 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.030230438882868516 0.03055110127354906 6.125855825029621e-06 2.167057908282934 -2.1628710201312877 4.521998277761523 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0006158715296021736 9.520435907095872e-05 0.002710122418266765 -3.4245266094056284 3.902499692881189 2.99883701418205 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.081008401228345e-05 0.004827412946186395 4.483351940271164e-11 4.05186913357941 2.818330247918638 6.587154663693872 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 0.004986133195426291 0.0033685567851754103 2.9941210791658745e-07 2.807928267339102 -2.93193644190598 5.123816675539011 +chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.629775934868511 0.0032786219354516257 0.03802402407151029 0.4820422473187418 -2.9403306275639056 2.074595666547732 +chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5595098204829343 5.1315106976375586e-05 0.012025540121556799 0.5835697449332469 4.049555046000217 2.511393982268917 +chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.003216073606046391 0.0055306726905717035 0.00022924443696242214 -2.9462932286120593 -2.7743818055769554 3.684397294574574 +chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.008928314591401266 7.14103207747527e-07 6.115423785857918e-07 -2.614786881491451 -4.957488355561393 4.987535965432151 +chr1 77900000 78500000 ID_0.01_49 -0.809386 . 0.32099041607424383 0.030960123115897433 0.02158985927361434 0.9924246566162215 -2.157584856684229 2.297507086558252 +chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.000621697204710699 0.00012207984276411976 0.000289635147178882 -3.421967604643488 3.841911528133773 3.624398133501732 +chr1 100200000 101600000 ID_0.01_65 -0.480589 . 0.2696554530687709 0.03750438635138998 0.04217312747454267 -1.1038563573935825 2.0802306050397386 2.0318076991127607 +chr1 109400000 110800000 ID_0.01_74 -0.327192 . 0.8719515577799544 4.067775971974873e-05 0.007150334840595598 -0.16118009530574245 4.103595971213147 2.689760345863624 +chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.00014045783392288526 0.0396948681031242 7.963547815901498e-06 -3.8073606560359816 2.0569101641013843 4.466161567031553 +chr1 127300000 129400000 ID_0.01_86 -0.702347 . 0.6151989343062929 0.013030884814290544 0.02644757894272022 0.5026662611685505 -2.482924103442399 2.219575764343504 +chr1 130700000 132300000 ID_0.01_88 -0.7337655 . 0.3313792760154809 0.013463601572888518 2.3322425005292974e-05 0.9713394377392744 -2.4712649795012656 4.230450030045437 +chr1 142600000 143800000 ID_0.01_95 -0.560399 . 0.11405480060793942 0.02498943527646134 0.007235404471539694 -1.5802273931817894 2.2415660029339977 2.685810811083112 +chr1 144700000 145600000 ID_0.01_97 -0.021447 . 0.06420778059889237 0.005915933786202155 0.01747092284081774 1.8507343443295508 -2.7524048347673724 2.376644375206907 +chr1 145600000 147800000 ID_0.01_98 -0.738409 . 0.011704014199319273 0.0024232283144502514 0.005179707699348202 -2.5209450069288897 3.0327667392849023 2.7956399072164286 +chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.010074561112534944 0.013340569405590395 2.0311415510577494e-07 2.573259593232858 2.4745458547284858 5.19646469403844 +chr1 154400000 155300000 ID_0.01_105 -0.4089925 . 0.08290762581038606 0.004488898188060745 0.04717516917172698 -1.7340589403721394 -2.841591405250457 1.9847241611135904 +chr1 161100000 162100000 ID_0.01_111 -0.601909 . 0.39963730606682835 0.00048013180818610735 0.0008523015251096703 -0.8422691660810344 -3.491602719703203 3.3352258309271323 +chr1 176400000 177800000 ID_0.01_125 0.0112955 . 0.6356274376221928 0.021734997211659477 6.325784122034014e-05 -0.4738211689117956 2.2949673200287624 4.0003164308551815 +chr1 178700000 179700000 ID_0.01_127 -0.2865335 . 0.3923180055901787 0.04550716311782837 2.6383293815311617e-05 0.85542121034293 -1.9999361117132166 4.2026288858569 +chr1 187300000 188600000 ID_0.01_134 -1.2024035 . 0.49143870397462885 0.022646678654874207 7.763551868301071e-05 -0.6880223548042432 -2.279343086591048 3.9515842867781994 +chr1 188600000 189900000 ID_0.01_135 -0.9273355 . 0.05908440312646483 0.01171597151998054 0.00010479145543859941 -1.8875647720051942 2.5205856687431933 3.8792211430563843 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/multichromosome_accepted.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/multichromosome_accepted.diff_tad new file mode 100644 index 00000000..6bd98e39 --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/multichromosome_accepted.diff_tad @@ -0,0 +1,211 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. +# Accepted regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 4400000 6200000 ID_0.01_1 -0.5630275 . nan 0.8268172476121132 1.1058975157219717e-05 nan -0.21878536516659502 4.395359153793844 +chr1 6200000 7300000 ID_0.01_2 -0.235798 . 0.7240996969343069 0.8243359234081221 0.0024356665657895523 -0.35298498529620814 0.2219716878036736 3.0312213039485765 +chr1 7300000 9500000 ID_0.01_3 -0.44334 . 0.7008731541371999 0.650310296312886 8.408429587003463e-08 0.38414206674794393 0.4533311629075967 5.358137379535459 +chr1 9500000 10100000 ID_0.01_4 -1.021538 . 0.775381473841675 0.04169142522984199 0.03824108000678763 0.2853428674485178 2.0365872132952734 2.0722612937584235 +chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 0.03886635487751637 0.554164823075991 0.0011349170069066487 2.0655990430354363 -0.5915308021170902 3.2547513054926425 +chr1 11600000 12900000 ID_0.01_6 -0.607587 . 0.8775507172147219 0.14300670825076836 3.723342500468501e-08 -0.1540748513296214 -1.4646856264851067 5.50349539982759 +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 0.10043295080776385 0.15901049598704675 0.0005125545788190994 -1.6427583014752256 -1.40840730970164 3.4741080553896504 +chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 0.22216806375823106 0.21229731104314642 1.083164714961291e-07 -1.2207833387937184 1.2472732808374114 5.312188506220233 +chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 0.19688386332905916 0.8248789609562149 0.0002659845110845362 1.2904805423981558 0.22127416988717524 3.6463568787355323 +chr1 17100000 18100000 ID_0.01_10 -0.230354 . 0.6773060416506496 0.03474017021549905 3.5997957192554745e-05 0.4161420771431718 -2.1113740910805427 4.1317706081302426 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 0.004933893894531303 0.09589931523564295 3.077331912182654e-07 2.811318367502185 -1.6650673726407532 5.118648311043724 +chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 0.04751915245141374 0.904050911399648 0.005175536195069642 -1.981643522124931 0.12054566060003176 2.7959003109619225 +chr1 21300000 22600000 ID_0.01_14 -0.859866 . 0.775168622700411 0.3945187634973626 1.476608408563463e-06 0.2856207321579987 -0.8514511947941247 4.814375615769073 +chr1 22600000 24300000 ID_0.01_15 -0.281294 . 0.4517230355955235 0.006600245133619858 0.01847468692656644 -0.7525455709410558 -2.716368288560635 2.3559644243362983 +chr1 33700000 34600000 ID_0.01_19 -1.33809 . 0.013383537582534024 0.6029863369698101 0.020907568598504074 -2.473397003078547 -0.5201108206732784 2.309649466814887 +chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 0.6067051125745504 0.7634577197763519 0.2396121095619237 -0.5147823611215394 0.30094331508019323 1.1759568747188343 +chr1 36400000 38100000 ID_0.01_21 -0.925006 . 0.7234142195281222 0.3494027566512913 0.17408908021704805 0.35389947629703 -0.9357483763091241 1.3591815058254761 +chr1 38100000 39000000 ID_0.01_22 -0.911804 . 0.4174483708095371 0.15435903209148993 0.0037812717498604915 -0.8108559999316329 -1.4243021268805818 2.8958549152450614 +chr1 39000000 39600000 ID_0.01_23 -0.474157 . 0.14703280928528345 0.5148715751262816 0.0011347156298055663 -1.450092202353357 0.6512709845176468 3.254801705957524 +chr1 39600000 40900000 ID_0.01_24 -0.483398 . 0.40888817047264736 0.020033161970560896 0.01046765700832177 0.8258517913622562 -2.3257261979627035 2.5599853690509846 +chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 0.029768372427647013 0.3232299806965241 5.661896787269534e-07 -2.173158733886599 0.9878421098318466 5.002406761573843 +chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 0.4238932930845717 0.31855216824530097 0.027231089546047107 0.7996850565201828 0.9974375586525043 2.2081891626495445 +chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 0.2593674551155798 0.8153952319211535 1.9632202705034285e-11 1.1278874489759811 0.23347158484910538 6.708732611216639 +chr1 45900000 47300000 ID_0.01_28 -0.656308 . 0.8624378083654324 0.6022635464423499 0.8654886280422122 0.17327177503085503 0.5211481849004947 -0.16939160282203797 +chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 0.5435679928715043 2.874689743232649e-06 0.0014020864555605958 0.6074263697261154 4.679575866063282 3.1942211896806025 +chr1 49100000 50200000 ID_0.01_30 0.046019 . 1.462991983438978e-06 0.0003647343839865502 0.10118859177318387 4.816225483456969 3.564367683212841 1.6391184573002755 +chr1 50200000 51500000 ID_0.01_31 0.1636485 . 9.279280726368033e-05 0.8454371355833938 0.0046151086387062525 3.908703389604525 0.19494355590096174 2.8327387569255187 +chr1 51500000 52200000 ID_0.01_32 -0.692286 . 0.9271311292713041 0.258929458622544 0.09999946543494605 0.09145491423778285 -1.1289250354194886 1.6448562185201652 +chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 0.35517009321681603 0.6540548808159248 0.007112713863390754 -0.9246075329536868 0.4481362318925992 2.691520444649401 +chr1 53100000 54700000 ID_0.01_34 -0.3917385 . 0.6274135919991417 0.2576928729588498 0.002042590170183633 0.4853704468922589 -1.13186101022841 3.083968797499583 +chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 0.3204559662272003 0.8607571669174674 0.013227891559998137 -0.9935213193022031 0.175410402983715 2.477574161123331 +chr1 57400000 58500000 ID_0.01_36 -0.8692615 . 0.9643398880083548 0.3531102128603071 0.0003919365784997684 0.04470821200905314 0.9285733991544985 3.5454545454545454 +chr1 58500000 59800000 ID_0.01_37 -0.793426 . 0.4311797824095879 0.011724455692841874 0.08194708998218529 0.7871743976503717 -2.5203309019134497 1.7394986471590186 +chr1 61100000 63200000 ID_0.01_39 -1.068387 . 0.06195469652396533 2.320703146298079e-05 9.54955812467016e-09 -1.866619828980462 -4.231565573647178 5.738541115971054 +chr1 63200000 64600000 ID_0.01_40 -1.4349735 . 3.1998179426018816e-05 0.9090783386043256 0.0001402398162148534 -4.15875863172037 0.11420115214739851 3.8077449244890746 +chr1 64600000 65300000 ID_0.01_41 -0.6812605 . 0.9799078880701289 0.4395451557789324 0.014375335496283982 0.02518438989152226 -0.7729615172332633 2.4477449990505264 +chr1 65300000 67100000 ID_0.01_42 -1.5001585 . 0.6052887178857895 0.5219186024777596 8.674627087508455e-06 -0.5168101156751135 -0.6403907384871393 4.44781975669886 +chr1 67100000 69200000 ID_0.01_43 -1.2359205 . 0.7906503578668709 0.11399561731585331 1.2129521659938234e-07 -0.26546618266990285 1.5804859703682583 5.291533122461273 +chr1 69200000 72300000 ID_0.01_44 -0.879535 . 0.112216850948871 0.010067587160355804 4.0304504067763294e-08 1.5883073736156892 2.573499227584165 5.48951230471138 +chr1 72300000 73900000 ID_0.01_45 -1.502847 . 0.005951077057798234 0.8941205362134248 0.01379204254338282 2.750464879122085 -0.13309210839403735 2.4626345182668112 +chr1 73900000 74500000 ID_0.01_46 -1.0827955 . 0.3313332753869537 0.8707485028548523 0.018581679780480545 -0.9714318483167035 0.16270780313525818 2.3538185347582092 +chr1 74500000 75600000 ID_0.01_47 -0.513854 . 0.9238588458891327 0.00031550435807928685 0.21680145643800885 0.09557408782506306 -3.6022256073047467 1.2350780532598715 +chr1 75600000 77900000 ID_0.01_48 -1.3889375 . 0.0003247535612809871 0.18454259326370037 3.237860112254183e-12 -3.594709638187899 1.3268974946039584 6.966993331914582 +chr1 77900000 78500000 ID_0.01_49 -0.809386 . 0.118872299825002 0.09332337155183495 0.007352875386775665 1.5595244603969194 -1.6781215551988444 2.680424934317961 +chr1 78500000 79800000 ID_0.01_50 -0.9250035 . 0.1239797088446756 0.1533952338122478 7.2966959465800866e-06 -1.5382818774730436 1.4276409387590285 4.4848449920512685 +chr1 79800000 81300000 ID_0.01_51 -0.4445345 . 0.11028839209007249 0.42422034349259397 0.003437760032436051 1.5968982404571548 0.7991208455689972 2.925615078141343 +chr1 81300000 82500000 ID_0.01_52 -0.548837 . 0.18859797704634573 0.9047287273528857 1.6939667078897195e-05 1.3147379814177793 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ID_0.01_21 -0.925006 . 0.7097522434979588 0.6305323133894596 0.0321324163398195 0.3721888549170316 0.48097774861358605 2.1427594822460274 +chr2 38100000 39000000 ID_0.01_22 -0.911804 . 0.7393292654773327 0.881325233306994 0.29519393230145974 0.33274170515122786 -0.1492894580583046 1.0467954436253115 +chr2 39000000 39600000 ID_0.01_23 -0.474157 . 0.6100584296663865 0.09177411159552243 0.5282444030584994 -0.5099900542174941 1.686112610223601 0.6306882198395203 +chr2 39600000 40900000 ID_0.01_24 -0.483398 . 0.07461114263487918 4.0609963411065196e-05 0.010501237199256202 1.7828474294215229 4.103981680942182 2.558872089916803 +chr2 42900000 44200000 ID_0.01_26 -0.6584895 . 0.0021975206441815654 0.20067758408950764 0.6380975269385074 3.0621516835802036 -1.2796234910268023 -0.4703604341917986 +chr2 44200000 45900000 ID_0.01_27 -1.4067435 . 0.22521157016748927 1.9510796109536805e-06 0.0007350515023349974 -1.2127862071029285 4.758426447825706 3.3761600350860053 +chr2 49100000 50200000 ID_0.01_30 0.046019 . 0.00022300982046490604 0.9447344417896487 0.2529345221959718 3.6914151198638283 -0.06932058361743652 1.143250688705234 +chr2 50200000 51500000 ID_0.01_31 0.1636485 . 0.951540897055784 0.10913756920793073 0.0010618782692566118 0.06077186539535113 1.6020815866769946 3.2735972940615 +chr2 51500000 52200000 ID_0.01_32 -0.692286 . 0.24118505156876602 0.6208598367844064 0.672470358702386 1.1720299009242017 -0.4946321031477141 0.42276002160669474 +chr2 52200000 53100000 ID_0.01_33 -0.7849475 . 0.39725134284435715 0.15447421559355445 0.5701831064617965 -0.8465404061607633 1.4239041663787457 0.5677818486223689 +chr2 53100000 54700000 ID_0.01_34 -0.3917385 . 0.1521280588110987 0.3799632165194018 0.002967803257668766 1.4320550794605422 0.8779640719156389 2.9710532409851655 +chr2 54700000 57400000 ID_0.01_35 -0.5543145 . 0.346755759830367 0.0014312329071657585 0.47352499353758404 0.9409006786256594 3.18827713599331 0.7167554683192523 +chr2 57400000 58500000 ID_0.01_36 -0.8692615 . 0.0024233876609619552 0.20626894756799574 0.7822405746331198 3.0327468948387115 -1.263891571071401 0.2764003673094582 +chr2 58500000 59800000 ID_0.01_37 -0.793426 . 0.18239853130591577 0.6218204561761443 0.13736616371185872 -1.3334062230862336 0.4932719344880407 1.4856710045655745 +chr2 59800000 61100000 ID_0.01_38 -1.1246435 . 0.5827287423546319 0.1054007296071133 0.21759194136983662 0.5494032527187045 1.6192163115233482 1.2329566411063124 +chr2 61100000 63200000 ID_0.01_39 -1.068387 . 0.10274298887110098 0.34115174774935353 0.07048470925924007 1.6316986297511233 -0.9518920185863162 1.8087830843232804 +chr2 63200000 64600000 ID_0.01_40 -1.4349735 . 0.48417731843647505 0.00033753405819330907 1.2801132462152629e-06 -0.6995997184577462 3.5846472757377863 4.842816771206897 +chr2 64600000 65300000 ID_0.01_41 -0.6812605 . 0.004359938857809953 0.20540528691175952 0.49742455539861163 2.8508729357203197 -1.2663011457719113 0.678547597704863 +chr2 65300000 67100000 ID_0.01_42 -1.5001585 . 0.17926714403352395 0.082391624771967 0.46883492695117224 -1.3430149159851612 1.7369747674578426 0.7243760049124582 +chr2 67100000 69200000 ID_0.01_43 -1.2359205 . 0.08238337439100206 0.4603363921737088 0.1723527397039586 1.7370215089379466 -0.7382930446473848 1.3646828897068228 +chr2 69200000 72300000 ID_0.01_44 -0.879535 . 0.47186254924794335 0.20435847184482636 0.5120848601408396 -0.7194518666231724 1.2692316051986414 0.6555948187181422 +chr2 72300000 73900000 ID_0.01_45 -1.502847 . 0.2019764189784251 0.07210576139432995 0.4268514825173947 1.2759408790576827 -1.7984497724014792 0.7945909532496019 +chr2 73900000 74500000 ID_0.01_46 -1.0827955 . 0.05624953467836868 0.01599081064223216 0.009588490917934598 -1.9090973489646446 2.409125214163984 2.5903266171980297 +chr2 74500000 75600000 ID_0.01_47 -0.513854 . 0.03355444523742217 0.05542743887521176 0.05648765699259401 2.125385667347831 -1.9155104411272263 1.9072543617998163 +chr2 75600000 77900000 ID_0.01_48 -1.3889375 . 0.06553467800613455 0.02122345376305353 0.8704438307617135 -1.8415931894192763 -2.30398556755355 0.16309475328230974 +chr2 78500000 79800000 ID_0.01_50 -0.9250035 . 0.0008305851034440484 0.04808908660969095 0.13502481037838385 3.342395876629217 -1.976580336704754 1.4945772376390287 +chr2 79800000 81300000 ID_0.01_51 -0.4445345 . 0.03995811680186064 0.007335033689831764 0.17880089751573314 -2.054181618455856 2.6812379562159783 1.3444562414603196 +chr2 81300000 82500000 ID_0.01_52 -0.548837 . 0.004438039067768516 0.4479494747926346 0.03585614473911171 2.8452226423748397 0.7588379936249628 2.0985550225691543 +chr2 82500000 87500000 ID_0.01_53 -0.8209955 . 0.5093232866302667 0.0035138888243136336 0.019678310085819 0.6598917690213242 -2.9187935263330775 -2.332425649107443 +chr2 87500000 88300000 ID_0.01_54 -1.9215335 . 0.004634877786222016 0.2216954296829935 0.14608442521660386 -2.8313720188917766 -1.222032254835529 -1.4535019984826383 +chr2 88300000 89100000 ID_0.01_55 -0.899375 . 0.244910008350822 0.003763742574571689 0.029772443535003953 -1.1628015987861107 2.8973128211932746 2.1731046272396166 +chr2 89100000 90200000 ID_0.01_56 -0.4054365 . 0.01030826760164906 0.19411185717270885 0.3344919216139357 2.5653133140994155 -1.298510830297501 0.9651056014692379 +chr2 90200000 91200000 ID_0.01_57 -0.78976 . 0.19482311541466302 0.3872162044489691 0.29679684491221225 -1.2964423911189213 -0.8646768038427621 1.0433270548028466 +chr2 91200000 92500000 ID_0.01_58 -0.2421285 . 0.4227784203801982 0.5834487844094985 0.3336025619146935 -0.8016102952787205 -0.5483541034377332 0.9668829280368689 +chr2 92500000 93400000 ID_0.01_59 -0.291361 . 0.48023513451797484 0.09651992187283932 0.0891317154479808 -0.705924429359093 -1.661964354209301 1.6999958004475058 +chr2 93400000 94800000 ID_0.01_60 -0.2776395 . 0.05863270833799688 0.5874252605886783 0.4952237214341225 -1.8909373463163015 -0.5425709271969614 -0.6820240850466266 +chr2 94800000 96000000 ID_0.01_61 -0.832662 . 0.6950543784533142 0.0032772769467099175 0.011218663998675783 -0.39200519078416285 2.940457748130579 2.5358129470289446 +chr2 97800000 98900000 ID_0.01_63 -0.276687 . 0.01182135449288108 0.9781360625835592 0.11444794246631047 2.517432718517982 -0.027405812127823743 1.578512396694215 +chr2 98900000 100200000 ID_0.01_64 -0.196956 . 0.9231075732967555 0.006380970470955413 0.8546925510997803 0.09652002151026357 2.727533878745341 -0.18313441757290147 +chr2 100200000 101600000 ID_0.01_65 -0.480589 . 0.019713998589890258 0.01605654685424601 0.8441535520280872 2.33174711595639 -2.407627673629528 0.19658341274873356 +chr2 101600000 102400000 ID_0.01_66 -0.1597755 . 0.015843566166002136 0.11038403054109522 0.010933411544174087 -2.4124993391137934 1.5964694081694553 2.5448198924253407 +chr2 102400000 103300000 ID_0.01_67 -0.2325575 . 0.07739196334618564 0.8920863632839254 0.004479508580355494 1.766023160471165 -0.13566468949384036 2.8422589885314458 +chr2 103300000 104300000 ID_0.01_68 -0.3313575 . 0.7682407326952878 0.07116112497945337 0.12194400706680208 -0.2946768717903739 -1.8044478663269963 1.5466651655508241 +chr2 104300000 105700000 ID_0.01_69 -0.3473065 . 0.06228140735132291 0.7066195504607469 0.6295784282194834 -1.8642870290828595 0.3763999939953517 0.4823203006669608 +chr2 105700000 106800000 ID_0.01_70 -0.5329025 . 0.6700182786304059 0.42087560865213913 0.4939032667187476 0.4261229215957268 -0.8049030839188904 0.6841138659320477 +chr2 106800000 107800000 ID_0.01_71 -0.404506 . 0.7314661136592258 0.8324328988453884 3.960360576478446e-05 -0.34317592706089095 -0.2115823261648799 4.109780108146108 +chr2 107800000 108700000 ID_0.01_72 -0.679396 . 0.8412726808275693 0.14875367516572954 0.010142593994358249 -0.20026583519734145 1.4439477438688086 2.570929609543765 +chr2 108700000 109400000 ID_0.01_73 -0.80483 . 0.046781600773732696 0.1109070316615554 0.00202042128660821 1.9882721355072683 -1.594129505098584 3.0872139392959475 +chr2 109400000 110800000 ID_0.01_74 -0.327192 . 0.0915352797518888 0.4400541989813883 0.1879067363032434 -1.6873541227319913 0.7721016940252946 1.3167968282534215 +chr2 110800000 112200000 ID_0.01_75 -0.168549 . 0.3847123825595731 0.6768860622762672 0.026973732909941883 0.8692463829025633 0.41671611971611583 2.211897718955138 +chr2 112200000 113500000 ID_0.01_76 -0.174322 . 0.7461011302024421 0.9632463458767686 0.0062423840221954045 0.32378458136544613 -0.046080176759473374 2.7347701931175226 +chr2 113500000 114400000 ID_0.01_77 -0.6967465 . 0.7935497657534414 0.008592001054516171 0.006971136756122058 -0.2617038582165721 2.6278752816769817 2.698219935488603 +chr2 115400000 116200000 ID_0.01_79 0.0065005 . 0.002794769727443374 0.7712804658813557 0.41512140421829624 2.989453511619916 0.29070039969652767 0.8149142352148562 +chr2 116200000 117100000 ID_0.01_80 -0.0989215 . 0.8604485472741461 0.22271495241320893 0.6840123446798727 0.17580321054464085 -1.2193405803749653 0.4069940684815211 +chr2 117100000 118400000 ID_0.01_81 -0.1478965 . 0.2315021025397601 0.033704773718936 0.1281855894415085 -1.1964984514034422 -2.123586042096408 1.5212959368593912 +chr2 118400000 120200000 ID_0.01_82 -0.13017 . 0.0343724402430932 0.8055360874068784 0.25821047039345024 -2.115675211386901 0.24618879702732402 1.1306309138089006 +chr2 120200000 123500000 ID_0.01_83 -0.6265325 . 0.8263054157245454 0.846247992608086 0.6848118044173057 0.21944243680230108 0.19390790663241042 -0.4059058161281474 +chr2 123500000 126000000 ID_0.01_84 -0.878022 . 0.8299313934948878 0.8690586942202709 0.04195680648346834 0.21478955917789536 0.16485426091950642 2.033948318776374 +chr2 126000000 127300000 ID_0.01_85 -0.1791345 . 0.9044013891860989 nan 0.4078273699642819 0.12010321050730002 nan 0.8277230362641474 diff --git a/hicexplorer/test/test_data/hicDifferentialTAD/multichromosome_rejected.diff_tad b/hicexplorer/test/test_data/hicDifferentialTAD/multichromosome_rejected.diff_tad new file mode 100644 index 00000000..b883133a --- /dev/null +++ b/hicexplorer/test/test_data/hicDifferentialTAD/multichromosome_rejected.diff_tad @@ -0,0 +1,22 @@ +# Created with HiCExplorer's hicDifferentialTAD version 3.7-dev +# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. +# Rejected regions with Wilcoxon rank-sum test to p-value: 0.05 with used mode: all and modeReject: all +# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 0.023812890829327776 0.016456650095058242 0.013780451222869307 -2.2601347205916467 2.3986274127154763 2.4629359982231134 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 0.0089215993395334 1.285472801127568e-06 0.00027371449872326916 -2.6150438783589705 4.841986839029572 3.638985227290415 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 5.62488175706287e-07 1.4504561507903456e-05 1.3778440238424469e-14 5.003670679515155 4.3360808453105735 7.698396376184418 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 1.5786397432173645e-05 0.022701527679266198 1.9076805322791016e-09 4.317419471951147 -2.2784206423969704 6.00547883263383 +chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 0.01586879590979828 0.03659340267092997 3.124179401591242e-05 -2.411919244204809 -2.0902716696341423 4.164220601406918 +chr1 96000000 97800000 ID_0.01_62 -1.285079 . 0.0017124997724517516 4.9680693940233185e-06 1.922983338658536e-05 -3.1360329241653946 4.5661316026435665 4.273650555054208 +chr1 115400000 116200000 ID_0.01_79 0.0065005 . 0.002826148476629719 0.0011343574929371728 0.023595609786263398 2.986040893455966 3.254891360536531 2.263650653374601 +chr1 123500000 126000000 ID_0.01_84 -0.878022 . 0.003332413744234827 0.005556795523194584 2.24757528005326e-07 -2.9352850775407884 2.772848668666098 5.17760078789867 +chr1 143800000 144700000 ID_0.01_96 0.08656 . 0.0009197364332563303 0.022759326510606574 0.002340427025911093 3.313993505947673 2.2774506820555747 3.0432437137075055 +chr1 144700000 145600000 ID_0.01_97 -0.021447 . 0.024067278280406255 0.027757272426992927 0.005130682934469564 2.2560535401012713 -2.200699949125614 2.798712298076633 +chr1 148600000 151600000 ID_0.01_100 -0.035126 . 0.002139568756318835 0.00348013763924427 1.4947314536052858e-09 3.0701422001103027 2.9218010495583786 6.044931876388202 +chr2 6200000 7300000 ID_0.01_2 -0.235798 . 0.0030071544754784697 3.3573055080321745e-05 0.005598205890746249 -2.9670056351141474 4.14776923065483 2.7704315886134068 +chr2 40900000 42900000 ID_0.01_25 -0.7016145 . 2.0772087272910948e-05 0.0008763900376773169 4.5966555611854654e-05 4.256425862879689 3.327468159433588 4.075241818610254 +chr2 45900000 47300000 ID_0.01_28 -0.656308 . 1.231296900689535e-07 0.010235964398398393 0.0003837953285890675 5.288787717864867 -2.5677544199764784 3.550982916000933 +chr2 47300000 49100000 ID_0.01_29 -0.0033885 . 0.027525391564099017 0.00017069331965971062 2.57653091365844e-07 -2.203985105864244 3.758854120987195 5.152050890095793 +chr2 77900000 78500000 ID_0.01_49 -0.809386 . 0.01855417571756637 0.0002025292493976715 0.03930313509400304 -2.3543691321852913 3.715840586511727 2.060999004118432 +chr2 96000000 97800000 ID_0.01_62 -1.285079 . 0.005308851713796463 0.02315236266375798 0.03434048057916755 2.787670456305292 2.270911058812528 2.1160508787767176 +chr2 114400000 115400000 ID_0.01_78 -0.4525885 . 0.004262135097073559 0.0021003189556864257 0.014354178641596564 2.8580795623163446 3.075667535012748 2.4482756649003568 diff --git a/hicexplorer/test/test_data/hicFindRestSite/hindIII_DpnII.bed b/hicexplorer/test/test_data/hicFindRestSite/hindIII_DpnII.bed new file mode 100644 index 00000000..7546776e --- /dev/null +++ b/hicexplorer/test/test_data/hicFindRestSite/hindIII_DpnII.bed @@ -0,0 +1,32 @@ +chrM 402 408 . 0 + +chrM 801 805 . 0 + +chrM 1617 1621 . 0 + +chrM 1981 1985 . 0 + +chrM 2001 2005 . 0 + +chrM 2023 2027 . 0 + +chrM 2100 2104 . 0 + +chrM 2145 2149 . 0 + +chrM 2836 2840 . 0 + +chrM 3154 3158 . 0 + +chrM 4263 4267 . 0 + +chrM 4596 4600 . 0 + +chrM 5267 5273 . 0 + +chrM 5318 5322 . 0 + +chrM 5689 5695 . 0 + +chrM 5713 5717 . 0 + +chrM 5736 5740 . 0 + +chrM 5950 5954 . 0 + +chrM 6193 6197 . 0 + +chrM 6544 6548 . 0 + +chrM 6554 6558 . 0 + +chrM 8414 8418 . 0 + +chrM 8489 8493 . 0 + +chrM 9407 9411 . 0 + +chrM 10600 10604 . 0 + +chrM 11110 11114 . 0 + +chrM 11344 11348 . 0 + +chrM 11476 11480 . 0 + +chrM 12852 12856 . 0 + +chrM 13020 13024 . 0 + +chrM 14117 14123 . 0 + +chrM 14348 14352 . 0 + diff --git a/hicexplorer/test/test_data/hicInterIntraTAD/GSM2644947_Auxin2days-R1.100000_chr1_chr2.cool b/hicexplorer/test/test_data/hicInterIntraTAD/GSM2644947_Auxin2days-R1.100000_chr1_chr2.cool new file mode 100644 index 00000000..765134d0 Binary files /dev/null and b/hicexplorer/test/test_data/hicInterIntraTAD/GSM2644947_Auxin2days-R1.100000_chr1_chr2.cool differ diff --git a/hicexplorer/test/test_data/hicInterIntraTAD/output_test.txt b/hicexplorer/test/test_data/hicInterIntraTAD/output_test.txt new file mode 100644 index 00000000..bd6a21d6 --- /dev/null +++ b/hicexplorer/test/test_data/hicInterIntraTAD/output_test.txt @@ -0,0 +1,227 @@ +# Created with HiCExplorer's hicInterIntraTAD version 3.7-dev +# Chromosome start end name score strand inter_left_sum inter_right_sum inter_left_density inter_right_density inter_left_number_of_contacts inter_right_number_of_contacts inter_left_number_of_contacts_nnz inter_right_number_of_contacts_nnz intra_sum intra_number_of_contacts intra_number_of_contacts_nnz intra_density inter_left_intra_ratio inter_right_intra_ratio inter_left_inter_right_intra_ratio +chr1 4400000 6200000 ID_0.01_1 -0.5630275 . 0 265.6981737879304 0 1.0 0 180 0 180 780.0186987409819 324 324 1.0 0.0 0.340630518494993 0.340630518494993 +chr1 6200000 7300000 ID_0.01_2 -0.235798 . 288.00513572726237 327.503479611623 1.0 1.0 198 231 198 231 339.91508704783513 121 121 1.0 0.8472855330682405 0.9634861531331044 1.8107716862013452 +chr1 7300000 9500000 ID_0.01_3 -0.44334 . 340.12385944568155 159.40880484157745 1.0 1.0 242 110 242 110 1078.1133262629996 484 484 1.0 0.31548061892958207 0.14785904316211984 0.46333966209170185 +chr1 9500000 10100000 ID_0.01_4 -1.021538 . 186.65816676710497 124.2235190772146 1.0 1.0 132 84 132 84 118.58286349492002 36 36 1.0 1.5740737005823884 1.0475672067282826 2.6216409073106712 +chr1 10100000 11600000 ID_0.01_5 -0.6844015 . 131.58549291278965 272.61351407375594 1.0 1.0 90 180 90 180 549.7750987796844 225 225 1.0 0.239344221309523 0.49586369895411075 0.7352079202636337 +chr1 11600000 12900000 ID_0.01_6 -0.607587 . 291.6352241871022 150.5794946648602 1.0 1.0 195 91 195 91 436.74972826807334 169 169 1.0 0.667739909864578 0.3447729555825522 1.0125128654471303 +chr1 12900000 13700000 ID_0.01_7 -0.6303795 . 168.48027938187317 134.58895474095965 1.0 1.0 104 88 104 88 195.67112396731414 64 64 1.0 0.8610380313960733 0.6878324814214388 1.548870512817512 +chr1 13700000 14900000 ID_0.01_8 -1.2063985 . 144.62201073549667 352.26933981751864 1.0 1.0 96 252 96 252 391.88190420845365 144 144 1.0 0.36904488107868316 0.898917087098097 1.2679619681767802 +chr1 14900000 17100000 ID_0.01_9 -0.3406565 . 365.5583939729056 277.35371965268376 1.0 1.0 264 198 264 198 1025.9990446573693 484 484 1.0 0.3562950627258949 0.27032551452843273 0.6266205772543276 +chr1 17100000 18100000 ID_0.01_10 -0.230354 . 305.01549550512163 151.28476510413458 1.0 1.0 220 90 220 90 286.2349158050838 100 100 1.0 1.0656124695591882 0.5285335811622448 1.594146050721433 +chr1 18100000 19100000 ID_0.01_11 -0.5135365 . 164.7300582447859 213.19454134995965 1.0 1.0 100 140 100 140 300.470028569374 100 100 1.0 0.5482412306781946 0.709536795949471 1.2577780266276657 +chr1 19100000 20600000 ID_0.01_12 -0.4202525 . 225.81990938044544 139.76163154045415 1.0 1.0 150 90 150 90 589.495485787105 225 225 1.0 0.38307317837884136 0.23708685632060758 0.6201600346994489 +chr1 20600000 21300000 ID_0.01_13 -0.9980865 . 160.10872364251864 135.89445630377475 1.0 1.0 105 84 105 84 156.98347680139352 49 49 1.0 1.0199081260321365 0.8656608903859392 1.8855690164180756 +chr1 21300000 22600000 ID_0.01_14 -0.859866 . 145.09396359580737 302.6918796200853 1.0 1.0 91 208 91 208 446.3865278020496 169 169 1.0 0.325041090084487 0.6780936716672465 1.0031347617517337 +chr1 22600000 24300000 ID_0.01_15 -0.281294 . 317.92695378401106 326.8941525587083 1.0 1.0 221 238 221 238 668.2801115420951 289 289 1.0 0.47573906254725457 0.48915738612118964 0.9648964486684442 +chr1 24300000 25800000 ID_0.01_16 -1.0366175 . 346.9866302510411 1133.9886552802805 1.0 1.0 255 720 255 720 559.8706523936909 225 225 1.0 0.6197621339277601 2.025447575135409 2.645209709063169 +chr1 25800000 30700000 ID_0.01_17 -0.1471245 . 1149.882672090284 1749.4996539384435 1.0 1.0 735 1421 735 1421 33023.50459512531 2401 2401 1.0 0.034820128456627256 0.052977407316020964 0.0877975357726482 +chr1 30700000 33700000 ID_0.01_18 -1.0134455 . 1804.0256984015848 302.8691059007878 1.0 1.0 1470 240 1470 240 1782.5452659721068 900 900 1.0 1.0120504274643278 0.16990822711905657 1.1819586545833844 +chr1 33700000 34600000 ID_0.01_19 -1.33809 . 336.9551008710529 213.8987190364382 1.0 1.0 270 153 270 153 241.21728719074298 81 81 1.0 1.3968944962249121 0.8867470550205526 2.2836415512454646 +chr1 34600000 36400000 ID_0.01_20 -0.6325015 . 224.7758694294482 355.62045180830626 1.0 1.0 162 288 162 288 816.3262559842592 324 324 1.0 0.27535053268430265 0.43563520002125655 0.7109857327055593 +chr1 36400000 38100000 ID_0.01_21 -0.925006 . 375.53511955331766 184.1653963923602 1.0 1.0 306 136 306 136 737.2993667600783 289 289 1.0 0.5093387251958933 0.24978374415488783 0.759122469350781 +chr1 38100000 39000000 ID_0.01_22 -0.911804 . 205.44010035241112 87.9936926197706 1.0 1.0 153 45 153 45 245.45808122307068 81 81 1.0 0.836966130138158 0.3584876577756774 1.1954537879138354 +chr1 39000000 39600000 ID_0.01_23 -0.474157 . 102.35144500050816 117.81813399791773 1.0 1.0 54 72 54 72 131.17238983108632 36 36 1.0 0.7802819261912393 0.8981930888781917 1.678475015069431 +chr1 39600000 40900000 ID_0.01_24 -0.483398 . 124.94881037455684 343.31390341283225 1.0 1.0 78 247 78 247 438.71990165523187 169 169 1.0 0.28480315094697456 0.7825355132455913 1.067338664192566 +chr1 40900000 42900000 ID_0.01_25 -0.7016145 . 359.15528103562735 315.1066837637684 1.0 1.0 260 240 260 240 943.7191199942096 400 400 1.0 0.38057433978643035 0.3338988021835372 0.7144731419699676 +chr1 42900000 44200000 ID_0.01_26 -0.6584895 . 337.4616559828976 259.9388458789232 1.0 1.0 260 208 260 208 407.5452223903218 169 169 1.0 0.8280348718201818 0.6378159566055953 1.4658508284257772 +chr1 44200000 45900000 ID_0.01_27 -1.4067435 . 275.0000667971437 1916.9267096113058 1.0 1.0 221 221 221 221 719.0292596533616 289 289 1.0 0.3824601893526824 2.665992633645314 3.048452822997996 +chr1 45900000 47300000 ID_0.01_28 -0.656308 . 1936.788727734827 1928.6906486268595 1.0 1.0 238 238 238 238 151544.45920955483 196 196 1.0 0.01278033349313449 0.012726896507379903 0.02550723000051439 +chr1 47300000 49100000 ID_0.01_29 -0.0033885 . 1977.836395681454 264.18077862905227 1.0 1.0 252 180 252 180 772.0417609792821 324 324 1.0 2.561825662348503 0.3421845708112435 2.904010233159746 +chr1 49100000 50200000 ID_0.01_30 0.046019 . 286.34674691306276 206.50756154235165 1.0 1.0 198 132 198 132 346.80865844176026 121 121 1.0 0.8256620471923688 0.5954509973026829 1.4211130444950517 +chr1 50200000 51500000 ID_0.01_31 0.1636485 . 220.25165721666815 121.41898184154596 1.0 1.0 143 78 143 78 452.78973895618924 169 169 1.0 0.48643252765491474 0.26815753846686474 0.7545900661217794 +chr1 51500000 52200000 ID_0.01_32 -0.692286 . 139.1147991444512 94.30814649283586 1.0 1.0 91 56 91 56 157.37391076134102 49 49 1.0 0.8839762478510182 0.5992616313377065 1.4832378791887246 +chr1 52200000 53100000 ID_0.01_33 -0.7849475 . 103.30880196103038 199.53535002975235 1.0 1.0 63 135 63 135 223.51506333492014 81 81 1.0 0.46220062495846237 0.8927154485814853 1.3549160735399477 +chr1 53100000 54700000 ID_0.01_34 -0.3917385 . 210.01226463030432 507.3728438042626 1.0 1.0 144 416 144 416 594.0201041685028 256 256 1.0 0.35354403522129135 0.8541341281949921 1.2076781634162834 +chr1 54700000 57400000 ID_0.01_35 -0.5543145 . 524.6254789917241 361.35021752831665 1.0 1.0 432 270 432 270 1464.1112754428707 729 729 1.0 0.35832350162936427 0.24680515995549168 0.605128661584856 +chr1 57400000 58500000 ID_0.01_36 -0.8692615 . 393.11363170223643 179.2834337604413 1.0 1.0 297 132 297 132 345.5283591650012 121 121 1.0 1.1377174153005245 0.518867493810624 1.6565849091111486 +chr1 58500000 59800000 ID_0.01_37 -0.793426 . 191.96651364329938 215.70333597531493 1.0 1.0 143 156 143 156 465.716735911298 169 169 1.0 0.41219586680230874 0.46316423555884095 0.8753601023611497 +chr1 59800000 61100000 ID_0.01_38 -1.1246435 . 230.39781429353206 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0.011295500000 . 176400000 177800000 31,120,180 +chr1 177800000 178700000 ID_0.01_126 -0.232881500000 . 177800000 178700000 51,160,44 +chr1 178700000 179700000 ID_0.01_127 -0.286533500000 . 178700000 179700000 31,120,180 +chr1 179700000 181400000 ID_0.01_128 -1.300036000000 . 179700000 181400000 51,160,44 +chr1 181400000 182800000 ID_0.01_129 -0.977387500000 . 181400000 182800000 31,120,180 +chr1 182800000 183800000 ID_0.01_130 -0.756317000000 . 182800000 183800000 51,160,44 +chr1 183800000 185100000 ID_0.01_131 -0.293619500000 . 183800000 185100000 31,120,180 +chr1 185100000 186600000 ID_0.01_132 -0.183922000000 . 185100000 186600000 51,160,44 +chr1 186600000 187300000 ID_0.01_133 -0.640236000000 . 186600000 187300000 31,120,180 +chr1 187300000 188600000 ID_0.01_134 -1.202403500000 . 187300000 188600000 51,160,44 +chr1 188600000 189900000 ID_0.01_135 -0.927335500000 . 188600000 189900000 31,120,180 +chr1 189900000 190800000 ID_0.01_136 0.306214000000 . 189900000 190800000 51,160,44 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52200000 53100000 31,120,180 +chr2 53100000 54700000 ID_0.01_34 -0.391738500000 . 53100000 54700000 51,160,44 +chr2 54700000 57400000 ID_0.01_35 -0.554314500000 . 54700000 57400000 31,120,180 +chr2 57400000 58500000 ID_0.01_36 -0.869261500000 . 57400000 58500000 51,160,44 +chr2 58500000 59800000 ID_0.01_37 -0.793426000000 . 58500000 59800000 31,120,180 +chr2 59800000 61100000 ID_0.01_38 -1.124643500000 . 59800000 61100000 51,160,44 +chr2 61100000 63200000 ID_0.01_39 -1.068387000000 . 61100000 63200000 31,120,180 +chr2 63200000 64600000 ID_0.01_40 -1.434973500000 . 63200000 64600000 51,160,44 +chr2 64600000 65300000 ID_0.01_41 -0.681260500000 . 64600000 65300000 31,120,180 +chr2 65300000 67100000 ID_0.01_42 -1.500158500000 . 65300000 67100000 51,160,44 +chr2 67100000 69200000 ID_0.01_43 -1.235920500000 . 67100000 69200000 31,120,180 +chr2 69200000 72300000 ID_0.01_44 -0.879535000000 . 69200000 72300000 51,160,44 +chr2 72300000 73900000 ID_0.01_45 -1.502847000000 . 72300000 73900000 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91200000 92500000 ID_0.01_58 -0.242128500000 . 91200000 92500000 51,160,44 +chr2 92500000 93400000 ID_0.01_59 -0.291361000000 . 92500000 93400000 31,120,180 +chr2 93400000 94800000 ID_0.01_60 -0.277639500000 . 93400000 94800000 51,160,44 +chr2 94800000 96000000 ID_0.01_61 -0.832662000000 . 94800000 96000000 31,120,180 +chr2 96000000 97800000 ID_0.01_62 -1.285079000000 . 96000000 97800000 51,160,44 +chr2 97800000 98900000 ID_0.01_63 -0.276687000000 . 97800000 98900000 31,120,180 +chr2 98900000 100200000 ID_0.01_64 -0.196956000000 . 98900000 100200000 51,160,44 +chr2 100200000 101600000 ID_0.01_65 -0.480589000000 . 100200000 101600000 31,120,180 +chr2 101600000 102400000 ID_0.01_66 -0.159775500000 . 101600000 102400000 51,160,44 +chr2 102400000 103300000 ID_0.01_67 -0.232557500000 . 102400000 103300000 31,120,180 +chr2 103300000 104300000 ID_0.01_68 -0.331357500000 . 103300000 104300000 51,160,44 +chr2 104300000 105700000 ID_0.01_69 -0.347306500000 . 104300000 105700000 31,120,180 +chr2 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118400000 31,120,180 +chr2 118400000 120200000 ID_0.01_82 -0.130170000000 . 118400000 120200000 51,160,44 +chr2 120200000 123500000 ID_0.01_83 -0.626532500000 . 120200000 123500000 31,120,180 +chr2 123500000 126000000 ID_0.01_84 -0.878022000000 . 123500000 126000000 51,160,44 +chr2 126000000 127300000 ID_0.01_85 -0.179134500000 . 126000000 127300000 31,120,180 diff --git a/hicexplorer/test/test_data/hicMergeLoops/gm12878_all.bedgraph b/hicexplorer/test/test_data/hicMergeLoops/gm12878_all.bedgraph index c9fbd063..fcd3e33c 100644 --- a/hicexplorer/test/test_data/hicMergeLoops/gm12878_all.bedgraph +++ b/hicexplorer/test/test_data/hicMergeLoops/gm12878_all.bedgraph @@ -8,7 +8,7 @@ 1 1050000 1075000 1 1175000 1200000 0.001 1 1310000 1320000 1 1410000 1420000 0.001 1 1710000 1720000 1 1830000 1840000 0.001 -1 1870000 1880000 1 3340000 3350000 0.0019430592210407133 +1 1870000 1880000 1 3340000 3350000 0.0019430592210407 1 2080000 2090000 1 3330000 3340000 0.001 1 2110000 2120000 1 2710000 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0.001 X 131425000 131450000 X 131725000 131750000 0.001 -X 131520000 131530000 X 131620000 131630000 0.00282181171267491 +X 131520000 131530000 X 131620000 131630000 0.0028218117126749 X 131850000 131860000 X 132810000 132820000 0.001 X 132130000 132140000 X 132800000 132810000 0.001 X 132920000 132930000 X 133530000 133540000 0.001 @@ -16546,4 +16546,4 @@ Y 13125000 13150000 Y 13850000 13875000 0.001 Y 13140000 13150000 Y 13840000 13850000 0.001 Y 13450000 13460000 Y 13840000 13850000 0.001 Y 13450000 13460000 Y 13650000 13660000 0.001 -Y 13650000 13675000 Y 13850000 13875000 0.001 \ No newline at end of file +Y 13650000 13675000 Y 13850000 13875000 0.001 diff --git a/hicexplorer/test/test_data/hicPCA/mm9_genes_sorted.bed12 b/hicexplorer/test/test_data/hicPCA/mm9_genes_sorted.bed12 new file mode 100644 index 00000000..723b1dcb --- /dev/null +++ b/hicexplorer/test/test_data/hicPCA/mm9_genes_sorted.bed12 @@ -0,0 +1,2437 @@ +chr1 3204562 3661579 NM_001011874 0 - 3206102 3661429 0 3 2487,200,947, 0,207220,456070, +chr1 4109946 4350384 NM_001370921 0 - 4110084 4342906 0 23 208,155,152,133,87,200,108,178,213,177,92,130,32,77,76,79,152,133,87,164,172,636,104, 0,22746,27946,28746,43989,50339,77668,86794,106745,108577,111187,123267,123551,123677,125165,141661,147603,164900,173060,191404,232044,232336,240334, +chr1 4280926 4399322 NM_001195662 0 - 4283061 4399268 0 4 2167,172,636,72, 0,61064,61356,118324, +chr1 4333587 4350395 NM_011283 0 - 4334680 4342906 0 4 6585,172,636,115, 0,8403,8695,16693, +chr1 4481008 4487435 NM_001289466 0 - 4481796 4485236 0 4 1741,92,63,1064, 0,2844,4208,5363, +chr1 4481008 4487435 NM_001289464 0 - 4481796 4483487 0 4 1741,391,92,1064, 0,2172,2844,5363, +chr1 4481008 4487435 NM_001289467 0 - 4481796 4482672 0 3 1741,92,1064, 0,2844,5363, +chr1 4481008 4487435 NM_011441 0 - 4481796 4483487 0 5 1741,367,92,807,1064, 0,2172,2844,4208,5363, +chr1 4481008 4487435 NM_001289465 0 - 4481796 4485236 0 4 1741,92,807,1064, 0,2844,4208,5363, +chr1 4763278 4775807 NR_033530 0 - 4775807 4775807 0 4 1319,124,166,154, 0,4327,9370,12375, +chr1 4763278 4775807 NM_001177658 0 - 4766544 4775758 0 5 3604,124,166,155,154, 0,4327,9370,10753,12375, +chr1 4763278 4775807 NM_025300 0 - 4764532 4775758 0 5 1319,124,166,155,154, 0,4327,9370,10753,12375, +chr1 4797903 4836816 NM_001355712 0 + 4797994 4835097 0 8 160,32,66,48,71,74,177,1773, 0,632,20761,22445,24488,29178,33133,37140, +chr1 4797903 4836816 NM_008866 0 + 4797994 4835097 0 9 160,32,66,48,71,74,102,177,1773, 0,632,20761,22445,24488,29178,31564,33133,37140, +chr1 4847774 4887990 NM_001159750 0 + 4847994 4886445 0 10 283,63,106,88,143,57,155,147,72,1554, 0,9776,20333,29050,31766,33046,34221,35723,37240,38662, +chr1 4847774 4887990 NM_011541 0 + 4847994 4886445 0 10 283,63,106,88,146,57,155,147,72,1554, 0,9776,20333,29050,31763,33046,34221,35723,37240,38662, +chr1 4848408 4887990 NM_001159751 0 + 4848488 4886445 0 10 176,63,106,88,146,57,155,147,72,1554, 0,9142,19699,28416,31129,32412,33587,35089,36606,38028, +chr1 4899656 5009620 NM_021374 0 - 4900554 5009460 0 5 1087,235,84,143,229, 0,2738,7321,14271,109735, +chr1 4899656 5060366 NM_001177795 0 - 4900554 5060258 0 6 1087,235,84,143,300,276, 0,2738,7321,14271,111162,160434, +chr1 4899656 5008815 NM_001290372 0 - 4900554 4914046 0 5 1087,235,84,143,159, 0,2738,7321,14271,109000, +chr1 5073166 5152630 NM_001310442 0 + 5074531 5152246 0 13 193,147,103,90,114,105,98,193,179,126,102,114,445, 0,1331,5923,10277,12529,14943,34304,41191,49998,52726,60664,66862,79019, +chr1 5073166 5152630 NM_133826 0 + 5074531 5152246 0 14 193,147,103,90,114,105,54,98,193,179,126,102,114,445, 0,1331,5923,10277,12529,14943,17984,34304,41191,49998,52726,60664,66862,79019, +chr1 5578573 5596214 NM_001318735 0 + 5579129 5592952 0 4 171,301,353,3882, 0,512,10097,13759, +chr1 5578573 5596214 NM_011011 0 + 5579129 5592865 0 4 171,271,353,3882, 0,542,10097,13759, +chr1 5578573 5596214 NM_001204371 0 + 5579129 5592865 0 4 171,301,353,3882, 0,512,10097,13759, +chr1 5903787 5907479 NM_010342 0 - 5906384 5907374 0 1 3692, 0, +chr1 6204742 6266185 NM_009826 0 + 6220083 6264356 0 24 296,110,115,127,171,203,427,171,185,187,82,62,104,127,1892,166,109,241,49,48,59,137,71,1907, 0,13278,15297,19299,19567,23600,25290,29443,30133,30496,30763,30936,33044,33404,33614,46268,48172,48362,49880,50912,54036,56029,58039,59536, +chr1 6349411 6384812 NM_001195732 0 + 6349411 6381185 0 5 184,54,81,77,462, 0,29242,30109,31709,34939, +chr1 6477311 6851021 NM_001244693 0 + 6758978 6848681 0 23 175,124,43,55,31,191,786,135,91,105,194,212,246,116,63,69,63,81,222,89,104,144,2481, 0,387,265763,281667,283713,308155,315089,320312,322046,323343,330372,332703,340545,346332,354908,355642,356890,357060,358340,361676,368138,370069,371229, +chr1 6477311 6851021 NM_001244692 0 + 6758978 6848681 0 24 175,124,78,43,55,31,191,786,135,91,105,194,212,246,116,63,69,63,81,222,89,104,144,2481, 0,387,250349,265763,281667,283713,308155,315089,320312,322046,323343,330372,332703,340545,346332,354908,355642,356890,357060,358340,361676,368138,370069,371229, +chr1 6720131 6851021 NM_173868 0 + 6758978 6848681 0 22 190,43,55,31,191,786,135,91,105,194,212,246,116,63,69,63,81,222,89,104,144,2481, 0,22943,38847,40893,65335,72269,77492,79226,80523,87552,89883,97725,103512,112088,112822,114070,114240,115520,118856,125318,127249,128409, +chr1 6720131 6851021 NR_045189 0 + 6851021 6851021 0 23 190,73,43,55,31,191,786,135,91,105,194,212,246,116,63,69,63,81,222,89,104,144,2481, 0,22245,22943,38847,40893,65335,72269,77492,79226,80523,87552,89883,97725,103512,112088,112822,114070,114240,115520,118856,125318,127249,128409, +chr1 6720131 6851021 NR_045188 0 + 6851021 6851021 0 24 190,78,73,43,55,31,191,786,135,91,105,194,212,246,116,63,69,63,81,222,89,104,144,2481, 0,7529,22245,22943,38847,40893,65335,72269,77492,79226,80523,87552,89883,97725,103512,112088,112822,114070,114240,115520,118856,125318,127249,128409, +chr1 7079000 7163709 NM_183028 0 + 7110389 7159963 0 6 297,422,103,172,124,4114, 0,31274,58717,71972,74328,80595, +chr1 8349819 9289958 NM_027671 0 - 8353555 8794024 0 21 3895,111,93,153,72,117,39,130,131,83,103,42,44,58,57,135,54,54,64,82,1745, 0,54464,85288,88241,103655,105698,194986,223466,235673,247331,265040,318068,318198,319334,322234,423024,444178,522422,639447,843440,938394, +chr1 8349819 9289958 NM_001290392 0 - 8353555 8573339 0 18 3895,111,93,153,72,117,39,130,103,42,44,58,57,135,54,64,82,1745, 0,54464,85288,88241,103655,105698,194986,223466,265040,318068,318198,319334,322234,423024,444178,639447,843440,938394, +chr1 8349819 9289958 NM_001290390 0 - 8353555 8794024 0 21 3895,111,93,153,72,117,39,130,131,83,103,42,41,58,57,135,54,54,64,82,1745, 0,54464,85288,88241,103655,105698,194986,223466,235673,247331,265040,318068,318198,319334,322234,423024,444178,522422,639447,843440,938394, +chr1 8349819 9289958 NM_001290393 0 - 8353555 8794024 0 20 3895,111,93,153,72,117,39,130,131,83,103,42,44,58,57,135,54,64,82,1745, 0,54464,85288,88241,103655,105698,194986,223466,235673,247331,265040,318068,318198,319334,322234,423024,444178,639447,843440,938394, +chr1 9535488 9537536 NM_021511 0 + 9535604 9536702 0 1 2048, 0, +chr1 9538028 9568051 NM_175236 0 + 9538173 9566355 0 14 204,38,41,54,155,197,78,106,153,99,79,97,158,1780, 0,1959,3769,4975,5370,5675,7590,9052,10185,12161,15561,15849,18833,28243, +chr1 9538028 9568051 NM_001357376 0 + 9543003 9566355 0 13 204,38,54,155,197,78,106,153,99,79,97,158,1780, 0,1959,4975,5370,5675,7590,9052,10185,12161,15561,15849,18833,28243, +chr1 9538028 9568051 NM_001357378 0 + 9543410 9566355 0 12 204,38,155,197,78,106,153,99,79,97,158,1780, 0,1959,5370,5675,7590,9052,10185,12161,15561,15849,18833,28243, +chr1 9538028 9568051 NM_001357377 0 + 9543003 9566355 0 15 204,177,38,41,54,155,197,78,106,153,99,79,97,158,1780, 0,492,1959,3769,4975,5370,5675,7590,9052,10185,12161,15561,15849,18833,28243, +chr1 9550913 9621173 NR_015470 0 - 9621173 9621173 0 5 946,49,90,128,32, 0,2990,58717,60122,70228, +chr1 9591347 9617223 NM_178399 0 + 9591664 9614977 0 6 384,56,163,62,92,2430, 0,5707,12045,18569,21326,23446, +chr1 9657491 9690290 NM_001290397 0 - 9659964 9690035 0 15 2602,105,117,115,143,369,234,105,72,175,221,93,72,106,275, 0,4801,5129,5690,6334,8556,10861,14374,15686,18225,20150,22670,25307,25876,32524, +chr1 9657491 9690290 NM_008651 0 - 9659964 9690035 0 16 2602,180,105,117,115,143,369,234,105,72,175,221,93,72,106,275, 0,4168,4801,5129,5690,6334,8556,10861,14374,15686,18225,20150,22670,25307,25876,32524, +chr1 9708702 9738463 NM_173443 0 - 9714562 9738237 0 3 6729,87,2933, 0,18344,26828, +chr1 9737728 9761337 NR_040462 0 + 9761337 9761337 0 4 957,116,124,297, 0,4801,23024,23312, +chr1 9788210 9892649 NM_133220 0 + 9855333 9888971 0 18 117,107,218,84,73,76,88,50,58,84,132,113,37,87,96,156,90,3849, 0,28883,67001,70253,73500,74128,79036,80896,82202,83448,83630,86277,86495,87537,87917,90740,93231,100590, +chr1 9788210 9892649 NM_177547 0 + 9855333 9888971 0 17 117,218,84,73,76,88,50,58,84,132,113,37,87,96,156,90,3849, 0,67001,70253,73500,74128,79036,80896,82202,83448,83630,86277,86495,87537,87917,90740,93231,100590, +chr1 9838361 9892649 NM_001037759 0 + 9855333 9888971 0 17 105,218,84,73,76,88,50,58,84,132,113,37,87,96,156,90,3849, 0,16850,20102,23349,23977,28885,30745,32051,33297,33479,36126,36344,37386,37766,40589,43080,50439, +chr1 9898718 9931035 NM_177722 0 + 9901799 9930625 0 15 53,138,131,60,196,123,105,126,238,206,167,180,143,110,577, 0,3037,3272,3476,6836,7678,7912,10382,11797,15419,22143,23364,25285,28358,31740, +chr1 9932105 9934199 NR_024067 0 - 9934199 9934199 0 4 131,69,108,99, 0,298,585,1995, +chr1 9932550 9932624 NR_004410 0 - 9932624 9932624 0 1 74, 0, +chr1 9950243 9957891 NM_001285425 0 - 9953488 9957566 0 3 3359,419,87, 0,6936,7561, +chr1 9958702 9999217 NR_110971 0 - 9999217 9999217 0 7 310,118,132,139,167,219,65, 0,16970,26524,30779,31349,34613,40450, +chr1 9958702 9999217 NM_145692 0 - 9958900 9993444 0 9 310,160,132,118,117,139,167,219,65, 0,7965,10194,16970,26524,30779,31349,34613,40450, +chr1 10014680 10028240 NM_001277101 0 - 10015059 10028091 0 8 464,149,112,86,66,129,235,241, 0,2503,5999,7739,8658,9408,10329,13319, +chr1 10014680 10028240 NR_102282 0 - 10028240 10028240 0 8 464,149,112,86,66,129,235,498, 0,2503,5999,7739,8658,9408,10329,13062, +chr1 10014680 10028240 NM_013715 0 - 10015059 10027893 0 8 464,149,112,86,66,129,235,490, 0,2503,5999,7739,8658,9408,10329,13070, +chr1 10028298 10126849 NM_026493 0 + 10035166 10126226 0 30 127,109,103,104,81,99,395,87,71,94,58,206,134,79,130,148,153,113,150,147,105,67,118,140,141,47,64,110,139,835, 0,6858,9206,20502,26115,27105,28208,36642,38954,44035,45283,47529,49833,50664,51970,57648,65994,70151,74175,74658,75385,77800,78396,88122,89205,91768,94236,94946,95874,97716, +chr1 10036573 10126849 NM_001368816 0 + 10036573 10126226 0 29 63,103,104,24,81,99,395,87,71,94,58,206,134,79,130,148,113,150,147,105,67,118,140,141,47,64,110,139,835, 0,931,12227,13331,17840,18830,19933,28367,30679,35760,37008,39254,41558,42389,43695,49373,61876,65900,66383,67110,69525,70121,79847,80930,83493,85961,86671,87599,89441, +chr1 10127587 10222751 NM_001102430 0 - 10128912 10222575 0 38 1490,118,139,169,140,133,73,139,136,130,131,161,173,152,170,41,91,151,159,129,152,172,85,206,112,202,109,240,235,134,176,102,277,180,147,157,31,300, 0,2960,4052,5069,7211,9896,14294,15879,16100,16774,19407,20393,22061,22370,23194,23456,26190,35327,35687,36560,42319,43363,46156,46469,46879,51250,51720,51932,56750,61336,62222,67301,71918,75537,76618,78330,79022,94864, +chr1 10314799 10710026 NM_177834 0 - 10315204 10709808 0 11 593,85,203,91,111,105,102,115,125,76,334, 0,4754,12548,83550,84538,152306,156295,159230,164106,270901,394893, +chr1 10314799 10710026 NM_001289497 0 - 10315204 10471100 0 10 593,85,203,91,111,105,102,115,76,334, 0,4754,12548,83550,84538,152306,156295,159230,270901,394893, +chr1 10983545 11293763 NM_029525 0 + 10983873 11287834 0 40 445,72,123,105,102,162,134,104,150,145,101,104,50,76,73,143,93,149,86,137,118,185,162,223,208,180,95,83,91,129,42,218,103,144,115,67,191,103,68,5975, 0,67861,72329,74546,86558,96252,104998,107599,114138,116817,119278,129656,130349,138873,143300,146491,146771,149184,156345,160078,162776,166631,168775,176388,177119,188390,190981,191665,192422,193172,200048,206370,210601,215047,238217,272214,272504,291592,295788,304243, +chr1 11254043 11293763 NM_001033636 0 + 11256052 11287834 0 6 133,67,191,103,68,5975, 0,1716,2006,21094,25290,33745, +chr1 11404185 11591902 NM_001160371 0 + 11404649 11587065 0 8 533,148,132,129,29,173,167,4857, 0,97813,104473,131049,148858,174269,182046,182860, +chr1 11404185 11591902 NM_001160370 0 + 11404649 11586415 0 7 533,148,132,129,29,173,5671, 0,97813,104473,131049,148858,174269,182046, +chr1 11404185 11965983 NM_001160369 0 + 11404649 11965047 0 14 533,148,132,129,29,173,167,136,86,77,48,94,57,980, 0,97813,104473,131049,148858,174269,182046,333860,384376,415710,519439,536858,557941,560818, +chr1 11404185 11965983 NM_001374633 0 + 11404649 11965047 0 13 533,148,132,129,29,173,167,136,86,77,94,57,980, 0,97813,104473,131049,148858,174269,182046,333860,384376,415710,536858,557941,560818, +chr1 11404185 11965983 NM_001374634 0 + 11508708 11965047 0 13 533,132,129,29,173,167,136,86,77,48,94,57,980, 0,104473,131049,148858,174269,182046,333860,384376,415710,519439,536858,557941,560818, +chr1 11404185 11965983 NM_177173 0 + 11404649 11965047 0 14 533,148,132,129,29,173,167,127,86,77,48,94,57,980, 0,97813,104473,131049,148858,174269,182046,333860,384376,415710,519439,536858,557941,560818, +chr1 11404185 11965983 NM_001310451 0 + 11404649 11965047 0 13 533,148,132,129,29,173,167,127,86,77,94,57,980, 0,97813,104473,131049,148858,174269,182046,333860,384376,415710,536858,557941,560818, +chr1 12416066 12416187 NR_105759 0 + 12416187 12416187 0 1 121, 0, +chr1 12657643 12663171 NR_045297 0 + 12663171 12663171 0 3 1530,40,1630, 0,3753,3898, +chr1 12682510 12850453 NM_001198565 0 + 12776607 12848923 0 22 255,95,73,231,240,152,170,151,176,129,57,130,217,253,97,95,66,176,143,124,34,1561, 0,36164,93649,94038,104336,112750,115424,124908,125948,127971,128365,129540,143683,145929,147399,147973,149013,150219,155665,155901,158330,166382, +chr1 12682510 12850453 NM_001198566 0 + 12776607 12848923 0 21 255,73,231,240,152,170,151,176,129,57,130,217,253,97,95,66,176,143,124,34,1561, 0,93649,94038,104336,112750,115424,124908,125948,127971,128365,129540,143683,145929,147399,147973,149013,150219,155665,155901,158330,166382, +chr1 12708625 12850453 NM_172294 0 + 12776607 12848923 0 22 239,95,73,231,240,152,170,151,176,129,57,130,217,253,97,95,66,176,143,124,34,1561, 0,10049,67534,67923,78221,86635,89309,98793,99833,101856,102250,103425,117568,119814,121284,121858,122898,124104,129550,129786,132215,140267, +chr1 12856630 12981216 NM_172841 0 - 12861948 12980576 0 9 5779,65,242,160,199,165,212,133,1556, 0,9760,12588,14743,27877,54488,72439,77430,123030, +chr1 13103508 13117244 NM_001081209 0 - 13104340 13115916 0 8 1060,102,203,271,158,54,691,54, 0,2352,5335,8933,10935,11191,11738,13682, +chr1 13129185 13364164 NM_008678 0 - 13132841 13214775 0 23 3668,90,199,178,229,78,279,166,130,216,207,211,1270,148,144,102,189,178,104,173,105,57,146, 0,7770,9212,9826,11585,13274,13692,17265,21056,22968,25791,27791,34974,37969,41376,42111,45070,47628,50982,82202,85504,146864,234833, +chr1 13129185 13362510 NM_001302702 0 - 13132841 13214775 0 22 3668,90,199,178,229,78,279,166,130,216,211,1270,148,144,102,189,178,104,173,105,57,247, 0,7770,9212,9826,11585,13274,13692,17265,21056,22968,27791,34974,37969,41376,42111,45070,47628,50982,82202,85504,146864,233078, +chr1 13554773 13579991 NM_028173 0 - 13556403 13579803 0 11 1704,161,144,105,71,85,59,117,122,64,311, 0,4778,5246,7110,7311,11675,13407,14757,14997,16330,24907, +chr1 13615979 13650590 NM_145381 0 - 13616941 13650531 0 7 1006,82,149,179,127,164,181, 0,1457,4166,12332,21486,24822,34430, +chr1 13658851 13691804 NM_001011873 0 + 13662573 13691464 0 4 97,639,221,969, 0,3355,15285,31984, +chr1 13775765 13777010 NR_004447 0 - 13777010 13777010 0 1 1245, 0, +chr1 14159038 14300280 NM_001252192 0 - 14160996 14294530 0 17 2039,101,122,115,161,59,90,84,140,187,83,138,143,70,78,50,554, 0,10522,14199,14423,15391,15668,39937,60535,62455,83470,84062,101747,105107,105576,114163,135467,140688, +chr1 14159038 14300280 NM_010164 0 - 14160996 14292974 0 18 2039,101,122,115,161,59,90,84,140,187,83,123,146,70,78,128,50,554, 0,10522,14199,14423,15391,15668,39937,60535,62455,83470,84062,101747,105107,105576,114163,133812,135467,140688, +chr1 14159038 14300280 NM_001310459 0 - 14160996 14292974 0 18 2039,101,122,115,161,59,90,84,140,187,83,138,143,70,78,128,50,554, 0,10522,14199,14423,15391,15668,39937,60535,62455,83470,84062,101747,105107,105576,114163,133812,135467,140688, +chr1 14743428 14746047 NM_001360810 0 - 14744599 14745829 0 3 978,37,737, 0,1158,1882, +chr1 14743428 14746047 NM_010827 0 - 14744319 14745829 0 2 978,737, 0,1882, +chr1 14862724 14908943 NM_177781 0 - 14863586 14908916 0 27 1085,98,111,69,183,130,170,90,166,71,99,60,94,167,115,165,170,101,100,49,137,146,109,108,176,160,138, 0,1720,3205,7555,8953,9468,11466,13106,14243,14951,16750,17751,18661,20539,23848,25365,25612,26703,27421,29218,30502,31503,31809,33279,38086,39716,46081, +chr1 14862724 14908943 NM_001348288 0 - 14863586 14908916 0 26 1085,98,111,69,183,130,170,166,71,99,60,94,167,115,165,170,101,100,49,137,146,109,108,176,160,138, 0,1720,3205,7555,8953,9468,11466,14243,14951,16750,17751,18661,20539,23848,25365,25612,26703,27421,29218,30502,31503,31809,33279,38086,39716,46081, +chr1 15277005 15713831 NM_001098528 0 + 15302532 15701710 0 3 560,668,14266, 0,25438,422560, +chr1 15795726 15834133 NR_152944 0 + 15834133 15834133 0 9 312,96,122,87,150,113,60,107,1132, 0,1995,7395,10240,13288,14005,25861,32536,37275, +chr1 15795726 15834133 NM_009352 0 + 15795758 15833163 0 10 312,96,122,87,150,113,60,89,107,1132, 0,1995,7395,10240,13288,14005,25861,27755,32536,37275, +chr1 15795726 15834133 NM_001286628 0 + 15795758 15833163 0 9 312,96,122,150,113,60,89,107,1132, 0,1995,7395,13288,14005,25861,27755,32536,37275, +chr1 15843942 15882803 NM_001033288 0 - 15845825 15882733 0 5 2001,177,91,195,284, 0,5027,6399,29784,38577, +chr1 16056059 16083406 NM_001243238 0 - 16056206 16071037 0 5 296,56,133,164,352, 0,2821,12589,14851,26995, +chr1 16056059 16083406 NM_001305227 0 - 16056206 16071037 0 6 296,56,133,164,843,352, 0,2821,12589,14851,15689,26995, +chr1 16091375 16094514 NM_011291 0 - 16091808 16094459 0 7 65,210,110,138,167,175,69, 0,432,1195,1397,1873,2215,3070, +chr1 16095962 16122631 NM_133832 0 + 16096098 16121498 0 6 425,236,99,146,132,1257, 0,1913,22283,23314,25193,25412, +chr1 16218890 16509383 NM_001111272 0 - 16219853 16499440 0 13 1057,89,308,61,132,138,213,108,160,136,160,67,130, 0,2193,116894,137269,140945,145864,161011,163707,165241,211513,234225,280532,290363, +chr1 16218890 16509383 NM_025303 0 - 16219853 16476214 0 14 1057,89,308,61,132,138,213,108,160,136,160,131,67,130, 0,2193,116894,137269,140945,145864,161011,163707,165241,211513,234225,257210,280532,290363, +chr1 16334373 16509196 NM_001347044 0 - 16335778 16476214 0 14 1719,61,132,138,213,108,160,136,160,131,67,54,37,108, 0,21786,25462,30381,45528,48224,49758,96030,118742,141727,165049,172589,174092,174715, +chr1 16334373 16509383 NM_001347045 0 - 16335778 16499440 0 11 1719,61,132,138,213,108,160,136,160,67,130, 0,21786,25462,30381,45528,48224,49758,96030,118742,165049,174880, +chr1 16530868 16609372 NM_001271016 0 - 16531852 16609332 0 7 1002,84,76,77,103,92,55, 0,3161,41139,44488,57163,61474,78449, +chr1 16558754 16609372 NM_025773 0 - 16561349 16609332 0 6 2609,76,156,103,92,55, 0,13253,16602,29277,33588,50563, +chr1 16558754 16609372 NR_073122 0 - 16609372 16609372 0 5 2609,76,156,92,55, 0,13253,16602,33588,50563, +chr1 16558754 16609372 NM_001271017 0 - 16561327 16609332 0 6 2609,76,77,103,92,55, 0,13253,16602,29277,33588,50563, +chr1 16631805 16647200 NM_001310470 0 - 16633368 16638039 0 5 1754,144,66,53,128, 0,3961,5263,6230,15267, +chr1 16632845 16646946 NM_026456 0 - 16633368 16638039 0 4 714,144,53,44, 0,2921,5190,14057, +chr1 16647632 16652359 NR_037998 0 + 16652359 16652359 0 4 2227,208,95,258, 0,2469,3003,4469, +chr1 16655271 16668356 NM_027415 0 + 16655388 16667506 0 3 315,106,1308, 0,2477,11777, +chr1 16655271 16668356 NM_026392 0 + 16655388 16667506 0 3 315,109,1308, 0,2474,11777, +chr1 16678536 16699686 NM_001159711 0 + 16678588 16699618 0 5 164,90,75,53,167, 0,3228,12393,17717,20983, +chr1 16678536 16699686 NM_016923 0 + 16678588 16699618 0 5 164,90,129,53,167, 0,3228,12339,17717,20983, +chr1 16985020 17087970 NM_020604 0 - 16987559 17087685 0 5 2620,644,119,760,664, 0,8951,21099,96358,102286, +chr1 17135453 17154351 NM_010267 0 + 17135552 17151590 0 6 216,193,174,95,115,3144, 0,1563,11588,13036,14551,15754, +chr1 17591981 17621020 NM_053191 0 + 17592659 17615051 0 6 142,308,119,133,116,6105, 0,676,17882,19500,19746,22934, +chr1 17666107 17717727 NR_130314 0 - 17717727 17717727 0 7 1078,158,57,210,145,68,548, 0,20969,31643,33659,36423,48495,51072, +chr1 17717125 17756425 NM_001356551 0 + 17718737 17754195 0 15 90,321,119,133,116,101,141,61,67,131,44,73,76,131,2282, 0,1549,18309,18735,19686,20456,22462,23220,23389,23689,25793,25923,29213,35067,37018, +chr1 17717497 17756288 NM_031402 0 + 17718737 17754195 0 15 347,321,119,133,116,101,141,61,67,131,44,73,76,131,2145, 0,1177,17937,18363,19314,20084,22090,22848,23017,23317,25421,25551,28841,34695,36646, +chr1 18105271 18135983 NM_001347048 0 - 18105709 18135934 0 8 566,89,98,149,91,135,65,59, 0,7547,9041,13451,14968,18848,21797,30653, +chr1 18105271 18135983 NM_001347047 0 - 18105709 18135934 0 9 566,89,98,149,91,135,65,117,59, 0,7547,9041,13451,14968,18848,21797,26225,30653, +chr1 18200133 18213645 NR_002879 0 - 18213645 18213645 0 2 178,44, 0,13468, +chr1 18226482 18227557 NM_001039123 0 - 18226553 18227524 0 2 259,103, 0,972, +chr1 18241058 18255219 NM_183124 0 - 18241280 18255161 0 2 356,113, 0,14048, +chr1 18250471 18255219 NM_001040027 0 - 18250604 18255161 0 2 276,113, 0,4635, +chr1 19053380 19094921 NR_151619 0 - 19094921 19094921 0 4 225,159,363,171, 0,1583,11802,41370, +chr1 19093102 19158668 NM_153154 0 + 19093336 19156259 0 8 273,498,61,166,119,142,114,2629, 0,1342,5228,15808,16140,39815,45282,62937, +chr1 19198994 19228926 NM_009334 0 + 19199248 19224428 0 7 335,459,61,220,119,142,4796, 0,5037,10279,17522,19528,22099,25136, +chr1 19198994 19228926 NM_001286340 0 + 19199248 19226711 0 8 335,459,61,220,119,142,257,2238, 0,5037,10279,17522,19528,22099,25136,27694, +chr1 19202134 19228926 NM_001025305 0 + 19202477 19224428 0 7 370,459,61,220,119,142,4796, 0,1897,7139,14382,16388,18959,21996, +chr1 20047859 20608138 NM_153179 0 - 20048378 20605404 0 67 932,123,159,108,88,136,1018,158,169,876,153,155,88,114,138,129,66,196,178,247,133,135,106,113,131,57,126,192,158,208,213,157,151,220,144,1602,68,196,136,131,276,106,123,185,128,139,176,128,143,91,90,279,115,142,96,102,71,40,65,75,79,58,109,142,78,137,147, 0,12599,15678,23407,45436,46763,59151,140239,141563,142741,151382,154058,162260,165080,181522,217740,230417,252746,254254,289432,292634,301061,303207,306340,316077,316933,319596,323624,333686,334233,356442,392442,445163,451114,462375,464885,476064,476757,479494,482535,489490,490312,491907,493068,495690,497299,500809,501642,504581,505844,506022,507820,508979,509669,512050,513560,526281,527379,527868,529045,530706,536132,550540,554923,555616,557490,560132, +chr1 20346534 20382381 NR_045734 0 + 20382381 20382381 0 3 252,125,409, 0,24641,35438, +chr1 20659962 20673039 NR_131249 0 + 20673039 20673039 0 3 120,155,246, 0,1068,12831, +chr1 20669090 20669163 NR_029593 0 + 20669163 20669163 0 1 73, 0, +chr1 20672849 20672968 NR_029902 0 + 20672968 20672968 0 1 119, 0, +chr1 20720985 20724577 NM_010552 0 + 20721042 20723940 0 3 84,212,875, 0,1191,2717, +chr1 20767229 20774351 NM_145856 0 - 20767847 20774280 0 3 856,221,98, 0,2142,7024, +chr1 20793048 20810393 NM_008563 0 - 20793536 20810289 0 17 687,91,77,104,141,151,127,175,209,132,154,109,239,131,209,113,182, 0,1849,2295,2829,3774,5753,6628,7090,8997,9596,9993,11431,11721,13681,14275,14825,17163, +chr1 20878730 20880554 NR_040492 0 - 20880554 20880554 0 4 490,180,84,366, 0,826,1196,1458, +chr1 20880628 20929731 NM_028829 0 + 20924704 20925769 0 3 139,180,5069, 0,41512,44034, +chr1 20907920 20929731 NM_001355122 0 + 20924704 20925769 0 3 50,180,5069, 0,14220,16742, +chr1 20941706 20980922 NM_027974 0 + 20941814 20980769 0 11 171,222,288,150,193,221,141,214,148,235,225, 0,3709,8504,9527,15698,21149,23273,27017,27784,37742,38991, +chr1 20991477 21069306 NM_177409 0 - 20991642 21069194 0 11 239,164,144,105,71,85,59,117,110,64,232, 0,1573,2441,2829,4170,4753,5456,11396,12005,36000,77597, +chr1 21208655 21220248 NM_029398 0 + 21215654 21219711 0 5 315,86,102,88,577, 0,6983,7370,8017,11016, +chr1 21208655 21220248 NM_001290679 0 + 21215654 21219666 0 5 315,86,102,88,760, 0,6983,7370,8017,10833, +chr1 21230665 21255656 NM_010356 0 + 21239852 21255043 0 7 75,108,52,133,142,132,733, 0,9166,16746,18263,19463,22208,24258, +chr1 21230665 21255656 NM_001288617 0 + 21248939 21255043 0 8 75,108,140,52,133,142,132,733, 0,9166,14099,16746,18263,19463,22208,24258, +chr1 21230665 21255656 NM_001077353 0 + 21239852 21255043 0 8 75,95,108,52,133,142,132,733, 0,4353,9166,16746,18263,19463,22208,24258, +chr1 21275326 21288393 NR_002858 0 - 21288393 21288393 0 6 488,132,71,133,52,272, 0,2896,6049,8234,9680,12795, +chr1 21339757 21342280 NM_183322 0 + 21340100 21341174 0 3 443,183,1324, 0,581,1199, +chr1 21358411 21359824 NM_001033904 0 + 21358738 21359808 0 3 427,183,234, 0,561,1179, +chr1 21373636 21376465 NM_001113187 0 + 21374017 21374980 0 3 481,183,1583, 0,619,1246, +chr1 21388479 21952731 NM_001310477 0 - 21392243 21951662 0 13 4727,127,132,109,221,95,96,111,126,176,127,91,1470, 0,6533,7394,25650,59005,71071,80975,88824,106901,107285,136662,195125,562782, +chr1 21388483 21952023 NM_023872 0 - 21392243 21951662 0 14 4723,127,132,109,221,27,95,96,111,126,176,127,91,762, 0,6529,7390,25646,59001,67980,71067,80971,88820,106897,107281,136658,195121,562778, +chr1 21388483 21952023 NM_001160139 0 - 21392243 21951662 0 15 4723,127,132,109,221,57,27,95,96,111,126,176,127,91,762, 0,6529,7390,25646,59001,63148,67980,71067,80971,88820,106897,107281,136658,195121,562778, +chr1 22276053 22812842 NM_053270 0 - 22278502 22812563 0 32 2668,140,102,113,139,236,167,113,113,183,72,84,90,63,126,157,72,131,113,47,124,100,111,65,73,235,338,12,214,69,81,443, 0,4087,5040,6849,10885,60320,87371,93455,111478,112626,118471,126238,135768,139898,141489,142492,146799,198976,203510,206473,210220,213939,215427,217373,264184,264791,269071,324878,327156,361197,457715,536346, +chr1 22276053 22812842 NM_001012625 0 - 22278502 22812563 0 27 2668,140,102,113,139,236,167,113,113,126,157,72,131,113,47,124,100,111,65,73,235,338,12,214,69,81,443, 0,4087,5040,6849,10885,60320,87371,93455,111478,141489,142492,146799,198976,203510,206473,210220,213939,215427,217373,264184,264791,269071,324878,327156,361197,457715,536346, +chr1 22276053 22812842 NM_001012624 0 - 22278502 22812563 0 29 2668,140,102,113,139,236,167,113,112,91,63,126,157,72,131,113,47,124,100,111,65,73,235,338,12,214,69,81,443, 0,4087,5040,6849,10885,60320,87371,93455,111478,135767,139898,141489,142492,146799,198976,203510,206473,210220,213939,215427,217373,264184,264791,269071,324878,327156,361197,457715,536346, +chr1 22276053 22812842 NM_183018 0 - 22278502 22812563 0 31 2668,140,102,113,139,236,167,113,113,183,72,90,63,126,157,72,131,113,47,124,100,111,65,73,235,338,12,214,69,81,443, 0,4087,5040,6849,10885,60320,87371,93455,111478,112626,118471,135768,139898,141489,142492,146799,198976,203510,206473,210220,213939,215427,217373,264184,264791,269071,324878,327156,361197,457715,536346, +chr1 22276053 22812842 NM_001012623 0 - 22278502 22812563 0 30 2668,140,102,113,139,236,167,113,112,73,90,63,126,157,72,131,113,47,124,100,111,65,73,235,338,12,214,69,81,443, 0,4087,5040,6849,10885,60320,87371,93455,111478,118470,135768,139898,141489,142492,146799,198976,203510,206473,210220,213939,215427,217373,264184,264791,269071,324878,327156,361197,457715,536346, +chr1 22905225 22911920 NR_151543 0 + 22911920 22911920 0 3 140,75,1232, 0,5022,5463, +chr1 23107312 23109092 NM_025746 0 - 23108608 23109070 0 1 1780, 0, +chr1 23279107 23279178 NR_029533 0 + 23279178 23279178 0 1 71, 0, +chr1 23298539 23298623 NR_029717 0 + 23298623 23298623 0 1 84, 0, +chr1 23373262 23390014 NM_001081079 0 - 23376587 23389890 0 7 4025,146,67,79,79,87,361, 0,9306,9564,9747,12302,12548,16391, +chr1 23581425 23603489 NR_151529 0 + 23603489 23603489 0 4 128,240,142,254, 0,1360,2088,21810, +chr1 23768764 23854697 NM_172124 0 + 23769473 23852026 0 4 1303,145,149,2758, 0,53295,82947,83175, +chr1 23851663 23916575 NR_110972 0 - 23916575 23916575 0 11 533,212,308,166,128,91,77,76,86,134,74, 0,1527,3439,4478,8598,14198,21392,31549,32884,47035,64838, +chr1 23852463 23929220 NM_028534 0 - 23853267 23928994 0 10 939,308,166,128,91,81,76,86,134,344, 0,2639,3678,7798,13398,20592,30749,32084,46235,76413, +chr1 23852463 23929220 NM_001357395 0 - 23853267 23928994 0 11 939,308,166,128,91,81,81,76,86,134,344, 0,2639,3678,7798,13398,20592,25813,30749,32084,46235,76413, +chr1 23852463 23916575 NM_001290683 0 - 23853267 23884630 0 10 939,308,166,128,91,81,76,86,134,74, 0,2639,3678,7798,13398,20592,30749,32084,46235,64038, +chr1 24002777 24012479 NM_026503 0 - 24003089 24012439 0 3 422,150,95, 0,7218,9607, +chr1 24017596 24107180 NM_026604 0 - 24019130 24092326 0 21 1740,114,111,152,98,92,161,2329,155,74,156,50,154,127,174,71,140,80,116,92,281, 0,4021,9917,11096,13455,14024,15850,17442,19984,21905,33356,35600,42425,43246,44986,46446,46608,57141,74653,75762,89303, +chr1 24184448 24259577 NM_007740 0 + 24184693 24258700 0 38 259,74,78,133,397,84,21,75,36,63,54,36,24,54,54,33,57,54,54,54,54,54,54,54,54,45,54,54,54,72,36,45,33,147,55,189,78,1062, 0,649,1674,1865,7428,17073,17907,19281,19690,19834,24404,24687,27048,27444,29776,30564,31449,32763,36929,39926,43134,43969,44160,44335,44812,45965,46894,47037,52586,53273,53841,54575,55961,59515,59832,61597,66748,74067, +chr1 24202041 24259577 NM_001290691 0 + 24202218 24258700 0 32 255,75,36,63,54,36,24,54,54,33,57,54,54,54,54,54,54,54,54,45,54,54,54,72,36,45,33,147,55,189,78,1062, 0,1688,2097,2241,6811,7094,9455,9851,12183,12971,13856,15170,19336,22333,25541,26376,26567,26742,27219,28372,29301,29444,34993,35680,36248,36982,38368,41922,42239,44004,49155,56474, +chr1 24264521 24594276 NM_007733 0 - 24271528 24582262 0 51 7135,78,129,67,171,45,36,63,45,45,54,27,45,51,45,54,54,54,54,105,42,54,54,36,78,45,90,54,54,54,36,36,63,42,54,54,54,36,54,54,45,45,63,126,81,276,124,100,66,127,88, 0,7282,12683,22249,24734,27370,27571,31984,32145,35389,39077,42910,43592,43717,45773,48577,49963,54364,54629,54765,57715,59709,59850,60007,64350,64531,65256,65999,67567,68296,68448,70353,74747,80215,94599,116900,152513,194079,196061,203793,250501,253160,267921,268702,272245,276350,279196,301971,303620,317650,329667, +chr1 24685382 24823146 NM_026719 0 + 24685595 24819581 0 16 273,177,61,98,68,89,74,126,153,65,103,105,150,79,92,3679, 0,56859,64403,76283,77439,82974,86371,100008,103209,115345,115718,116328,118267,120262,133654,134085, +chr1 24685756 24823144 NM_001310483 0 + 24742391 24819581 0 16 117,177,61,98,68,89,74,126,153,65,103,105,150,79,92,3677, 0,56485,64029,75909,77065,82600,85997,99634,102835,114971,115344,115954,117893,119888,133280,133711, +chr1 25124320 25886552 NM_175642 0 - 25125012 25883605 0 31 881,105,36,644,40,96,172,99,86,67,70,151,103,104,127,44,103,76,150,109,69,195,107,102,165,165,165,162,111,772,246, 0,7209,16768,26289,31400,33957,44216,44701,49813,59165,61343,63775,154284,159244,160945,328960,353082,363947,364951,389516,393267,420449,436957,437437,464394,464999,479940,486199,492279,758528,761986, +chr1 25333248 25334799 NM_001204913 0 - 25333416 25333791 0 1 1551, 0, +chr1 26738645 26744305 NM_001033764 0 - 26738796 26744271 0 2 4111,220, 0,5440, +chr1 27940890 27959032 NR_151583 0 + 27959032 27959032 0 2 33,1760, 0,16382, +chr1 28832966 28837097 NM_001013750 0 - 28833103 28837043 0 2 2663,219, 0,3912, +chr1 29478332 29478457 NR_105760 0 + 29478457 29478457 0 1 125, 0, +chr1 30177857 30195681 NR_157039 0 - 30195681 30195681 0 4 941,203,69,992, 0,1681,9030,16832, +chr1 30177857 30195681 NR_157038 0 - 30195681 30195681 0 4 941,203,185,992, 0,1681,9030,16832, +chr1 30177857 30195681 NR_157037 0 - 30195681 30195681 0 5 941,203,185,43,992, 0,1681,9030,14155,16832, +chr1 30859186 30920101 NM_001081080 0 - 30860643 30920075 0 15 3601,196,90,148,196,136,132,117,157,145,184,310,1717,162,270, 0,3827,6381,8341,9430,10675,11618,14126,17739,18341,18789,21868,27501,34763,60645, +chr1 30997147 31006600 NM_011200 0 - 31000050 31002987 0 6 3021,75,131,93,602,207, 0,3629,4233,4635,5735,9246, +chr1 30998436 31006555 NR_002688 0 - 31006555 31006555 0 7 1732,75,131,93,197,394,162, 0,2340,2944,3346,4446,4654,7957, +chr1 31006715 31008180 NR_164183 0 + 31008180 31008180 0 1 1465, 0, +chr1 31076032 31153299 NR_136907 0 - 31153299 31153299 0 4 498,112,188,83, 0,1664,28397,77184, +chr1 31197922 31279501 NR_033445 0 - 31279501 31279501 0 3 691,222,181, 0,63174,81398, +chr1 31233279 31261570 NM_153601 0 + 31233295 31261375 0 5 46,133,162,167,1395, 0,12931,13928,20347,26896, +chr1 31279683 31281132 NM_029062 0 + 31279783 31280440 0 1 1449, 0, +chr1 31321691 31324906 NR_015347 0 + 31324906 31324906 0 2 143,771, 0,2444, +chr1 32229566 32715414 NM_133235 0 + 32229762 32714386 0 9 287,128,117,147,128,199,83,59,1126, 0,71178,160744,242149,295038,299845,446449,471371,484722, +chr1 32576407 32577844 NM_001199956 0 - 32576407 32577844 0 1 1437, 0, +chr1 32600390 32604138 NM_001164286 0 - 32602235 32603672 0 1 3748, 0, +chr1 33510652 33726639 NM_008922 0 - 33510930 33725856 0 14 497,69,83,127,186,73,68,138,96,121,80,104,163,171, 0,10245,26650,30874,58208,60337,79488,174587,176530,208438,209969,213237,215050,215816, +chr1 33726668 33727557 NR_033199 0 + 33727557 33727557 0 1 889, 0, +chr1 33771025 33776691 NR_157041 0 - 33776691 33776691 0 4 160,93,95,67, 0,277,2786,5599, +chr1 33776740 33799409 NM_008999 0 + 33780695 33796237 0 8 278,92,220,86,157,83,93,3312, 0,1712,3890,5038,14806,16904,18392,19357, +chr1 33777263 33799409 NM_001159729 0 + 33780695 33796237 0 8 166,92,220,86,157,83,93,3312, 0,1189,3367,4515,14283,16381,17869,18834, +chr1 33802328 33814595 NM_145392 0 - 33803451 33814536 0 3 1533,110,172, 0,2733,12095, +chr1 33818385 33871440 NM_001290699 0 - 33819007 33839977 0 13 669,66,187,131,141,1595,148,154,127,151,81,84,258, 0,4303,8180,9228,11352,14728,17503,18355,20527,21500,43798,52186,52797, +chr1 33818385 33871440 NM_133817 0 - 33819007 33871203 0 15 669,66,187,131,141,1595,148,154,127,151,112,126,81,84,258, 0,4303,8180,9228,11352,14728,17503,18355,20527,21500,22312,24866,43798,52186,52797, +chr1 33818389 33871440 NM_001359275 0 - 33821373 33871203 0 16 665,56,66,187,131,141,1595,148,154,127,151,112,126,81,84,258, 0,2969,4299,8176,9224,11348,14724,17499,18351,20523,21496,22308,24862,43794,52182,52793, +chr1 33818389 33871440 NM_001359274 0 - 33819007 33871203 0 14 665,66,187,131,1595,148,154,127,151,112,126,81,84,258, 0,4299,8176,9224,14724,17499,18351,20523,21496,22308,24862,43794,52182,52793, +chr1 33858804 33871440 NM_001290700 0 - 33858964 33871203 0 4 1654,81,84,258, 0,3379,11767,12378, +chr1 33892743 33895759 NM_001161816 0 - 33892966 33895525 0 1 3016, 0, +chr1 33908896 33964612 NM_001310484 0 - 33910198 33935216 0 6 1316,120,193,221,178,202, 0,10602,11690,12471,26208,55514, +chr1 33908896 33964466 NM_177235 0 - 33910198 33940405 0 7 1316,120,193,221,178,208,56, 0,10602,11690,12471,26208,31389,55514, +chr1 33965069 34365507 NM_001276764 0 + 33965116 34364437 0 103 228,35,201,208,62,90,78,93,167,113,107,120,96,128,94,155,463,129,78,162,105,96,126,150,155,127,184,158,179,139,194,163,84,108,99,129,89,133,5292,150,216,150,234,153,234,267,546,177,124,209,318,167,157,127,63,242,130,200,496,1472,162,171,167,160,327,85,242,207,120,108,219,204,232,227,123,102,102,174,156,198,129,171,156,207,120,170,160,195,129,144,189,130,164,163,155,75,18,118,72,203,111,124,1333, 0,774,60478,97966,178017,205708,207893,209207,226865,243977,244188,246288,248374,248556,252395,252779,254784,255401,255672,255851,256102,256833,257955,258717,259051,259386,259598,260939,261525,262135,262891,263958,264777,265890,266472,275791,277737,278594,279747,285167,285780,286290,287603,288976,290293,291067,292645,294220,300329,302929,303997,304677,306309,307261,309585,310110,311171,315579,317284,319550,334394,336119,339424,341254,341579,342385,343471,344586,348007,348317,349497,351939,353795,355039,356300,356525,358632,360004,360510,362603,363130,365943,366980,367448,369795,374198,376034,378962,379666,381299,382134,383562,385095,386159,386929,387237,388517,391496,393636,394605,395196,398303,399105, +chr1 34068439 34365501 NM_133833 0 + 34068669 34364437 0 93 321,62,90,78,93,167,113,107,120,96,128,94,155,463,129,78,162,105,96,126,150,155,127,184,158,179,139,194,163,84,108,99,129,89,133,153,234,267,546,177,124,209,318,167,157,127,63,242,130,200,496,1472,162,171,167,160,85,242,207,120,108,219,204,232,227,123,102,102,174,156,198,129,171,156,207,120,170,160,195,129,144,189,130,164,163,155,75,18,118,72,203,124,1327, 0,74647,102338,104523,105837,123495,140607,140818,142918,145004,145186,149025,149409,151414,152031,152302,152481,152732,153463,154585,155347,155681,156016,156228,157569,158155,158765,159521,160588,161407,162520,163102,172421,174367,175224,185606,186923,187697,189275,190850,196959,199559,200627,201307,202939,203891,206215,206740,207801,212209,213914,216180,231024,232749,236054,237884,239015,240101,241216,244637,244947,246127,248569,250425,251669,252930,253155,255262,256634,257140,259233,259760,262573,263610,264078,266425,270828,272664,275592,276296,277929,278764,280192,281725,282789,283559,283867,285147,288126,290266,291235,294933,295735, +chr1 34068439 34365501 NM_134448 0 + 34068669 34364437 0 98 321,62,90,78,93,167,113,107,120,96,128,94,155,463,129,78,162,105,96,126,150,155,127,184,158,179,139,194,163,84,108,99,129,89,133,5292,150,216,150,234,153,234,267,546,177,124,209,318,167,157,127,63,242,130,200,496,1472,162,171,167,160,85,242,207,120,108,219,204,232,227,123,102,102,174,156,198,129,171,156,207,120,170,160,195,129,144,189,130,164,163,155,75,18,118,72,203,124,1327, 0,74647,102338,104523,105837,123495,140607,140818,142918,145004,145186,149025,149409,151414,152031,152302,152481,152732,153463,154585,155347,155681,156016,156228,157569,158155,158765,159521,160588,161407,162520,163102,172421,174367,175224,176377,181797,182410,182920,184233,185606,186923,187697,189275,190850,196959,199559,200627,201307,202939,203891,206215,206740,207801,212209,213914,216180,231024,232749,236054,237884,239015,240101,241216,244637,244947,246127,248569,250425,251669,252930,253155,255262,256634,257140,259233,259760,262573,263610,264078,266425,270828,272664,275592,276296,277929,278764,280192,281725,282789,283559,283867,285147,288126,290266,291235,294933,295735, +chr1 34174203 34174276 NR_105861 0 + 34174276 34174276 0 1 73, 0, +chr1 34217104 34240748 NM_010081 0 + 34217174 34239881 0 24 237,94,155,463,129,78,162,105,96,126,150,155,127,184,158,179,139,194,163,84,108,99,2703,2769, 0,360,744,2749,3366,3637,3816,4067,4798,5920,6682,7016,7351,7563,8904,9490,10100,10856,11923,12742,13855,14437,17536,20875, +chr1 34489965 34490044 NR_039562 0 - 34490044 34490044 0 1 79, 0, +chr1 34493514 34496517 NM_027159 0 - 34494342 34496183 0 5 941,132,83,104,445, 0,1057,2180,2373,2558, +chr1 34496673 34502592 NM_178601 0 + 34496769 34501315 0 9 99,109,84,110,133,155,95,74,1390, 0,212,3081,3549,3734,3940,4168,4367,4529, +chr1 34516590 34530624 NM_011206 0 + 34516668 34530491 0 15 171,109,77,96,39,69,63,143,67,78,90,89,206,75,201, 0,2956,3361,3523,3720,8547,10094,10454,11747,11895,12066,12357,13017,13589,13833, +chr1 34555256 34559907 NM_009355 0 + 34555301 34559792 0 5 217,163,275,170,439, 0,816,1604,3615,4212, +chr1 34555256 34559907 NM_001360855 0 + 34556936 34559792 0 6 217,163,66,275,170,439, 0,816,1232,1604,3615,4212, +chr1 34592492 34601156 NM_007685 0 + 34592747 34600982 0 6 308,50,168,115,110,287, 0,550,702,1484,1678,8377, +chr1 34592492 34601156 NR_153806 0 + 34601156 34601156 0 5 308,50,168,110,287, 0,550,702,1678,8377, +chr1 34609176 34617788 NM_009356 0 - 34609339 34617749 0 5 478,170,275,163,214, 0,3637,5521,7411,8398, +chr1 34636537 34647789 NM_213727 0 + 34643526 34645869 0 2 74,4282, 0,6970, +chr1 34690379 34693055 NR_033627 0 - 34693055 34693055 0 1 2676, 0, +chr1 34735026 34869583 NM_001368773 0 + 34735068 34868674 0 14 81,3456,300,127,137,180,180,180,233,130,132,244,78,1061, 0,43522,53927,67136,115044,126732,127774,128133,128877,129460,131515,132129,132904,133496, +chr1 34858585 34869583 NM_183019 0 + 34861812 34868674 0 10 261,180,180,180,233,130,132,244,78,1061, 0,3173,4215,4574,5318,5901,7956,8570,9345,9937, +chr1 34870062 34899895 NM_001160236 0 - 34874858 34893647 0 7 4187,130,199,143,81,81,223, 0,4779,6374,6649,15549,23515,29610, +chr1 34870062 34899895 NM_001160235 0 - 34874858 34893647 0 8 4187,130,178,143,36,81,81,223, 0,4779,6374,6649,10802,15549,23515,29610, +chr1 34870062 34899895 NM_174997 0 - 34874858 34893647 0 7 4187,130,178,143,81,81,223, 0,4779,6374,6649,15549,23515,29610, +chr1 34906803 34928402 NM_175421 0 + 34918725 34926336 0 7 105,45,153,103,40,90,2258, 0,11914,13047,13512,14514,16182,19341, +chr1 34906803 34936430 NM_145516 0 + 34918725 34933892 0 8 105,45,153,103,40,90,106,2675, 0,11914,13047,13512,14514,16182,19341,26952, +chr1 34906833 34936399 NM_001357425 0 + 34918725 34933892 0 9 75,112,45,153,103,40,90,106,2644, 0,2236,11884,13017,13482,14484,16152,19311,26922, +chr1 36125244 36163291 NM_015818 0 + 36125502 36161066 0 2 785,2934, 0,35113, +chr1 36196872 36301147 NM_198899 0 - 36201070 36300972 0 41 4224,154,117,115,161,183,85,102,89,85,86,159,190,80,103,96,131,132,207,95,24,99,121,165,132,136,86,120,151,92,61,100,101,79,97,175,113,131,83,136,233, 0,6004,6597,10017,11606,15045,16199,17372,18080,19914,21648,22177,23193,24416,25481,30171,33407,34051,34868,36205,36748,37490,39531,42442,44328,45805,51501,52358,55822,57516,61677,62751,67914,69958,71362,76104,81184,87456,90630,94779,104042, +chr1 36201096 36201158 NR_105862 0 - 36201158 36201158 0 1 62, 0, +chr1 36321446 36330270 NM_153408 0 - 36323204 36330210 0 4 1952,54,489,88, 0,4054,4611,8736, +chr1 36364577 36380874 NR_033310 0 + 36380874 36380874 0 6 104,119,53,98,166,5038, 0,8476,9877,10351,10755,11259, +chr1 36364577 36380874 NM_001290726 0 + 36368722 36377048 0 8 104,95,119,121,53,98,166,5038, 0,4141,8476,9471,9877,10351,10755,11259, +chr1 36364577 36380874 NM_001290727 0 + 36375414 36377048 0 6 104,116,53,98,166,5038, 0,8479,9877,10351,10755,11259, +chr1 36364577 36380874 NM_001172206 0 + 36364677 36377048 0 7 104,116,121,53,98,166,5038, 0,8479,9471,9877,10351,10755,11259, +chr1 36364577 36380874 NM_001172205 0 + 36364677 36377048 0 7 104,119,121,53,98,166,5038, 0,8476,9471,9877,10351,10755,11259, +chr1 36364577 36380874 NM_145996 0 + 36364677 36377048 0 5 104,119,98,166,5038, 0,8476,10351,10755,11259, +chr1 36392574 36426026 NM_172652 0 - 36394475 36424828 0 21 1922,134,223,110,131,82,192,157,201,64,158,75,72,102,117,132,186,91,171,266,77, 0,7521,7943,8340,9186,9655,10108,12795,13088,13672,15903,16196,17864,18042,18368,18919,22310,22640,29752,32039,33375, +chr1 36392574 36426026 NM_001310513 0 - 36394475 36424828 0 22 1922,134,223,110,131,82,192,78,157,201,64,158,75,72,102,117,132,186,91,171,266,77, 0,7521,7943,8340,9186,9655,10108,11487,12795,13088,13672,15903,16196,17864,18042,18368,18919,22310,22640,29752,32039,33375, +chr1 36405526 36405603 NR_105863 0 - 36405603 36405603 0 1 77, 0, +chr1 36429034 36478955 NM_001277076 0 + 36429135 36478754 0 53 186,53,92,109,55,110,129,63,51,31,116,121,53,69,44,83,95,129,178,125,101,178,156,129,164,115,103,176,171,133,78,182,162,105,147,163,26,51,105,120,162,92,171,149,140,89,96,142,100,191,110,148,372, 0,1496,2326,2982,4539,5665,6197,7288,8174,10595,12895,13248,13901,14991,16396,16527,16701,18338,20113,29164,30307,31027,31282,32564,34319,34739,35693,36305,36583,36952,37190,38672,39039,39372,40367,40589,40900,42586,42743,43401,44277,44683,45175,45534,45912,47490,47789,48052,48407,48583,48937,49291,49549, +chr1 36480030 36502116 NM_001310517 0 - 36481205 36502078 0 9 1318,120,115,162,33,83,118,119,222, 0,1652,4916,5114,6237,15564,16423,20305,21864, +chr1 36480030 36502116 NM_001013374 0 - 36481205 36502078 0 8 1318,120,115,162,83,118,119,222, 0,1652,4916,5114,15564,16423,20305,21864, +chr1 36528441 36565621 NM_033570 0 + 36528537 36563451 0 7 1489,144,135,170,97,179,2368, 0,26393,26798,27814,28288,34004,34812, +chr1 36568711 36585081 NM_001331209 0 + 36568755 36582075 0 8 1287,144,147,170,97,134,139,3071, 0,7085,8214,8652,8952,9338,9834,13299, +chr1 36568711 36585081 NM_053186 0 + 36568755 36582075 0 8 1287,144,150,170,97,134,139,3071, 0,7085,8211,8652,8952,9338,9834,13299, +chr1 36568711 36585081 NM_001039551 0 + 36568755 36580928 0 9 1287,144,150,170,97,134,139,99,3071, 0,7085,8211,8652,8952,9338,9834,12167,13299, +chr1 36587037 36593401 NM_001310521 0 - 36588390 36589512 0 9 1449,99,99,99,99,126,129,147,60, 0,1530,1716,1919,2109,2388,3794,4098,6304, +chr1 36587037 36592584 NM_153502 0 - 36588390 36592553 0 9 1449,99,99,99,99,126,129,147,58, 0,1530,1716,1919,2109,2388,3794,4098,5489, +chr1 36595015 36604097 NM_026241 0 - 36596235 36604030 0 4 1364,204,104,167, 0,3688,4591,8915, +chr1 36595015 36604097 NM_001310533 0 - 36596318 36604030 0 4 1364,239,104,167, 0,3653,4591,8915, +chr1 36595015 36604097 NR_132321 0 - 36604097 36604097 0 4 1364,204,104,343, 0,3688,4591,8739, +chr1 36605483 36614402 NM_001304329 0 - 36606383 36612885 0 15 1730,71,161,113,223,145,176,152,117,97,99,63,149,149,198, 0,1867,2029,3087,3288,3613,4080,4340,4585,4832,5077,5287,5613,7293,8721, +chr1 36605483 36614402 NM_001304330 0 - 36606383 36612885 0 16 1730,71,161,113,223,145,176,152,117,97,99,63,149,146,283,198, 0,1867,2029,3087,3288,3613,4080,4340,4585,4832,5077,5287,5613,7293,8164,8721, +chr1 36605483 36615226 NM_001126047 0 - 36606383 36612885 0 15 1730,71,161,113,223,145,176,152,117,97,99,63,149,146,366, 0,1867,2029,3087,3288,3613,4080,4340,4585,4832,5077,5287,5613,7293,9377, +chr1 36619540 36650177 NM_027957 0 - 36619832 36642808 0 6 325,153,78,126,88,135, 0,1634,2135,15823,23220,30502, +chr1 36619540 36740028 NM_001126046 0 - 36619832 36717792 0 15 325,153,78,126,88,98,177,85,115,85,106,153,62,315,316, 0,1634,2135,15823,23220,37427,37712,38171,45721,69724,72471,81514,96668,98039,120172, +chr1 36619542 36739992 NM_001372417 0 - 36619832 36717792 0 16 323,153,78,126,88,98,177,85,115,85,106,153,123,62,315,280, 0,1632,2133,15821,23218,37425,37710,38169,45719,69722,72469,81512,94113,96666,98037,120170, +chr1 36619542 36739992 NM_001372416 0 - 36619832 36717792 0 17 323,153,78,126,88,98,177,85,162,115,85,106,153,123,62,315,280, 0,1632,2133,15821,23218,37425,37710,38169,39021,45719,69722,72469,81512,94113,96666,98037,120170, +chr1 36656818 36740028 NM_201365 0 - 36656921 36717792 0 10 247,177,85,115,85,106,153,62,315,316, 0,434,893,8443,32446,35193,44236,59390,60761,82894, +chr1 36748331 36750233 NM_009942 0 + 36748431 36750154 0 4 203,74,100,192, 0,724,964,1710, +chr1 36756046 36766770 NM_146107 0 - 36756920 36766698 0 11 977,41,62,175,93,217,125,126,76,65,120, 0,1135,1334,1932,2219,2483,2857,3273,7668,8989,10604, +chr1 36771381 36814804 NM_001374322 0 + 36771457 36803339 0 9 161,63,87,84,102,99,151,210,170, 0,4285,8828,10678,19311,27741,29974,31825,43253, +chr1 36818642 36839665 NM_009539 0 + 36827655 36839429 0 13 145,411,161,139,85,44,52,196,207,193,141,113,360, 0,9004,9991,16355,16582,16749,16953,17319,17887,19039,19321,19548,20663, +chr1 36821359 36839665 NM_001289766 0 + 36821449 36839429 0 13 153,411,161,139,85,44,52,196,207,193,141,113,360, 0,6287,7274,13638,13865,14032,14236,14602,15170,16322,16604,16831,17946, +chr1 36823778 36839665 NM_001289765 0 + 36827655 36839429 0 13 188,411,161,139,85,44,52,196,207,193,141,113,360, 0,3868,4855,11219,11446,11613,11817,12183,12751,13903,14185,14412,15527, +chr1 36835828 36839665 NM_001289612 0 + 36835996 36839429 0 6 329,207,193,141,113,360, 0,701,1853,2135,2362,3477, +chr1 36849033 36996372 NM_018872 0 - 36849765 36996190 0 41 1017,155,98,97,122,163,150,125,128,179,593,159,186,187,143,152,67,110,139,118,76,153,87,105,135,111,171,154,109,109,62,57,151,81,123,117,124,69,41,62,363, 0,1855,2615,2912,3106,3973,6753,7090,9636,12279,15695,16638,18092,19219,19972,20368,23266,23698,23920,26469,26704,26874,30878,32527,33023,33240,34822,35073,35876,37377,41307,42427,42573,45770,48200,49405,62655,80323,89145,97075,146976, +chr1 37086157 37244452 NM_001370828 0 + 37092598 37243815 0 28 116,232,95,251,163,170,116,126,191,155,139,132,99,177,131,158,114,88,157,119,51,202,112,125,138,101,177,716, 0,6324,12982,15645,22404,31017,34121,55920,71323,79683,85148,86345,94638,99571,106122,108417,111778,113416,113598,128020,135187,136333,144522,146183,148016,149804,157216,157579, +chr1 37086157 37198180 NM_001370829 0 + 37092598 37198156 0 17 116,161,95,251,163,170,116,126,191,155,139,132,99,177,131,158,245, 0,6395,12982,15645,22404,31017,34121,55920,71323,79683,85148,86345,94638,99571,106122,108417,111778, +chr1 37275122 37320229 NM_001282010 0 + 37289089 37318941 0 8 164,111,137,114,180,108,107,2688, 0,1150,13931,23549,26555,35679,39715,42419, +chr1 37276049 37320229 NM_009918 0 + 37289089 37318941 0 6 334,137,180,108,107,2688, 0,13004,25628,34752,38788,41492, +chr1 37356682 37467585 NM_030266 0 + 37414763 37465104 0 26 281,62,210,45,119,117,80,112,91,148,131,105,109,18,184,219,139,33,173,124,127,141,98,113,155,2614, 0,57505,57977,58670,64272,66325,66701,67032,67919,68439,69520,71864,72473,74434,77740,79003,80084,83501,87860,88949,89812,90211,93105,96232,98928,108289, +chr1 37356682 37467585 NM_001290797 0 + 37414763 37465104 0 26 281,62,210,45,119,117,80,112,91,148,131,105,109,15,184,219,256,33,173,124,127,141,98,113,155,2614, 0,57505,57977,58670,64272,66325,66701,67032,67919,68439,69520,71864,72473,74437,77740,79003,80084,83501,87860,88949,89812,90211,93105,96232,98928,108289, +chr1 37356740 37467580 NM_001374630 0 + 37414763 37465104 0 25 223,62,210,45,119,117,80,112,91,148,131,105,109,184,219,139,33,173,124,127,141,98,113,155,2609, 0,57447,57919,58612,64214,66267,66643,66974,67861,68381,69462,71806,72415,77682,78945,80026,83443,87802,88891,89754,90153,93047,96174,98870,108231, +chr1 37356740 37467580 NM_001374629 0 + 37414763 37465104 0 25 223,62,210,45,119,117,80,112,91,148,131,105,109,184,219,256,33,173,124,127,141,98,113,155,2609, 0,57447,57919,58612,64214,66267,66643,66974,67861,68381,69462,71806,72415,77682,78945,80026,83443,87802,88891,89754,90153,93047,96174,98870,108231, +chr1 37426061 37461287 NM_172971 0 + 37426179 37460474 0 16 272,105,109,18,184,219,139,33,173,124,127,141,98,113,155,994, 0,2485,3094,5055,8361,9624,10705,14122,18481,19570,20433,20832,23726,26853,29549,34232, +chr1 37426061 37461287 NM_001290799 0 + 37426179 37460474 0 15 272,105,109,15,184,219,139,173,124,127,141,98,113,155,994, 0,2485,3094,5058,8361,9624,10705,18481,19570,20433,20832,23726,26853,29549,34232, +chr1 37426061 37461287 NM_001290798 0 + 37426179 37460474 0 15 272,105,109,18,184,219,139,173,124,127,141,98,113,155,994, 0,2485,3094,5055,8361,9624,10705,18481,19570,20433,20832,23726,26853,29549,34232, +chr1 37473929 37486948 NM_198006 0 - 37477430 37486812 0 3 3543,84,235, 0,11257,12784, +chr1 37486983 37495831 NM_001356528 0 + 37488141 37495663 0 6 144,284,121,140,102,305, 0,1154,2412,7023,7238,8543, +chr1 37486983 37495831 NM_026123 0 + 37488141 37495663 0 6 355,284,121,140,102,305, 0,1154,2412,7023,7238,8543, +chr1 37496184 37597861 NM_173870 0 - 37501503 37592977 0 16 5346,113,67,79,194,108,131,115,76,114,47,134,141,168,366,52, 0,5467,9756,10989,12891,13182,15404,17250,23552,25081,27197,50920,56533,59233,96699,101625, +chr1 37496184 37593249 NM_001290801 0 - 37501503 37592977 0 15 5346,113,67,79,194,108,131,115,76,114,47,134,141,141,366, 0,5467,9756,10989,12891,13182,15404,17250,23552,25081,27197,50920,56533,59260,96699, +chr1 37542695 37545450 NR_024017 0 - 37545450 37545450 0 1 2755, 0, +chr1 37668520 37776656 NM_028096 0 - 37669101 37701475 0 10 721,145,188,2308,210,162,136,169,80,242, 0,1661,2805,12085,16541,19645,20140,26185,32885,107894, +chr1 37811416 37921927 NM_207228 0 - 37812341 37898080 0 20 950,147,105,203,210,186,111,169,56,155,116,152,78,171,159,168,66,216,129,60, 0,6377,6858,8735,29245,47148,50057,52365,56400,60960,64953,79614,80686,80850,85927,86613,87883,94659,100673,110451, +chr1 37817668 37912218 NM_001290721 0 - 37817789 37898080 0 18 272,105,203,210,186,111,169,56,155,116,152,78,171,159,168,66,216,129, 0,606,2483,22993,40896,43805,46113,50148,54708,58701,73362,74434,74598,79675,80361,81631,88407,94421, +chr1 37817668 37922143 NM_001290720 0 - 37817789 37898080 0 18 272,105,203,186,111,169,56,155,116,152,78,171,159,168,66,216,129,193, 0,606,2483,40896,43805,46113,50148,54708,58701,73362,74434,74598,79675,80361,81631,88407,94421,104282, +chr1 37858307 37912218 NR_110976 0 - 37912218 37912218 0 13 443,111,169,56,116,152,78,171,159,168,66,216,129, 0,3166,5474,9509,18062,32723,33795,33959,39036,39722,40992,47768,53782, +chr1 37929050 37933143 NM_001037918 0 + 37931709 37932831 0 2 120,1435, 0,2658, +chr1 37931645 37947256 NM_001356262 0 - 37936112 37947155 0 8 325,99,61,116,87,137,102,252, 0,4464,4759,6132,6898,7761,10414,15359, +chr1 37935732 37947256 NM_026913 0 - 37936112 37947155 0 7 476,61,116,87,137,102,252, 0,672,2045,2811,3674,6327,11272, +chr1 37947321 37955183 NM_027098 0 + 37950809 37955109 0 6 108,81,77,81,147,278, 0,2466,3462,4853,7211,7584, +chr1 37947321 37955183 NM_001356482 0 + 37950809 37955109 0 5 108,77,81,147,278, 0,3462,4853,7211,7584, +chr1 37962767 37973338 NM_001033427 0 - 37964401 37972607 0 6 1753,139,197,144,73,258, 0,2946,3973,5136,9797,10313, +chr1 38003582 38014604 NM_027111 0 - 38003729 38009627 0 6 266,133,194,105,75,25, 0,439,3058,3919,6002,10997, +chr1 38040711 38054053 NM_172054 0 - 38044506 38052666 0 5 3913,255,119,209,100, 0,6336,10125,11766,13242, +chr1 38054854 38112424 NM_198303 0 + 38055134 38108558 0 24 315,126,85,670,218,151,99,90,75,281,108,111,68,142,132,183,162,132,132,77,165,139,162,3974, 0,19796,20015,20855,23584,24154,34267,35058,36019,37983,39193,39537,42663,43687,46694,47314,47638,48602,50783,51007,51166,52177,53113,53596, +chr1 38109630 38186511 NM_019570 0 - 38109931 38165302 0 23 413,103,157,212,121,234,203,166,103,173,221,120,155,129,109,117,108,704,153,169,127,64,205, 0,830,1054,1298,1959,2505,3478,3931,4888,6336,10329,14714,18557,21529,26504,30918,32759,35185,39277,46067,54782,55618,76676, +chr1 38109630 38186511 NM_001359288 0 - 38109931 38131266 0 26 413,103,157,212,121,234,203,166,103,173,221,120,155,129,125,109,200,117,108,704,153,169,127,64,64,205, 0,830,1054,1298,1959,2505,3478,3931,4888,6336,10329,14714,18557,21529,22113,26504,28373,30918,32759,35185,39277,46067,54782,55618,75466,76676, +chr1 38109630 38186511 NM_001359287 0 - 38109931 38131362 0 24 413,103,157,212,121,234,203,166,103,173,221,120,155,709,106,117,108,704,153,169,127,66,6,207, 0,830,1054,1298,1959,2505,3478,3931,4888,6336,10329,14714,18557,21529,26504,30918,32759,35185,39277,46067,54782,55618,59280,76674, +chr1 38188927 38216737 NR_151587 0 + 38216737 38216737 0 6 88,172,138,1262,47,141, 0,11940,13116,25373,27132,27669, +chr1 38232835 38684089 NM_001290814 0 - 38236293 38683986 0 22 3580,224,50,94,72,137,64,128,202,125,1095,193,41,52,52,37,81,48,386,313,121,156, 0,5269,5624,9334,10945,15180,17575,27820,28899,31915,33562,42272,76650,93719,144121,153881,165730,230505,358915,359420,360835,451098, +chr1 38850513 38893532 NM_001029878 0 - 38854873 38893273 0 12 4555,150,163,159,122,115,97,208,156,123,119,917, 0,6982,10570,13372,14167,18043,18875,19544,22296,24393,27478,42102, +chr1 38920717 38955005 NM_001368780 0 - 38922342 38941294 0 8 2163,106,235,92,132,108,120,271, 0,4108,7728,10076,20477,30691,32064,34017, +chr1 38920717 38955005 NM_145142 0 - 38922342 38952803 0 7 2163,106,235,92,132,120,271, 0,4108,7728,10076,20477,32064,34017, +chr1 38995993 39007121 NM_001011684 0 + 38996130 39005512 0 10 213,56,51,24,54,84,36,42,47,394, 0,2362,2718,4789,4907,6907,7806,8411,9480,10734, +chr1 38995993 39007121 NM_001311788 0 + 38996130 39005512 0 9 213,56,51,54,84,36,42,47,394, 0,2362,2718,4907,6907,7806,8411,9480,10734, +chr1 39044658 39054081 NM_026850 0 + 39044688 39053128 0 6 36,130,91,144,209,1096, 0,3432,7101,7431,7921,8327, +chr1 39243740 39243837 NR_105767 0 - 39243837 39243837 0 1 97, 0, +chr1 39251116 39420085 NM_008719 0 + 39320188 39418852 0 21 471,57,149,92,90,121,114,119,83,107,148,85,142,110,102,147,198,191,93,175,1386, 0,69047,93196,98415,106372,117569,118683,130168,131024,131816,134035,136665,139538,140431,141723,143781,150997,153219,154160,165377,167583, +chr1 39424695 39428755 NM_001252219 0 + 39424993 39428178 0 5 156,107,126,113,609, 0,298,2163,3103,3451, +chr1 39424695 39428755 NM_001252218 0 + 39424993 39428178 0 4 405,126,113,609, 0,2163,3103,3451, +chr1 39424695 39428755 NM_053257 0 + 39424993 39428178 0 5 84,107,126,113,609, 0,298,2163,3103,3451, +chr1 39428340 39535600 NM_001357521 0 - 39429193 39535411 0 20 1291,98,90,66,241,69,99,130,286,118,215,151,171,198,208,241,229,119,156,316, 0,2231,2586,4928,5382,7959,8499,8732,9781,13625,14502,17812,19621,20561,22569,31187,33795,35256,54527,106944, +chr1 39428341 39535592 NM_018775 0 - 39429193 39535411 0 20 1290,98,90,66,241,69,99,130,286,118,215,151,171,198,208,241,229,119,111,308, 0,2230,2585,4927,5381,7958,8498,8731,9780,13624,14501,17811,19620,20560,22568,31186,33794,35255,54571,106943, +chr1 39430157 39535600 NM_001357522 0 - 39430517 39535411 0 19 512,90,66,241,69,99,130,286,118,215,151,171,198,208,241,229,119,111,316, 0,769,3111,3565,6142,6682,6915,7964,11808,12685,15995,17804,18744,20752,29370,31978,33439,52755,105127, +chr1 39592545 39603722 NM_028043 0 + 39592683 39602111 0 7 637,165,153,203,203,97,1809, 0,1715,2570,4172,6699,9191,9368, +chr1 39605591 39605685 NR_028555 0 - 39605685 39605685 0 1 94, 0, +chr1 39608143 39634192 NM_001033135 0 - 39609316 39634119 0 7 1217,193,97,83,69,251,521, 0,4179,7016,9394,12749,13783,25528, +chr1 39675250 39708027 NM_170597 0 - 39679940 39707785 0 4 4838,114,170,677, 0,6464,29370,32100, +chr1 39722145 39777834 NM_001145660 0 - 39722307 39777787 0 15 357,314,115,95,157,59,151,114,78,111,64,87,62,124,112, 0,4969,6885,13356,15541,17608,18299,20194,23272,24790,30597,44857,46077,53117,55577, +chr1 39860985 39862177 NM_001177348 0 - 39861027 39862022 0 2 199,160, 0,1032, +chr1 39899272 39904175 NR_040465 0 - 39904175 39904175 0 5 129,86,112,182,22, 0,1590,2800,3237,4881, +chr1 39957757 40083155 NM_001252200 0 + 39958074 40081557 0 32 374,66,57,126,111,91,131,55,79,176,73,211,162,87,126,162,231,107,152,98,9,176,121,118,171,144,135,101,150,160,140,1682, 0,596,61265,73014,75794,79647,82226,82970,84269,85712,88057,89176,96108,98975,99711,100517,102844,103894,105758,106520,107418,108775,109644,113193,113614,116197,118631,120171,121792,122447,123397,123716, +chr1 39957757 40083155 NM_001252202 0 + 39958074 40081557 0 30 374,66,57,126,111,91,131,55,79,176,73,211,162,87,126,162,107,152,98,176,121,118,171,144,135,101,150,160,140,1682, 0,596,61265,73014,75794,79647,82226,82970,84269,85712,88057,89176,96108,98975,99711,100517,103894,105758,106520,108775,109644,113193,113614,116197,118631,120171,121792,122447,123397,123716, +chr1 39957757 40083155 NM_001252201 0 + 39958074 40081557 0 31 374,66,57,126,111,91,131,55,79,176,73,211,162,87,126,107,152,98,9,176,121,192,118,171,144,135,101,150,160,140,1682, 0,596,61265,73014,75794,79647,82226,82970,84269,85712,88057,89176,96108,98975,99711,103894,105758,106520,107418,108775,109644,110737,113193,113614,116197,118631,120171,121792,122447,123397,123716, +chr1 39957757 40083155 NM_008696 0 + 39958074 40081557 0 31 374,66,57,126,111,91,131,55,79,176,73,211,162,87,126,231,107,152,98,9,176,121,118,171,144,135,101,150,160,140,1682, 0,596,61265,73014,75794,79647,82226,82970,84269,85712,88057,89176,96108,98975,99711,102844,103894,105758,106520,107418,108775,109644,113193,113614,116197,118631,120171,121792,122447,123397,123716, +chr1 40133056 40142696 NR_037980 0 - 40142696 40142696 0 4 427,48,144,239, 0,8755,8932,9401, +chr1 40141558 40182075 NM_001360801 0 + 40168821 40182052 0 8 106,149,181,175,63,136,143,190, 0,17675,27241,30310,33241,36195,38408,40327, +chr1 40141558 40182075 NM_010555 0 + 40159273 40182052 0 9 106,149,259,181,175,63,136,143,190, 0,17675,20550,27241,30310,33241,36195,38408,40327, +chr1 40142937 40182075 NM_001360800 0 + 40143273 40182052 0 9 350,149,259,181,175,63,136,143,190, 0,16296,19171,25862,28931,31862,34816,37029,38948, +chr1 40281924 40373022 NM_008362 0 + 40282148 40370238 0 11 227,64,238,190,169,66,118,152,144,168,3203, 0,57153,68040,68378,69678,72829,75680,77198,85206,87267,87895, +chr1 40323430 40373022 NM_001123382 0 + 40339083 40370238 0 11 296,64,238,190,169,66,118,152,144,168,3203, 0,15647,26534,26872,28172,31323,34174,35692,43700,45761,46389, +chr1 40381433 40424398 NM_133193 0 + 40383339 40422290 0 11 231,70,235,199,163,72,130,137,144,162,2527, 0,1900,2783,4382,18439,21217,26347,27173,32230,38603,40438, +chr1 40381433 40424398 NM_001356478 0 + 40383339 40422290 0 11 161,70,235,199,163,72,130,137,144,162,2527, 0,1900,2783,4382,18439,21217,26347,27173,32230,38603,40438, +chr1 40486414 40505256 NM_001294171 0 + 40497594 40503549 0 8 61,201,211,175,163,69,142,1882, 0,11058,11722,12736,13029,14764,16517,16960, +chr1 40496473 40505256 NM_010743 0 + 40497594 40503549 0 8 228,201,211,175,163,69,142,1882, 0,999,1663,2677,2970,4705,6458,6901, +chr1 40496473 40522259 NM_001025602 0 + 40497594 40519014 0 11 228,201,211,175,163,69,142,146,147,168,3649, 0,999,1663,2677,2970,4705,6458,6901,10446,12064,22137, +chr1 40522396 40548423 NM_001161842 0 + 40528601 40548078 0 10 230,197,86,247,166,145,63,124,140,521, 0,609,6177,9142,12833,15370,18729,21423,24049,25506, +chr1 40522465 40548425 NM_001161843 0 + 40528601 40548078 0 10 190,109,86,247,166,145,63,124,140,523, 0,540,6108,9073,12764,15301,18660,21354,23980,25437, +chr1 40522850 40557699 NM_008365 0 + 40528601 40555535 0 11 352,86,247,166,145,63,124,140,159,159,2517, 0,5723,8688,12379,14916,18275,20969,23595,25052,29743,32332, +chr1 40572206 40608550 NM_010553 0 + 40581157 40605933 0 13 115,76,139,167,322,184,151,66,124,152,138,174,3081, 0,338,1035,8854,9432,9842,16114,21696,23862,26525,27628,32405,33263, +chr1 40637071 40687576 NM_177084 0 + 40637360 40686437 0 12 545,464,260,218,203,87,71,162,97,132,88,1495, 0,3632,20543,22626,26782,27522,30090,31896,38813,43166,43987,49010, +chr1 40738556 40825730 NM_001033289 0 + 40738718 40824844 0 12 454,464,251,218,203,90,71,162,97,132,91,1260, 0,36883,44496,60908,62091,73997,74547,80189,81831,83853,84531,85914, +chr1 40828884 40847502 NM_172499 0 - 40830597 40847464 0 6 2507,210,130,44,88,173, 0,9341,12337,14127,15490,18445, +chr1 40862445 40912112 NM_001081198 0 + 40862600 40911861 0 5 287,100,99,138,472, 0,498,2021,32697,49195, +chr1 41224404 41238097 NR_040475 0 - 41238097 41238097 0 3 279,40,254, 0,8816,13439, +chr1 42705044 42751670 NR_027826 0 - 42751670 42751670 0 4 257,47,163,79, 0,15356,18641,46547, +chr1 42752612 42757054 NM_008900 0 + 42753990 42755484 0 1 4442, 0, +chr1 42757180 42760021 NR_027891 0 + 42760021 42760021 0 1 2841, 0, +chr1 42763907 42770299 NR_110495 0 - 42770299 42770299 0 4 196,62,103,100, 0,1294,5140,6292, +chr1 42807556 42809731 NR_130904 0 + 42809731 42809731 0 1 2175, 0, +chr1 42908077 42962528 NM_023514 0 + 42908136 42962341 0 11 194,180,63,31,80,68,76,169,109,170,279, 0,11236,28522,28663,36474,44117,44860,47207,48208,52062,54172, +chr1 43009716 43092294 NM_053107 0 + 43089043 43090165 0 2 362,3498, 0,79080, +chr1 43104044 43155473 NM_001013025 0 - 43106503 43132783 0 13 2636,434,160,147,144,58,342,83,155,195,702,198,359, 0,4358,6211,7319,9412,11898,12680,15317,20274,24261,28051,49652,51070, +chr1 43104044 43149331 NM_001357299 0 - 43106503 43132783 0 12 2636,434,160,147,144,58,342,83,155,195,702,106, 0,4358,6211,7319,9412,11898,12680,15317,20274,24261,28051,45181, +chr1 43155554 43172791 NM_133818 0 + 43155608 43170087 0 4 153,167,376,2761, 0,2005,12288,14476, +chr1 43179915 43220806 NM_010212 0 - 43180358 43210076 0 6 595,187,170,175,179,260, 0,5173,8581,18627,30005,40631, +chr1 43179915 43253606 NM_001289533 0 - 43180358 43210076 0 6 595,187,170,175,179,111, 0,5173,8581,18627,30005,73580, +chr1 43502595 43627363 NM_010879 0 + 43590412 43626187 0 5 277,163,242,722,1371, 0,63870,87801,108110,123397, +chr1 43787446 43799409 NM_024283 0 + 43787729 43799251 0 4 362,48,158,320, 0,6598,7958,11643, +chr1 43803805 43884684 NM_026430 0 - 43807075 43884553 0 15 3402,104,58,61,44,120,122,60,105,181,61,44,49,28,225, 0,6756,8738,10011,13560,17929,24720,27856,33104,43503,50284,58392,58665,60389,80654, +chr1 43803805 43884684 NR_160750 0 - 43884684 43884684 0 14 3402,104,58,61,44,120,122,60,105,61,44,64,28,225, 0,6756,8738,10011,13560,17929,24720,27856,33104,50284,58392,58665,60389,80654, +chr1 43803805 43883429 NM_001368289 0 - 43807075 43864199 0 15 3402,104,58,61,44,120,122,60,105,181,61,44,49,28,198, 0,6756,8738,10011,13560,17929,24720,27856,33104,43503,50284,58392,58665,60389,79426, +chr1 43803805 43884684 NM_001368288 0 - 43807075 43864199 0 15 3402,104,58,61,44,120,122,60,105,181,61,44,49,28,134, 0,6756,8738,10011,13560,17929,24720,27856,33104,43503,50284,58392,58665,60389,80745, +chr1 43803805 43884684 NM_001368287 0 - 43807075 43884553 0 15 3402,104,58,61,44,120,122,60,105,181,61,44,64,28,225, 0,6756,8738,10011,13560,17929,24720,27856,33104,43503,50284,58392,58665,60389,80654, +chr1 43803805 43884684 NR_160751 0 - 43884684 43884684 0 14 3402,104,58,61,44,120,122,60,105,61,44,49,28,225, 0,6756,8738,10011,13560,17929,24720,27856,33104,50284,58392,58665,60389,80654, +chr1 43803805 43884684 NR_160749 0 - 43884684 43884684 0 15 3402,104,58,61,44,120,122,60,105,87,61,44,49,28,225, 0,6756,8738,10011,13560,17929,24720,27856,33104,43503,50284,58392,58665,60389,80654, +chr1 43990838 44059845 NM_001310540 0 + 43990933 44059038 0 29 260,129,96,105,125,164,155,77,128,100,149,116,169,158,77,107,155,117,101,97,138,245,79,152,97,131,208,120,897, 0,6116,15318,17113,19263,20583,22477,23442,26090,26874,34888,36407,37570,38536,39450,41422,43213,44419,44741,46314,47736,49078,49520,56517,57269,58270,65634,67325,68110, +chr1 43990838 44059845 NM_009418 0 + 43990933 44059038 0 30 260,129,96,105,125,164,155,77,128,100,149,116,169,158,77,107,155,117,101,97,138,245,79,39,152,97,131,208,120,897, 0,6116,15318,17113,19263,20583,22477,23442,26090,26874,34888,36407,37570,38536,39450,41422,43213,44419,44741,46314,47736,49078,49520,51422,56517,57269,58270,65634,67325,68110, +chr1 44066252 44076851 NM_001013799 0 - 44066483 44074112 0 5 626,118,152,91,99, 0,1124,4214,7778,10500, +chr1 44143457 44159286 NM_001356297 0 - 44143734 44156707 0 6 451,206,52,231,154,114, 0,1230,1863,4748,13235,15715, +chr1 44143457 44159286 NM_001356296 0 - 44143734 44156707 0 7 451,206,52,231,88,58,114, 0,1230,1863,4748,13235,15287,15715, +chr1 44143457 44159286 NM_029368 0 - 44143734 44156707 0 8 451,206,52,231,154,56,58,114, 0,1230,1863,4748,13235,14854,15287,15715, +chr1 44163390 44175618 NM_023645 0 - 44163931 44175344 0 10 559,108,90,210,238,173,78,206,206,456, 0,1219,3448,4189,6099,6457,7895,8148,10492,11772, +chr1 44175801 44201362 NM_001357046 0 + 44183236 44199987 0 11 239,101,601,127,96,105,95,133,87,97,1669, 0,1217,7309,8681,9771,10303,10626,18027,19616,22821,23892, +chr1 44176006 44201362 NM_001357047 0 + 44183236 44199987 0 11 209,101,601,127,96,105,95,133,87,97,1669, 0,1012,7104,8476,9566,10098,10421,17822,19411,22616,23687, +chr1 44176372 44201362 NM_001357048 0 + 44183236 44199987 0 11 202,101,601,127,96,105,95,133,87,97,1669, 0,646,6738,8110,9200,9732,10055,17456,19045,22250,23321, +chr1 44176812 44201616 NM_144558 0 + 44183236 44199987 0 10 307,601,127,96,105,95,133,87,97,1923, 0,6298,7670,8760,9292,9615,17016,18605,21810,22881, +chr1 44204588 44238105 NM_011729 0 + 44204907 44237927 0 15 407,176,116,87,61,144,208,1074,242,120,214,145,201,85,730, 0,9193,10400,11061,13233,14066,16133,19065,25594,26168,26418,28095,30430,31403,32787, +chr1 44260914 44275776 NM_207281 0 - 44263194 44275001 0 5 2684,118,167,120,92, 0,6094,6962,14041,14770, +chr1 44608515 44853681 NM_028450 0 + 44746032 44851866 0 11 202,72,62,72,99,138,117,93,139,95,1887, 0,137473,156946,192803,202672,214343,221600,222382,229297,236777,243279, +chr1 44796519 44801794 NR_040602 0 - 44801794 44801794 0 3 807,81,18, 0,4481,5257, +chr1 45368382 45406551 NM_009930 0 + 45368592 45405592 0 51 295,200,51,114,75,54,54,54,54,54,54,45,54,45,54,99,45,99,54,108,54,99,54,99,54,54,54,54,45,99,108,54,54,54,54,108,54,54,162,108,108,54,108,54,108,54,108,295,188,243,1106, 0,9959,10404,10868,12185,13822,14267,15033,16051,16272,16895,17339,17515,18565,19017,19568,19979,20140,20435,20597,21427,22025,22469,22676,23059,23223,23597,24190,25122,25703,25888,26420,27036,27172,27821,28336,28717,29092,29328,29600,30585,31718,31856,32428,32921,33259,33414,34310,35582,36098,37063, +chr1 45431175 45560127 NM_007737 0 - 45432928 45559759 0 54 1900,240,188,292,108,54,108,54,108,54,108,108,162,54,54,108,54,54,54,54,108,99,45,54,54,54,54,99,54,99,54,108,54,99,45,99,54,45,54,45,54,54,54,54,54,45,78,111,54,33,33,14,222,462, 0,2308,3976,5669,7785,8836,9260,10069,10631,12502,13882,15041,15701,16745,17331,17493,17973,18484,18722,20051,20390,21730,22119,26490,27748,28785,28929,29090,29870,30402,30909,31909,32213,32691,32902,33371,37103,39139,40417,42596,43257,44168,46890,47613,48055,49351,52657,55567,60561,62048,63133,64539,68316,128490, +chr1 45852010 45880483 NM_028599 0 + 45852366 45880360 0 21 439,130,66,91,125,71,120,89,159,60,116,176,158,181,95,96,170,60,147,92,331, 0,3850,5995,6873,8711,10211,11507,12505,16875,17879,18024,19375,21311,22097,23004,23656,24323,24965,27282,27717,28142, +chr1 45964914 45982439 NM_016917 0 - 45966250 45982108 0 8 1650,639,246,127,116,160,68,374, 0,2822,4166,10239,10815,13086,16647,17151, +chr1 46077259 46087282 NR_037690 0 - 46087282 46087282 0 3 1533,190,1640, 0,4489,8383, +chr1 46077259 46087282 NR_037691 0 - 46087282 46087282 0 4 1533,190,120,1640, 0,4489,6084,8383, +chr1 46123697 46430391 NM_001368717 0 + 46123834 46430284 0 65 152,63,63,109,148,88,181,76,126,120,184,180,273,128,79,225,147,686,187,194,199,141,213,110,169,103,128,213,99,249,150,183,177,132,225,198,156,169,127,220,873,230,331,347,181,186,164,155,191,134,336,127,195,93,177,162,201,162,186,138,231,153,178,104,314, 0,11670,14582,16852,18702,31145,32565,42412,49316,52407,56764,57490,59809,61255,64453,67649,70559,72653,75125,108434,110377,115488,120302,121723,124798,128182,128396,134339,137365,140592,144396,146485,147445,150224,152468,154726,156219,157756,158913,159965,166626,169740,173928,175127,176402,182920,186517,201752,210108,222680,223702,231395,232961,236693,255397,257854,258855,270577,273265,276881,285962,289652,291276,296050,306380, +chr1 46482362 46864322 NM_001310335 0 + 46482457 46864210 0 65 110,63,63,109,148,88,181,76,126,120,184,180,273,128,79,225,147,686,187,194,199,141,213,110,169,103,128,213,99,249,150,183,177,132,225,198,156,169,127,220,873,230,331,347,181,186,164,155,191,134,336,127,195,93,177,162,201,162,186,138,231,153,178,104,319, 0,5254,14955,30237,31689,40326,41733,56463,69082,78515,89035,89762,93571,94995,98528,101946,104981,107056,109540,169423,171373,177159,181895,183368,187046,189537,189751,200417,203365,206582,210930,213047,214009,221476,223692,228468,229959,231559,232695,233805,239944,242642,246833,254940,256214,259886,263407,299508,305300,314025,315047,323032,324589,334747,341051,343506,344521,349588,352215,355138,358887,366248,367898,372675,381641, +chr1 46864388 46910463 NM_001356416 0 - 46866797 46892985 0 11 2568,191,81,369,121,189,170,208,1025,134,148, 0,4442,10519,11521,12979,18549,19799,25012,27583,34204,45927, +chr1 46864388 46910463 NM_172653 0 - 46866797 46892985 0 10 2568,191,81,369,121,189,170,208,1025,148, 0,4442,10519,11521,12979,18549,19799,25012,27583,45927, +chr1 46864388 46982621 NM_001356417 0 - 46866797 46892985 0 11 2568,191,81,369,121,189,170,208,1025,101,75, 0,4442,10519,11521,12979,18549,19799,25012,27583,85256,118158, +chr1 47523864 47523969 NR_105768 0 - 47523969 47523969 0 1 105, 0, +chr1 49301459 49397275 NR_151585 0 + 49397275 49397275 0 5 113,150,100,137,42, 0,66204,90753,93466,95774, +chr1 50984366 51244114 NM_019790 0 + 50984791 51242325 0 10 597,110,130,27,97,149,60,124,159,1886, 0,3026,10690,15674,143945,204620,205536,252729,254214,257862, +chr1 51275229 51390623 NR_045151 0 - 51390623 51390623 0 5 2055,221,46,134,96, 0,32881,40999,109402,115298, +chr1 51345969 51359804 NM_138741 0 + 51346229 51358266 0 2 743,2312, 0,11523, +chr1 51526331 51535243 NM_028696 0 - 51528088 51534759 0 6 1924,52,76,72,139,575, 0,2841,3518,5046,7990,8337, +chr1 51526331 51535243 NM_001310549 0 - 51528088 51531439 0 6 1924,52,76,72,139,28, 0,2841,3518,5046,7990,8884, +chr1 51526331 51535243 NM_001310548 0 - 51528088 51531439 0 6 1924,52,76,72,139,99, 0,2841,3518,5046,7990,8813, +chr1 51566348 51653562 NR_151621 0 - 51653562 51653562 0 4 540,419,93,418, 0,72855,80879,86796, +chr1 51806601 51972822 NM_001290982 0 - 51808016 51940061 0 29 1539,128,153,133,107,135,75,87,69,150,94,201,227,201,63,105,66,87,119,148,104,99,64,47,105,95,116,144,218, 0,5885,7347,8118,10537,12734,14132,19246,21028,23475,24554,26446,28563,29803,32212,34679,43882,44554,47241,47630,49774,51426,63245,70383,74339,84691,113561,133325,166003, +chr1 51806601 51972822 NM_010863 0 - 51808016 51940061 0 30 1539,128,153,133,107,135,75,87,87,69,150,94,201,227,201,63,105,66,87,119,148,104,99,64,47,105,95,116,144,218, 0,5885,7347,8118,10537,12734,14132,17064,19246,21028,23475,24554,26446,28563,29803,32212,34679,43882,44554,47241,47630,49774,51426,63245,70383,74339,84691,113561,133325,166003, +chr1 51806601 51972822 NM_001161817 0 - 51808016 51940061 0 31 1539,128,153,133,107,135,75,87,87,87,69,150,94,201,227,201,63,105,66,87,119,148,104,99,64,47,105,95,116,144,218, 0,5885,7347,8118,10537,12734,14132,17064,18892,19246,21028,23475,24554,26446,28563,29803,32212,34679,43882,44554,47241,47630,49774,51426,63245,70383,74339,84691,113561,133325,166003, +chr1 52043991 52164033 NM_001308266 0 + 52068627 52163780 0 25 73,88,129,145,99,93,79,86,152,159,93,60,18,94,45,84,99,136,50,95,137,192,67,109,280, 0,9114,24635,26642,78167,81598,84713,87529,89385,91346,92593,95370,95714,95830,96931,109637,111239,113176,114704,114969,115333,115700,118058,118520,119762, +chr1 52065083 52164033 NM_011487 0 + 52068627 52163780 0 24 489,129,145,99,93,79,86,152,159,93,60,18,94,45,84,99,136,50,95,137,192,67,109,280, 0,3543,5550,57075,60506,63621,66437,68293,70254,71501,74278,74622,74738,75839,88545,90147,92084,93612,93877,94241,94608,96966,97428,98670, +chr1 52176281 52218709 NM_001205314 0 + 52179437 52216141 0 25 171,161,131,145,99,90,79,92,152,159,93,60,30,94,42,84,99,136,50,95,146,186,76,100,2583, 0,474,3153,3676,7082,13106,16165,17441,17841,19756,21139,23463,24648,24766,25712,27856,28463,29465,31181,31800,32795,34406,35548,36545,39845, +chr1 52176281 52218709 NM_001357627 0 + 52179437 52216141 0 25 186,124,131,145,99,90,79,92,152,159,93,60,30,94,42,84,99,136,50,95,146,186,76,100,2583, 0,474,3153,3676,7082,13106,16165,17441,17841,19756,21139,23463,24648,24766,25712,27856,28463,29465,31181,31800,32795,34406,35548,36545,39845, +chr1 52176281 52218709 NM_009283 0 + 52179437 52216141 0 25 186,161,131,145,99,90,79,92,152,159,93,60,30,94,42,84,99,136,50,95,146,186,76,100,2583, 0,474,3153,3676,7082,13106,16165,17441,17841,19756,21139,23463,24648,24766,25712,27856,28463,29465,31181,31800,32795,34406,35548,36545,39845, +chr1 52176465 52218709 NM_001205313 0 + 52179437 52216141 0 25 172,124,131,145,99,90,79,92,152,159,93,60,30,94,42,84,117,136,50,95,146,186,76,100,2583, 0,290,2969,3492,6898,12922,15981,17257,17657,19572,20955,23279,24464,24582,25528,27672,28261,29281,30997,31616,32611,34222,35364,36361,39661, +chr1 52220293 52290076 NM_001081081 0 - 52223001 52289836 0 18 2865,64,77,62,93,132,177,51,67,59,33,59,164,80,130,122,97,641, 0,4886,5035,5447,25229,25973,27661,32715,33293,36261,36405,43851,48753,51028,52115,56038,56493,69142, +chr1 52242124 52290076 NM_001113383 0 - 52244491 52289836 0 15 2514,93,132,177,51,67,59,33,59,164,80,130,122,97,641, 0,3398,4142,5830,10884,11462,14430,14574,22020,26922,29197,30284,34207,34662,47311, +chr1 52512692 52557292 NM_008667 0 - 52516061 52547580 0 8 3458,117,163,90,52,134,835,239, 0,6239,8936,11041,23389,25022,34072,44361, +chr1 52626857 52637136 NR_151614 0 - 52637136 52637136 0 6 2475,128,93,91,126,31, 0,5121,6360,6560,8764,10248, +chr1 52687548 52708763 NR_024590 0 + 52708763 52708763 0 9 147,116,232,73,94,69,226,177,2214, 0,6660,10124,10466,11614,12463,14556,18045,19001, +chr1 52687548 52708763 NM_001142647 0 + 52687601 52706688 0 9 147,116,232,73,94,115,226,177,2214, 0,6660,10124,10466,11614,12417,14556,18045,19001, +chr1 52713129 52784202 NM_001357464 0 - 52715378 52766548 0 8 2260,25,281,99,162,98,1592,336, 0,2413,4521,6104,6999,20192,51878,70737, +chr1 52713147 52784162 NM_133829 0 - 52715185 52766548 0 7 2242,281,99,162,98,1592,296, 0,4503,6086,6981,20174,51860,70719, +chr1 52716829 52784162 NM_178081 0 - 52717503 52766548 0 6 1102,99,162,98,1592,296, 0,2404,3299,16492,48178,67037, +chr1 52846263 52874532 NM_008384 0 - 52846511 52856332 0 6 798,175,201,61,252,287, 0,2268,5050,7621,9865,27982, +chr1 52901881 52977830 NM_146108 0 + 52901953 52977222 0 14 107,43,138,85,81,53,79,146,87,59,82,120,34,724, 0,8630,14990,17230,20511,23868,40065,56150,57809,59604,60333,68693,71599,75225, +chr1 52979167 53004824 NM_001368281 0 - 52982090 52982411 0 2 3411,19, 0,25638, +chr1 52979167 53020075 NM_001368278 0 - 52982090 52982411 0 2 3411,179, 0,40729, +chr1 52979167 53010194 NM_001368280 0 - 52982090 52982411 0 2 3411,154, 0,30873, +chr1 52979167 53009684 NM_144953 0 - 52982090 52982411 0 2 3411,226, 0,30291, +chr1 52979167 53049501 NM_001368274 0 - 52982090 52982411 0 3 3411,75,32, 0,68945,70302, +chr1 52979167 53010458 NM_001368279 0 - 52982090 52982411 0 2 3411,73, 0,31218, +chr1 52979167 53049501 NM_001368276 0 - 52982090 52982411 0 4 3411,59,75,32, 0,67782,68945,70302, +chr1 52979167 53028890 NM_001368277 0 - 52982090 52982411 0 2 3411,76, 0,49647, +chr1 53118483 53124923 NM_010834 0 + 53118609 53123475 0 3 502,374,1829, 0,2243,4611, +chr1 53215420 53244461 NM_027070 0 - 53215590 53244445 0 9 212,20,23,71,58,53,50,76,64, 0,4649,11661,11811,19193,23266,23918,26638,28977, +chr1 53215420 53244461 NM_001368200 0 - 53215590 53244219 0 10 212,20,23,71,58,53,50,76,131,64, 0,4649,11661,11811,19193,23266,23918,26638,28751,28977, +chr1 53246030 53353872 NM_153556 0 - 53246177 53338916 0 13 312,161,131,480,851,144,123,117,164,103,183,152,143, 0,2913,5741,7636,17375,18389,18776,27044,67442,78641,85883,92754,107699, +chr1 53353938 53367089 NM_145517 0 + 53355822 53365806 0 4 94,181,152,1419, 0,1877,8360,11732, +chr1 53370467 53383186 NR_104360 0 + 53383186 53383186 0 7 235,244,383,354,131,104,339, 0,1232,4283,6319,7456,9543,12380, +chr1 53370467 53383186 NR_151661 0 + 53383186 53383186 0 7 235,244,388,354,131,104,339, 0,1232,4278,6319,7456,9543,12380, +chr1 53370467 53383186 NM_001285839 0 + 53371722 53380089 0 8 235,244,388,354,131,72,104,339, 0,1232,4278,6319,7456,7872,9543,12380, +chr1 53370467 53383186 NR_104361 0 + 53383186 53383186 0 9 235,244,388,354,131,80,72,104,339, 0,1232,4278,6319,7456,7681,7872,9543,12380, +chr1 53401460 53409596 NM_133728 0 - 53401573 53405310 0 6 363,182,1544,76,54,223, 0,1963,2398,5370,6263,7913, +chr1 53401460 53409596 NM_001290984 0 - 53401573 53405310 0 6 363,182,113,76,54,223, 0,1963,3829,5370,6263,7913, +chr1 53405172 53409596 NM_001353501 0 - 53405322 53409463 0 4 230,76,54,223, 0,1658,2551,4201, +chr1 53453845 53763628 NM_001252070 0 - 53453950 53763536 0 66 312,104,178,153,231,138,186,162,201,162,177,93,195,127,336,134,191,155,164,186,181,347,331,230,873,220,127,169,156,198,225,132,177,183,150,249,99,213,128,103,169,110,213,141,199,194,187,686,147,225,79,128,273,180,184,120,126,76,181,88,59,89,109,63,63,107, 0,8674,14504,16730,22543,26227,28165,30824,35889,36949,40429,47439,50316,51927,59534,60669,71618,75799,82650,86295,97576,98684,99814,104476,106502,121619,124096,125209,126787,127936,131671,134106,137419,138373,140495,143877,147426,150141,162038,162277,164900,168661,170033,180187,185492,187456,208796,220723,223641,226341,230032,233193,234464,238262,238992,243334,246439,250245,265326,266802,287839,287964,289497,301630,305016,309676, +chr1 53812355 53842059 NM_133810 0 - 53814331 53833482 0 8 2259,180,49,127,145,213,163,142, 0,5470,7077,8520,10409,16098,21005,29562, +chr1 53863717 54251878 NM_001001883 0 - 53870065 54097336 0 29 6460,113,86,115,147,130,99,153,114,121,110,84,97,103,135,186,125,104,151,96,1374,101,140,170,76,95,108,327,59, 0,20002,21011,23768,24636,25748,32138,33840,44699,46295,58167,61962,78455,80709,84252,97375,106367,106893,107608,117025,118436,120191,124096,126245,130184,135832,143940,233327,388102, +chr1 53906267 53906339 NR_106149 0 + 53906339 53906339 0 1 72, 0, +chr1 53987658 54251878 NM_172655 0 - 53987809 54097336 0 7 295,170,76,95,108,327,59, 0,2304,6243,11891,19999,109386,264161, +chr1 54307526 54425571 NM_030025 0 + 54307672 54425243 0 28 203,164,221,179,69,117,130,44,93,108,125,178,69,114,72,108,63,129,170,94,170,127,195,69,162,87,120,427, 0,9241,12761,13091,21795,26971,28028,31047,34852,38152,40019,49623,50317,54181,63462,78274,78800,102313,103936,105004,105981,110309,113735,114212,114365,115450,117231,117618, +chr1 54452720 54495870 NM_001033194 0 - 54454723 54495758 0 18 2126,153,125,191,238,136,102,203,172,104,73,148,166,192,124,185,112,214, 0,3252,7634,9103,9960,20007,20845,21782,23506,24519,27624,28132,31523,32885,34622,38177,41955,42936, +chr1 54529843 54614528 NM_001163314 0 - 54537549 54614424 0 27 7845,105,188,51,136,198,91,94,39,109,67,52,74,76,78,52,47,84,56,106,67,53,158,172,176,154,251, 0,8852,13470,17221,19029,20209,21801,24534,37028,38394,38901,39597,39772,41837,48292,51316,52368,55512,57117,57854,59022,60419,62955,70038,74939,77977,84434, +chr1 54702183 54983231 NM_001081433 0 - 54705120 54983010 0 28 2996,92,83,83,146,84,88,217,118,88,202,72,112,81,141,69,64,83,115,79,213,143,88,201,71,79,84,248, 0,6329,8403,9740,10321,12276,13579,15661,17314,18559,22032,35780,77674,82150,84394,87588,89656,90890,97974,107550,116921,118305,121010,121444,132947,147113,183272,280800, +chr1 55042012 55084322 NM_031179 0 - 55044177 55084210 0 25 2324,217,273,132,121,112,183,222,126,147,146,271,87,180,102,198,122,213,238,171,80,115,105,167,140, 0,2770,5134,9161,10197,11648,11843,12869,14458,14846,15073,15475,15843,16214,17935,18124,20633,21002,22311,26933,29314,31207,31610,34065,42170, +chr1 55109613 55129546 NM_001039710 0 + 55109718 55128647 0 5 221,150,193,102,1067, 0,8505,11411,14727,18866, +chr1 55109613 55129546 NM_026424 0 + 55109718 55128647 0 4 221,193,102,1067, 0,11411,14727,18866, +chr1 55134676 55145087 NM_001356512 0 - 55135131 55143783 0 12 608,179,175,246,100,169,94,96,83,253,176,255, 0,696,1223,2269,3240,3827,4225,5234,5892,6700,8933,10156, +chr1 55134677 55144776 NM_010477 0 - 55135131 55143783 0 12 607,179,175,246,100,169,94,96,83,253,176,154, 0,695,1222,2268,3239,3826,4224,5233,5891,6699,8932,9945, +chr1 55144991 55148161 NM_008303 0 + 55145253 55147964 0 4 265,165,90,248, 0,903,2565,2922, +chr1 55188088 55211743 NM_025283 0 + 55188143 55209650 0 8 115,63,101,43,87,80,112,2225, 0,5432,13879,17074,17303,18901,19726,21430, +chr1 55188088 55211743 NM_001310585 0 + 55188143 55209650 0 7 115,101,43,87,80,112,2225, 0,13879,17074,17303,18901,19726,21430, +chr1 55227003 55283626 NM_001356288 0 - 55228653 55268059 0 8 1923,79,104,122,210,280,112,662, 0,14790,24084,25356,34023,36176,40990,55961, +chr1 55227003 55283626 NM_028713 0 - 55228653 55283103 0 9 1923,79,104,122,210,280,112,184,662, 0,14790,24084,25356,34023,36176,40990,43960,55961, +chr1 55227003 55283626 NM_001356287 0 - 55228653 55282997 0 8 1923,79,104,122,78,210,280,662, 0,14790,24084,25356,31185,34023,36176,55961, +chr1 55294020 55296902 NM_175439 0 + 55294083 55295844 0 1 2882, 0, +chr1 55305554 55420597 NM_001368767 0 - 55305649 55420163 0 11 254,99,129,48,72,128,76,55,92,144,455, 0,51376,55787,56965,74939,91762,97666,100170,106937,111905,114588, +chr1 55325699 55420597 NM_001367887 0 - 55327485 55420163 0 11 1810,99,129,48,72,128,76,55,92,144,455, 0,31231,35642,36820,54794,71617,77521,80025,86792,91760,94443, +chr1 55356578 55419572 NM_001368768 0 - 55356912 55397433 0 10 451,129,48,72,128,63,55,92,144,247, 0,4763,5941,23915,40738,46655,49146,55913,60881,62747, +chr1 55356578 55419572 NM_001113367 0 - 55356912 55397433 0 10 451,129,48,72,128,76,55,92,144,247, 0,4763,5941,23915,40738,46642,49146,55913,60881,62747, +chr1 55356578 55420597 NM_029267 0 - 55356912 55420163 0 10 451,129,48,72,128,76,55,92,144,455, 0,4763,5941,23915,40738,46642,49146,55913,60881,63564, +chr1 55462789 55811129 NM_001114663 0 + 55463231 55808307 0 6 685,2475,204,76,110,3005, 0,289799,295984,307475,309548,345335, +chr1 55988084 56028942 NR_045837 0 + 56028942 56028942 0 6 102,135,110,362,178,1019, 0,3045,25594,26404,29744,39839, +chr1 56075821 56077047 NR_126075 0 + 56077047 56077047 0 2 76,406, 0,820, +chr1 56075821 56077047 NR_126076 0 + 56077047 56077047 0 2 76,348, 0,878, +chr1 56692892 56694295 NM_027661 0 - 56693041 56694220 0 1 1403, 0, +chr1 56850824 57035494 NM_001358581 0 - 56853626 57026665 0 12 3264,198,156,213,473,103,124,127,177,228,83,230, 0,37458,51595,56190,77331,97182,103965,105010,154098,175672,180258,184440, +chr1 56850824 57037092 NM_001358580 0 - 56853626 57026665 0 12 3264,198,156,213,473,103,124,127,177,228,83,231, 0,37458,51595,56190,77331,97182,103965,105010,154098,175672,180258,186037, +chr1 56850824 57028178 NM_139146 0 - 56853626 57026665 0 11 3264,198,156,213,473,103,124,127,177,228,223, 0,37458,51595,56190,77331,97182,103965,105010,154098,175672,177131, +chr1 57028312 57032040 NR_024325 0 + 57032040 57032040 0 1 3728, 0, +chr1 57028312 57032040 NR_024326 0 + 57032040 57032040 0 2 303,939, 0,2789, +chr1 57257488 57271840 NR_037990 0 - 57271840 57271840 0 7 2203,80,186,240,234,184,177, 0,3884,6069,8155,11761,13068,14175, +chr1 57416065 57434388 NR_037999 0 - 57434388 57434388 0 4 1442,198,272,140, 0,3344,16026,18183, +chr1 57434463 57442266 NM_028546 0 + 57434514 57440408 0 2 327,2680, 0,5123, +chr1 57445087 57463518 NM_001302963 0 - 57445339 57450274 0 8 509,102,88,138,45,70,136,291, 0,2398,3205,5106,5803,8483,13144,18140, +chr1 57445087 57463518 NM_001037742 0 - 57445339 57463305 0 8 509,117,88,138,45,70,155,291, 0,2398,3205,5106,5803,8483,13125,18140, +chr1 57445087 57463518 NM_001302964 0 - 57445339 57450274 0 8 509,117,88,138,45,70,136,291, 0,2398,3205,5106,5803,8483,13144,18140, +chr1 57445087 57463518 NM_001302962 0 - 57445339 57463305 0 9 509,117,88,138,25,45,70,136,291, 0,2398,3205,5106,5426,5803,8483,13144,18140, +chr1 57463109 57474796 NM_001081181 0 + 57463616 57472578 0 5 957,72,127,148,2297, 0,3646,5457,6974,9390, +chr1 57831704 58005241 NM_144882 0 + 57888943 58003307 0 14 164,50,85,61,109,50,247,207,136,59,110,103,221,2330, 0,24444,57192,80603,104647,107845,110842,125773,127228,148505,163051,165512,168160,171207, +chr1 57831704 58005241 NM_001368787 0 + 57912329 58003307 0 14 164,50,81,61,109,50,247,207,136,59,110,103,221,2330, 0,24444,57192,80603,104647,107845,110842,125773,127228,148505,163051,165512,168160,171207, +chr1 57902414 58005241 NM_001164566 0 + 57912329 58003307 0 12 113,61,109,50,247,207,136,59,110,103,221,2327, 0,9893,33937,37135,40132,55063,56518,77795,92341,94802,97450,100500, +chr1 58011944 58026928 NM_001159864 0 - 58013171 58024533 0 7 1720,103,95,194,212,227,64, 0,4042,6800,7967,10228,12396,14920, +chr1 58011944 58026368 NR_027630 0 - 58026368 58026368 0 7 1720,103,95,194,190,227,118, 0,4042,6800,7967,10250,12396,14306, +chr1 58011944 58026928 NM_001159865 0 - 58013171 58024533 0 4 1720,103,227,64, 0,4042,12396,14920, +chr1 58042183 58082741 NM_001177867 0 + 58042207 58081643 0 6 102,86,236,2625,154,1114, 0,17554,28167,30019,34249,39444, +chr1 58052817 58083121 NM_199007 0 + 58054941 58081643 0 9 339,126,176,78,86,236,2625,154,1494, 0,2122,3990,5244,6920,17533,19385,23615,28810, +chr1 58086812 58163254 NM_009676 0 + 58086860 58162922 0 35 90,58,97,109,127,62,90,81,145,93,152,94,110,185,163,93,170,115,123,97,125,134,88,87,192,228,96,129,75,53,115,66,189,168,383, 0,11467,13573,17166,19394,23695,24679,26245,27445,28163,29066,29410,31227,32163,33403,35305,38301,38763,40072,43209,46095,47474,48457,51534,52043,55465,62525,64452,65186,66991,67897,72616,74350,74996,76059, +chr1 58169979 58257296 NM_023617 0 + 58170102 58257067 0 35 177,58,97,109,127,62,81,81,145,93,152,94,110,185,163,93,170,115,123,97,125,134,88,87,192,228,96,129,75,53,115,66,189,168,283, 0,1735,5462,6345,7842,11882,14491,25080,28215,29534,33288,34058,37159,39418,39885,40344,45065,45769,46501,50213,52701,54467,56642,57521,58606,58985,63338,64383,66181,67470,70330,73141,75199,81490,87034, +chr1 58267240 58325440 NM_023631 0 + 58267418 58324657 0 35 232,58,97,109,127,62,84,81,145,93,152,94,113,185,163,93,170,115,123,97,125,134,88,87,192,228,96,129,75,53,115,66,186,168,837, 0,2625,7036,9590,11431,13769,17675,18457,20708,21084,23441,24722,26270,28720,30284,34663,35404,35842,36809,38451,39738,41668,43129,43512,43743,45078,46818,48645,52168,52946,53437,53945,54562,56231,57363, +chr1 58335169 58436108 NM_001008419 0 + 58335262 58433159 0 36 150,58,97,109,127,62,84,81,145,93,152,94,110,185,187,93,170,115,123,97,125,134,88,87,192,228,96,129,75,53,115,66,189,168,75,624, 0,2851,4340,5161,7245,9366,11582,13872,15975,17537,21437,22289,25201,26103,26878,29024,30533,31655,33949,44453,52444,54217,56354,58274,59009,61133,65330,67899,70727,71911,72829,75836,75984,80592,97936,100315, +chr1 58449741 58464198 NM_025824 0 + 58451055 58461910 0 12 319,74,177,95,66,136,110,171,147,139,123,2320, 0,1304,4778,6106,7181,7809,8216,8443,9989,10717,11334,12137, +chr1 58468831 58480932 NR_027854 0 - 58480932 58480932 0 11 353,91,80,83,130,95,167,117,1642,161,169, 0,659,959,1402,2384,2602,5025,5279,7679,9786,11932, +chr1 58468831 58480932 NR_027853 0 - 58480932 58480932 0 12 353,91,80,83,130,95,167,117,67,226,161,169, 0,659,959,1402,2384,2602,5025,5279,7679,9095,9786,11932, +chr1 58468831 58480932 NM_001042634 0 - 58469040 58478778 0 13 353,91,80,83,130,95,167,117,67,91,226,161,169, 0,659,959,1402,2384,2602,5025,5279,7679,8133,9095,9786,11932, +chr1 58487836 58502330 NM_001285827 0 - 58488047 58501435 0 7 338,119,68,94,75,51,341, 0,3338,7351,9850,11532,13596,14153, +chr1 58487836 58502330 NM_001285826 0 - 58488047 58501435 0 7 338,119,68,94,75,51,676, 0,3338,7351,9850,11532,13596,13818, +chr1 58487836 58502330 NM_027351 0 - 58488047 58501435 0 7 338,119,68,94,75,51,155, 0,3338,7351,9850,11532,13596,14339, +chr1 58490630 58502330 NM_027374 0 - 58491170 58501435 0 6 663,68,94,75,51,341, 0,4557,7056,8738,10802,11359, +chr1 58501994 58519120 NM_022988 0 + 58504500 58518169 0 7 484,456,163,127,139,84,1136, 0,2483,5236,6938,10446,12629,15990, +chr1 58519614 58558270 NM_001025378 0 - 58521047 58558260 0 15 1520,119,62,172,147,97,133,110,99,194,61,32,90,90,104, 0,3224,4880,6897,8169,9534,12038,13663,17480,18189,20872,30086,30890,34605,38552, +chr1 58519614 58561953 NM_001271526 0 - 58521047 58558260 0 18 1520,119,62,172,147,97,133,110,99,194,61,32,90,90,144,104,43,338, 0,3224,4880,6897,8169,9534,12038,13663,17480,18189,20872,30086,30890,34605,37470,38552,39071,42001, +chr1 58519614 58561953 NM_008765 0 - 58521047 58558260 0 18 1520,119,62,172,147,97,133,110,99,194,61,32,90,90,144,104,49,338, 0,3224,4880,6897,8169,9534,12038,13663,17480,18189,20872,30086,30890,34605,37470,38552,39071,42001, +chr1 58579649 58643177 NM_001310598 0 - 58586501 58614871 0 13 7454,168,160,88,117,96,116,81,180,102,81,98,122, 0,11679,12584,16753,17328,21861,23301,25833,29344,34466,35171,43051,63406, +chr1 58579649 58643177 NM_172513 0 - 58586501 58614871 0 12 7454,160,88,117,96,116,81,180,102,81,98,122, 0,12584,16753,17328,21861,23301,25833,29344,34466,35171,43051,63406, +chr1 58579649 58642998 NM_001310599 0 - 58586501 58614871 0 12 7454,160,88,117,96,116,81,180,102,81,98,52, 0,12584,16753,17328,21861,23301,25833,29344,34466,35171,43051,63297, +chr1 58643240 58652808 NM_025597 0 + 58647935 58652649 0 3 274,160,316, 0,4693,9252, +chr1 58709484 58712675 NR_045007 0 + 58712675 58712675 0 2 49,887, 0,2304, +chr1 58714964 58749289 NM_001347056 0 - 58715151 58749257 0 14 314,110,90,63,104,100,53,98,62,94,134,46,78,145, 0,875,1102,3279,8706,9608,11307,12249,18408,20165,21743,32792,33584,34180, +chr1 58714964 58752833 NM_175370 0 - 58715267 58749257 0 15 310,110,90,63,104,100,53,98,62,94,134,46,78,145,88, 0,875,1102,3279,8706,9608,11307,12249,18408,20165,21743,32792,33584,34180,37781, +chr1 58768334 58815726 NM_001289704 0 + 58783280 58810766 0 10 102,427,106,136,74,55,50,82,508,5099, 0,14815,17565,19661,20762,24167,28772,29474,40848,42293, +chr1 58768334 58771146 NR_149256 0 + 58771146 58771146 0 3 102,87,186, 0,2080,2626, +chr1 58768334 58815726 NM_001293804 0 + 58789116 58810766 0 10 102,89,427,136,74,55,50,82,508,5099, 0,2080,14815,19661,20762,24167,28772,29474,40848,42293, +chr1 58768334 58770733 NR_149258 0 + 58770733 58770733 0 2 102,594, 0,1805, +chr1 58768334 58770733 NR_149257 0 + 58770733 58770733 0 2 102,319, 0,2080, +chr1 58770129 58790071 NR_149255 0 + 58790071 58790071 0 4 374,427,136,975, 0,13020,17866,18967, +chr1 58770129 58815726 NM_001355056 0 + 58789116 58810766 0 9 374,427,136,74,55,50,82,508,5099, 0,13020,17866,18967,22372,26977,27679,39053,40498, +chr1 58770129 58815726 NM_207653 0 + 58783280 58810766 0 10 374,427,106,136,74,55,50,82,508,5099, 0,13020,15770,17866,18967,22372,26977,27679,39053,40498, +chr1 58770129 58790071 NM_009805 0 + 58783280 58789206 0 5 374,427,106,136,975, 0,13020,15770,17866,18967, +chr1 58787395 58815726 NM_001293805 0 + 58789116 58810766 0 8 111,136,74,55,50,82,508,5099, 0,600,1701,5106,9711,10413,21787,23232, +chr1 58852217 58904347 NM_009812 0 + 58880786 58903598 0 9 365,333,106,139,54,62,142,502,882, 0,28541,31833,33499,33722,36232,38259,48970,51248, +chr1 58859345 58904347 NM_001277926 0 + 58860926 58903598 0 10 192,116,333,106,139,54,62,142,502,882, 0,1497,21413,24705,26371,26594,29104,31131,41842,44120, +chr1 58859345 58904347 NM_001080126 0 + 58880786 58903598 0 9 192,333,106,139,54,62,142,502,882, 0,21413,24705,26371,26594,29104,31131,41842,44120, +chr1 58957293 59030326 NM_172406 0 - 58960347 59003181 0 16 3733,106,267,299,201,77,138,75,131,79,210,117,77,195,289,246, 0,6256,8073,9500,11186,11736,15236,18322,18771,20624,21230,23072,26201,35296,45797,72787, +chr1 59030365 59051965 NR_151686 0 + 59051965 59051965 0 11 329,107,81,100,122,109,124,105,245,43,829, 0,3437,6412,11767,14984,16168,17491,19129,19371,20039,20771, +chr1 59030365 59051965 NM_172656 0 + 59033897 59051280 0 12 329,107,81,100,122,109,124,172,105,245,43,829, 0,3437,6412,11767,14984,16168,17491,18682,19129,19371,20039,20771, +chr1 59053960 59151737 NM_026600 0 - 59054106 59151704 0 19 485,4674,75,63,62,37,288,38,64,106,135,80,69,45,126,146,52,87,396, 0,6024,12952,15517,21633,25762,53881,55379,61539,63455,65279,69033,70660,71566,72600,77880,79554,80766,97381, +chr1 59107349 59151744 NM_175200 0 - 59107766 59151704 0 13 780,38,64,106,135,80,69,45,126,146,52,87,403, 0,1990,8150,10066,11890,15644,17271,18177,19211,24491,26165,27377,43992, +chr1 59157427 59176940 NM_001033449 0 - 59157980 59176858 0 13 615,122,91,74,192,124,158,118,138,57,11,32,145, 0,4962,5960,6870,7454,8091,8455,9404,13497,15289,16747,17391,19368, +chr1 59157427 59177252 NM_001361413 0 - 59157980 59177203 0 14 615,122,91,74,192,124,158,118,138,57,63,11,32,91, 0,4962,5960,6870,7454,8091,8455,9404,13497,15289,16258,16747,17391,19734, +chr1 59157427 59176650 NM_001037812 0 - 59157980 59176579 0 13 615,122,91,74,192,124,158,118,138,57,11,32,104, 0,4962,5960,6870,7454,8091,8455,9404,13497,15289,16747,17391,19119, +chr1 59177778 59218480 NM_145143 0 - 59178096 59215505 0 22 510,135,109,94,81,171,42,15,21,39,18,65,197,72,86,82,132,81,78,122,90,105, 0,2508,3696,4588,7997,8990,10987,12880,15904,18827,20009,22821,23719,25407,25812,28079,28586,29536,30724,36439,37651,40597, +chr1 59177778 59220233 NM_001164682 0 - 59178096 59218358 0 23 510,135,109,94,81,171,42,15,21,39,18,65,197,72,86,82,132,81,78,122,90,60,682, 0,2508,3696,4588,7997,8990,10987,12880,15904,18827,20009,22821,23719,25407,25812,28079,28586,29536,30724,36439,37651,40537,41773, +chr1 59219599 59293937 NM_001159948 0 - 59221020 59277238 0 34 1460,97,150,62,46,177,123,158,118,168,134,78,112,165,99,66,203,67,71,129,132,163,66,181,172,183,78,97,169,358,920,155,78,246, 0,4427,4707,5395,5633,7081,7681,10400,12168,15776,16304,17350,17793,20408,21025,22457,22641,23256,23700,24565,24979,29133,31277,33435,36264,40159,43763,45004,46193,48375,52346,55171,57619,74092, +chr1 59219599 59294075 NM_028717 0 - 59221020 59277238 0 34 1460,97,150,62,46,177,123,158,118,168,134,78,112,165,99,66,203,67,71,129,132,163,66,181,172,183,78,97,169,358,920,155,78,77, 0,4427,4707,5395,5633,7081,7681,10400,12168,15776,16304,17350,17793,20408,21025,22457,22641,23256,23700,24565,24979,29133,31277,33435,36264,40159,43763,45004,46193,48375,52346,55171,57619,74399, +chr1 59248466 59294075 NM_146109 0 - 59248507 59277238 0 13 429,66,181,172,183,78,97,169,358,920,155,78,77, 0,2410,4568,7397,11292,14896,16137,17326,19508,23479,26304,28752,45532, +chr1 59313749 59409340 NM_001356389 0 + 59313816 59401201 0 14 193,141,92,80,95,63,124,121,94,64,49,140,119,227, 0,910,1800,8698,23663,24503,30856,32753,44289,53890,69765,73953,87342,95364, +chr1 59313749 59409340 NM_001033373 0 + 59313816 59401201 0 14 193,141,95,80,95,63,124,121,94,64,49,140,119,227, 0,910,1797,8698,23663,24503,30856,32753,44289,53890,69765,73953,87342,95364, +chr1 59538990 59543799 NM_008057 0 + 59539803 59541522 0 1 4809, 0, +chr1 59573107 59691353 NM_001013771 0 + 59573275 59691106 0 20 255,267,160,156,128,163,143,169,141,168,111,80,73,91,151,115,332,203,173,516, 0,10447,25050,28310,33648,34870,36156,39892,41822,46379,50330,66132,91469,108823,111193,111906,113731,115950,116883,117730, +chr1 59581137 59693260 NM_001357842 0 + 59581501 59693067 0 19 448,267,160,156,128,169,141,168,111,80,73,91,151,115,332,203,173,220,332, 0,2417,17020,20280,25618,31862,33792,38349,42300,58102,83439,100793,103163,103876,105701,107920,108853,109700,111791, +chr1 59696277 59727678 NM_009460 0 - 59697043 59727535 0 5 835,72,78,75,155, 0,2984,5083,16024,31246, +chr1 59741849 59768354 NM_018868 0 + 59742025 59768165 0 15 221,77,53,122,137,65,135,146,127,164,135,62,134,158,240, 0,5480,7331,10972,13317,15879,17807,19057,19618,20587,21627,21997,23997,25489,26265, +chr1 59748801 59748854 NR_028554 0 + 59748854 59748854 0 1 53, 0, +chr1 59761651 59761714 NR_028521 0 + 59761714 59761714 0 1 63, 0, +chr1 59821122 59934925 NM_007561 0 + 59821496 59927329 0 13 450,171,171,111,92,231,115,161,148,137,173,1280,7847, 0,49309,50962,77152,78464,81199,82779,86899,88015,94894,99502,103057,105956, +chr1 59969849 60042192 NM_001037725 0 + 59970007 60038571 0 8 747,152,90,114,144,226,121,3940, 0,36047,39929,45316,55948,57480,61877,68403, +chr1 60045911 60099966 NM_001357296 0 - 60047967 60085073 0 11 2172,261,50,86,99,126,199,124,73,169,53, 0,8383,14588,17166,18740,21041,24752,26644,33510,39000,54002, +chr1 60045911 60099966 NM_027407 0 - 60047967 60085073 0 11 2172,261,50,86,99,126,199,124,73,169,326, 0,8383,14588,17166,18740,21041,24752,26644,33510,39000,53729, +chr1 60045911 60099966 NM_001316694 0 - 60047967 60085073 0 11 2172,261,50,86,99,126,199,124,73,179,53, 0,8383,14588,17166,18740,21041,24752,26644,33510,39000,54002, +chr1 60077634 60099966 NM_001316695 0 - 60078130 60085073 0 4 594,73,169,53, 0,1787,7277,22279, +chr1 60133711 60154978 NM_001199061 0 - 60135007 60154391 0 14 1374,73,133,106,141,86,46,155,116,107,95,95,221,90, 0,3651,5169,5423,5641,6887,8843,10178,11173,12384,14152,17564,20639,21177, +chr1 60133711 60155344 NM_001199060 0 - 60135007 60154391 0 14 1374,73,133,106,141,86,46,155,116,107,95,95,221,358, 0,3651,5169,5423,5641,6887,8843,10178,11173,12384,14152,17564,20639,21275, +chr1 60133711 60154751 NM_021312 0 - 60135007 60154391 0 13 1374,73,133,106,141,86,46,155,116,107,95,95,401, 0,3651,5169,5423,5641,6887,8843,10178,11173,12384,14152,17564,20639, +chr1 60155090 60210797 NM_139150 0 + 60164969 60207531 0 16 61,117,118,228,61,115,85,190,121,144,234,163,64,113,370,3373, 0,7064,9836,10975,26604,27673,29742,33597,38017,40953,43088,45747,47862,49121,49586,52334, +chr1 60155090 60210797 NM_001285463 0 + 60181982 60207531 0 18 61,158,124,118,123,61,67,115,85,190,121,144,234,163,64,113,370,3373, 0,4380,7064,9836,11080,26604,26832,27673,29742,33597,38017,40953,43088,45747,47862,49121,49586,52334, +chr1 60164926 60210797 NR_104344 0 + 60210797 60210797 0 12 118,123,61,115,85,190,234,163,64,113,370,3373, 0,1244,16768,17837,19906,23761,33252,35911,38026,39285,39750,42498, +chr1 60164926 60210797 NM_001285473 0 + 60164969 60207531 0 14 118,123,61,115,85,190,121,144,234,163,64,113,370,3373, 0,1244,16768,17837,19906,23761,28181,31117,33252,35911,38026,39285,39750,42498, +chr1 60237442 60391549 NM_173444 0 + 60238547 60387836 0 55 87,292,92,162,82,128,83,86,307,107,84,99,581,133,120,304,86,90,169,134,160,103,157,159,160,89,561,176,154,129,306,150,158,125,127,149,134,102,96,125,141,131,110,118,98,117,90,110,173,95,117,162,149,136,3815, 0,864,13905,14416,19506,20265,25735,36597,41468,44026,50003,54198,54382,55772,56498,57973,61940,64195,67017,67764,70436,70705,72753,74295,76831,78051,79634,80811,83680,84283,87160,87784,89673,91534,96526,97314,98068,99100,100648,101226,103384,106712,109316,111235,112268,115280,124676,129605,130328,131552,138718,139072,147461,148728,150292, +chr1 60400143 60444904 NM_001313721 0 + 60411374 60444133 0 12 158,50,143,168,79,116,55,121,112,65,90,922, 0,8821,11214,19890,23349,27921,29290,32767,36074,39104,43605,43839, +chr1 60400143 60444904 NM_030013 0 + 60400229 60444133 0 13 158,50,167,143,168,79,116,55,121,112,65,90,922, 0,8821,9609,11214,19890,23349,27921,29290,32767,36074,39104,43605,43839, +chr1 60466462 60538007 NM_198127 0 + 60466646 60533759 0 9 301,168,177,98,147,125,159,174,4424, 0,24624,27437,34366,37641,38459,43985,61047,67121, +chr1 60466462 60538007 NM_001198571 0 + 60466646 60533759 0 11 301,168,177,18,98,147,125,84,159,174,4424, 0,24624,27437,29323,34366,37641,38459,40551,43985,61047,67121, +chr1 60466462 60538007 NM_001198570 0 + 60466646 60534851 0 12 301,168,177,18,98,147,125,183,159,174,93,3161, 0,24624,27437,29323,34366,37641,38459,40452,43985,61047,67121,68384, +chr1 60540028 60623609 NM_001045513 0 - 60545143 60590250 0 14 7137,143,121,99,111,144,66,122,160,78,509,106,120,201, 0,10353,12230,13040,15239,16295,17370,18571,19640,20333,42407,44199,50102,83380, +chr1 60803231 60830203 NM_007642 0 + 60803317 60826629 0 4 141,357,116,3703, 0,16591,18889,23269, +chr1 60965868 60972676 NM_009843 0 + 60966014 60971561 0 4 255,348,110,1220, 0,3398,4194,5588, +chr1 60965868 60972676 NM_001281976 0 + 60966014 60971524 0 3 255,348,1220, 0,3398,5588, +chr1 61034757 61057164 NM_017480 0 + 61034802 61054558 0 5 103,339,107,85,2620, 0,15788,16696,17610,19787, +chr1 61435275 61452748 NR_040483 0 + 61452748 61452748 0 5 125,159,234,100,274, 0,578,1564,15676,17199, +chr1 61685397 62688858 NM_001081050 0 + 61685816 62684497 0 23 539,102,172,110,89,87,126,359,140,129,186,171,133,100,116,45,207,238,111,297,136,80,4719, 0,129124,371483,437561,506023,515109,520611,522286,525256,527530,559753,572710,577599,591355,600013,637059,705110,706046,801187,840675,893821,948913,998742, +chr1 62177682 62182683 NR_151537 0 - 62182683 62182683 0 3 572,132,152, 0,2784,4849, +chr1 62749890 62843665 NM_001077406 0 + 62750778 62842563 0 16 961,178,182,231,156,170,156,145,350,145,117,141,263,97,36,1383, 0,15613,34972,40858,42041,43841,45816,57458,59374,61533,65683,68388,79977,81728,82964,92392, +chr1 62749890 62865266 NM_001077403 0 + 62750778 62862211 0 17 961,178,182,231,156,170,156,145,350,145,117,141,263,97,36,51,3360, 0,15613,34972,40858,42041,43841,45816,57458,59374,61533,65683,68388,79977,81728,82964,109217,112016, +chr1 62749890 62865266 NM_010939 0 + 62750778 62862211 0 16 961,178,182,231,156,170,156,145,350,145,117,141,263,97,36,3360, 0,15613,34972,40858,42041,43841,45816,57458,59374,61533,65683,68388,79977,81728,82964,112016, +chr1 62749890 62843665 NM_001077407 0 + 62750778 62842563 0 16 961,178,182,231,156,170,156,145,350,145,117,141,263,97,21,1383, 0,15613,34972,40858,42041,43841,45816,57458,59374,61533,65683,68388,79977,81728,82964,92392, +chr1 62749890 62865266 NM_001077405 0 + 62750778 62862211 0 16 961,178,182,231,156,170,156,145,350,145,117,141,263,97,21,3360, 0,15613,34972,40858,42041,43841,45816,57458,59374,61533,65683,68388,79977,81728,82964,112016, +chr1 62749890 62865266 NM_001077404 0 + 62750778 62862211 0 17 961,178,182,231,156,170,156,145,350,145,117,141,263,97,21,51,3360, 0,15613,34972,40858,42041,43841,45816,57458,59374,61533,65683,68388,79977,81728,82964,109217,112016, +chr1 62837491 62841306 NR_040601 0 - 62841306 62841306 0 3 639,76,180, 0,3478,3635, +chr1 63094374 63160841 NM_001081436 0 - 63104556 63132875 0 12 11345,158,218,134,110,225,109,731,156,91,104,57, 0,13239,14235,17903,20383,26521,31152,37867,45484,45839,57855,66410, +chr1 63094374 63160841 NM_001114609 0 - 63104556 63140076 0 12 11345,158,218,134,110,225,109,731,247,91,104,57, 0,13239,14235,17903,20383,26521,31152,37867,45484,45839,57855,66410, +chr1 63161044 63204869 NR_045915 0 + 63204869 63204869 0 4 74,67,102,1338, 0,29648,41749,42487, +chr1 63161313 63204869 NR_045914 0 + 63204869 63204869 0 4 221,67,102,1338, 0,29379,41480,42218, +chr1 63190165 63223396 NM_001160040 0 - 63190404 63217483 0 19 331,73,135,176,155,161,130,129,146,115,135,186,131,82,77,108,92,66,395, 0,3528,3698,4804,6365,7959,9183,12612,13540,16158,17288,20075,21138,21357,22699,25637,26458,27257,32836, +chr1 63190165 63223396 NM_001160039 0 - 63190404 63217483 0 20 331,73,135,176,155,161,130,129,146,115,135,186,131,82,77,108,92,66,104,237, 0,3528,3698,4804,6365,7959,9183,12612,13540,16158,17288,20075,21138,21357,22699,25637,26458,27257,28562,32994, +chr1 63190165 63223396 NM_145518 0 - 63190404 63217483 0 19 331,73,135,176,155,161,130,129,146,115,135,186,131,82,77,108,92,66,237, 0,3528,3698,4804,6365,7959,9183,12612,13540,16158,17288,20075,21138,21357,22699,25637,26458,27257,32994, +chr1 63190165 63223396 NM_001160038 0 - 63190404 63217483 0 20 331,73,135,176,155,161,130,129,146,115,135,186,131,82,77,108,92,66,104,395, 0,3528,3698,4804,6365,7959,9183,12612,13540,16158,17288,20075,21138,21357,22699,25637,26458,27257,28562,32836, +chr1 63223404 63227060 NM_018796 0 + 63223785 63226186 0 6 461,123,127,67,126,1029, 0,923,1608,2001,2417,2627, +chr1 63225596 63225709 NR_028558 0 + 63225709 63225709 0 1 113, 0, +chr1 63229144 63260855 NM_146250 0 - 63229586 63230648 0 3 1534,146,118, 0,27183,31593, +chr1 63229144 63257290 NM_001357045 0 - 63229586 63230648 0 3 1534,146,147, 0,27183,27999, +chr1 63246931 63361149 NM_001285937 0 + 63327391 63356519 0 6 317,100,53,111,131,11936, 0,7157,77573,80409,94558,102282, +chr1 63246931 63361149 NM_001285936 0 + 63327391 63356519 0 7 317,100,57,53,111,131,11936, 0,7157,63141,77573,80409,94558,102282, +chr1 63319842 63361149 NM_028673 0 + 63337311 63356519 0 7 204,83,53,111,103,131,11936, 0,1827,4662,7498,17411,21647,29371, +chr1 63319842 63361149 NM_001267872 0 + 63337311 63356519 0 6 204,53,111,136,131,11936, 0,4662,7498,17378,21647,29371, +chr1 63492464 63642675 NM_011780 0 + 63492784 63639230 0 26 522,221,77,64,83,64,73,74,66,72,164,85,91,49,100,72,90,81,51,64,106,120,169,112,91,3494, 0,1837,31788,69686,82867,84344,88395,89244,91028,97228,99540,100525,101836,103856,105870,109264,109923,111517,117518,118254,120711,121958,125019,126996,139474,146717, +chr1 63662541 63667395 NM_001370842 0 + 63662541 63666834 0 2 412,695, 0,4159, +chr1 63669424 63733501 NM_001081658 0 - 63669588 63731693 0 15 301,481,160,71,136,146,112,164,72,101,86,202,75,147,173, 0,10567,18204,20452,24546,36019,38288,41549,41922,52005,52887,54266,55930,62250,63904, +chr1 63745400 63776892 NM_029696 0 - 63745582 63776866 0 11 211,66,52,140,164,142,497,143,135,113,48, 0,2749,12288,12625,16365,19692,20695,22661,22981,26781,31444, +chr1 63777198 63799959 NM_172422 0 + 63778060 63798978 0 12 67,822,104,109,124,140,173,164,213,85,115,1089, 0,775,4107,4838,5220,7154,8557,15217,17333,19061,20639,21672, +chr1 63801482 63815841 NM_001256158 0 - 63802672 63815779 0 3 1511,158,87, 0,13476,14272, +chr1 64011300 64015573 NR_027824 0 + 64015573 64015573 0 2 72,1360, 0,2913, +chr1 64082246 64167963 NM_033563 0 - 64082286 64167575 0 4 92,124,628,490, 0,6641,43034,85227, +chr1 64089011 64089075 NR_105864 0 - 64089075 64089075 0 1 64, 0, +chr1 64579377 64651122 NM_009952 0 + 64597430 64643952 0 9 217,122,147,42,101,143,183,151,7315, 0,18045,25699,26923,33413,37330,41269,43375,64430, +chr1 64579377 64651122 NM_001037726 0 + 64605082 64643952 0 7 217,147,101,143,183,151,7315, 0,25699,33413,37330,41269,43375,64430, +chr1 64579377 64651122 NM_133828 0 + 64597430 64643952 0 8 217,122,147,101,143,183,151,7315, 0,18045,25699,33413,37330,41269,43375,64430, +chr1 64653046 64664338 NM_001368284 0 - 64654313 64662993 0 4 1665,112,172,603, 0,8625,9800,10689, +chr1 64653046 64664338 NM_001368283 0 - 64654313 64662993 0 4 1665,112,172,833, 0,8625,9800,10459, +chr1 64653046 64664338 NM_025964 0 - 64654313 64662993 0 3 1665,112,1492, 0,8625,9800, +chr1 64726442 64737233 NR_038009 0 - 64737233 64737233 0 2 517,196, 0,10595, +chr1 64737918 64772216 NM_001097644 0 + 64737964 64770213 0 10 56,75,35,101,36,52,120,167,163,2120, 0,9624,11001,17033,20073,21766,23224,26786,30282,32178, +chr1 64777131 64784324 NM_001042659 0 - 64781416 64783174 0 2 6296,511, 0,6682, +chr1 64777131 64784324 NM_022721 0 - 64781416 64783174 0 2 6296,618, 0,6575, +chr1 64835694 65003398 NM_001039493 0 - 64841610 64984883 0 8 6094,158,64,194,146,933,843,130, 0,30815,72066,94008,103631,132429,148576,167574, +chr1 65059651 65079333 NM_001310617 0 - 65059840 65072292 0 9 232,83,166,110,123,78,117,168,174, 0,1599,2989,3587,8305,8841,11585,12485,19508, +chr1 65059651 65079333 NM_027582 0 - 65059840 65077222 0 10 232,83,166,110,123,78,117,168,121,174, 0,1599,2989,3587,8305,8841,11585,12485,17490,19508, +chr1 65095130 65097737 NM_007777 0 - 65095197 65097687 0 3 340,243,59, 0,2213,2548, +chr1 65108411 65110014 NM_007776 0 - 65108483 65109976 0 3 345,243,47, 0,1221,1556, +chr1 65118098 65120106 NM_001082573 0 - 65118172 65120079 0 3 350,243,36, 0,1637,1972, +chr1 65118098 65120106 NM_007775 0 - 65118172 65120079 0 3 347,243,36, 0,1637,1972, +chr1 65126795 65128864 NM_144761 0 - 65126865 65128829 0 3 346,243,44, 0,1693,2025, +chr1 65146962 65149937 NM_007774 0 - 65147026 65149911 0 3 337,243,35, 0,2592,2940, +chr1 65151858 65169788 NM_001285882 0 - 65152302 65169667 0 8 466,115,88,72,88,83,82,162, 0,4177,4592,11396,11837,14254,16072,17768, +chr1 65153886 65169788 NM_175293 0 - 65155270 65169667 0 8 1493,115,88,72,88,83,100,162, 0,2149,2564,9368,9809,12226,14026,15740, +chr1 65153886 65169788 NM_001285881 0 - 65155270 65169667 0 8 1493,115,88,72,88,83,82,162, 0,2149,2564,9368,9809,12226,14044,15740, +chr1 65205189 65225716 NM_010497 0 - 65206038 65221926 0 9 940,163,141,152,178,106,292,138,153, 0,2434,3184,6484,7491,9883,12343,16615,20374, +chr1 65205189 65233053 NM_001111320 0 - 65206038 65221926 0 9 940,163,141,152,178,106,292,138,175, 0,2434,3184,6484,7491,9883,12343,16615,27689, +chr1 65233258 65325270 NM_001310624 0 + 65236901 65320332 0 42 149,181,150,119,172,208,90,139,158,112,148,168,60,130,181,75,108,141,127,1157,101,72,172,179,114,109,155,91,61,138,121,96,84,98,165,60,177,104,129,262,75,5054, 0,3634,5460,8971,9927,16031,18904,29249,33069,35585,36820,37477,44109,47045,47569,48325,51750,57711,59025,59377,63501,64920,65727,66667,68357,68837,69254,69863,71224,72098,73314,76195,77662,78564,79077,81141,82013,83188,84583,85762,86348,86958, +chr1 65233258 65325270 NM_011086 0 + 65236901 65320332 0 42 149,181,150,33,119,172,208,90,139,158,112,148,60,130,181,75,108,141,127,1157,101,72,172,179,114,109,155,91,61,138,121,96,84,98,165,60,177,104,129,262,75,5054, 0,3634,5460,5849,8971,9927,16031,18904,29249,33069,35585,36820,44109,47045,47569,48325,51750,57711,59025,59377,63501,64920,65727,66667,68357,68837,69254,69863,71224,72098,73314,76195,77662,78564,79077,81141,82013,83188,84583,85762,86348,86958, +chr1 65357830 65435818 NM_139270 0 + 65358169 65435384 0 13 414,103,111,116,98,190,154,61,64,95,139,42,827, 0,10712,25491,25717,32223,34050,35556,40279,51995,61021,72606,75044,77161, +chr1 65973095 65974886 NM_001360779 0 + 65973131 65974651 0 3 45,243,328, 0,126,1463, +chr1 65973095 65974886 NM_027010 0 + 65973131 65974817 0 3 45,243,342, 0,126,1449, +chr1 66221902 66489157 NM_001039934 0 + 66427085 66485581 0 15 167,63,51,65,78,285,114,78,62,145,332,93,82,113,3792, 0,17790,76333,147075,186874,205160,224060,226115,244806,246317,249868,256198,258185,262925,263463, +chr1 66221902 66489157 NM_008632 0 + 66427085 66485581 0 14 167,63,51,65,78,285,114,78,62,145,332,82,113,3792, 0,17790,76333,147075,186874,205160,224060,226115,244806,246317,249868,258185,262925,263463, +chr1 66368297 66489157 NM_001310634 0 + 66427085 66485581 0 15 419,65,78,285,114,78,3741,207,135,62,145,332,82,113,3792, 0,680,40479,58765,77665,79720,90683,94620,95008,98411,99922,103473,111790,116530,117068, +chr1 66514507 66745724 NM_175510 0 + 66515020 66742170 0 65 605,49,157,302,124,77,140,262,135,217,141,269,375,147,148,149,167,99,209,107,97,173,213,136,134,166,204,101,201,108,139,182,132,187,129,144,101,87,184,95,90,102,181,269,135,139,97,171,93,36,219,201,124,126,124,207,185,166,180,139,57,82,112,200,3821, 0,1530,4042,5297,15307,17831,23058,35596,36989,38696,39392,41333,42616,53521,57709,59938,62038,62821,81794,83012,84220,86993,101856,122261,125731,133121,138518,140458,144154,150228,151491,154522,155276,158494,159260,163454,167923,168994,169980,171312,172617,173682,176338,178437,180447,180967,181740,183526,185362,186076,186450,201162,203652,204723,206053,206953,209382,210131,211630,215215,217682,224574,225758,226431,227396, +chr1 66514507 66745724 NM_001368825 0 + 66515020 66742170 0 64 605,49,157,302,124,77,140,262,135,217,141,269,375,147,148,149,167,99,215,107,97,173,213,136,134,166,101,201,108,139,182,132,187,132,144,101,87,184,95,90,102,181,269,135,139,97,171,93,36,219,201,124,126,124,207,185,166,180,139,57,82,112,200,3821, 0,1530,4042,5297,15307,17831,23058,35596,36989,38696,39392,41333,42616,53521,57709,59938,62038,62821,81794,83012,84220,86993,101856,122261,125731,133121,140458,144154,150228,151491,154522,155276,158494,159257,163454,167923,168994,169980,171312,172617,173682,176338,178437,180447,180967,181740,183526,185362,186076,186450,201162,203652,204723,206053,206953,209382,210131,211630,215215,217682,224574,225758,226431,227396, +chr1 66514507 66745724 NM_001368824 0 + 66515020 66742170 0 65 605,49,157,302,124,77,140,262,135,217,141,269,375,147,148,149,167,99,215,107,97,173,213,172,134,166,204,101,201,108,139,182,132,187,132,144,101,87,184,95,90,102,181,269,135,139,97,171,93,36,219,201,124,126,124,207,185,166,180,139,57,82,112,200,3821, 0,1530,4042,5297,15307,17831,23058,35596,36989,38696,39392,41333,42616,53521,57709,59938,62038,62821,81794,83012,84220,86993,101856,122261,125731,133121,138518,140458,144154,150228,151491,154522,155276,158494,159257,163454,167923,168994,169980,171312,172617,173682,176338,178437,180447,180967,181740,183526,185362,186076,186450,201162,203652,204723,206053,206953,209382,210131,211630,215215,217682,224574,225758,226431,227396, +chr1 66747404 66766379 NM_025683 0 + 66747480 66764450 0 6 198,80,140,135,87,2052, 0,5615,13746,14282,15128,16923, +chr1 66747404 66766379 NM_001310644 0 + 66747589 66764450 0 6 187,80,140,135,87,2052, 0,5615,13746,14282,15128,16923, +chr1 66747404 66766379 NM_001310643 0 + 66761152 66764450 0 7 198,32,80,140,135,87,2052, 0,786,5615,13746,14282,15128,16923, +chr1 66747404 66766379 NM_001310642 0 + 66747480 66764450 0 7 187,32,80,140,135,87,2052, 0,786,5615,13746,14282,15128,16923, +chr1 66765816 66864169 NM_001122738 0 - 66767349 66848713 0 15 1764,169,113,55,125,122,132,108,163,205,122,93,142,1120,222, 0,2562,4020,5315,6631,7444,9201,16394,18808,42805,53663,54179,58724,81806,98131, +chr1 66765816 66864169 NM_177645 0 - 66767349 66848713 0 14 1764,169,113,55,125,122,108,163,205,122,198,142,1120,222, 0,2562,4020,5315,6631,7444,16394,18808,42805,53663,54179,58724,81806,98131, +chr1 66765821 66864169 NM_001357156 0 - 66767349 66848713 0 15 1759,169,113,55,125,122,108,163,205,122,198,142,1120,80,186, 0,2557,4015,5310,6626,7439,16389,18803,42800,53658,54174,58719,81801,88277,98162, +chr1 66765821 66855368 NM_001357157 0 - 66767349 66848713 0 15 1759,169,113,55,125,119,108,163,205,122,198,142,1120,80,491, 0,2557,4015,5310,6626,7439,16389,18803,42800,53658,54174,58719,81801,88277,89056, +chr1 66765821 66864169 NM_001368830 0 - 66767349 66848713 0 14 1759,169,113,55,125,122,108,163,205,122,93,142,1120,222, 0,2557,4015,5310,6626,7439,16389,18803,42800,53658,54174,58719,81801,98126, +chr1 66877412 66909883 NM_007381 0 - 66878007 66909823 0 11 689,87,128,114,102,165,67,165,138,156,137, 0,6123,7440,10783,12242,14329,17561,22288,23785,26560,32334, +chr1 66970869 66981940 NM_001113387 0 - 66971610 66981852 0 7 262,43,78,174,144,25,91, 0,727,1912,2238,5890,10222,10980, +chr1 66970869 66991630 NM_021285 0 - 66971610 66991479 0 7 262,43,78,174,144,28,265, 0,727,1912,2238,5890,9950,20496, +chr1 67047090 67085446 NM_021295 0 - 67050054 67085149 0 10 3041,73,177,183,147,136,208,118,97,97, 0,3822,4273,6351,8711,9394,20341,33607,37978,38259, +chr1 67047090 67085408 NM_001190984 0 - 67050054 67085149 0 10 3041,73,177,183,147,136,208,118,97,63, 0,3822,4273,6351,8711,9394,20341,33607,37978,38255, +chr1 67047090 67085446 NM_001190985 0 - 67050054 67085149 0 9 3041,73,177,183,147,136,208,118,378, 0,3822,4273,6351,8711,9394,20341,33607,37978, +chr1 67169600 67277841 NM_001080809 0 + 67169738 67276920 0 38 264,110,145,90,57,93,90,129,107,139,78,99,96,190,158,129,145,211,199,177,119,142,66,64,182,195,68,76,78,108,90,171,75,99,60,113,130,1020, 0,16730,19838,20839,22760,25683,29255,33106,33797,34712,35837,37832,39554,42355,43342,45214,47822,49629,51276,53882,57044,72116,73511,73978,75274,81481,82105,83729,86569,89376,90990,92383,94825,97476,104097,105209,106362,107221, +chr1 68078760 69154633 NM_010154 0 - 68086614 69154330 0 27 8300,298,171,98,147,76,156,186,99,123,133,75,155,94,133,200,91,74,127,114,142,119,66,135,187,152,385, 0,10254,39331,40911,43231,46349,48453,166655,218393,222342,226994,258056,266100,273658,277408,295881,298005,299033,307170,311653,314359,317114,338268,363994,528309,708195,1075488, +chr1 69577783 69732534 NM_011770 0 - 69585341 69730731 0 8 8283,144,138,168,267,105,49,267, 0,11017,17389,39283,46571,152000,152914,154484, +chr1 69873543 69972824 NM_001271533 0 + 69873577 69970487 0 11 152,47,96,119,138,108,118,67,45,110,2589, 0,15999,17309,26353,31503,43294,46164,60522,68257,69502,96692, +chr1 69873543 70771706 NM_029160 0 + 69873577 70771516 0 17 152,47,96,119,138,108,118,67,45,110,128,144,186,127,66,127,366, 0,15999,17309,26353,31503,43294,46164,60522,68257,69502,169811,437936,472613,554309,634096,666811,897797, +chr1 69998188 70771706 NM_025728 0 + 70043375 70771516 0 8 159,128,144,186,127,66,127,366, 0,45166,313291,347968,429664,509451,542166,773152, +chr1 70772288 70931971 NM_177164 0 + 70775352 70928789 0 4 724,470,130,3331, 0,2984,25222,156352, +chr1 70772288 70931955 NM_001310658 0 + 70775352 70928670 0 3 724,470,3315, 0,2984,156352, +chr1 71074108 71149546 NM_007525 0 - 71077093 71149381 0 11 3318,98,93,133,109,173,81,938,143,57,305, 0,3824,19143,20105,26078,37944,39573,47008,60574,61936,75133, +chr1 71289663 71461484 NM_175210 0 - 71289870 71461156 0 53 315,138,106,93,104,135,142,110,205,254,160,116,178,55,106,88,128,94,87,253,151,237,161,197,219,187,156,135,70,330,115,316,180,91,120,140,211,165,174,122,113,257,107,119,70,113,179,186,98,92,154,94,397, 0,1642,4042,5255,6765,15001,16268,16699,17691,20322,21634,22772,24339,25092,29274,31323,32981,35722,36285,37251,39712,40855,42488,43369,45448,48242,49324,50291,50511,51637,57830,59541,60376,63946,66678,69471,70869,71388,74010,76783,78310,78505,86074,87157,92602,98373,103496,105927,108618,110580,119511,158561,171424, +chr1 71603729 71625977 NM_026195 0 + 71603829 71625245 0 16 119,127,77,67,89,152,157,126,108,86,90,129,93,183,156,852, 0,341,2070,3733,6603,7250,7655,10658,11807,12684,13684,15752,18885,19461,20630,21396, +chr1 71632046 71699808 NM_001276411 0 - 71632785 71699556 0 44 811,114,107,126,165,139,392,90,180,90,177,88,188,114,156,165,117,270,90,183,192,87,169,95,267,273,195,90,129,177,178,122,144,129,153,177,180,192,156,138,132,138,129,403, 0,1357,4625,5294,7598,10191,11808,12901,13742,14130,14817,15728,16837,19497,20412,21230,22431,23940,25456,26995,29887,33106,33911,35252,38605,40501,41690,42584,42935,43843,44193,46568,51779,52984,54819,55679,56479,57487,60074,62536,63721,65089,66048,67359, +chr1 71632046 71699808 NM_001276410 0 - 71632785 71699556 0 44 811,114,107,126,165,139,467,90,180,90,177,88,188,114,156,165,117,270,90,183,192,87,169,95,267,273,195,90,129,177,178,122,144,129,153,177,180,192,156,138,132,138,129,403, 0,1357,4625,5294,7598,10191,11808,12901,13742,14130,14817,15728,16837,19497,20412,21230,22431,23940,25456,26995,29887,33106,33911,35252,38605,40501,41690,42584,42935,43843,44193,46568,51779,52984,54819,55679,56479,57487,60074,62536,63721,65089,66048,67359, +chr1 71632046 71699808 NM_001276413 0 - 71632785 71699556 0 44 811,114,107,126,165,139,107,90,180,90,177,88,188,114,156,165,117,270,90,183,192,87,169,95,267,273,195,90,129,177,178,122,144,129,153,177,180,192,156,138,132,138,129,403, 0,1357,4625,5294,7598,10191,11808,12901,13742,14130,14817,15728,16837,19497,20412,21230,22431,23940,25456,26995,29887,33106,33911,35252,38605,40501,41690,42584,42935,43843,44193,46568,51779,52984,54819,55679,56479,57487,60074,62536,63721,65089,66048,67359, +chr1 71632046 71699808 NM_001276412 0 - 71632785 71699556 0 45 811,114,107,126,165,139,107,90,180,90,177,88,188,270,114,156,165,117,270,90,183,192,87,169,95,267,273,195,90,129,177,178,122,144,129,153,177,180,192,156,138,132,138,129,403, 0,1357,4625,5294,7598,10191,11808,12901,13742,14130,14817,15728,16837,18187,19497,20412,21230,22431,23940,25456,26995,29887,33106,33911,35252,38605,40501,41690,42584,42935,43843,44193,46568,51779,52984,54819,55679,56479,57487,60074,62536,63721,65089,66048,67359, +chr1 71632046 71699808 NM_010233 0 - 71632785 71699556 0 46 811,114,107,126,165,139,467,90,180,90,177,88,188,270,114,156,165,117,270,90,183,273,192,87,169,95,267,273,195,90,129,177,178,122,144,129,153,177,180,192,156,138,132,138,129,403, 0,1357,4625,5294,7598,10191,11808,12901,13742,14130,14817,15728,16837,18187,19497,20412,21230,22431,23940,25456,26995,28290,29887,33106,33911,35252,38605,40501,41690,42584,42935,43843,44193,46568,51779,52984,54819,55679,56479,57487,60074,62536,63721,65089,66048,67359, +chr1 71632046 71699808 NM_001276409 0 - 71632785 71699556 0 45 811,114,107,126,165,139,392,90,180,90,177,88,188,270,114,156,165,117,270,90,183,192,87,169,95,267,273,195,90,129,177,178,122,144,129,153,177,180,192,156,138,132,138,129,403, 0,1357,4625,5294,7598,10191,11808,12901,13742,14130,14817,15728,16837,18187,19497,20412,21230,22431,23940,25456,26995,29887,33106,33911,35252,38605,40501,41690,42584,42935,43843,44193,46568,51779,52984,54819,55679,56479,57487,60074,62536,63721,65089,66048,67359, +chr1 71632046 71699808 NM_001276408 0 - 71632785 71699556 0 45 811,114,107,126,165,139,467,90,180,90,177,88,188,270,114,156,165,117,270,90,183,192,87,169,95,267,273,195,90,129,177,178,122,144,129,153,177,180,192,156,138,132,138,129,403, 0,1357,4625,5294,7598,10191,11808,12901,13742,14130,14817,15728,16837,18187,19497,20412,21230,22431,23940,25456,26995,29887,33106,33911,35252,38605,40501,41690,42584,42935,43843,44193,46568,51779,52984,54819,55679,56479,57487,60074,62536,63721,65089,66048,67359, +chr1 71699908 71709417 NR_040308 0 + 71709417 71709417 0 4 52,122,194,825, 0,3710,7417,8684, +chr1 71934685 71937778 NR_027659 0 + 71937778 71937778 0 3 90,96,513, 0,507,2580, +chr1 71934685 71937778 NR_027658 0 + 71937778 71937778 0 3 410,96,513, 0,507,2580, +chr1 72005571 72051769 NR_040454 0 - 72051769 72051769 0 3 630,279,184, 0,4516,46014, +chr1 72205806 72258888 NM_001357488 0 - 72207458 72242502 0 6 1787,164,91,160,1030,298, 0,3089,4839,32810,36679,52784, +chr1 72205806 72258881 NM_001005423 0 - 72207458 72258685 0 5 1787,164,91,160,291, 0,3089,4839,32810,52784, +chr1 72290566 72321443 NR_155355 0 + 72321443 72321443 0 4 171,150,81,2722, 0,20750,25475,28155, +chr1 72305745 72330895 NM_023523 0 - 72305921 72330790 0 8 262,112,111,97,82,166,134,229, 0,2780,8235,11105,15714,16994,18115,24921, +chr1 72305745 72330895 NM_001356516 0 - 72305921 72321527 0 7 262,112,111,97,82,134,229, 0,2780,8235,11105,15714,18115,24921, +chr1 72330946 72349569 NM_175564 0 + 72344481 72347880 0 3 94,409,2312, 0,13397,16311, +chr1 72353994 72441527 NM_009533 0 + 72354120 72441296 0 21 147,114,184,49,123,192,115,139,113,63,138,91,134,197,94,70,110,97,68,72,246, 0,3014,4987,6733,8038,11578,17653,18795,22505,27215,31539,32568,35588,38807,46822,49396,74198,75937,76281,86475,87287, +chr1 72353994 72441527 NM_001357520 0 + 72357044 72441296 0 21 440,110,184,49,123,192,115,139,113,63,138,91,134,197,94,70,110,97,68,72,246, 0,3018,4987,6733,8038,11578,17653,18795,22505,27215,31539,32568,35588,38807,46822,49396,74198,75937,76281,86475,87287, +chr1 72353994 72441527 NM_001357519 0 + 72357044 72441296 0 21 440,114,184,49,123,192,115,139,113,63,138,91,134,197,94,70,110,97,68,72,246, 0,3014,4987,6733,8038,11578,17653,18795,22505,27215,31539,32568,35588,38807,46822,49396,74198,75937,76281,86475,87287, +chr1 72473685 72583733 NM_001045533 0 - 72475215 72581711 0 4 1898,193,156,2535, 0,20044,25330,107513, +chr1 72629824 72683364 NM_018817 0 + 72632269 72679628 0 17 188,767,51,213,51,187,151,159,66,141,216,71,103,183,101,97,3970, 0,2387,3800,7812,8574,12537,14128,15520,18118,28044,29558,33257,36781,43212,44850,46124,49570, +chr1 72689553 72747138 NM_176980 0 - 72689580 72745595 0 24 332,47,197,110,118,159,123,107,162,154,242,169,242,105,209,202,39,220,181,104,164,438,636,113, 0,1944,4014,7142,7952,8716,9359,13127,15431,15670,15998,22108,23365,27112,30991,32689,36529,37001,38830,44745,45570,46966,55441,57472, +chr1 72689553 72747153 NM_001347063 0 - 72689580 72745595 0 24 332,47,197,110,118,159,123,107,162,154,242,169,242,105,209,202,36,220,181,104,164,438,636,128, 0,1944,4014,7142,7952,8716,9359,13127,15431,15670,15998,22108,23365,27112,30991,32689,36529,37001,38830,44745,45570,46966,55441,57472, +chr1 72757833 72760387 NM_009084 0 + 72757894 72760139 0 4 64,129,83,312, 0,412,882,2242, +chr1 72871053 72899045 NM_008342 0 + 72871153 72898736 0 4 485,227,141,474, 0,24606,25084,27518, +chr1 72871960 72899045 NM_001310659 0 + 72895715 72898736 0 4 88,227,141,474, 0,23699,24177,26611, +chr1 72904638 72921439 NM_010518 0 - 72908950 72920713 0 4 4444,120,230,1060, 0,5078,5786,15741, +chr1 73061648 73062473 NM_009407 0 - 73061870 73062437 0 2 251,175, 0,650, +chr1 73062609 73072082 NR_038001 0 + 73072082 73072082 0 3 59,96,187, 0,1470,9286, +chr1 73071159 73072082 NR_038002 0 + 73072082 73072082 0 2 229,187, 0,736, +chr1 73437958 73454143 NR_003202 0 - 73454143 73454143 0 5 1016,184,73,58,229, 0,5646,8819,13611,15956, +chr1 73445541 73477353 NR_040605 0 + 73477353 73477353 0 3 134,129,288, 0,3619,31524, +chr1 73664954 73911040 NR_045311 0 - 73911040 73911040 0 9 286,229,71,33,297,251,84,458,92, 0,1815,54615,239684,240183,241236,242588,244278,245994, +chr1 73902050 73902149 NR_105769 0 - 73902149 73902149 0 1 99, 0, +chr1 73956805 74171122 NM_027884 0 - 73961103 74171021 0 35 4443,33,69,169,72,78,93,132,87,1064,199,39,24,93,76,197,1530,117,66,130,76,61,113,84,65,123,51,181,56,51,42,42,38,115,257, 0,6207,6634,7401,7766,9422,10275,10726,11535,14474,17680,25666,26100,26993,30746,31678,42189,70682,72001,74787,75471,75643,76031,80079,81443,81868,82931,84969,86817,92055,93285,105913,158377,168967,214060, +chr1 73956805 74171122 NM_001289895 0 - 73961103 74171021 0 33 4443,33,69,169,72,78,93,132,87,1064,199,93,76,197,1530,117,66,130,76,61,113,84,65,123,51,181,56,51,42,42,38,115,257, 0,6207,6634,7401,7766,9422,10275,10726,11535,14474,17680,26993,30746,31678,42189,70682,72001,74787,75471,75643,76031,80079,81443,81868,82931,84969,86817,92055,93285,105913,158377,168967,214060, +chr1 74172114 74194804 NM_001170641 0 + 74174251 74194320 0 12 74,132,107,126,107,144,70,627,104,147,111,587, 0,2051,2305,3407,3798,4157,5637,7179,8563,15378,21113,22103, +chr1 74172114 74194797 NM_001034060 0 + 74175620 74194320 0 12 74,132,84,126,107,144,70,627,104,147,111,580, 0,2051,2328,3407,3798,4157,5637,7179,8563,15378,21113,22103, +chr1 74200567 74207820 NM_009909 0 + 74204922 74206002 0 2 126,2917, 0,4336, +chr1 74238359 74241205 NM_178241 0 - 74238379 74239435 0 2 1084,40, 0,2806, +chr1 74253127 74253194 NR_035449 0 - 74253194 74253194 0 1 67, 0, +chr1 74283090 74314783 NM_001357387 0 + 74283399 74314369 0 11 94,82,35,113,46,187,94,127,101,101,439, 0,301,9563,11615,14737,18311,19441,25942,27226,27836,31254, +chr1 74283090 74314783 NM_029711 0 + 74283399 74314369 0 10 383,35,113,46,187,94,127,101,101,439, 0,9563,11615,14737,18311,19441,25942,27226,27836,31254, +chr1 74325173 74326163 NM_174985 0 + 74325173 74326163 0 1 990, 0, +chr1 74326413 74331312 NM_146110 0 - 74326807 74331197 0 11 470,155,91,104,116,84,145,140,120,156,236, 0,943,1249,1489,1687,1896,2187,2571,3254,4046,4663, +chr1 74326413 74331312 NM_001190444 0 - 74326807 74331197 0 11 470,155,91,104,116,84,145,140,120,159,236, 0,943,1249,1489,1687,1896,2187,2571,3254,4046,4663, +chr1 74331607 74334027 NM_025580 0 + 74331644 74333858 0 3 104,169,362, 0,808,2058, +chr1 74331607 74400266 NM_001039509 0 + 74331644 74398505 0 10 104,169,116,113,59,93,164,87,116,1935, 0,808,62351,62618,63729,64274,64680,65583,66503,66724, +chr1 74334820 74350910 NM_027154 0 - 74335945 74341973 0 12 1272,54,96,88,38,40,51,54,65,95,242,214, 0,1624,2505,2953,3184,3448,4210,4588,4758,5661,6951,15876, +chr1 74379183 74400266 NM_019999 0 + 74379204 74398505 0 9 182,116,113,59,93,164,87,116,1935, 0,14775,15042,16153,16698,17104,18007,18927,19148, +chr1 74408681 74415895 NM_001033345 0 + 74409208 74415647 0 10 79,293,198,56,87,168,125,77,89,929, 0,259,642,1144,2209,2441,4509,5679,6026,6285, +chr1 74421776 74432625 NM_013612 0 + 74421888 74432080 0 15 119,134,123,120,107,71,68,156,159,90,120,150,74,154,659, 0,515,1590,1954,4580,4994,5406,5639,6533,8235,8422,8821,9494,9938,10190, +chr1 74438182 74443859 NM_153088 0 + 74438471 74442158 0 7 356,149,105,57,93,186,1830, 0,1669,2188,2410,3031,3228,3847, +chr1 74440883 74440968 NR_029743 0 + 74440968 74440968 0 1 85, 0, +chr1 74455957 74482134 NM_009509 0 + 74461653 74481565 0 20 53,86,75,197,109,111,203,79,99,154,101,138,159,180,146,145,189,69,141,683, 0,5685,6582,8976,10185,10411,11869,12177,12395,13543,14291,14479,16153,17168,17856,18095,18683,21233,22907,25494, +chr1 74482083 74552395 NM_001310662 0 - 74485964 74542359 0 24 3969,139,70,116,61,167,256,142,165,80,118,191,124,132,159,85,98,75,179,101,172,224,145,162, 0,4450,6022,8903,14985,17177,18318,20569,26056,31405,32757,35027,35786,36045,39476,42537,44142,50471,51109,54580,57395,60120,64446,70150, +chr1 74482083 74590860 NM_176972 0 - 74485964 74542359 0 26 3969,139,70,116,61,167,256,142,66,165,80,118,191,124,132,159,85,98,75,179,101,172,224,145,50,112, 0,4450,6022,8903,14985,17177,18318,20569,24405,26056,31405,32757,35027,35786,36045,39476,42537,44142,50471,51109,54580,57395,60120,64446,95553,108665, +chr1 74552633 74577416 NM_021383 0 + 74553011 74575428 0 8 402,180,116,110,110,99,92,2157, 0,11010,12841,16258,17444,20932,21532,22626, +chr1 74589462 74612551 NM_001081456 0 + 74594520 74611940 0 17 140,56,159,229,130,232,202,145,153,204,169,117,173,136,150,108,231, 0,5024,5216,6286,8131,9099,11601,13054,14831,17401,19166,19825,20562,21488,22143,22371,22858, +chr1 74590933 74612551 NM_148937 0 + 74594520 74611940 0 18 291,56,159,229,130,232,202,145,153,204,96,169,117,173,136,150,108,231, 0,3553,3745,4815,6660,7628,10130,11583,13360,15930,17482,17695,18354,19091,20017,20672,20900,21387, +chr1 74612999 74634602 NM_029888 0 - 74613451 74632237 0 9 922,106,2905,178,825,165,294,314,465, 0,2125,3253,7113,9354,11697,12899,18958,21138, +chr1 74612999 74634602 NM_001310668 0 - 74613451 74632237 0 9 922,106,2905,178,825,165,603,314,465, 0,2125,3253,7113,9354,11697,12899,18958,21138, +chr1 74634862 74639017 NM_025784 0 + 74636132 74638645 0 8 199,393,140,195,64,170,118,622, 0,1197,1671,1976,2382,2671,3300,3533, +chr1 74634862 74639017 NM_001305652 0 + 74636132 74638645 0 8 105,393,140,195,64,170,118,622, 0,1197,1671,1976,2382,2671,3300,3533, +chr1 74640321 74647971 NM_021313 0 - 74640397 74647939 0 10 655,135,93,138,72,70,68,100,75,73, 0,812,1461,1883,2118,4614,4782,4945,5318,7577, +chr1 74640321 74647971 NM_001305230 0 - 74640397 74647939 0 10 655,135,90,138,72,70,68,100,75,73, 0,812,1461,1883,2118,4614,4782,4945,5318,7577, +chr1 74648028 74683467 NM_175031 0 + 74648691 74682432 0 27 159,173,141,78,131,250,94,170,188,100,144,180,98,106,151,128,105,99,89,64,111,81,172,148,148,747,1179, 0,574,1683,1942,3934,7557,9317,9634,9946,11231,15121,20741,21830,22375,24038,24558,25088,25940,26130,26463,26687,30131,31274,31687,32052,32555,34260, +chr1 74708275 74748406 NM_001014974 0 + 74725565 74744273 0 20 188,167,1566,110,64,125,111,77,192,83,129,123,99,135,147,103,211,71,71,4392, 0,11142,17196,19598,20057,23617,24158,24615,25502,25776,26021,26462,26865,27621,28258,34006,34703,35040,35477,35739, +chr1 74760108 74784471 NM_024264 0 + 74760204 74784233 0 9 357,191,200,198,173,167,82,213,355, 0,18384,21742,22019,22329,23146,23482,23644,24008, +chr1 74785495 74795529 NM_153744 0 - 74787278 74795424 0 14 1139,235,147,38,166,127,55,46,59,82,407,153,40,138, 0,1665,2230,2545,5534,5799,6395,6629,6775,6948,8230,8950,9550,9896, +chr1 74818465 74831893 NM_009526 0 + 74818719 74831174 0 4 331,221,335,1181, 0,10210,10668,12247, +chr1 74838592 74850749 NM_009518 0 + 74838744 74850194 0 4 265,263,380,1053, 0,1344,8514,11104, +chr1 74897468 74926527 NR_151618 0 + 74926527 74926527 0 4 68,173,100,1589, 0,3448,17841,27470, +chr1 74901602 74904306 NM_009872 0 + 74901671 74902781 0 1 2704, 0, +chr1 74928082 74931982 NM_153111 0 - 74928649 74931784 0 3 1154,75,250, 0,2898,3650, +chr1 74936507 74939717 NM_021541 0 - 74936562 74939461 0 5 203,143,142,165,67, 0,597,2012,2793,3143, +chr1 74947231 74947295 NR_029876 0 - 74947295 74947295 0 1 64, 0, +chr1 74948653 74982173 NM_001039495 0 - 74948708 74979772 0 33 164,138,453,126,203,45,108,114,144,159,192,111,67,177,129,226,129,151,159,225,246,138,375,201,266,223,146,200,167,103,185,169,79, 0,259,1017,1941,2553,2966,3527,3820,4230,5248,5525,8364,8623,8934,14683,15070,16286,16754,17104,18306,19351,20848,22713,23293,24351,24934,25517,25925,26254,27175,29764,30990,33441, +chr1 74991888 74998246 NM_010544 0 - 74992662 74997788 0 3 1433,262,773, 0,2989,5585, +chr1 74994296 74998246 NM_001313683 0 - 74994665 74997788 0 2 843,773, 0,3177, +chr1 75013919 75121800 NM_029342 0 - 75014267 75093214 0 6 423,107,118,59,140,91, 0,823,1449,77963,79155,107790, +chr1 75122115 75130464 NM_194333 0 - 75122302 75130429 0 12 477,96,168,106,254,115,121,182,77,98,158,206, 0,800,2931,3362,3856,6119,6610,7057,7409,7653,7859,8143, +chr1 75132335 75138265 NM_001356264 0 - 75132972 75138058 0 8 1171,118,62,129,121,82,109,276, 0,1564,1993,3585,3797,4059,5136,5654, +chr1 75132335 75139285 NM_026977 0 - 75132972 75138058 0 10 1171,118,62,129,121,82,109,88,503,69, 0,1564,1993,3585,3797,4059,5136,5654,6296,6881, +chr1 75139359 75144483 NM_001305231 0 + 75139436 75143629 0 10 343,107,31,136,85,144,95,136,290,1079, 0,583,1137,1518,1836,2174,2473,2894,3644,4045, +chr1 75139359 75144483 NM_170755 0 + 75139436 75143629 0 9 343,107,31,136,85,144,95,136,1480, 0,583,1137,1518,1836,2174,2473,2894,3644, +chr1 75139731 75144483 NM_001305232 0 + 75141261 75143629 0 9 119,107,31,136,85,144,95,136,1480, 0,211,765,1146,1464,1802,2101,2522,3272, +chr1 75165219 75168200 NM_001159906 0 + 75165425 75167854 0 10 62,73,95,132,152,93,61,68,73,391, 0,188,539,854,1119,1721,1893,2040,2330,2590, +chr1 75165219 75168200 NM_001159905 0 + 75165425 75167854 0 10 62,76,95,132,152,93,61,68,73,391, 0,185,539,854,1119,1721,1893,2040,2330,2590, +chr1 75165308 75168200 NM_026846 0 + 75165425 75167854 0 9 172,95,132,152,93,61,68,73,391, 0,450,765,1030,1632,1804,1951,2241,2501, +chr1 75168214 75176966 NM_023732 0 - 75168453 75176692 0 19 348,69,95,113,175,105,58,86,64,77,126,66,110,122,184,102,181,138,823, 0,473,625,914,1150,1904,2221,2498,2685,2837,3061,3332,3867,4449,5662,6024,6281,7290,7929, +chr1 75177434 75188584 NM_001003917 0 - 75178499 75186979 0 16 1071,146,223,118,179,249,180,154,749,142,162,65,44,132,55,187, 0,1731,2033,3595,3828,4192,4805,5090,5329,6824,7084,8702,9251,9442,9962,10963, +chr1 75177434 75188584 NM_001288613 0 - 75178499 75183374 0 16 1071,146,223,118,179,249,180,154,997,142,162,65,44,132,55,187, 0,1731,2033,3595,3828,4192,4805,5090,5329,6824,7084,8702,9251,9442,9962,10963, +chr1 75177434 75188584 NR_109938 0 - 75188584 75188584 0 16 1071,146,223,118,179,249,180,95,749,142,162,65,44,132,58,187, 0,1731,2033,3595,3828,4192,4805,5149,5329,6824,7084,8702,9251,9442,9962,10963, +chr1 75177434 75188584 NM_001288612 0 - 75178499 75186979 0 16 1071,146,223,118,179,249,180,154,749,142,162,65,44,132,58,187, 0,1731,2033,3595,3828,4192,4805,5090,5329,6824,7084,8702,9251,9442,9962,10963, +chr1 75188733 75195960 NR_051998 0 + 75195960 75195960 0 13 519,107,103,194,144,148,229,156,481,112,168,86,322, 0,2019,2682,2904,3410,3642,3994,4355,5485,6106,6318,6621,6905, +chr1 75188733 75192113 NM_001267620 0 + 75189025 75191921 0 5 430,88,107,103,476, 0,431,2019,2682,2904, +chr1 75188733 75195960 NM_026187 0 + 75189025 75195762 0 14 430,88,107,103,194,113,148,229,156,481,112,168,86,322, 0,431,2019,2682,2904,3441,3642,3994,4355,5485,6106,6318,6621,6905, +chr1 75188733 75192113 NR_051999 0 + 75192113 75192113 0 3 519,103,476, 0,2682,2904, +chr1 75194809 75207353 NM_029010 0 - 75196068 75206015 0 17 1523,216,132,114,90,75,119,41,122,59,175,95,61,151,167,123,188, 0,1676,2095,2709,2963,3164,3508,3815,3952,4173,4340,4612,10084,10452,10821,11146,12356, +chr1 75207403 75212181 NR_102731 0 + 75212181 75212181 0 8 224,175,220,134,121,116,122,1793, 0,411,1096,1771,2057,2284,2747,2985, +chr1 75207403 75212181 NM_001277992 0 + 75207903 75210527 0 8 196,175,220,134,121,96,122,1793, 0,411,1096,1771,2057,2304,2747,2985, +chr1 75207403 75212181 NM_011494 0 + 75207903 75210527 0 8 224,175,220,134,121,96,122,1793, 0,411,1096,1771,2057,2304,2747,2985, +chr1 75211546 75215869 NM_001313724 0 - 75212196 75213084 0 3 2004,223,102, 0,2240,4221, +chr1 75211546 75215869 NM_001313723 0 - 75212196 75212937 0 4 1477,149,223,102, 0,1855,2240,4221, +chr1 75211546 75215869 NM_009447 0 - 75212196 75215770 0 4 1622,149,223,102, 0,1855,2240,4221, +chr1 75216669 75228668 NM_001243090 0 - 75217034 75228649 0 3 479,137,119, 0,3199,11880, +chr1 75216669 75220229 NM_001243091 0 - 75217034 75219991 0 3 479,137,32, 0,3199,3528, +chr1 75232997 75242267 NM_178055 0 + 75233458 75241379 0 10 167,97,110,54,123,93,103,71,204,899, 0,429,1032,2857,3085,4469,4748,4986,7035,8371, +chr1 75232997 75242267 NM_001159883 0 + 75233458 75240388 0 9 167,97,110,54,123,93,103,71,2235, 0,429,1032,2857,3085,4469,4748,4986,7035, +chr1 75232997 75242267 NM_001159884 0 + 75233458 75241379 0 10 115,97,110,54,123,93,103,71,204,899, 0,429,1032,2857,3085,4469,4748,4986,7035,8371, +chr1 75232997 75242267 NM_020266 0 + 75233458 75241379 0 9 167,97,110,123,93,103,71,204,899, 0,429,1032,3085,4469,4748,4986,7035,8371, +chr1 75233276 75242267 NM_001159885 0 + 75233458 75241379 0 9 247,110,54,123,93,103,71,204,899, 0,753,2578,2806,4190,4469,4707,6756,8092, +chr1 75243615 75260783 NM_008985 0 - 75244123 75260702 0 23 580,74,65,54,167,120,78,74,148,201,219,65,80,87,275,38,132,352,259,97,114,51,205, 0,796,1061,1685,4710,5215,5427,5730,5971,6219,6882,7544,7738,8084,8586,9802,10252,10904,11338,13530,14986,15282,16963, +chr1 75243615 75260346 NM_001359281 0 - 75244123 75258611 0 23 580,74,65,54,167,120,78,74,148,201,219,65,80,87,275,38,132,352,259,97,114,51,175, 0,796,1061,1685,4710,5215,5427,5730,5971,6219,6882,7544,7738,8084,8586,9802,10252,10904,11338,13530,14986,15282,16556, +chr1 75268771 75274990 NM_009049 0 - 75268885 75274882 0 6 165,90,43,133,105,214, 0,1760,1971,2200,3416,6005, +chr1 75268771 75274990 NR_138251 0 - 75274990 75274990 0 5 165,90,133,105,214, 0,1760,2200,3416,6005, +chr1 75305139 75313592 NM_016878 0 - 75305233 75313378 0 15 145,168,102,40,161,84,78,108,76,131,126,114,89,94,127, 0,734,3227,3427,3840,4861,5799,6565,6780,7054,7380,7765,7976,8145,8326, +chr1 75305139 75314212 NM_001110831 0 - 75305233 75313915 0 15 145,168,102,40,161,84,78,108,76,131,126,114,89,94,303, 0,734,3227,3427,3840,4861,5799,6565,6780,7054,7380,7765,7976,8145,8770, +chr1 75356866 75365154 NM_010043 0 + 75356992 75363625 0 9 701,61,96,162,126,221,44,83,1571, 0,1866,2021,2273,2602,3179,5036,6468,6717, +chr1 75364784 75371590 NR_037976 0 - 75371590 75371590 0 4 222,209,116,129, 0,1530,5171,6677, +chr1 75371871 75428881 NM_007463 0 + 75372014 75428026 0 41 537,90,337,1307,144,183,176,89,176,261,159,190,224,120,105,207,124,176,113,169,97,201,58,78,179,27,153,43,69,1969,132,117,168,123,168,580,240,224,76,150,1048, 0,9359,9531,12501,15682,16465,25758,26166,27001,29590,31009,31282,31579,34657,34992,35260,35782,35989,39019,39703,40023,40245,41746,42366,42530,43134,43674,44932,45994,46263,48519,51467,51747,52017,52314,52595,53763,54100,55142,55500,55962, +chr1 75378688 75401140 NM_001085371 0 + 75378716 75400359 0 11 61,43,90,337,1307,144,183,176,89,176,789, 0,1023,2542,2714,5684,8865,9648,18941,19349,20184,21663, +chr1 75382184 75428879 NM_001085370 0 + 75387630 75428026 0 39 67,1304,144,183,176,89,176,261,159,190,224,120,105,207,124,176,113,169,97,201,58,78,179,27,153,43,69,1969,132,117,168,123,168,580,240,224,76,150,1046, 0,2191,5369,6152,15445,15853,16688,19277,20696,20969,21266,24344,24679,24947,25469,25676,28706,29390,29710,29932,31433,32053,32217,32821,33361,34619,35681,35950,38206,41154,41434,41704,42001,42282,43450,43787,44829,45187,45649, +chr1 75396659 75401140 NM_001173477 0 + 75397736 75400359 0 5 178,176,89,176,789, 0,970,1378,2213,3692, +chr1 75432510 75439754 NM_001357169 0 + 75433373 75439576 0 14 76,166,61,98,104,187,60,131,135,98,47,93,169,279, 0,211,842,1001,2315,2906,3409,4476,5539,5794,6049,6249,6508,6965, +chr1 75432510 75439754 NM_001357171 0 + 75433373 75439576 0 14 258,61,98,104,187,60,131,15,135,98,47,93,169,279, 0,842,1001,2315,2906,3409,4476,5224,5539,5794,6049,6249,6508,6965, +chr1 75432510 75439754 NM_133708 0 + 75433373 75439576 0 13 76,61,98,104,187,60,131,135,98,47,93,169,279, 0,842,1001,2315,2906,3409,4476,5539,5794,6049,6249,6508,6965, +chr1 75432510 75439754 NM_001357170 0 + 75433373 75439576 0 13 377,61,98,104,187,60,131,135,98,47,93,169,279, 0,842,1001,2315,2906,3409,4476,5539,5794,6049,6249,6508,6965, +chr1 75447084 75470915 NM_183022 0 + 75447406 75470207 0 10 904,145,128,163,57,154,92,80,105,822, 0,18601,18847,19161,19769,21774,22312,22482,22733,23009, +chr1 75471143 75476046 NM_001001565 0 - 75471544 75474221 0 5 1658,180,574,143,680, 0,1991,2676,3701,4223, +chr1 75471143 75476046 NM_001001566 0 - 75471544 75475680 0 4 1658,180,574,680, 0,1991,2676,4223, +chr1 75476106 75482268 NM_177056 0 + 75476806 75481559 0 5 354,205,576,203,847, 0,661,3037,4843,5315, +chr1 75482399 75503027 NM_178884 0 - 75482526 75502799 0 20 135,270,105,162,157,113,267,273,270,288,276,273,273,273,273,297,303,252,270,1240, 0,815,1398,1804,2081,2764,3658,4971,5363,6681,7045,7960,11183,12250,14077,16134,17088,17542,17872,19388, +chr1 75492912 75503027 NM_001310679 0 - 75493074 75502799 0 9 287,273,273,273,297,303,252,270,1240, 0,670,1737,3564,5621,6575,7029,7359,8875, +chr1 75503651 75506941 NM_010564 0 + 75503822 75506738 0 2 442,1033, 0,2257, +chr1 75504183 75506941 NM_001329843 0 + 75506126 75506738 0 2 861,1033, 0,1725, +chr1 75518103 75533910 NM_027886 0 + 75518363 75532810 0 25 114,86,206,75,96,108,72,127,104,96,42,150,85,351,206,117,178,213,104,98,179,82,71,248,1250, 0,235,3154,3559,3890,4323,4558,5529,5834,6047,6273,6440,6780,7382,7882,8405,8644,10774,11098,12031,12224,12643,12875,13649,14557, +chr1 75542840 75556006 NM_009208 0 + 75543445 75555465 0 23 117,150,166,278,116,197,149,181,136,184,100,185,226,219,149,195,219,90,167,254,170,174,619, 0,506,967,1678,2050,2603,4238,4489,4981,5371,5887,6357,6990,7358,7894,8236,8657,9145,9673,10478,11007,11361,12547, +chr1 75542840 75555658 NM_001357149 0 + 75543445 75555465 0 23 117,107,166,278,116,197,149,181,136,184,100,185,226,219,149,195,219,90,167,254,170,174,271, 0,549,967,1678,2050,2603,4238,4489,4981,5371,5887,6357,6990,7358,7894,8236,8657,9145,9673,10478,11007,11361,12547, +chr1 75543036 75555658 NM_001357150 0 + 75543445 75555465 0 23 152,150,166,278,116,197,149,181,136,184,100,185,226,219,149,195,219,90,167,254,170,174,271, 0,310,771,1482,1854,2407,4042,4293,4785,5175,5691,6161,6794,7162,7698,8040,8461,8949,9477,10282,10811,11165,12351, +chr1 76485707 76498603 NR_038012 0 + 76498603 76498603 0 5 82,99,60,250,1697, 0,5293,6297,8401,11199, +chr1 76485707 76498603 NR_038013 0 + 76498603 76498603 0 5 82,99,60,66,1697, 0,5293,6297,8401,11199, +chr1 76506134 76506218 NR_105761 0 + 76506218 76506218 0 1 84, 0, +chr1 77363759 77511663 NM_007936 0 - 77370307 77511606 0 18 2487,938,156,194,150,210,62,186,114,59,112,160,125,339,156,664,68,148, 0,5725,7586,10229,13679,15684,16338,20612,21288,22848,31309,32453,34015,59366,77680,139363,144498,147756, +chr1 77493227 77493343 NR_105770 0 - 77493343 77493343 0 1 116, 0, +chr1 78097841 78193711 NM_001159520 0 - 78099375 78193324 0 9 1569,247,215,166,206,135,130,236,472, 0,2061,20311,21324,30961,91175,92473,93984,95398, +chr1 78097841 78193711 NM_008781 0 - 78099882 78193324 0 8 2308,215,166,206,135,130,236,472, 0,20311,21324,30961,91175,92473,93984,95398, +chr1 78306920 78416861 NM_001004173 0 + 78306993 78414001 0 5 157,159,180,90,3412, 0,49725,80129,83013,106529, +chr1 78414532 78485472 NM_001278075 0 - 78421768 78485417 0 18 265,153,156,118,93,81,208,62,52,62,71,109,151,116,70,155,56,113, 0,7235,25677,36796,40607,44348,44877,45314,49009,50013,51294,53125,54526,58232,60235,61999,64350,70827, +chr1 78421319 78485472 NR_102758 0 - 78485472 78485472 0 16 601,156,118,93,81,208,62,52,62,71,109,151,116,70,155,113, 0,18890,30009,33820,37561,38090,38527,42222,43226,44507,46338,47739,51445,53448,55212,64040, +chr1 78421319 78485472 NR_102757 0 - 78485472 78485472 0 17 601,156,118,93,81,208,62,52,62,71,109,151,116,70,57,56,113, 0,18890,30009,33820,37561,38090,38527,42222,43226,44507,46338,47739,51445,53448,55212,57563,64040, +chr1 78421319 78485472 NM_011811 0 - 78421768 78485417 0 17 601,156,118,93,81,208,62,52,62,71,109,151,116,70,155,56,113, 0,18890,30009,33820,37561,38090,38527,42222,43226,44507,46338,47739,51445,53448,55212,57563,64040, +chr1 78507634 78534748 NM_026713 0 + 78508536 78534673 0 7 29,188,179,205,175,200,230, 0,808,11625,12514,16510,17993,26884, +chr1 78654399 78704318 NM_001033606 0 + 78678207 78702990 0 15 279,418,178,110,139,151,124,72,140,173,75,192,115,158,1486, 0,23768,30412,32444,34257,36371,38256,38604,39065,41171,41931,43444,45661,47409,48433, +chr1 78654399 78704318 NM_001136222 0 + 78684889 78702990 0 14 279,178,110,139,151,124,72,140,173,75,192,115,158,1486, 0,30412,32444,34257,36371,38256,38604,39065,41171,41931,43444,45661,47409,48433, +chr1 78654399 78664176 NM_001001981 0 + 78660961 78663304 0 3 279,140,3276, 0,5316,6501, +chr1 78654399 78704318 NM_028817 0 + 78678207 78702990 0 16 279,140,418,178,110,139,151,124,72,140,173,75,192,115,158,1486, 0,5316,23768,30412,32444,34257,36371,38256,38604,39065,41171,41931,43444,45661,47409,48433, +chr1 78655014 78664176 NM_001136226 0 + 78660961 78663304 0 4 221,65,140,3276, 0,1886,4701,5886, +chr1 78788197 79221086 NR_151519 0 - 79221086 79221086 0 4 2671,80,156,376, 0,157210,394975,432513, +chr1 78813485 78816607 NM_021342 0 + 78814211 78814724 0 2 86,2422, 0,700, +chr1 79430942 79436601 NM_001310680 0 - 79431725 79433579 0 3 1564,967,71, 0,1684,5588, +chr1 79430942 79436601 NM_009129 0 - 79431725 79433579 0 2 2651,71, 0,5588, +chr1 79603450 79668547 NM_183027 0 - 79605741 79668427 0 5 2327,138,109,179,123, 0,7327,16806,18231,64974, +chr1 79698836 79758344 NM_001111279 0 - 79702085 79758275 0 12 3309,109,131,102,106,127,113,151,55,74,68,206, 0,3982,5190,6831,11596,12612,22383,24304,27394,31538,37800,59302, +chr1 79722977 79758344 NM_027057 0 - 79723061 79758275 0 5 314,55,74,68,206, 0,3253,7397,13659,35161, +chr1 79772592 79778020 NM_001081210 0 + 79772707 79777713 0 4 294,469,179,482, 0,1840,3470,4946, +chr1 79790895 79855240 NM_009255 0 - 79791579 79818110 0 9 722,84,87,101,199,198,228,281,155, 0,2505,5147,7135,8526,16233,22407,26956,64190, +chr1 80195273 80210519 NM_173425 0 - 80196484 80210239 0 2 1850,1012, 0,14234, +chr1 80261497 80337265 NM_001313728 0 - 80263730 80318470 0 17 2365,146,187,135,97,125,108,171,177,146,229,115,161,114,128,198,445, 0,4287,6601,11491,12452,13041,15910,16460,17700,18753,21976,23821,25159,39157,56862,57936,75323, +chr1 80261497 80337265 NM_016716 0 - 80263730 80336886 0 16 2365,146,187,135,97,125,108,171,177,146,229,115,161,114,198,445, 0,4287,6601,11491,12452,13041,15910,16460,17700,18753,21976,23821,25159,39157,57936,75323, +chr1 80442506 80472235 NR_040460 0 + 80472235 80472235 0 3 63,60,271, 0,4145,29458, +chr1 80497642 80755128 NM_175291 0 - 80498281 80755023 0 56 759,139,101,191,211,147,114,123,107,99,58,216,111,183,138,113,125,102,48,67,115,122,112,117,176,45,97,84,147,72,114,70,119,93,87,122,124,93,66,188,80,123,83,123,222,156,84,86,184,135,123,73,83,90,120,228, 0,4257,4553,9209,11359,14421,22648,22902,25156,27165,27581,29010,30106,31254,32718,34785,35777,37715,38742,39017,39176,39389,40160,42032,42273,48065,48638,50387,51610,58099,59833,63434,65660,66224,66928,67370,67679,71389,72412,73012,74791,77518,83928,85261,85581,91449,91705,92091,94473,104723,105097,105485,114224,133132,147145,257258, +chr1 80497642 80661927 NM_001285927 0 - 80498281 80661770 0 56 759,139,101,191,211,147,114,123,107,99,58,216,111,183,138,113,125,102,48,67,115,122,112,117,176,45,97,84,147,72,114,70,119,93,87,122,124,93,66,188,80,123,83,123,222,156,84,86,184,135,123,73,83,90,120,244, 0,4257,4553,9209,11359,14421,22648,22902,25156,27165,27581,29010,30106,31254,32718,34785,35777,37715,38742,39017,39176,39389,40160,42032,42273,48065,48638,50387,51610,58099,59833,63434,65660,66224,66928,67370,67679,71389,72412,73012,74791,77518,83928,85261,85581,91449,91705,92091,94473,104723,105097,105485,114224,133132,147145,164041, +chr1 81073524 81296671 NM_001356399 0 + 81083847 81294670 0 7 98,487,237,302,1086,210,2135, 0,457,10307,114801,163934,192094,221012, +chr1 81073778 81296671 NM_001356398 0 + 81083847 81294670 0 7 105,487,237,398,1086,210,2135, 0,203,10053,114547,163680,191840,220758, +chr1 81073882 81296671 NM_001356400 0 + 81083847 81294670 0 6 586,237,302,1086,210,2135, 0,9949,114443,163576,191736,220654, +chr1 81073981 81338339 NM_001356397 0 + 81083847 81333316 0 7 487,237,302,1086,210,104,5251, 0,9850,114344,163477,191637,220555,259107, +chr1 82128490 82128594 NR_105762 0 + 82128594 82128594 0 1 104, 0, +chr1 82229679 82288014 NM_010570 0 - 82283372 82287068 0 2 4500,4663, 0,53672, +chr1 82313153 82441941 NM_029777 0 + 82336972 82439529 0 7 70,512,133,89,57,144,2504, 0,23740,26151,51713,53755,60982,126284, +chr1 82335623 82441941 NM_001122685 0 + 82336972 82439529 0 7 248,512,133,89,57,144,2504, 0,1270,3681,29243,31285,38512,103814, +chr1 82447297 82583424 NM_007735 0 - 82449705 82567990 0 48 2672,287,189,117,128,6,109,156,114,129,72,108,108,75,64,182,105,144,171,162,219,108,69,184,107,73,164,90,165,105,70,54,45,60,54,81,42,36,63,36,69,117,45,135,78,43,167,231, 0,3054,5000,6056,11328,11604,15764,18756,20260,20466,21755,29135,29759,33668,34858,35760,36789,38288,38977,40802,41725,42770,45048,46431,47105,48212,56223,58445,68206,73128,74264,75142,76806,77729,78029,78842,80635,80877,82194,83872,85018,88308,89231,90447,112680,119081,120646,135896, +chr1 82583495 82718634 NM_007734 0 + 82583919 82715459 0 52 511,57,90,45,45,63,54,27,78,63,36,42,78,63,60,45,54,42,85,36,165,90,96,71,183,169,93,102,98,151,114,168,90,135,99,90,140,127,81,99,48,186,131,73,72,126,99,213,178,115,173,3260, 0,54518,56288,61657,62835,63640,64333,65240,66380,68033,68205,69930,70225,73303,73905,75281,75975,77656,79600,79974,81999,82751,83254,84386,85676,87058,88988,89745,91646,92158,92628,93759,95365,95782,102186,103065,103600,106498,109335,109759,110819,113317,113836,121669,123879,124038,124919,128321,129091,129377,130912,131879, +chr1 82721464 82748964 NM_029409 0 + 82725830 82748291 0 9 195,109,221,170,89,159,60,85,805, 0,2338,4326,6223,10529,16928,22193,25630,26695, +chr1 82721464 82748964 NM_001310695 0 + 82725830 82748291 0 8 195,109,221,170,92,60,85,805, 0,2338,4326,6223,10526,22193,25630,26695, +chr1 82721464 82748964 NM_001310699 0 + 82725830 82748291 0 7 195,109,221,170,89,85,805, 0,2338,4326,6223,10529,25630,26695, +chr1 82721464 82748964 NM_001310697 0 + 82725830 82748291 0 8 195,109,221,170,89,60,85,805, 0,2338,4326,6223,10529,22193,25630,26695, +chr1 82721492 82748964 NM_001372412 0 + 82725830 82748291 0 9 167,109,221,170,92,33,60,85,805, 0,2310,4298,6195,10498,20606,22165,25602,26667, +chr1 82721492 82748964 NM_001372411 0 + 82725830 82748291 0 8 167,109,221,170,89,159,85,805, 0,2310,4298,6195,10501,16900,25602,26667, +chr1 82721492 82748964 NM_001372413 0 + 82725830 82748291 0 9 167,109,221,170,89,33,60,85,805, 0,2310,4298,6195,10501,20606,22165,25602,26667, +chr1 82721492 82748964 NM_001372409 0 + 82725830 82748291 0 8 167,109,221,170,92,159,85,805, 0,2310,4298,6195,10498,16900,25602,26667, +chr1 82721492 82748964 NM_001372408 0 + 82725830 82748291 0 9 167,109,221,170,92,159,60,85,805, 0,2310,4298,6195,10498,16900,22165,25602,26667, +chr1 82721492 82748964 NM_001372407 0 + 82725830 82748291 0 10 167,109,221,170,89,159,33,60,85,805, 0,2310,4298,6195,10501,16900,20606,22165,25602,26667, +chr1 82721492 82748964 NM_001372414 0 + 82725830 82748291 0 7 167,109,221,170,92,85,805, 0,2310,4298,6195,10498,25602,26667, +chr1 82721492 82748964 NM_001372406 0 + 82725830 82748291 0 10 167,109,221,170,92,159,33,60,85,805, 0,2310,4298,6195,10498,16900,20606,22165,25602,26667, +chr1 82721492 82748964 NM_001372405 0 + 82724775 82748291 0 10 167,109,172,221,170,89,159,60,85,805, 0,2310,3149,4298,6195,10501,16900,22165,25602,26667, +chr1 82753221 82765036 NM_001368252 0 - 82754283 82764992 0 3 1065,66,227, 0,7280,11588, +chr1 82753221 82765036 NM_025453 0 - 82754006 82764992 0 4 1065,152,66,227, 0,3521,7280,11588, +chr1 82836034 82897570 NM_001347077 0 + 82836297 82891633 0 13 430,94,116,163,154,210,181,77,93,48,159,92,5997, 0,18896,31225,35828,36711,42768,43721,46651,46915,52000,53964,55016,55539, +chr1 82836034 82897576 NM_001310713 0 + 82836297 82891633 0 12 430,94,116,163,154,120,210,181,77,159,92,6003, 0,18896,31225,35828,36711,40548,42768,43721,46651,53964,55016,55539, +chr1 82836034 82897576 NM_001368850 0 + 82836297 82891633 0 13 430,94,116,163,154,120,210,181,77,93,159,92,6003, 0,18896,31225,35828,36711,40548,42768,43721,46651,46915,53964,55016,55539, +chr1 82836034 82897576 NM_010472 0 + 82836297 82891633 0 13 430,94,116,163,154,120,210,181,77,93,159,86,6003, 0,18896,31225,35828,36711,40548,42768,43721,46651,46915,53964,55022,55539, +chr1 83009097 83035023 NM_030556 0 - 83010393 83022953 0 7 1467,142,193,808,155,130,79, 0,2180,6809,9811,13703,15490,25847, +chr1 83057504 83058496 NM_027778 0 + 83057570 83057987 0 1 992, 0, +chr1 83113340 83115742 NM_001159738 0 + 83113398 83115292 0 4 137,112,78,472, 0,1033,1233,1930, +chr1 83113340 83115742 NM_016960 0 + 83113398 83115292 0 4 137,115,78,472, 0,1030,1233,1930, +chr1 83156329 83207147 NM_001372243 0 + 83156373 83206764 0 13 84,73,184,59,123,100,108,107,103,115,77,163,418, 0,19538,20551,22495,23501,28151,31589,32862,37466,38331,46134,49451,50400, +chr1 83156329 83207147 NM_001372245 0 + 83156373 83206764 0 10 84,73,184,59,123,103,115,77,163,418, 0,19538,20551,22495,23501,37466,38331,46134,49451,50400, +chr1 83156329 83207147 NR_164164 0 + 83207147 83207147 0 10 84,73,122,59,123,103,115,77,163,418, 0,19538,20613,22495,23501,37466,38331,46134,49451,50400, +chr1 83156329 83207147 NR_164165 0 + 83207147 83207147 0 13 84,73,184,59,123,100,107,103,115,77,163,103,122, 0,19538,20551,22495,23501,28151,32862,37466,38331,46134,49451,50400,50696, +chr1 83156329 83207147 NM_001372244 0 + 83156373 83206764 0 13 84,73,145,59,123,100,108,107,103,115,77,163,418, 0,19538,20590,22495,23501,28151,31589,32862,37466,38331,46134,49451,50400, +chr1 83156336 83207147 NM_027725 0 + 83156373 83206764 0 10 77,73,145,59,123,103,115,77,163,418, 0,19531,20583,22488,23494,37459,38324,46127,49444,50393, +chr1 83156336 83207147 NR_027636 0 + 83207147 83207147 0 13 77,73,125,59,123,100,108,107,103,115,77,163,418, 0,19531,20603,22488,23494,28144,31582,32855,37459,38324,46127,49444,50393, +chr1 83252018 83404775 NM_172430 0 - 83253701 83404586 0 11 1827,185,53,186,3718,256,135,60,108,100,221, 0,8065,8338,11858,20174,24886,33318,35526,84091,106785,152536, +chr1 83252018 83404775 NM_001356547 0 - 83253701 83404582 0 12 1827,185,53,186,3718,256,135,60,108,100,79,221, 0,8065,8338,11858,20174,24886,33318,35526,84091,106785,129450,152536, +chr1 84032867 84281220 NM_001003948 0 - 84034605 84280945 0 3 2215,147,305, 0,122939,248048, +chr1 84215423 84215536 NR_105771 0 - 84215536 84215536 0 1 113, 0, +chr1 84366413 84692796 NM_152915 0 - 84367338 84692303 0 13 1037,247,132,114,123,225,114,154,146,167,95,309,769, 0,13946,25776,36100,48810,75556,106506,124892,165013,210817,213165,215474,325614, +chr1 84692413 84692490 NR_039588 0 + 84692490 84692490 0 1 77, 0, +chr1 84717763 84835879 NM_133975 0 - 84721192 84811495 0 41 3626,104,95,114,165,165,155,115,99,157,143,152,128,200,74,173,152,192,142,175,101,208,119,229,154,157,118,166,69,162,93,96,36,149,96,84,137,106,803,147,76, 0,4207,4547,5014,6936,9343,10434,10824,15793,17489,18325,20998,21905,22631,23489,23824,25989,27969,29169,30350,30691,33082,36228,36533,37785,39574,39822,40675,40930,42139,42650,44791,44970,47394,55128,56235,61638,64902,72336,93634,118040, +chr1 84836415 84897061 NM_025386 0 + 84836447 84896760 0 4 128,109,173,490, 0,41251,56649,60156, +chr1 84903279 84931658 NM_027921 0 - 84903852 84926126 0 5 725,978,144,278,224, 0,5491,16149,22582,28155, +chr1 85084713 85106428 NM_213615 0 - 85085352 85105943 0 7 678,54,113,63,172,163,517, 0,1388,2938,6158,11338,12393,21198, +chr1 85102667 85110613 NR_163968 0 + 85110613 85110613 0 4 598,151,135,992, 0,5716,6358,6954, +chr1 85196185 85210337 NM_001081746 0 + 85209224 85210115 0 4 112,169,194,1136, 0,2529,8393,13016, +chr1 85242918 85267141 NM_175219 0 - 85243511 85266639 0 8 793,81,81,63,84,172,163,534, 0,1955,7759,8170,11042,13351,14393,23689, +chr1 85242918 85267141 NM_001037909 0 - 85243511 85266639 0 7 793,81,81,63,172,163,534, 0,1955,7759,8170,13351,14393,23689, +chr1 85309981 85323954 NM_001372515 0 - 85310900 85323857 0 3 1114,160,123, 0,3718,13850, +chr1 87473474 87500466 NM_175397 0 - 87473866 87492683 0 13 446,143,102,69,150,81,78,78,267,169,148,151,57, 0,2157,2744,6612,8003,9315,10562,12214,14623,17365,19062,21729,26935, +chr1 87473474 87495385 NM_030194 0 - 87473866 87492683 0 12 446,143,102,69,150,81,78,78,267,169,148,182, 0,2157,2744,6612,8003,9315,10562,12214,14623,17365,19062,21729, +chr1 87497277 87541611 NM_001013817 0 + 87497734 87541257 0 17 489,163,172,51,84,102,54,66,105,143,48,42,116,106,78,144,453, 0,8991,10036,14101,14485,19353,20951,25397,29757,31775,34856,37121,41030,41839,42232,42500,43881, +chr1 87546562 87598147 NM_001313712 0 + 87546676 87598033 0 17 140,160,169,72,66,90,81,147,72,51,54,75,51,105,143,33,168, 0,9715,12485,13538,15291,16926,20014,23637,25207,29071,31098,41987,44271,47018,49619,51129,51417, +chr1 87546562 87606572 NM_013673 0 + 87546676 87605693 0 20 140,160,169,72,66,90,81,147,72,51,54,75,51,105,143,33,39,72,144,1005, 0,9715,12485,13538,15291,16926,20014,23637,25207,29071,31098,41987,44271,47018,49619,51129,51417,57239,57994,59005, +chr1 87546562 87598147 NM_001313713 0 + 87546676 87598033 0 16 140,160,169,72,66,90,81,147,72,51,75,51,105,143,33,168, 0,9715,12485,13538,15291,16926,20014,23637,25207,29071,41987,44271,47018,49619,51129,51417, +chr1 87546562 87579693 NM_001313714 0 + 87546676 87578850 0 12 140,160,169,72,66,90,81,147,72,51,54,902, 0,9715,12485,13538,15291,16926,20014,23637,25207,29071,31098,32229, +chr1 87546588 87606572 NM_001372231 0 + 87546676 87605693 0 22 114,160,169,72,66,90,81,147,72,51,54,75,51,105,143,33,39,116,118,72,144,1005, 0,9689,12459,13512,15265,16900,19988,23611,25181,29045,31072,41961,44245,46992,49593,51103,51391,54929,56823,57213,57968,58979, +chr1 87546588 87606572 NM_001372232 0 + 87546676 87605693 0 21 114,160,169,72,66,90,81,147,72,51,54,51,105,143,33,39,116,118,72,144,1005, 0,9689,12459,13512,15265,16900,19988,23611,25181,29045,31072,44245,46992,49593,51103,51391,54929,56823,57213,57968,58979, +chr1 87613657 87633181 NM_177055 0 - 87614767 87623189 0 6 1286,105,84,169,157,135, 0,1942,6015,8038,9376,19389, +chr1 87648522 87648649 NR_106172 0 + 87648649 87648649 0 1 127, 0, +chr1 87671845 87681269 NR_108086 0 + 87681269 87681269 0 4 49,51,87,634, 0,2230,6172,8790, +chr1 87690015 87748152 NM_133781 0 + 87714974 87745796 0 9 381,157,165,119,169,60,66,144,2545, 0,24916,41882,43845,48757,51152,53969,54836,55592, +chr1 87690015 87748152 NM_001355046 0 + 87714974 87745796 0 10 381,117,157,165,119,169,60,66,144,2545, 0,1916,24916,41882,43845,48757,51152,53969,54836,55592, +chr1 87690591 87748152 NM_001355047 0 + 87714974 87745796 0 10 225,117,157,165,119,169,60,66,144,2545, 0,1340,24340,41306,43269,48181,50576,53393,54260,55016, +chr1 87791084 87805273 NM_022417 0 + 87791238 87804213 0 6 280,141,189,111,151,1152, 0,8500,10704,11912,12498,13037, +chr1 87825057 87828331 NR_037692 0 + 87828331 87828331 0 3 610,66,472, 0,1988,2802, +chr1 87836111 87857630 NM_001033290 0 - 87837448 87838432 0 2 2329,221, 0,21298, +chr1 87918516 87926533 NM_001122732 0 + 87918623 87923094 0 4 408,172,144,380, 0,2388,4472,7637, +chr1 87918516 87923753 NM_028647 0 + 87918623 87923094 0 4 408,172,144,327, 0,2388,4472,4910, +chr1 87918516 87921244 NM_027029 0 + 87918623 87921116 0 2 408,340, 0,2388, +chr1 87918516 87926533 NM_027300 0 + 87918623 87923094 0 4 408,175,144,380, 0,2385,4472,7637, +chr1 87942437 87952031 NM_001144992 0 + 87942537 87949664 0 3 710,114,2507, 0,2725,7087, +chr1 87942437 87952031 NM_001144993 0 + 87942537 87949664 0 3 710,111,2507, 0,2728,7087, +chr1 87961193 88035870 NM_027357 0 + 87961364 88033684 0 25 187,44,74,170,206,144,227,61,129,89,79,174,112,197,96,65,115,117,103,170,93,87,147,154,216, 0,5964,6995,7208,11180,12737,13949,17418,18528,20563,21411,21956,24190,25375,27384,29657,51956,53891,61837,63517,66018,68095,69019,72344,74461, +chr1 87995611 88008555 NM_008311 0 - 87995917 88007457 0 4 1196,201,583,102, 0,3385,11497,12842, +chr1 88051354 88174859 NM_001310702 0 + 88053529 88172257 0 25 64,88,129,171,156,93,25,158,99,35,112,93,91,124,140,77,75,91,56,105,116,137,127,173,2625, 0,2138,5215,7885,9916,15130,17344,18777,22034,31325,34097,36230,39497,41539,43462,45058,47710,53173,58270,89786,97497,102446,107259,119603,120880, +chr1 88051354 88174859 NM_030184 0 + 88053529 88172257 0 25 64,88,129,171,156,93,25,158,99,35,112,93,91,124,140,77,75,91,56,105,116,137,124,173,2625, 0,2138,5215,7885,9916,15130,17344,18777,22034,31325,34097,36230,39497,41539,43462,45058,47710,53173,58270,89786,97497,102446,107262,119603,120880, +chr1 88051354 88149066 NM_027456 0 + 88053529 88148971 0 21 64,88,129,171,156,93,25,158,99,35,112,93,91,124,140,77,75,91,56,105,215, 0,2138,5215,7885,9916,15130,17344,18777,22034,31325,34097,36230,39497,41539,43462,45058,47710,53173,58270,89786,97497, +chr1 88199637 88200635 NR_151592 0 - 88200635 88200635 0 2 556,97, 0,901, +chr1 88199795 88203880 NM_145222 0 + 88200118 88202802 0 2 334,2261, 0,1824, +chr1 88241293 88256030 NM_010880 0 - 88247194 88255798 0 14 5978,224,127,122,124,155,124,125,142,87,186,496,117,250, 0,6093,6648,7479,7791,8407,9013,10301,11333,11652,11837,12238,13388,14487, +chr1 88247744 88247860 NR_028478 0 - 88247860 88247860 0 1 116, 0, +chr1 88248555 88248702 NR_106184 0 - 88248702 88248702 0 1 147, 0, +chr1 88252834 88252902 NR_002851 0 - 88252902 88252902 0 1 68, 0, +chr1 88256158 88265082 NR_015507 0 + 88265082 88265082 0 2 424,1375, 0,7549, +chr1 88282816 88285936 NM_001319227 0 - 88282899 88285919 0 3 472,895,20, 0,1071,3100, +chr1 88282899 88284716 NM_010341 0 - 88282899 88284716 0 2 389,829, 0,988, +chr1 88322903 88324624 NM_027966 0 + 88322945 88324538 0 1 1721, 0, +chr1 88423131 88427286 NM_001360830 0 + 88423480 88426365 0 5 394,72,101,69,747, 0,2616,2899,3179,3408, +chr1 88423131 88427286 NR_153834 0 + 88427286 88427286 0 5 394,72,97,66,747, 0,2616,2899,3182,3408, +chr1 88423131 88427286 NM_001360831 0 + 88423480 88426587 0 5 394,72,97,35,711, 0,2616,2899,3174,3444, +chr1 88423131 88427286 NM_008972 0 + 88423480 88426587 0 5 394,72,97,74,747, 0,2616,2899,3174,3408, +chr1 88423131 88427286 NR_153833 0 + 88427286 88427286 0 4 394,72,74,747, 0,2616,3174,3408, +chr1 88439586 88479360 NM_001360817 0 - 88440076 88443286 0 5 572,106,126,182,486, 0,2690,3645,4424,39288, +chr1 88439586 88479360 NM_008801 0 - 88440076 88478924 0 5 572,106,126,89,486, 0,2690,3645,4517,39288, +chr1 88439586 88479360 NM_001360816 0 - 88440141 88478924 0 4 572,126,89,486, 0,3645,4517,39288, +chr1 88479495 88503403 NM_001360888 0 + 88495613 88501791 0 7 176,220,178,76,203,106,1771, 0,4095,6243,9370,16082,18162,22137, +chr1 88479495 88503403 NM_001360887 0 + 88485754 88501791 0 7 176,178,76,89,203,106,1771, 0,6243,9370,13830,16082,18162,22137, +chr1 88479495 88503403 NM_172974 0 + 88485754 88501791 0 8 176,220,178,76,89,203,106,1771, 0,4095,6243,9370,13830,16082,18162,22137, +chr1 88562867 88567148 NM_010933 0 - 88566238 88567013 0 3 506,311,225, 0,3351,4056, +chr1 88600378 88946672 NM_001172157 0 + 88641351 88946320 0 22 68,148,158,54,102,42,229,101,248,174,80,113,108,234,80,184,87,148,131,105,102,475, 0,40877,41537,50423,56484,87612,117418,150556,153323,174599,226950,255939,269596,286288,317234,340213,341026,343233,343644,343884,345029,345819, +chr1 88600378 88946672 NM_153530 0 + 88641351 88946320 0 21 68,148,158,54,102,229,101,248,174,80,113,108,234,80,184,87,148,131,105,102,475, 0,40877,41537,50423,56484,117418,150556,153323,174599,226950,255939,269596,286288,317234,340213,341026,343233,343644,343884,345029,345819, +chr1 88983265 88986503 NM_007433 0 - 88983622 88986338 0 11 650,117,192,135,73,135,173,175,116,117,229, 0,738,967,1242,1483,1665,2015,2259,2582,2804,3009, +chr1 88994576 88998181 NM_001081082 0 - 88995177 88998110 0 11 963,117,192,135,73,135,173,175,116,117,141, 0,1050,1368,1647,1903,2069,2447,2687,3029,3262,3464, +chr1 89021528 89025303 NM_007432 0 + 89021582 89024487 0 11 121,117,116,175,173,135,73,135,192,114,1199, 0,204,438,673,926,1356,1572,1774,1982,2376,2576, +chr1 89044229 89052931 NM_021306 0 - 89044561 89051564 0 18 432,77,96,66,125,68,52,59,104,75,99,223,125,93,111,69,885,109, 0,571,970,1479,1841,2129,2822,2951,3245,3480,3794,4328,5164,5465,5646,5863,6549,8593, +chr1 89044229 89052711 NM_001277925 0 - 89044561 89051564 0 18 432,77,96,66,125,68,52,59,104,75,99,223,125,93,111,69,885,117, 0,571,970,1479,1841,2129,2822,2951,3245,3480,3794,4328,5164,5465,5646,5863,6549,8365, +chr1 89079888 89084980 NM_027084 0 + 89080067 89084795 0 13 285,108,54,190,100,160,143,163,180,165,63,107,461, 0,841,1289,1439,2010,2196,2580,2957,3261,3570,3832,4182,4631, +chr1 89087171 89096645 NM_021600 0 + 89087265 89095337 0 12 146,155,45,110,156,110,201,112,115,205,119,1491, 0,378,923,1617,1889,2249,4203,4888,5086,6686,6978,7983, +chr1 89102385 89108410 NM_009604 0 + 89102399 89108063 0 12 69,140,45,110,156,98,201,115,115,217,134,521, 0,264,657,839,1576,2397,3204,3616,3953,4713,5092,5504, +chr1 89110485 89137063 NM_001347083 0 + 89110574 89129023 0 8 109,115,135,105,153,137,79,2643, 0,5670,7009,10442,11939,12186,18492,23935, +chr1 89110488 89137063 NM_023314 0 + 89110574 89134460 0 7 106,115,135,105,153,137,2643, 0,5667,7006,10439,11936,12183,23932, +chr1 89110488 89125433 NM_001039170 0 + 89110574 89124448 0 7 106,115,135,105,153,137,1058, 0,5667,7006,10439,11936,12183,13887, +chr1 89110513 89125433 NM_001039169 0 + 89111065 89124448 0 7 557,115,135,105,153,137,1058, 0,5642,6981,10414,11911,12158,13862, +chr1 89160927 89207416 NR_151447 0 + 89207416 89207416 0 5 402,148,135,186,870, 0,25115,33276,45308,45619, +chr1 89160927 89207416 NM_028889 0 + 89161024 89206370 0 4 402,148,135,1181, 0,25115,33276,45308, +chr1 89223572 89347385 NM_146112 0 + 89251020 89345720 0 29 95,65,83,130,96,115,112,41,180,218,163,189,197,160,167,92,108,101,101,162,159,237,123,225,206,155,182,148,1733, 0,7272,27406,37106,38186,46999,51974,52970,76669,79986,80295,80537,83664,84710,89820,92090,93287,94493,96183,98067,101572,106682,109771,113390,113719,115013,116647,119314,122080, +chr1 89223572 89347385 NM_001110212 0 + 89251020 89345720 0 29 95,65,83,130,96,115,112,41,180,200,163,189,197,160,167,92,108,101,101,162,159,237,123,225,206,155,182,148,1733, 0,7272,27406,37106,38186,46999,51974,52970,76669,80004,80295,80537,83664,84710,89820,92090,93287,94493,96183,98067,101572,106682,109771,113390,113719,115013,116647,119314,122080, +chr1 89281151 89291304 NM_001110227 0 - 89282990 89285964 0 3 2462,476,118, 0,4353,10035, +chr1 89366775 89372057 NM_001356490 0 + 89366913 89372013 0 3 211,180,154, 0,4825,5128, +chr1 89366775 89372057 NM_028473 0 + 89366913 89372013 0 3 211,183,154, 0,4822,5128, +chr1 89373403 89470445 NM_001111314 0 - 89374128 89442633 0 15 916,105,80,156,164,90,75,130,153,161,308,143,115,335,183, 0,2274,3008,3758,4287,5794,7770,9327,10970,12755,26437,32416,63830,68968,96859, +chr1 89373403 89406937 NM_019867 0 - 89374128 89406774 0 13 916,105,80,156,164,90,75,130,153,161,308,143,270, 0,2274,3008,3758,4287,5794,7770,9327,10970,12755,26437,32416,33264, +chr1 89470601 89494415 NM_001160163 0 + 89476079 89494051 0 4 100,102,212,1303, 0,5407,20851,22511, +chr1 89470601 89494415 NM_001160164 0 + 89491463 89494051 0 3 100,212,1303, 0,20851,22511, +chr1 89480596 89494415 NM_001160165 0 + 89480817 89494051 0 3 228,212,1303, 0,10856,12516, +chr1 89491124 89494415 NM_015750 0 + 89491463 89494051 0 3 68,212,1303, 0,328,1988, +chr1 89516886 89617085 NM_001110192 0 + 89517063 89615898 0 27 320,64,151,172,141,88,81,72,124,107,103,197,118,97,139,109,89,82,90,114,83,88,150,97,276,595,1190, 0,14980,45075,47580,49330,55971,61177,61375,63431,71313,75021,77037,77801,78716,79328,80848,81103,82806,85622,87784,89306,90753,91719,92881,94726,97378,99009, +chr1 89516886 89617085 NR_122078 0 + 89617085 89617085 0 28 320,64,151,172,141,88,81,72,124,107,103,197,118,97,139,109,89,82,90,114,83,88,150,97,56,53,595,1190, 0,14980,45075,47580,49330,55971,61177,61375,63431,71313,75021,77037,77801,78716,79328,80848,81103,82806,85622,87784,89306,90753,91719,92881,94726,94949,97378,99009, +chr1 89516886 89617085 NM_001110193 0 + 89517063 89615898 0 28 320,64,151,175,141,88,81,72,124,107,103,197,118,97,139,109,89,82,90,114,83,88,150,97,56,37,595,1190, 0,14980,45075,47577,49330,55971,61177,61375,63431,71313,75021,77037,77801,78716,79328,80848,81103,82806,85622,87784,89306,90753,91719,92881,94726,94965,97378,99009, +chr1 89516886 89617085 NM_010566 0 + 89517063 89615898 0 27 320,64,151,175,141,88,81,72,124,107,103,197,118,97,139,109,89,82,90,114,83,88,150,97,276,595,1190, 0,14980,45075,47577,49330,55971,61177,61375,63431,71313,75021,77037,77801,78716,79328,80848,81103,82806,85622,87784,89306,90753,91719,92881,94726,97378,99009, +chr1 89625142 89652321 NR_157047 0 - 89652321 89652321 0 4 1170,105,161,422, 0,11213,12134,26757, +chr1 89625142 89652321 NR_157046 0 - 89652321 89652321 0 5 1170,105,161,1425,422, 0,11213,12134,18777,26757, +chr1 89652585 89689003 NM_029846 0 + 89652774 89687884 0 18 304,94,106,74,252,66,87,57,103,106,71,72,121,106,150,48,102,1213, 0,4040,9327,10098,10795,15381,18134,18802,19746,22911,24114,25660,29865,30230,33320,33561,34575,35205, +chr1 89652585 89689003 NM_001205391 0 + 89652774 89687884 0 19 304,94,106,74,252,66,87,57,48,103,106,71,72,121,106,150,48,102,1213, 0,4040,9327,10098,10795,15381,18134,18802,19070,19746,22911,24114,25660,29865,30230,33320,33561,34575,35205, +chr1 89652585 89689003 NM_001205392 0 + 89652774 89687884 0 17 304,94,106,74,252,66,87,103,106,71,72,121,106,150,48,102,1213, 0,4040,9327,10098,10795,15381,18134,19746,22911,24114,25660,29865,30230,33320,33561,34575,35205, +chr1 89681145 89681393 NR_028519 0 + 89681393 89681393 0 1 248, 0, +chr1 89700254 89741732 NM_009118 0 + 89701886 89741598 0 16 333,105,61,45,194,60,77,136,85,73,138,78,24,56,10,243, 0,1593,6627,9305,11000,13836,17627,19637,20746,24717,28159,30870,33630,37112,40432,41235, +chr1 89749861 89841064 NM_177646 0 + 89749875 89839047 0 30 170,111,81,105,133,107,126,103,163,109,140,85,95,100,274,159,126,97,111,97,108,114,135,152,112,93,120,130,131,2107, 0,27081,28572,61813,62205,63082,63520,64605,65272,68286,70785,71193,72407,72586,72764,73579,74398,76454,78645,80819,81107,82051,82997,83462,84867,85059,85909,86890,88082,89096, +chr1 89749921 89750874 NR_136921 0 - 89750874 89750874 0 2 512,329, 0,624, +chr1 89841695 89905126 NM_001198573 0 - 89843170 89903998 0 32 1587,95,96,211,66,119,95,124,75,65,37,87,89,54,58,124,323,71,85,172,82,298,108,96,129,144,147,165,114,68,218,114, 0,3381,4811,5038,6522,7219,9030,12090,14668,17303,20185,22063,22389,23275,28956,30687,33190,34894,35850,36888,38633,40781,43764,44941,49053,50590,52692,54619,57288,59126,62104,63317, +chr1 89841695 89905126 NM_001033291 0 - 89843170 89903998 0 28 1587,95,96,211,66,119,95,124,75,65,58,124,323,71,85,172,82,298,108,96,129,144,147,165,114,68,218,114, 0,3381,4811,5038,6522,7219,9030,12090,14668,17303,28956,30687,33190,34894,35850,36888,38633,40781,43764,44941,49053,50590,52692,54619,57288,59126,62104,63317, +chr1 89951985 90116577 NM_201641 0 + 89952056 90114999 0 5 926,132,88,220,1876, 0,159633,160384,160727,162716, +chr1 89967353 90116577 NM_201644 0 + 89967404 90114999 0 5 900,132,88,220,1876, 0,144265,145016,145359,147348, +chr1 89991575 90116577 NM_201642 0 + 89991695 90114999 0 5 978,132,88,220,1876, 0,120043,120794,121137,123126, +chr1 89999831 90115573 NM_201410 0 + 90003516 90114999 0 6 122,859,132,88,220,872, 0,3684,111787,112538,112881,114870, +chr1 90031383 90116577 NM_145079 0 + 90035048 90114999 0 6 127,859,132,88,220,1876, 0,3664,80235,80986,81329,83318, +chr1 90062586 90116577 NM_201643 0 + 90062626 90114999 0 5 892,132,88,220,1876, 0,49032,49783,50126,52115, +chr1 90097185 90116577 NM_013701 0 + 90097211 90114999 0 5 890,132,88,220,1876, 0,14433,15184,15527,17516, +chr1 90101306 90102323 NM_008299 0 - 90101524 90102253 0 1 1017, 0, +chr1 90108533 90116577 NM_201645 0 + 90108576 90114999 0 5 913,132,88,220,1876, 0,3085,3836,4179,6168, +chr1 90123594 90158864 NM_001281466 0 + 90124642 90156601 0 42 209,93,182,132,163,99,152,144,93,79,114,77,120,111,148,41,142,53,108,120,123,153,123,80,109,96,105,124,119,153,155,160,194,138,115,150,183,156,132,103,66,2385, 0,1034,1207,3322,3606,5224,6297,6982,7950,8170,8353,9635,10453,10825,11874,13099,13659,14051,14523,15384,15649,16911,17924,18968,20116,20728,21532,22683,23245,24225,25316,27838,28070,28523,29037,29380,29631,30690,31563,32099,32510,32885, +chr1 90155430 90174154 NM_198652 0 - 90161755 90174044 0 8 7803,79,93,98,37,56,67,206, 0,9092,10465,11346,13873,16186,18363,18518, +chr1 90159687 90165983 NR_040291 0 - 90165983 90165983 0 5 3166,238,67,79,88, 0,3217,3479,4835,6208, +chr1 90161402 90174132 NM_172505 0 - 90161755 90174044 0 5 1831,79,58,65,184, 0,3120,10214,12393,12546, +chr1 90203309 90285426 NM_134252 0 + 90215544 90281288 0 27 57,93,122,74,157,178,173,175,68,198,103,119,291,96,130,146,113,217,92,142,172,178,191,100,34,91,311, 0,1075,12230,14129,18647,19670,21416,23961,25940,30378,34570,36498,41309,43112,44121,44615,47674,48396,52917,53850,55176,58305,67514,73005,74234,77928,81806, +chr1 90303584 90323013 NM_029269 0 + 90303724 90317243 0 8 207,125,120,108,55,51,96,117, 0,307,4099,5241,10228,11377,13573,19312, +chr1 90396445 90406641 NM_008132 0 - 90397697 90406461 0 3 1272,409,276, 0,3271,9920, +chr1 90448091 90458741 NR_037971 0 + 90458741 90458741 0 6 251,96,451,110,123,1591, 0,3640,4808,5692,8351,9059, +chr1 90594800 90598766 NM_177305 0 - 90597660 90598239 0 1 3966, 0, +chr1 90651464 90652308 NR_040493 0 + 90652308 90652308 0 3 69,207,200, 0,194,644, +chr1 90912687 90918785 NR_040471 0 + 90918785 90918785 0 3 260,104,239, 0,433,5859, +chr1 90966989 91051662 NM_133816 0 + 91034260 91049926 0 6 183,79,245,2357,189,1961, 0,36843,67144,73135,81785,82712, +chr1 91256916 91302708 NR_040482 0 - 91302708 91302708 0 3 375,116,100, 0,1532,45692, +chr1 91351385 91791857 NM_178119 0 + 91352004 91785469 0 18 782,59,88,86,142,135,128,156,93,105,169,159,162,155,91,223,256,6592, 0,149787,154685,172950,175577,179349,208850,210223,216368,271150,288917,311495,334352,379623,382901,388210,432695,433880, +chr1 91351385 91791857 NM_001037136 0 + 91352004 91785469 0 17 782,59,88,86,142,135,128,156,93,105,169,162,155,91,223,256,6592, 0,149787,154685,172950,175577,179349,208850,210223,216368,271150,288917,334352,379623,382901,388210,432695,433880, +chr1 91573081 91580467 NR_015540 0 - 91580467 91580467 0 4 3162,133,110,206, 0,3465,4649,7180, +chr1 91824536 91827751 NM_010262 0 - 91825194 91827330 0 2 1182,944, 0,2271, +chr1 91849165 91911241 NM_001355134 0 - 91849252 91911152 0 5 273,114,508,268,294, 0,1798,15622,40367,61782, +chr1 91849165 91911241 NR_149309 0 - 91911241 91911241 0 4 273,114,268,294, 0,1798,40367,61782, +chr1 91849165 91911241 NM_139152 0 - 91849252 91911152 0 6 273,114,508,268,123,294, 0,1798,15622,40367,43621,61782, +chr1 91938706 92050011 NM_001368722 0 - 91939200 92049750 0 19 611,239,178,87,200,108,83,68,93,107,76,153,85,206,72,192,117,325,272, 0,3460,5657,10256,24593,28380,31615,35675,38728,39184,47343,55779,61691,87921,96019,97751,100544,102689,111033, +chr1 91938706 92049976 NM_029122 0 - 91939200 92049750 0 19 611,239,178,87,200,108,83,68,93,107,76,126,85,206,72,192,117,325,237, 0,3460,5657,10256,24593,28380,31615,35675,38728,39184,47343,55806,61691,87921,96019,97751,100544,102689,111033, +chr1 92100554 92112297 NM_001271607 0 + 92110395 92111484 0 3 108,283,1928, 0,5608,9815, +chr1 92100554 92112297 NM_007722 0 + 92110395 92111484 0 2 108,1928, 0,9815, +chr1 92499999 92509916 NM_133805 0 + 92500124 92508828 0 8 203,71,49,133,108,63,48,1168, 0,950,2039,3112,6668,7550,8115,8749, +chr1 92663434 92740548 NM_001243009 0 - 92664166 92726807 0 43 746,165,99,264,220,4,531,103,699,97,494,12,37,33,63,63,36,51,63,63,63,63,36,54,66,63,54,45,27,72,54,93,146,79,338,600,615,606,603,573,585,116,226, 0,1464,6092,6577,8671,8892,8897,10583,11898,13130,14777,15359,15483,15601,17368,18349,18864,19032,19780,21065,21357,22173,22686,25066,25552,26156,27152,27318,27466,28154,29057,29622,31194,33138,34352,35234,36781,40613,43268,44401,49093,63285,76888, +chr1 92663434 92740548 NM_001243008 0 - 92664166 92726807 0 46 746,165,99,264,220,4,531,103,699,97,494,12,37,33,63,63,36,51,63,63,63,63,36,54,66,63,54,45,27,72,54,93,146,79,338,600,615,606,603,573,600,585,603,618,116,226, 0,1464,6092,6577,8671,8892,8897,10583,11898,13130,14777,15359,15483,15601,17368,18349,18864,19032,19780,21065,21357,22173,22686,25066,25552,26156,27152,27318,27466,28154,29057,29622,31194,33138,34352,35234,36781,40613,43268,44401,46357,49093,54944,61002,63285,76888, +chr1 92811676 92847719 NM_053015 0 + 92818445 92845186 0 16 154,134,222,113,104,123,205,140,84,153,156,93,87,55,101,2560, 0,6745,12883,13223,14990,16394,18217,20213,22554,24259,24620,26588,27772,28595,30514,33483, +chr1 92849684 92850589 NM_001101647 0 + 92849684 92850589 0 2 97,164, 0,741, +chr1 92854709 92864244 NM_001159725 0 - 92855460 92860877 0 6 867,94,126,152,160,160, 0,1035,1869,2978,6011,9375, +chr1 92854709 92866197 NM_008998 0 - 92855460 92860877 0 6 867,94,126,152,160,391, 0,1035,1869,2978,6011,11097, +chr1 92895303 93025521 NM_001111312 0 + 92895374 93024773 0 13 167,87,36,126,72,171,93,142,50,118,80,105,859, 0,69836,101850,102458,104520,106400,108571,113429,121414,123695,124351,126914,129359, +chr1 92950020 93025521 NM_001310732 0 + 92950234 93024773 0 25 280,87,18,48,45,51,39,60,66,78,66,78,36,126,72,171,93,93,93,142,50,118,80,105,859, 0,15119,19880,23500,24947,25587,28697,31502,33615,35190,38158,40116,47133,47741,49803,51683,53854,55136,56911,58712,66697,68978,69634,72197,74642, +chr1 92950020 93025521 NM_008515 0 + 92950234 93024773 0 23 280,87,18,48,45,51,60,78,66,78,36,126,72,171,93,93,93,142,50,118,80,105,859, 0,15119,19880,23500,24947,25587,31502,35190,38158,40116,47133,47741,49803,51683,53854,55136,56911,58712,66697,68978,69634,72197,74642, +chr1 92950020 93013899 NM_001111311 0 + 92950234 93012641 0 8 280,87,36,126,171,93,142,2727, 0,15119,47133,47741,51683,53854,58712,61152, +chr1 93041679 93067372 NM_001033408 0 + 93046677 93065657 0 16 67,91,1496,59,171,184,23,85,115,129,80,71,286,146,140,708, 0,4980,7062,8791,10282,11552,11815,11961,17255,17949,19811,19992,21696,23590,23854,24985, +chr1 93076398 93103367 NM_001168392 0 + 93076665 93103021 0 4 319,139,79,394, 0,16949,25425,26575, +chr1 93076398 93121773 NM_016894 0 + 93076665 93119938 0 3 319,139,2091, 0,16949,43284, +chr1 93076398 93103367 NM_178401 0 + 93076665 93103094 0 3 319,139,394, 0,16949,26575, +chr1 93146880 93183098 NM_001355763 0 + 93150852 93181932 0 10 134,179,30,66,68,71,58,33,63,1217, 0,3911,11963,14914,24946,26082,27957,29201,33643,35001, +chr1 93146880 93183098 NM_001355761 0 + 93150852 93181932 0 11 134,68,134,30,66,68,71,58,33,63,1217, 0,3456,3956,11963,14914,24946,26082,27957,29201,33643,35001, +chr1 93146880 93183098 NM_026454 0 + 93150852 93181932 0 10 134,134,30,66,68,71,58,33,63,1217, 0,3956,11963,14914,24946,26082,27957,29201,33643,35001, +chr1 93146880 93183098 NR_149825 0 + 93183098 93183098 0 10 134,134,30,66,99,71,58,33,63,1217, 0,3956,11963,14914,24915,26082,27957,29201,33643,35001, +chr1 93146880 93183098 NM_001355762 0 + 93150852 93181932 0 10 134,131,30,66,68,71,58,33,63,1217, 0,3959,11963,14914,24946,26082,27957,29201,33643,35001, +chr1 93147142 93183098 NM_001355764 0 + 93150852 93181932 0 11 288,68,179,30,66,68,71,58,33,63,1217, 0,3194,3649,11701,14652,24684,25820,27695,28939,33381,34739, +chr1 93194914 93217657 NM_016717 0 + 93194972 93216807 0 12 111,113,101,181,128,165,107,37,84,100,76,1004, 0,2190,4431,6936,9976,10313,11459,17151,18726,19254,20700,21739, +chr1 93218651 93244880 NM_001033292 0 + 93218709 93242514 0 9 352,191,187,183,132,115,98,195,3989, 0,1404,2961,5401,12615,18434,19771,20466,22240, +chr1 93247649 93258981 NM_027551 0 + 93250255 93257843 0 8 63,847,136,87,156,189,146,1396, 0,2533,4379,6261,6682,7715,8263,9936, +chr1 93263006 93270794 NM_173395 0 + 93263057 93269053 0 8 219,117,103,257,109,91,79,1840, 0,1935,2941,3656,3985,4195,4952,5948, +chr1 93270437 93295400 NM_001355152 0 - 93271983 93283856 0 12 1678,82,120,122,88,94,107,127,92,57,66,173, 0,2457,4605,7990,9443,10704,11379,13354,14494,16746,17271,24790, +chr1 93272403 93295400 NM_023343 0 - 93272518 93295282 0 12 256,82,120,122,88,94,107,127,120,57,66,173, 0,491,2639,6024,7477,8738,9413,11388,12518,14780,15305,22824, +chr1 93301456 93302606 NR_026924 0 - 93302606 93302606 0 3 303,119,124, 0,616,1026, +chr1 93308059 93310615 NM_001360900 0 - 93308634 93309000 0 4 1000,82,87,68, 0,1238,1410,2488, +chr1 93308059 93309799 NM_001360899 0 - 93308634 93309714 0 4 1000,76,87,166, 0,1238,1410,1574, +chr1 93308059 93309799 NM_019479 0 - 93308634 93309714 0 4 1000,82,87,166, 0,1238,1410,1574, +chr1 93312558 93355905 NM_011066 0 - 93314447 93347402 0 23 2039,151,193,187,797,240,165,107,163,85,126,109,154,107,79,143,52,202,122,155,66,239,156, 0,3393,4424,5386,7708,11757,13402,14792,14996,16826,17414,18640,19035,19668,22352,23905,24850,28603,29519,32726,33831,34623,43191, +chr1 93391244 93425884 NM_028718 0 + 93391342 93424360 0 15 221,69,162,138,420,72,76,21,85,84,124,37,77,224,1690, 0,3285,4834,6105,6337,10755,12825,23626,24910,25388,26216,26519,28163,31211,32950, +chr1 93437141 93456167 NM_001039126 0 + 93437389 93451455 0 5 300,142,303,386,4840, 0,3591,6363,11489,14186, +chr1 93437656 93456167 NM_023046 0 + 93437729 93451455 0 5 96,147,303,386,4840, 0,3071,5848,10974,13671, +chr1 93698037 93744611 NM_007855 0 + 93698203 93698686 0 2 689,646, 0,45928, +chr1 93825355 94076918 NM_207225 0 - 93829923 94044854 0 27 4608,142,85,134,119,98,120,88,56,108,47,106,134,187,255,224,196,117,113,132,122,121,151,242,72,239,84, 0,4877,5823,17121,18639,26511,27263,29576,30632,32674,36001,39574,42164,43921,46660,53250,55599,55882,58766,62704,67278,73376,83890,101176,126122,219477,251479, +chr1 94336295 94370335 NM_024197 0 - 94336415 94370314 0 10 189,109,86,55,80,122,87,216,169,96, 0,12292,20661,22572,23359,24642,27662,30144,31098,33944, +chr1 94361059 94361119 NR_105865 0 - 94361119 94361119 0 1 60, 0, +chr1 94376257 94377196 NM_147038 0 - 94376257 94377196 0 1 939, 0, +chr1 94387394 94388330 NM_001011525 0 - 94387394 94388330 0 1 936, 0, +chr1 94407624 94415092 NM_147039 0 - 94407664 94408603 0 2 989,200, 0,7268, +chr1 94469701 94470783 NM_147037 0 + 94469749 94470721 0 1 1082, 0, +chr1 94484908 94485874 NM_146277 0 + 94484908 94485874 0 1 966, 0, +chr1 94493097 94494069 NM_146490 0 + 94493097 94494069 0 1 972, 0, +chr1 94504415 94505384 NM_146491 0 + 94504415 94505384 0 1 969, 0, +chr1 94516457 94517578 NM_206896 0 + 94516484 94517486 0 1 1121, 0, +chr1 94533721 94538525 NR_028108 0 - 94538525 94538525 0 3 259,73,342, 0,2542,4462, +chr1 94533721 94538562 NM_001163425 0 - 94533942 94538519 0 3 259,73,106, 0,2542,4735, +chr1 94540794 94545418 NM_153114 0 - 94540909 94541968 0 5 300,27,93,193,91, 0,964,1116,1466,4533, +chr1 94728221 94756788 NM_016696 0 + 94728508 94755141 0 9 453,159,389,166,131,120,134,176,1880, 0,21702,23213,24262,25342,25603,25827,26210,26687, +chr1 94746954 94747020 NR_029559 0 + 94747020 94747020 0 1 66, 0, +chr1 94766705 94799483 NM_172850 0 - 94766848 94799160 0 18 190,161,73,166,114,132,108,141,141,172,431,159,217,470,144,190,157,77, 0,680,1544,6406,6882,8202,9186,10851,11622,13613,14706,16007,16494,18318,25940,29370,32315,32701, +chr1 94766705 94799483 NM_001347091 0 - 94766848 94799160 0 18 190,161,76,166,114,132,108,141,141,172,431,159,217,470,144,190,157,77, 0,680,1544,6406,6882,8202,9186,10851,11622,13613,14706,16007,16494,18318,25940,29370,32315,32701, +chr1 94803565 94805197 NM_175118 0 + 94803631 94804264 0 2 435,1056, 0,576, +chr1 94804954 94807341 NR_138578 0 - 94807341 94807341 0 2 1601,186, 0,2201, +chr1 94804954 94807266 NR_138577 0 - 94807266 94807266 0 2 1601,268, 0,2044, +chr1 94807401 94817162 NM_181405 0 + 94807547 94816432 0 11 659,141,152,117,236,114,113,109,231,143,1024, 0,4234,4989,5530,5886,6322,6809,7193,8048,8359,8737, +chr1 94830119 94847167 NR_015525 0 - 94847167 94847167 0 2 1561,111, 0,16937, +chr1 94830984 94844525 NM_011796 0 + 94831450 94844115 0 12 607,132,197,218,142,167,263,203,262,200,46,440, 0,3537,4915,5875,8074,8892,9271,10287,10609,12366,12807,13101, +chr1 94869695 94882968 NM_001104529 0 + 94879144 94880068 0 2 163,3834, 0,9439, +chr1 94871923 94882968 NM_001271766 0 + 94879144 94880068 0 2 102,3834, 0,7211, +chr1 94875479 94882968 NM_022320 0 + 94879144 94880068 0 2 399,3834, 0,3655, +chr1 94902910 94908846 NM_001159658 0 + 94902979 94908700 0 3 676,114,295, 0,2230,5641, +chr1 94902910 94908846 NM_177587 0 + 94902979 94908700 0 3 676,117,295, 0,2227,5641, +chr1 94912031 94998451 NM_008440 0 - 94915033 94978998 0 48 3045,119,193,153,125,78,201,146,62,134,115,24,106,85,67,109,56,119,91,169,139,86,119,138,179,149,94,73,181,84,107,80,76,80,134,143,79,76,18,66,78,112,179,66,180,77,165,112, 0,3497,4352,5003,5758,6271,6866,7471,8004,9124,10166,11377,21391,23580,23762,24290,25164,26119,26630,26888,27161,28134,31197,36969,38805,39361,40230,40502,40645,43359,44742,45283,47045,47412,48694,50592,51601,53030,56853,57584,58353,59501,60696,61587,62233,63306,66861,86308, +chr1 94912031 94998451 NM_001368847 0 - 94915033 94978998 0 49 3045,119,193,153,125,78,201,146,62,134,115,24,106,85,67,109,56,119,91,169,139,86,119,138,179,149,94,73,181,84,107,80,76,80,134,27,143,79,76,18,66,78,112,179,66,180,77,165,112, 0,3497,4352,5003,5758,6271,6866,7471,8004,9124,10166,11377,21391,23580,23762,24290,25164,26119,26630,26888,27161,28134,31197,36969,38805,39361,40230,40502,40645,43359,44742,45283,47045,47412,48694,50097,50592,51601,53030,56853,57584,58353,59501,60696,61587,62233,63306,66861,86308, +chr1 94912031 94998451 NM_001110315 0 - 94915033 94978998 0 47 3045,119,193,153,125,78,201,146,62,134,115,106,85,67,109,56,119,91,169,139,86,119,138,179,149,94,73,181,84,107,80,76,80,134,143,79,76,18,66,78,112,179,66,180,77,165,112, 0,3497,4352,5003,5758,6271,6866,7471,8004,9124,10166,21391,23580,23762,24290,25164,26119,26630,26888,27161,28134,31197,36969,38805,39361,40230,40502,40645,43359,44742,45283,47045,47412,48694,50592,51601,53030,56853,57584,58353,59501,60696,61587,62233,63306,66861,86308, +chr1 94912031 94979057 NM_001294150 0 - 94915033 94978998 0 47 3045,119,193,153,125,78,201,146,62,134,115,106,85,67,109,56,119,91,169,139,86,119,138,179,149,94,73,181,84,107,80,76,80,134,27,143,79,76,18,66,78,112,179,66,180,77,165, 0,3497,4352,5003,5758,6271,6866,7471,8004,9124,10166,21391,23580,23762,24290,25164,26119,26630,26888,27161,28134,31197,36969,38805,39361,40230,40502,40645,43359,44742,45283,47045,47412,48694,50097,50592,51601,53030,56853,57584,58353,59501,60696,61587,62233,63306,66861, +chr1 94912031 94998451 NM_001294149 0 - 94915033 94978998 0 48 3045,119,193,153,125,78,201,146,62,134,115,27,106,85,67,109,56,119,91,169,139,86,119,138,179,149,94,73,181,84,107,80,76,80,134,143,79,76,18,66,78,112,179,66,180,77,165,112, 0,3497,4352,5003,5758,6271,6866,7471,8004,9124,10166,19091,21391,23580,23762,24290,25164,26119,26630,26888,27161,28134,31197,36969,38805,39361,40230,40502,40645,43359,44742,45283,47045,47412,48694,50592,51601,53030,56853,57584,58353,59501,60696,61587,62233,63306,66861,86308, +chr1 95031816 95041998 NM_016702 0 + 95031870 95041744 0 11 285,193,65,101,71,85,96,70,96,129,362, 0,369,2055,2660,4041,5082,6074,6828,8815,9271,9820, +chr1 95031816 95041998 NM_001276710 0 + 95031936 95041744 0 11 285,193,65,101,71,85,96,70,96,129,362, 0,369,2055,2660,4041,5082,6074,6828,8815,9271,9820, +chr1 95047931 95057447 NM_001159940 0 - 95048584 95056706 0 6 746,357,154,226,750,69, 0,1562,3132,4624,8246,9447, +chr1 95047931 95057525 NM_172411 0 - 95048584 95056706 0 6 746,357,154,226,750,60, 0,1562,3132,4624,8246,9534, +chr1 95064999 95127643 NM_001310428 0 + 95065301 95125434 0 32 380,151,149,107,142,104,198,97,90,207,200,183,145,147,231,194,128,170,177,114,144,218,160,168,355,179,121,134,99,126,132,2278, 0,11585,12650,14942,16539,20473,21102,21641,21819,22050,22469,24613,25151,25559,25962,30044,32975,33357,34297,37473,40811,44363,45078,45596,46957,47535,48549,49333,55137,55662,58178,60366, +chr1 95132473 95193025 NM_172463 0 + 95132565 95192855 0 31 305,288,141,163,126,114,114,114,126,105,114,117,117,117,114,174,114,114,114,114,297,184,113,282,145,83,96,117,88,82,182, 0,20368,23069,23748,25752,26207,29141,29382,35245,35702,35958,36595,38152,38447,38708,39400,44584,45340,45755,46372,46795,47305,47678,48488,49899,50115,51031,53411,54101,59823,60370, +chr1 95171125 95171187 NR_105866 0 + 95171187 95171187 0 1 62, 0, +chr1 95197781 95202456 NM_001310756 0 - 95197954 95202422 0 4 380,185,499,55, 0,1513,3403,4620, +chr1 95197781 95202456 NM_178051 0 - 95198036 95202422 0 4 591,185,499,55, 0,1513,3403,4620, +chr1 95202540 95213889 NR_151531 0 + 95213889 95213889 0 3 144,82,662, 0,579,10687, +chr1 95206013 95239365 NM_080850 0 - 95206668 95234108 0 18 813,147,134,200,135,126,168,182,1448,154,169,261,135,141,171,236,236,263, 0,1331,3359,4844,7348,7584,10523,11057,11338,14765,15927,17779,21318,22122,25106,26173,27908,33089, +chr1 95240204 95264193 NM_023200 0 + 95240236 95261643 0 10 84,132,56,66,131,163,117,105,87,2727, 0,2528,6697,7321,7878,8889,10701,14129,17098,21262, +chr1 95242668 95242732 NR_105867 0 + 95242732 95242732 0 1 64, 0, +chr1 95248734 95248862 NR_105763 0 + 95248862 95248862 0 1 128, 0, +chr1 95270472 95300881 NM_001271884 0 + 95271718 95299673 0 24 152,115,58,131,108,137,58,111,166,91,97,144,138,99,103,112,55,98,131,206,143,91,120,1235, 0,1239,3379,6519,10915,11651,13339,14701,16383,17505,18307,20441,20652,21391,21569,23381,23736,25189,26548,27535,27865,28241,28745,29174, +chr1 95270472 95300881 NM_207031 0 + 95271718 95299601 0 24 152,115,58,131,108,137,58,111,166,91,97,144,138,99,103,112,55,98,131,206,143,91,120,1355, 0,1239,3379,6519,10915,11651,13339,14701,16383,17505,18307,20441,20652,21391,21569,23381,23736,25189,26548,27535,27865,28241,28745,29054, +chr1 95302516 95375494 NM_133808 0 - 95304749 95337332 0 28 2320,129,117,186,144,135,105,155,139,219,222,219,132,87,114,105,140,79,105,108,207,216,207,216,158,113,65,205, 0,2429,2749,3011,6423,7551,7887,8872,10561,11232,11528,14129,15144,15403,17324,17830,19327,21618,22208,23438,24158,25015,25372,31154,32286,34740,36246,72773, +chr1 95302516 95342278 NM_001301364 0 - 95304749 95337332 0 28 2320,129,117,186,144,135,105,155,139,219,222,219,132,87,114,105,140,79,105,108,207,216,207,216,158,113,65,122, 0,2429,2749,3011,6423,7551,7887,8872,10561,11232,11528,14129,15144,15403,17324,17830,19327,21618,22208,23438,24158,25015,25372,31154,32286,34740,36246,39640, +chr1 95302516 95374954 NM_001357556 0 - 95304749 95337332 0 28 2320,129,117,186,144,135,105,155,139,219,222,219,132,87,114,105,140,79,105,108,207,216,207,216,158,113,65,171, 0,2429,2749,3011,6423,7551,7887,8872,10561,11232,11528,14129,15144,15403,17324,17830,19327,21618,22208,23438,24158,25015,25372,31154,32286,34740,36246,72267, +chr1 95375569 95406309 NM_001159718 0 + 95387844 95403641 0 12 76,121,87,124,135,118,102,146,84,58,120,2020, 0,12164,16586,18348,20019,20280,21465,22514,24442,26551,27970,28720, +chr1 95375569 95406309 NM_001159717 0 + 95385722 95403641 0 13 76,27,121,87,124,135,118,102,146,84,58,120,2020, 0,10135,12164,16586,18348,20019,20280,21465,22514,24442,26551,27970,28720, +chr1 95375569 95406309 NM_010891 0 + 95385722 95403641 0 13 76,31,121,87,124,135,118,102,146,84,58,120,2020, 0,10131,12164,16586,18348,20019,20280,21465,22514,24442,26551,27970,28720, +chr1 95375637 95406309 NM_001159719 0 + 95385722 95403641 0 13 120,31,121,87,124,135,118,102,146,84,58,120,2020, 0,10063,12096,16518,18280,19951,20212,21397,22446,24374,26483,27902,28652, +chr1 95408680 95518553 NM_145519 0 + 95425173 95517948 0 27 81,211,105,43,79,98,115,148,96,164,69,58,259,179,90,134,82,238,131,69,90,83,119,158,108,152,753, 0,16465,48132,49040,51205,55313,56977,57769,62267,64266,64719,65544,67636,87819,91274,92106,93238,95329,97872,100288,101014,105448,106399,106789,108050,108389,109120, +chr1 95517327 95532304 NM_021537 0 - 95519063 95531904 0 12 1776,137,72,115,146,186,158,109,57,231,86,181, 0,2645,3802,4283,4710,5030,5300,6274,6903,8283,14547,14796, +chr1 95582151 95592347 NM_016778 0 + 95583023 95591739 0 5 280,252,129,164,734, 0,843,3582,8485,9462, +chr1 95601967 95651415 NM_025920 0 - 95602112 95651110 0 6 265,104,110,160,1139,382, 0,9507,11241,19766,44456,49066, +chr1 95601967 95628503 NM_001310761 0 - 95602112 95628437 0 5 265,104,110,160,70, 0,9507,11241,19766,26466, +chr1 95651481 95686179 NM_001368266 0 + 95651621 95684336 0 12 150,102,72,102,73,80,194,79,146,57,94,1917, 0,13148,13348,20228,20723,23380,25813,29507,29848,31005,31606,32781, +chr1 95651481 95686179 NM_174874 0 + 95651621 95684336 0 13 150,102,72,99,102,73,80,194,79,146,57,94,1917, 0,13148,13348,18865,20228,20723,23380,25813,29507,29848,31005,31606,32781, +chr1 95689152 95698511 NM_001105667 0 - 95689409 95698404 0 5 368,198,91,109,237, 0,2150,5804,8226,9122, +chr1 95697071 95698511 NM_023136 0 - 95697374 95698404 0 2 416,237, 0,1203, +chr1 95700541 95718677 NM_025454 0 + 95700579 95714900 0 8 75,72,167,112,94,136,62,3820, 0,2083,7817,8442,8701,12410,12673,14316, +chr1 95721816 95748938 NM_001310767 0 + 95722113 95747403 0 10 341,356,58,140,194,169,144,143,166,1795, 0,1045,3966,4517,7356,10047,12700,13581,22863,25327, +chr1 95721816 95748938 NM_178882 0 + 95722883 95747403 0 10 80,356,58,140,194,169,144,143,166,1795, 0,1045,3966,4517,7356,10047,12700,13581,22863,25327, +chr1 95757920 95773071 NM_199366 0 + 95758170 95771666 0 4 276,87,259,2224, 0,11111,12246,12927, +chr1 95815013 95837816 NM_001205249 0 + 95815013 95837816 0 4 20,87,259,819, 0,20168,21303,21984, +chr1 95887081 95908116 NM_001039219 0 + 95892954 95906102 0 8 178,319,144,151,92,87,259,2833, 0,941,4612,5406,5807,16413,17536,18202, +chr1 95917069 95924907 NM_173772 0 + 95918966 95921993 0 4 124,233,256,3894, 0,1865,2200,3944, +chr1 95917069 95924907 NM_001310769 0 + 95918172 95921993 0 5 124,84,233,256,3894, 0,1056,1865,2200,3944, +chr1 95934881 95949130 NM_008798 0 - 95935881 95949067 0 5 1234,35,162,360,139, 0,1787,2405,2851,14110, +chr1 96694018 96699049 NR_040473 0 + 96699049 96699049 0 4 268,1019,119,159, 0,1924,3556,4872, +chr1 97210204 97231861 NM_026321 0 + 97210393 97230516 0 3 623,135,1349, 0,11481,20308, +chr1 97484258 97564171 NM_009183 0 - 97488258 97563838 0 5 4283,294,258,132,446, 0,39825,65831,73182,79467, +chr1 97523819 97564171 NM_001159745 0 - 97524079 97563838 0 4 558,258,132,446, 0,26270,33621,39906, +chr1 97597760 97613095 NR_040479 0 - 97613095 97613095 0 4 313,103,63,282, 0,11418,14803,15053, +chr1 97887235 97918335 NR_040467 0 - 97918335 97918335 0 3 245,79,32, 0,4755,31068, +chr1 98508633 98559150 NR_040478 0 - 98559150 98559150 0 3 275,153,155, 0,2962,50362, +chr1 98715360 98768748 NM_172658 0 - 98715523 98768686 0 13 324,138,65,185,154,196,145,119,122,97,180,264,405, 0,2399,4913,10007,13202,18096,18670,20383,22346,23670,25692,48941,52983, +chr1 98767702 98777811 NR_131964 0 + 98777811 98777811 0 4 131,201,184,3401, 0,1064,1359,6708, +chr1 98802752 98894137 NR_120500 0 - 98894137 98894137 0 15 165,50,159,138,65,188,154,196,145,110,116,97,192,261,439, 0,4035,5638,15742,18113,23516,35699,41304,46841,54899,59102,81641,82366,88848,90946, +chr1 98956025 99024880 NM_028942 0 - 98958970 99024751 0 14 160,160,138,65,188,154,196,145,110,119,97,189,261,451, 0,2922,6584,9535,13346,16380,21872,28424,39003,45339,59090,60356,66143,68404, +chr1 99540478 99558253 NM_001355072 0 - 99542291 99542915 0 3 2460,90,946, 0,10698,16829, +chr1 99540478 99558595 NM_133825 0 - 99542291 99542915 0 3 2460,90,188, 0,10698,17929, +chr1 99540478 99558253 NM_001355073 0 - 99542291 99542915 0 3 2460,90,389, 0,10698,17386, +chr1 99540478 99558595 NM_001355071 0 - 99542291 99542915 0 2 2460,188, 0,17929, +chr1 99540478 99558253 NM_001355074 0 - 99542291 99542915 0 3 2460,90,122, 0,10698,17653, +chr1 99602619 99666669 NM_173760 0 - 99604294 99658133 0 28 1788,126,141,73,165,117,108,115,128,224,142,183,122,126,86,110,76,87,102,122,162,102,155,86,91,196,397,238, 0,5680,6961,13791,17627,21146,21352,22875,23868,27843,28924,34419,34781,35027,38014,39120,39352,40375,41504,43499,44524,46661,49012,49843,50801,53126,55382,63812, +chr1 99666748 99690285 NM_001310773 0 + 99672030 99689148 0 8 84,146,194,39,192,168,283,1412, 0,5275,7154,13022,14581,14883,15804,22125, +chr1 99666748 99690285 NM_026250 0 + 99672030 99689148 0 8 84,146,194,306,192,168,283,1412, 0,5275,7154,12755,14581,14883,15804,22125, +chr1 99717670 99992209 NM_013626 0 - 99718386 99873534 0 26 895,54,201,54,109,116,201,211,73,117,130,318,72,185,104,77,81,68,49,84,86,88,58,121,403,148, 0,1842,4743,10361,13314,16869,19186,19605,21138,23502,32009,43109,63032,64508,73267,74538,74875,76114,77247,102000,103337,113557,123526,154691,155763,274391, +chr1 99717670 99992223 NM_001357127 0 - 99718386 99873534 0 26 895,54,204,54,109,116,201,211,73,117,130,318,72,185,104,77,81,68,49,84,86,88,58,121,403,162, 0,1842,4743,10361,13314,16869,19186,19605,21138,23502,32009,43109,63032,64508,73267,74538,74875,76114,77247,102000,103337,113557,123526,154691,155763,274391, +chr1 99927699 99944370 NR_037993 0 - 99944370 99944370 0 3 986,100,92, 0,1993,16579, +chr1 100028043 100041232 NR_040439 0 + 100041232 100041232 0 3 238,90,1359, 0,2045,11830, +chr1 100070224 100087274 NR_151613 0 + 100087274 100087274 0 4 92,92,137,3854, 0,1427,11782,13196, +chr1 100317700 100405957 NM_027584 0 + 100317782 100404190 0 14 374,261,186,97,119,110,145,196,154,188,65,138,133,162, 0,1965,7142,11109,22504,25589,45534,59467,69373,75061,76353,78635,86389,88095, +chr1 100317700 100405957 NM_001164233 0 + 100317782 100405797 0 13 374,261,186,97,119,110,145,196,154,188,65,138,162, 0,1965,7142,11109,22504,25589,45534,59467,69373,75061,76353,78635,88095, +chr1 101668977 102387175 NM_172851 0 + 101669341 102381278 0 24 446,105,194,148,204,185,141,265,150,172,107,120,201,118,128,171,219,240,225,131,85,219,72,6094, 0,168242,194791,278241,299647,303629,325333,368773,387637,391667,441266,482658,501960,586253,597356,597657,606650,610980,618066,659315,674433,705957,709504,712104, +chr1 103052344 103071779 NR_037989 0 + 103071779 103071779 0 3 245,75,566, 0,12863,18869, +chr1 106665096 106892058 NM_011800 0 + 106830673 106890962 0 12 379,386,295,120,168,188,254,137,122,118,252,1602, 0,165437,172512,173578,176672,178804,185309,202301,206474,210460,216151,225360, +chr1 107173493 107253287 NM_001160368 0 - 107180795 107181407 0 2 8038,368, 0,79426, +chr1 107173493 107253287 NM_178779 0 - 107180795 107181407 0 3 8038,123,368, 0,78124,79426, +chr1 107252583 107258314 NR_151540 0 + 107258314 107258314 0 2 899,149, 0,5582, +chr1 107252583 107258314 NR_151538 0 + 107258314 107258314 0 2 1243,149, 0,5582, +chr1 107252583 107258314 NR_151539 0 + 107258314 107258314 0 2 951,149, 0,5582, +chr1 107414998 107560253 NM_013784 0 - 107418580 107554399 0 31 3706,53,43,74,76,56,87,103,103,109,109,92,93,100,140,183,79,56,93,60,41,117,131,125,107,99,122,249,120,74,177, 0,28242,30643,33950,35642,36022,39041,39566,47726,61500,66567,69558,70627,70804,73200,79246,80627,119088,119761,122243,126057,128276,129687,130861,134682,137512,138244,139180,140465,140871,145078, +chr1 107560437 107651708 NM_029349 0 + 107560684 107650200 0 28 773,90,56,114,204,92,294,76,96,113,91,72,141,165,148,157,124,49,80,107,100,83,64,139,117,89,71,1629, 0,14302,23269,23421,28045,28351,29023,31567,32640,40070,49988,52917,54914,55591,57407,61788,62482,64079,67340,70657,72062,76574,77436,79350,82208,86461,87112,89642, +chr1 107560437 107651708 NM_173187 0 + 107560684 107650200 0 29 773,90,72,56,114,204,92,294,76,96,113,91,72,141,165,148,157,124,49,80,107,100,83,64,139,117,89,71,1629, 0,14302,23088,23269,23421,28045,28351,29023,31567,32640,40070,49988,52917,54914,55591,57407,61788,62482,64079,67340,70657,72062,76574,77436,79350,82208,86461,87112,89642, +chr1 107677299 107744558 NM_009399 0 + 107677328 107741443 0 10 107,82,126,144,94,95,114,53,745,3462, 0,27420,28607,32928,36946,39147,40755,44277,46268,63797, +chr1 107875926 107886859 NR_151625 0 - 107886859 107886859 0 3 275,85,111, 0,9669,10822, +chr1 107886982 107930654 NM_001122676 0 + 107887366 107928740 0 14 1302,112,77,72,113,95,84,58,133,65,95,129,1482,1982, 0,10525,13694,15609,21296,25593,27813,29442,31320,32794,33258,36997,39346,41690, +chr1 107886982 107930654 NM_001122675 0 + 107887366 107927845 0 13 1302,112,77,72,113,95,84,58,133,65,95,129,4326, 0,10525,13694,15609,21296,25593,27813,29442,31320,32794,33258,36997,39346, +chr1 108049201 108068101 NR_040630 0 - 108068101 108068101 0 3 123,237,185, 0,10938,18715, +chr1 108068445 108290822 NM_133821 0 + 108068580 108289917 0 17 1579,197,126,167,147,231,203,61,96,156,201,163,131,105,195,229,2117, 0,109494,115122,146980,166868,167571,171508,172991,175216,178663,192372,197145,204292,208449,214458,217805,220260, +chr1 108434752 108610867 NM_009741 0 - 108439840 108609457 0 2 5223,1986, 0,174129, +chr1 108443072 108443208 NR_106164 0 - 108443208 108443208 0 1 136, 0, +chr1 108608741 108610867 NM_177410 0 - 108608857 108609457 0 1 2126, 0, +chr1 108616986 108656319 NM_027534 0 - 108621478 108656228 0 10 4612,102,84,84,192,96,66,57,90,199, 0,7219,14137,18921,23259,27078,27361,32802,35034,39134, +chr1 108627778 108656319 NM_001316750 0 - 108627890 108656228 0 9 139,84,84,192,96,66,57,90,199, 0,3345,8129,12467,16286,16569,22010,24242,28342, +chr1 108667364 108693302 NM_009190 0 - 108669023 108693024 0 11 1761,141,220,82,149,157,120,68,157,112,305, 0,3219,6482,8181,9174,9716,11878,15915,19141,20890,25633, +chr1 108757751 108779925 NM_001360853 0 + 108766859 108778570 0 8 86,130,169,138,118,143,168,1748, 0,8304,9107,11075,13868,14835,19001,20426, +chr1 108757751 108779925 NM_001360854 0 + 108772675 108778570 0 6 86,138,118,143,168,1748, 0,11075,13868,14835,19001,20426, +chr1 108757751 108779925 NM_009257 0 + 108766859 108778570 0 7 86,169,138,118,143,168,1748, 0,9107,11075,13868,14835,19001,20426, +chr1 108831025 108853657 NM_027971 0 + 108843123 108853374 0 8 116,186,132,138,118,143,168,688, 0,12080,14675,15113,16253,19242,20873,21944, +chr1 108835533 108853657 NM_001199213 0 + 108843123 108853374 0 8 46,186,132,138,118,143,168,688, 0,7572,10167,10605,11745,14734,16365,17436, +chr1 108877560 108897772 NM_172852 0 + 108878731 108897398 0 8 46,182,57,129,118,143,156,776, 0,1154,1829,14805,15296,17582,17904,19436, +chr1 108942163 108948880 NM_009126 0 - 108942592 108948347 0 8 834,156,143,118,123,57,187,11, 0,1456,1886,2903,3740,5422,6022,6706, +chr1 108974769 108980057 NM_201376 0 - 108974769 108980057 0 7 405,156,143,118,123,57,162, 0,1025,1459,2481,3389,4545,5126, +chr1 109050537 109057691 NM_198680 0 - 109050945 109056354 0 8 813,156,143,118,123,57,187,35, 0,1451,1884,2869,3707,5060,5655,7119, +chr1 109167777 109174948 NM_201363 0 - 109168205 109173591 0 8 830,156,143,118,123,57,187,45, 0,1452,1882,2897,3734,5061,5652,7126, +chr1 109258890 109277052 NM_025867 0 + 109265972 109276584 0 8 46,186,60,120,118,143,156,870, 0,7064,8475,9840,11761,14459,15191,17292, +chr1 109319265 109349266 NM_027548 0 + 109324825 109348584 0 8 44,186,51,117,118,143,147,1081, 0,5542,12047,12638,23303,25419,27487,28920, +chr1 109407999 109422177 NM_001174170 0 + 109412049 109421518 0 8 56,177,120,129,118,143,165,1064, 0,4041,8229,10724,11269,11642,12374,13114, +chr1 109408086 109422177 NM_011111 0 + 109412049 109421518 0 8 75,177,120,129,118,143,165,1064, 0,3954,8142,10637,11182,11555,12287,13027, +chr1 109425579 109445848 NM_001160307 0 + 109432084 109443649 0 7 89,66,138,118,143,156,2604, 0,6442,6990,9424,11885,13189,17665, +chr1 109425579 109445848 NM_198028 0 + 109429067 109443649 0 8 89,176,66,138,118,143,156,2604, 0,3360,6442,6990,9424,11885,13189,17665, +chr1 109486582 109505555 NM_011459 0 + 109494046 109503902 0 7 282,183,138,118,143,153,2058, 0,7449,8894,12794,14598,15778,16915, +chr1 109486582 109502727 NM_001159748 0 + 109494046 109502531 0 6 282,183,138,118,143,367, 0,7449,8894,12794,14598,15778, +chr1 109813835 109847524 NR_102307 0 + 109847524 109847524 0 5 94,114,108,104,1799, 0,19450,20299,24449,31890, +chr1 109813835 109847524 NR_102306 0 + 109847524 109847524 0 4 94,108,104,1799, 0,20299,24449,31890, +chr1 111879476 112036480 NM_001316743 0 + 111890756 112034932 0 12 152,404,295,120,168,188,254,137,122,118,252,2042, 0,11086,65917,69949,78095,82710,102020,115371,116328,117121,125804,154962, +chr1 111879878 112036480 NM_001316744 0 + 111894392 112034932 0 13 590,404,156,295,120,168,188,254,137,122,118,252,2042, 0,10684,14394,65515,69547,77693,82308,101618,114969,115926,116719,125402,154560, +chr1 111880299 112036480 NM_172853 0 + 111890756 112034932 0 12 169,404,295,120,168,188,254,137,122,118,252,2042, 0,10263,65094,69126,77272,81887,101197,114548,115505,116298,124981,154139, +chr1 112784902 112874170 NM_001356415 0 - 112786274 112851337 0 13 1863,252,118,122,122,254,185,165,120,292,304,130,347, 0,4859,7057,19733,31222,36670,37430,41508,43820,60798,66243,84187,88921, +chr1 112784902 112874170 NM_001081386 0 - 112786274 112851337 0 12 1863,252,118,122,122,254,185,165,120,292,304,347, 0,4859,7057,19733,31222,36670,37430,41508,43820,60798,66243,88921, +chr1 113755278 113761495 NM_001081316 0 - 113755756 113759380 0 2 4939,824, 0,5393, +chr1 114273905 114313495 NR_157044 0 - 114313495 114313495 0 5 4153,45,265,675,435, 0,23667,25458,26853,39155, +chr1 117581313 118483899 NM_001077425 0 + 117581713 118477251 0 24 482,105,194,148,204,185,141,265,150,172,107,120,201,157,128,171,219,240,225,131,85,219,72,6842, 0,216193,230404,375385,404471,416814,432837,472656,499569,503527,537105,574716,607598,727350,743735,744044,757448,761772,770256,833376,839497,886715,893127,895744, +chr1 117581313 118483899 NM_001371013 0 + 117581713 118477251 0 24 482,105,194,148,204,185,144,265,150,172,107,120,201,157,128,171,219,240,225,131,85,219,72,6842, 0,216193,230404,375385,404471,416814,432837,472656,499569,503527,537105,574716,607598,727350,743735,744044,757448,761772,770256,833376,839497,886715,893127,895744, +chr1 119677711 119699936 NM_001372356 0 + 119678076 119698988 0 5 96,201,127,988,1297, 0,179,1746,19772,20928, +chr1 120195090 120207305 NR_153836 0 - 120207305 120207305 0 6 2524,80,116,97,94,92, 0,6177,6686,10231,11259,12123, +chr1 120195090 120207923 NM_011650 0 - 120197380 120207643 0 6 2524,80,116,97,94,346, 0,6177,6686,10231,11259,12487, +chr1 120218419 120230408 NM_026472 0 + 120218469 120229518 0 7 155,144,109,212,57,135,1082, 0,1739,5782,7510,8763,10501,10907, +chr1 120285634 120506039 NM_001359342 0 + 120316300 120503571 0 38 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,159,108,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,136239,142920,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359330 0 + 120316300 120503571 0 40 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,108,104,24,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,142920,150208,152617,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359337 0 + 120316300 120503571 0 40 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,24,108,27,159,108,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,142920,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001293301 0 + 120316300 120503571 0 36 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,159,104,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,136239,150208,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359341 0 + 120316300 120503571 0 38 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,108,104,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,142920,150208,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359336 0 + 120316300 120503571 0 40 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,24,108,27,159,104,24,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,150208,152617,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359338 0 + 120316300 120503571 0 39 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,104,24,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,150208,152617,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359335 0 + 120316300 120503571 0 40 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,24,108,27,159,108,63,104,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,142920,147077,150208,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359346 0 + 120316300 120503571 0 38 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359343 0 + 120316300 120503571 0 39 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,63,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,147077,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359328 0 + 120316300 120503571 0 42 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,24,108,27,159,108,63,104,24,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,142920,147077,150208,152617,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359331 0 + 120316300 120503571 0 41 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,24,108,27,159,108,63,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,142920,147077,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359347 0 + 120400448 120503571 0 41 464,479,79,104,92,76,98,68,153,74,93,117,136,71,60,78,168,50,171,24,108,27,159,108,104,24,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,142920,150208,152617,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_029709 0 + 120316300 120503571 0 37 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,159,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,136239,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359340 0 + 120316300 120503571 0 38 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,104,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,150208,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001293300 0 + 120316300 120503571 0 41 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,24,108,27,159,108,104,24,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,142920,150208,152617,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359334 0 + 120316300 120503571 0 40 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,108,63,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,142920,147077,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359329 0 + 120316300 120503571 0 41 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,108,63,104,24,245,67,164,79,144,144,107,117,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,142920,147077,150208,152617,154044,156335,158807,162029,162955,170928,171953,176085,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359339 0 + 120316300 120503571 0 39 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,108,27,159,108,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,132769,134263,136239,142920,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120285634 120506039 NM_001359345 0 + 120316300 120503571 0 39 464,479,79,104,92,76,98,68,153,74,93,146,136,71,60,78,168,50,171,24,108,27,159,104,24,245,67,164,79,144,144,107,151,244,191,129,207,117,2555, 0,30382,70743,72129,73408,75470,78822,82714,108576,110590,112244,113795,114762,115838,116424,117882,119757,120514,121148,123647,132769,134263,136239,150208,152617,154044,156335,158807,162029,162955,170928,171953,181791,189763,192215,201363,211320,213307,217850, +chr1 120355245 120355842 NR_027901 0 - 120355842 120355842 0 1 597, 0, +chr1 120524521 120581745 NM_023755 0 + 120524617 120574011 0 15 158,152,77,106,107,153,111,92,49,94,91,104,143,52,7781, 0,4297,24356,24924,25771,28423,31063,34035,36814,36953,38171,40686,41444,47630,49443, +chr1 120730637 120950196 NM_001081125 0 - 120732361 120898752 0 14 4117,337,282,165,150,135,123,217,202,186,203,106,167,318, 0,6193,7855,10290,11856,14322,19197,20380,21375,32511,33918,56235,167979,219241, +chr1 120850796 120850876 NR_105764 0 + 120850876 120850876 0 1 80, 0, +chr1 121312039 121318825 NM_008381 0 - 121313898 121317663 0 2 2635,1622, 0,5164, +chr1 121366881 121401359 NM_022327 0 - 121368282 121380184 0 5 1521,178,209,163,206, 0,5590,7610,13189,34272, +chr1 121422730 121425560 NM_146103 0 + 121423087 121424140 0 1 2830, 0, +chr1 121426056 121432742 NR_126486 0 - 121432742 121432742 0 4 2117,45,149,103, 0,5498,6282,6583, +chr1 121441609 121545577 NM_145506 0 - 121445705 121539233 0 25 4163,131,42,75,91,65,129,98,164,116,40,28,107,170,70,89,88,121,53,45,79,43,105,182,216, 0,4854,5489,9173,10019,22763,25012,27773,33881,53972,55165,60195,62954,64084,70313,71368,72331,72521,75134,75642,76853,78893,88512,97444,103752, +chr1 121491400 121545577 NM_001113416 0 - 121492455 121539233 0 17 1236,116,40,28,107,170,70,89,88,121,53,45,79,43,105,182,216, 0,4181,5374,10404,13163,14293,20522,21577,22540,22730,25343,25851,27062,29102,38721,47653,53961, +chr1 121554669 121733648 NM_019933 0 - 121556407 121699037 0 27 1825,136,149,129,147,62,91,167,157,57,84,160,159,126,69,173,64,89,88,121,53,45,79,43,108,155,170, 0,9421,17456,20662,21956,24391,24612,26374,29517,33508,33653,34657,48062,49683,57854,63771,67940,83262,85259,106938,107336,107785,114956,115136,125389,144230,178809, +chr1 121804475 121809760 NM_175106 0 - 121806588 121807524 0 2 3256,51, 0,5234, +chr1 121819916 121893809 NM_001115074 0 - 121820095 121891787 0 24 288,96,93,92,159,132,108,81,128,106,99,90,88,109,112,118,160,104,101,99,87,101,186,54, 0,2221,4274,7549,9434,10742,11181,12751,13902,22443,24712,26331,27710,30261,30562,30808,32309,38532,58374,61390,61676,66090,71732,73839, +chr1 121903556 121960109 NM_001311077 0 + 121903833 121959859 0 13 352,115,108,104,98,133,154,61,70,92,127,42,415, 0,15178,24584,29355,36471,37651,39679,46694,47292,48405,49414,54914,56138, +chr1 121903556 121960109 NM_001012322 0 + 121903833 121959859 0 14 352,115,45,108,104,98,133,154,61,70,92,127,42,421, 0,15178,15486,24584,29355,36471,37651,39679,46694,47292,48405,49414,54914,56132, +chr1 121963953 121970357 NM_019432 0 - 121964286 121970309 0 2 948,69, 0,6335, +chr1 122009856 122017673 NM_007830 0 - 122010036 122017530 0 4 254,63,118,152, 0,3106,6615,7665, +chr1 122009856 122017496 NM_001037999 0 - 122010036 122017491 0 4 254,63,118,158, 0,3106,6615,7482, +chr1 122017763 122084766 NM_001172074 0 + 122047191 122084761 0 5 624,145,51,38,149, 0,29416,39419,44948,66854, +chr1 122017763 122084766 NM_028439 0 + 122047191 122084694 0 6 31,145,51,38,82,149, 0,29416,39419,44948,50214,66854, +chr1 122122992 122161857 NM_133186 0 - 122124223 122140836 0 5 1513,165,528,500,49, 0,7826,15016,17352,38816, +chr1 122122992 122167659 NM_001085409 0 - 122124223 122140836 0 6 1513,165,528,500,277,145, 0,7826,15016,17352,43567,44522, +chr1 122237158 122239751 NM_207233 0 + 122237694 122239151 0 2 1220,780, 0,1813, +chr1 122371114 122401601 NM_010766 0 - 122371235 122401354 0 17 252,177,45,99,45,63,99,36,99,108,45,45,99,36,219,102,356, 0,2016,2828,3314,4806,10087,10236,11151,11294,13609,13994,16375,17494,19082,19506,20203,30131, +chr1 122499063 122504568 NM_010133 0 + 122499609 122503766 0 2 1435,1119, 0,4386, +chr1 122983981 123017552 NR_038008 0 + 123017552 123017552 0 5 152,49,104,157,1118, 0,11634,26353,29904,32453, +chr1 122983981 123017552 NR_110450 0 + 123017552 123017552 0 3 152,49,1118, 0,11634,32453, +chr1 123200929 123224255 NM_001271531 0 - 123202482 123216417 0 6 1595,100,167,125,309,158, 0,2511,2787,7848,15244,23168, +chr1 123200929 123229166 NM_178082 0 - 123202482 123216417 0 6 1595,100,167,125,376,98, 0,2511,2787,7848,15244,28139, +chr1 123200929 123224601 NM_001271532 0 - 123202482 123208822 0 5 1595,100,167,125,334, 0,2511,2787,7848,23338, +chr1 123200929 123224601 NM_133748 0 - 123202482 123216417 0 6 1595,100,167,125,376,334, 0,2511,2787,7848,15244,23338, +chr1 123200929 123224601 NM_001357251 0 - 123202482 123216417 0 6 1595,100,167,125,309,334, 0,2511,2787,7848,15244,23338, +chr1 123327643 123403037 NM_001025156 0 + 123327792 123397820 0 24 191,114,95,112,99,57,101,37,93,51,87,117,63,74,82,66,54,63,109,83,38,85,114,5271, 0,3466,6729,10715,14573,17157,25004,30397,30820,31166,32032,44965,46768,49748,50929,51534,52220,55536,60055,61838,63329,65917,68141,70123, +chr1 123327643 123403037 NM_029955 0 + 123327792 123397820 0 24 191,114,95,112,99,57,101,37,93,48,87,117,63,74,82,66,54,63,109,83,38,85,114,5271, 0,3466,6729,10715,14573,17157,25004,30397,30820,31169,32032,44965,46768,49748,50929,51534,52220,55536,60055,61838,63329,65917,68141,70123, +chr1 123406349 123425042 NM_010483 0 - 123406964 123424766 0 2 951,1053, 0,17640, +chr1 123450411 123464557 NM_025860 0 - 123450572 123464452 0 13 304,178,57,114,153,162,140,315,101,136,111,288,190, 0,1381,1856,3570,4576,5331,6297,7446,7855,8224,10658,12046,13956, +chr1 124101721 124148757 NR_151524 0 + 124148757 124148757 0 6 112,108,99,90,191,1009, 0,23667,26982,43865,45192,46027, +chr1 125228714 125942136 NM_199021 0 - 125230825 125942020 0 26 2246,74,73,59,100,55,195,70,99,48,122,48,92,108,39,124,98,155,121,82,53,75,95,96,115,188, 0,4686,8967,9182,9479,20496,21274,35460,35637,44489,45989,52147,52784,66383,70695,79573,91475,100793,113063,153756,153935,318150,354083,522028,572924,713234, +chr1 127289481 127332304 NM_023735 0 - 127290571 127331905 0 12 1186,84,126,93,174,144,108,96,111,125,56,443, 0,2163,4202,4547,10488,12940,14387,15615,18359,23351,25344,42380, +chr1 127289481 127332304 NM_001205385 0 - 127290571 127331905 0 13 1186,84,126,93,174,144,108,96,111,125,56,173,78, 0,2163,4202,4547,10488,12940,14387,15615,18359,23351,25344,42380,42745, +chr1 127289481 127332304 NM_001205386 0 - 127290571 127331905 0 13 1186,84,126,93,174,144,108,96,111,125,56,173,75, 0,2163,4202,4547,10488,12940,14387,15615,18359,23351,25344,42380,42748, +chr1 127457171 127492411 NM_001356294 0 + 127457288 127487685 0 16 223,91,142,144,63,82,191,82,88,65,105,160,91,155,97,922, 0,1680,1905,5873,7952,9952,11718,14071,15577,18668,23858,24479,26770,29216,30438,34318, +chr1 127457578 127492411 NM_028787 0 + 127457821 127487685 0 16 283,91,142,144,63,82,191,82,88,65,105,160,91,155,97,922, 0,1273,1498,5466,7545,9545,11311,13664,15170,18261,23451,24072,26363,28809,30031,33911, +chr1 127573572 127770438 NM_027677 0 + 127573913 127769461 0 2 1197,1492, 0,195374, +chr1 127764198 127808791 NM_145100 0 - 127769912 127808467 0 3 5950,138,376, 0,42769,44217, +chr1 127764198 127807964 NM_001311090 0 - 127769912 127807001 0 3 5950,138,85, 0,42769,43681, +chr1 127764198 127809505 NM_001311089 0 - 127769912 127807001 0 3 5950,138,55, 0,42769,45252, +chr1 127810212 128727209 NM_001081756 0 - 127811319 128592331 0 17 1386,137,315,79,178,3740,192,120,39,69,153,88,134,64,74,129,316, 0,63290,67747,100935,109397,110640,120137,188908,196573,210407,308973,344755,468416,534818,615046,782050,916681, +chr1 127810212 128727209 NM_176957 0 - 127811581 128592331 0 13 1386,315,79,120,39,69,153,88,134,64,74,129,316, 0,67747,100935,188908,196573,210407,308973,344755,468416,534818,615046,782050,916681, +chr1 127810212 128389504 NM_172484 0 - 127811319 128345033 0 15 1386,137,315,79,178,3740,192,120,39,69,153,88,134,64,380, 0,63290,67747,100935,109397,110640,120137,188908,196573,210407,308973,344755,468416,534818,578912, +chr1 129101562 129379549 NM_145128 0 + 129203352 129379302 0 18 442,50,383,162,77,90,72,162,170,135,134,134,150,147,117,75,158,446, 0,44804,101648,115618,160162,161417,177935,179782,182357,185758,192521,207141,241256,254850,264206,266515,274479,277541, +chr1 129386918 129574598 NM_028135 0 - 129388176 129574206 0 8 1319,142,112,97,92,44,120,591, 0,5376,9842,29003,60984,62419,178309,187089, +chr1 129625989 129664141 NM_001033041 0 + 129626062 129662922 0 10 130,45,97,50,237,94,96,173,99,1282, 0,9138,10530,16363,19576,24375,28591,30246,36467,36870, +chr1 129650193 129670631 NR_045298 0 - 129670631 129670631 0 2 337,127, 0,20311, +chr1 129670740 129701414 NM_028399 0 + 129670804 129700136 0 9 222,82,129,61,63,46,164,71,2676, 0,937,17441,19194,21091,23677,25226,27442,27998, +chr1 129711847 129736867 NM_011737 0 - 129711847 129736867 0 10 67,698,147,2421,44,260,73,91,113,22, 0,1964,5116,6706,13785,15000,17453,19264,23168,24998, +chr1 129765349 129840453 NM_178690 0 + 129765388 129839187 0 24 57,56,76,133,79,120,166,100,82,69,74,93,167,90,173,55,372,138,228,97,104,116,103,1503, 0,152,5307,20383,22245,32806,34899,41078,46866,49448,50795,55955,56502,58687,59176,61617,61934,65644,68565,69216,69425,69802,70273,73601, +chr1 129850755 129999624 NM_001285945 0 - 129851543 129999549 0 21 887,132,391,111,143,102,92,198,406,150,180,120,120,117,172,86,232,179,19,168,80, 0,2358,5531,6580,9582,10884,13699,18768,21960,33818,38621,42674,45162,61864,63379,78670,82219,86639,103803,137664,148789, +chr1 129850755 129999578 NM_001357573 0 - 129851543 129988580 0 21 887,132,391,111,143,102,92,198,406,150,180,120,120,117,172,86,232,179,19,168,1227, 0,2358,5531,6580,9582,10884,13699,18768,21960,33818,38621,42674,45162,61864,63379,78670,82219,86639,103803,137664,147596, +chr1 129850755 129999048 NM_027678 0 - 129851543 129988580 0 21 887,132,391,111,143,102,92,198,406,150,180,120,120,117,172,86,232,179,19,168,219, 0,2358,5531,6580,9582,10884,13699,18768,21960,33818,38621,42674,45162,61864,63379,78670,82219,86639,103803,137664,148074, +chr1 129999882 130134312 NM_181750 0 + 130049805 130133335 0 27 178,209,211,42,90,115,79,60,141,109,96,38,51,227,255,152,102,297,124,155,152,104,173,145,83,85,1339, 0,48438,49883,58896,59463,64587,65673,71643,71786,75577,75781,78411,78532,78680,81094,83452,87332,90154,93668,107899,113095,118294,120163,128017,131760,132236,133091, +chr1 130038563 130134315 NM_001357482 0 + 130049805 130133335 0 27 106,209,211,42,90,115,79,60,141,109,96,38,51,227,255,152,102,297,124,155,152,104,173,145,83,85,1342, 0,9757,11202,20215,20782,25906,26992,32962,33105,36896,37100,39730,39851,39999,42413,44771,48651,51473,54987,69218,74414,79613,81482,89336,93079,93555,94410, +chr1 130098937 130099007 NR_029543 0 + 130099007 130099007 0 1 70, 0, +chr1 130140713 130175955 NM_026390 0 + 130141047 130173672 0 13 416,103,29,119,172,94,55,165,125,103,132,203,2422, 0,8066,11296,11982,14695,15307,16697,18656,22153,25732,28684,30665,32820, +chr1 130140713 130175955 NM_001356529 0 + 130141047 130173672 0 13 416,103,29,119,172,94,58,165,125,103,132,203,2422, 0,8066,11296,11982,14695,15307,16694,18656,22153,25732,28684,30665,32820, +chr1 130181332 130224895 NM_001081078 0 - 130181695 130224880 0 17 581,231,224,135,110,203,199,291,269,1557,646,721,79,103,84,80,661, 0,1700,2735,4195,7167,8871,9370,10317,13710,15083,18996,22800,25761,26779,28299,34303,42902, +chr1 130228151 130256282 NM_001313695 0 - 130230057 130256142 0 16 2082,156,136,162,129,156,108,142,142,151,146,166,250,111,147,247, 0,3188,4155,6541,7775,9710,11836,12722,14297,16794,17350,17729,19858,21885,23938,27884, +chr1 130228151 130256282 NM_008567 0 - 130228511 130256142 0 17 477,140,156,136,162,129,156,108,142,142,151,146,166,250,111,147,247, 0,1942,3188,4155,6541,7775,9710,11836,12722,14297,16794,17350,17729,19858,21885,23938,27884, +chr1 130260283 130313993 NM_177445 0 - 130260810 130313794 0 16 619,72,112,81,43,147,148,135,112,60,81,103,103,93,58,265, 0,2991,3214,4658,5786,8433,10230,12471,15059,23410,25412,27564,41659,49953,51647,53445, +chr1 130308694 130313993 NM_145507 0 - 130308924 130313794 0 4 277,93,58,265, 0,1542,3236,5034, +chr1 130484775 130488876 NM_001356509 0 - 130485419 130488786 0 2 1703,105, 0,3996, +chr1 130484775 130488876 NM_009911 0 - 130485419 130488786 0 2 1703,111, 0,3990, +chr1 131169880 132115855 NM_172485 0 + 131327407 132114757 0 28 297,173,811,249,170,156,198,192,235,116,130,104,195,267,179,134,151,142,116,118,146,160,174,96,83,193,88,1180, 0,157493,322066,339806,355573,394510,404745,485142,486965,502989,543339,549288,642249,647944,678086,829767,843256,886270,889516,891745,907048,915156,916552,916827,919250,921803,936937,944795, +chr1 132285104 132319620 NM_001317361 0 - 132285184 132319535 0 8 202,21,63,86,100,192,186,179, 0,21344,22101,28311,29580,31073,33587,34337, +chr1 132285104 132319620 NM_007827 0 - 132285184 132319535 0 10 202,21,63,147,192,86,100,192,186,179, 0,21344,22101,22865,25521,28311,29580,31073,33587,34337, +chr1 132319400 132334491 NR_151525 0 + 132334491 132334491 0 4 239,68,144,1987, 0,3090,12523,13104, +chr1 132335602 132359321 NM_010016 0 - 132336888 132359246 0 10 1354,21,81,147,192,86,100,192,186,175, 0,8593,9302,10391,13358,17795,19061,20556,22796,23544, +chr1 132473282 132526183 NM_009581 0 - 132473495 132516014 0 12 420,203,90,201,198,183,195,86,100,183,104,71, 0,1180,6143,6694,14658,19953,22101,22454,38453,41589,42638,52830, +chr1 132532497 132558195 NM_007576 0 - 132532782 132553874 0 10 450,176,165,180,192,86,97,183,183,171, 0,780,3148,7013,12108,12463,17404,19960,21211,25527, +chr1 132566778 132578148 NR_028304 0 - 132578148 132578148 0 6 200,127,84,38,72,233, 0,745,4023,7481,7637,11137, +chr1 132585619 132612398 NR_027859 0 - 132612398 132612398 0 16 2106,1069,65,63,130,105,147,208,125,57,75,67,97,126,111,101, 0,7974,9636,10145,10938,11727,12662,13188,16334,17383,17800,18009,18466,19033,25423,26678, +chr1 132585619 132612625 NM_001368843 0 - 132587659 132611133 0 16 2106,180,65,63,130,105,147,208,125,57,75,67,97,126,111,167, 0,8863,9636,10145,10938,11727,12662,13188,16334,17383,17800,18009,18466,19033,25423,26839, +chr1 132585619 132625830 NM_001162415 0 - 132587659 132611133 0 16 2106,65,63,130,105,147,208,125,57,75,67,97,126,111,154,53, 0,9636,10145,10938,11727,12662,13188,16334,17383,17800,18009,18466,19033,25423,29779,40158, +chr1 132588831 132612398 NM_008825 0 - 132594461 132611133 0 15 5831,65,63,130,105,147,208,125,57,75,67,97,126,111,101, 0,6424,6933,7726,8515,9450,9976,13122,14171,14588,14797,15254,15821,22211,23466, +chr1 132593593 132611153 NM_001162416 0 - 132594461 132611133 0 13 1069,65,130,105,147,208,125,57,75,67,97,126,111, 0,1662,2964,3753,4688,5214,8360,9409,9826,10035,10492,11059,17449, +chr1 132613903 132618634 NM_178691 0 + 132614060 132615996 0 2 485,3342, 0,1389, +chr1 132628552 132641199 NM_177604 0 + 132634159 132640440 0 4 248,186,181,2294, 0,5526,9027,10353, +chr1 132662960 132681010 NR_151623 0 + 132681010 132681010 0 4 196,145,165,2322, 0,372,14558,15728, +chr1 132697478 132711317 NM_144960 0 + 132697526 132711230 0 7 87,58,141,339,757,119,242, 0,2317,3641,10469,11689,13092,13597, +chr1 132697478 132711317 NM_001170632 0 + 132697526 132711230 0 7 87,226,141,339,757,119,242, 0,2149,3641,10469,11689,13092,13597, +chr1 132723260 132748826 NM_011082 0 + 132731005 132747473 0 11 124,99,345,654,333,333,193,128,132,59,1449, 0,7689,14813,17751,19643,20529,21754,22307,22804,23047,24117, +chr1 132762353 132777367 NM_026976 0 + 132762436 132777228 0 8 120,333,132,220,152,159,59,316, 0,8271,9245,10186,11976,12406,12676,14698, +chr1 132778650 132783988 NM_053095 0 - 132779031 132783916 0 6 465,75,159,63,194,160, 0,1260,1760,2714,3503,5178, +chr1 132803561 132807873 NM_021380 0 - 132803991 132807803 0 5 508,75,153,66,229, 0,1367,2590,3749,4083, +chr1 132803561 132807873 NM_001311091 0 - 132803991 132807803 0 4 508,75,153,229, 0,1367,2590,4083, +chr1 132829232 132836692 NM_001009940 0 - 132829724 132835818 0 6 588,75,153,63,181,64, 0,2319,3237,6261,6442,7396, +chr1 132829232 132836692 NM_001355135 0 - 132829724 132832604 0 4 588,75,153,64, 0,2319,3237,7396, +chr1 132916421 132921547 NM_010548 0 + 132916488 132920845 0 5 232,60,153,66,795, 0,1119,1484,2644,4331, +chr1 132950277 132994420 NM_008551 0 - 132951668 132994102 0 10 1535,81,86,125,76,127,80,65,140,555, 0,2058,2228,2713,3188,3793,4300,4651,4922,43588, +chr1 133025017 133034811 NM_145508 0 - 133025250 133034733 0 3 1805,112,155, 0,7819,9639, +chr1 133049783 133068811 NM_010709 0 + 133049946 133068511 0 15 219,191,84,91,108,215,118,46,104,150,90,96,121,175,314, 0,1022,1961,2426,4985,7203,8078,10313,11196,11413,11913,13120,14913,17730,18714, +chr1 133049783 133070048 NM_001136070 0 + 133049946 133069948 0 15 219,191,84,91,108,215,118,46,104,150,90,96,121,175,168, 0,1022,1961,2426,4985,7203,8078,10313,11196,11413,11913,13120,14913,17730,20097, +chr1 133072986 133141755 NM_018750 0 - 133075101 133141707 0 6 2268,116,298,111,122,490, 0,4143,4744,5734,35847,68279, +chr1 133072986 133141755 NM_001313731 0 - 133077155 133141707 0 6 2268,116,201,111,122,490, 0,4143,4841,5734,35847,68279, +chr1 133072986 133096762 NM_001311094 0 - 133075101 133096549 0 5 2268,116,298,111,333, 0,4143,4744,5734,23443, +chr1 133151178 133176140 NM_019777 0 - 133151881 133173131 0 22 737,72,107,97,102,40,77,116,76,87,92,65,197,180,111,161,182,130,141,111,89,233, 0,2285,2515,3299,4580,5404,8671,11037,11273,15199,15416,15584,16285,17161,17506,18769,19039,20548,21105,21866,24097,24729, +chr1 133181827 133423938 NM_001081011 0 - 133185933 133421581 0 23 4490,325,147,181,80,225,106,135,78,61,25,28,85,198,102,225,129,216,63,163,193,656,129, 0,7270,11069,13081,15142,25223,31878,34274,35184,39837,46866,48606,51139,59098,60511,64201,70260,71439,78751,126549,151424,239687,241982, +chr1 133424479 133435612 NM_175382 0 + 133425277 133435506 0 4 950,78,125,201, 0,2751,5906,10932, +chr1 133495690 133508577 NM_011924 0 + 133496317 133506322 0 2 1558,2590, 0,10297, +chr1 133534890 133572084 NM_007799 0 + 133558572 133571522 0 10 244,191,157,118,119,200,123,142,99,727, 0,23562,24299,24997,25970,29723,32372,33890,34131,36467, +chr1 133585271 133612016 NM_145509 0 + 133593590 133608274 0 6 141,68,127,216,126,3820, 0,8304,9134,9721,16901,22925, +chr1 133585271 133612016 NM_001311096 0 + 133593590 133608274 0 5 141,68,127,216,3820, 0,8304,9134,9721,22925, +chr1 133640598 133666982 NM_177243 0 + 133647174 133665825 0 21 92,143,140,111,176,165,153,83,148,114,78,96,107,70,93,114,282,55,143,72,1205, 0,6558,8822,9098,9805,11350,12167,12615,13366,14449,14737,15376,17684,18734,18893,19123,19772,20965,21862,23787,25179, +chr1 133693971 133714692 NM_178079 0 + 133693994 133712687 0 13 192,87,233,87,134,120,76,62,79,72,169,100,2129, 0,1201,3699,4331,4906,5325,6657,7192,7498,9504,14640,16496,18592, +chr1 133693974 133718049 NM_001357478 0 + 133693994 133712687 0 14 189,87,233,87,134,120,76,62,79,72,169,100,125,771, 0,1198,3696,4328,4903,5322,6654,7189,7495,9501,14637,16493,18589,23304, +chr1 133724588 133745440 NM_173865 0 + 133727198 133743312 0 11 382,980,108,72,145,147,148,80,135,149,2314, 0,1999,11103,12165,12843,13116,13973,14937,15907,16326,18538, +chr1 133763853 133769464 NM_144875 0 + 133764228 133769157 0 6 134,257,72,182,122,422, 0,242,2656,3403,4790,5189, +chr1 133807034 133832898 NM_175294 0 + 133807310 133827783 0 7 293,50,106,56,153,150,5288, 0,8547,11485,14128,17606,19155,20576, +chr1 133807034 133832898 NM_001145804 0 + 133807310 133827783 0 7 293,50,106,56,153,147,5288, 0,8547,11485,14128,17606,19158,20576, +chr1 133859491 133879549 NM_001177628 0 + 133873517 133878305 0 5 138,395,786,266,1682, 0,13803,14498,15833,18376, +chr1 133867185 133879549 NM_145977 0 + 133873517 133878305 0 5 219,395,786,266,1682, 0,6109,6804,8139,10682, +chr1 133904181 133922261 NM_007923 0 + 133910968 133920228 0 5 336,216,870,117,2132, 0,6778,9988,11745,15948, +chr1 133923197 133964639 NM_172510 0 - 133925062 133964469 0 11 920,95,121,71,148,174,116,166,252,199,400, 0,1832,13919,15237,19685,25759,26928,27438,31095,32539,41042, +chr1 133933359 133964639 NM_001114662 0 - 133935494 133964469 0 10 2191,121,71,148,174,116,166,252,199,400, 0,3757,5075,9523,15597,16766,17276,20933,22377,30880, +chr1 134010123 134036262 NM_008795 0 - 134011512 134019012 0 16 1424,78,91,43,106,98,121,124,63,95,115,57,126,80,149,276, 0,1918,2315,2900,3049,3337,3935,4203,4974,5303,5553,6421,7901,8490,8765,25863, +chr1 134088012 134153959 NM_001311104 0 + 134124798 134153303 0 5 54,120,123,71,686, 0,36748,37478,40831,65261, +chr1 134088012 134153959 NM_001033250 0 + 134124798 134153458 0 4 54,120,123,686, 0,36748,37478,65261, +chr1 134094664 134094761 NR_029777 0 + 134094761 134094761 0 1 97, 0, +chr1 134122890 134153959 NM_001311102 0 + 134124798 134153535 0 6 58,120,123,71,74,686, 0,1870,2600,5953,29107,30383, +chr1 134122890 134153959 NM_001311103 0 + 134125601 134153535 0 5 58,120,123,74,686, 0,1870,2600,29107,30383, +chr1 134122890 134153959 NR_132336 0 + 134153959 134153959 0 5 58,120,123,140,686, 0,1870,2600,29041,30383, +chr1 134195202 134203934 NM_144810 0 + 134195853 134201369 0 5 1027,165,216,102,2759, 0,3899,4314,5103,5973, +chr1 134212701 134230065 NM_028778 0 + 134212806 134228958 0 7 348,121,152,66,120,133,2168, 0,8828,11572,12006,13833,14434,15196, +chr1 134212701 134230065 NM_001195025 0 + 134212806 134228958 0 8 348,121,24,152,66,120,133,2168, 0,8828,10081,11572,12006,13833,14434,15196, +chr1 134252891 134286895 NM_001311107 0 - 134254082 134277731 0 5 1503,136,941,525,417, 0,2588,3960,24342,33587, +chr1 134252891 134287963 NM_178874 0 - 134254082 134287760 0 5 1503,136,941,525,410, 0,2588,3960,24342,34662, +chr1 134252891 134264525 NM_001311108 0 - 134254082 134264301 0 4 1503,136,941,251, 0,2588,3960,11383, +chr1 134314029 134363536 NM_172516 0 + 134314182 134360088 0 13 418,389,664,233,84,177,130,157,133,114,115,135,3636, 0,16646,31859,35634,36608,37779,38407,38872,39416,40864,42423,45460,45871, +chr1 134373943 134402242 NM_001357486 0 + 134374085 134400369 0 14 161,26,173,141,163,110,120,154,72,118,70,230,78,1902, 0,6685,7379,12221,13056,15186,16448,16654,16903,17490,18839,19432,20563,26397, +chr1 134373943 134402242 NM_172517 0 + 134374085 134400369 0 14 161,26,173,141,163,110,120,154,72,118,70,230,192,1902, 0,6685,7379,12221,13056,15186,16448,16654,16903,17490,18839,19432,20563,26397, +chr1 134373943 134402242 NM_001357487 0 + 134387021 134400369 0 15 161,26,56,58,141,163,110,120,154,72,118,70,230,78,1902, 0,6685,7379,8081,12221,13056,15186,16448,16654,16903,17490,18839,19432,20563,26397, +chr1 134402806 134405216 NM_029025 0 + 134404034 134404814 0 2 267,1475, 0,935, +chr1 134406001 134439517 NM_177129 0 - 134412110 134430309 0 23 6213,169,113,187,113,235,71,150,159,121,176,128,151,130,137,176,100,210,96,176,145,161,218, 0,6596,7099,7476,8872,9237,9744,11714,12296,12908,13510,13933,14168,15882,16393,16863,18270,18651,19187,19485,19762,24232,33298, +chr1 134461266 134539435 NM_001160316 0 - 134466996 134539345 0 27 5962,70,132,15,174,123,205,116,223,71,198,102,45,125,148,167,112,144,132,185,112,51,171,123,197,106,181, 0,9080,11596,28661,30794,31836,33075,35409,37281,39108,40351,40794,42313,43693,45067,45621,46085,46840,54699,56235,56822,63182,66995,69478,69934,72296,77988, +chr1 134461266 134603903 NM_001160318 0 - 134466996 134539345 0 27 5962,70,132,15,174,123,205,116,223,71,198,102,125,148,167,112,144,132,185,112,171,123,197,106,181,109,228, 0,9080,11596,28661,30794,31836,33075,35409,37281,39108,40351,40794,43693,45067,45621,46085,46840,54699,56235,56822,66995,69478,69934,72296,77988,100789,142409, +chr1 134461266 134638374 NM_182716 0 - 134466996 134539345 0 30 5962,70,132,153,117,237,15,174,123,223,71,198,102,45,125,148,167,112,144,132,185,112,171,123,197,106,18,181,109,127, 0,9080,11596,18305,19674,23384,28661,30794,31836,37281,39108,40351,40794,42313,43693,45067,45621,46085,46840,54699,56235,56822,66995,69478,69934,72296,73174,77988,100789,176981, +chr1 134461266 134638374 NM_001160317 0 - 134466996 134539345 0 28 5962,70,132,15,174,123,205,116,223,71,198,102,125,148,167,112,144,132,185,112,51,171,123,197,106,181,109,127, 0,9080,11596,28661,30794,31836,33075,35409,37281,39108,40351,40794,43693,45067,45621,46085,46840,54699,56235,56822,63182,66995,69478,69934,72296,77988,100789,176981, +chr1 134625929 134629403 NR_045892 0 + 134629403 134629403 0 3 1093,67,719, 0,2247,2755, +chr1 134776931 134836582 NM_010732 0 + 134833775 134835968 0 2 321,3025, 0,56626, +chr1 134882681 134921993 NM_008575 0 - 134888232 134915431 0 12 6121,81,147,161,100,68,56,134,75,108,78,169, 0,8398,10458,15178,17686,18549,23032,24960,26532,32672,33249,39143, +chr1 134882681 134921993 NR_126506 0 - 134921993 134921993 0 10 6121,81,147,161,100,56,134,78,108,169, 0,8398,10458,15178,17686,23032,24960,26532,32672,39143, +chr1 134882681 134921993 NM_001302804 0 - 134888232 134901260 0 11 6121,81,147,161,100,39,56,134,78,108,169, 0,8398,10458,15178,17686,18549,23032,24960,26532,32672,39143, +chr1 134882681 134921993 NM_001302803 0 - 134888232 134915431 0 11 6121,81,147,161,100,68,56,134,75,108,169, 0,8398,10458,15178,17686,18549,23032,24960,26532,32672,39143, +chr1 134882681 134927164 NM_001302802 0 - 134888232 134915431 0 11 6121,81,147,161,100,68,56,134,78,108,53, 0,8398,10458,15178,17686,18549,23032,24960,26532,32672,44430, +chr1 134882681 134921993 NM_001302801 0 - 134888232 134915431 0 11 6121,81,147,161,100,68,56,134,78,108,169, 0,8398,10458,15178,17686,18549,23032,24960,26532,32672,39143, +chr1 134942588 135005265 NM_001099276 0 + 134962876 135002735 0 33 412,1018,101,155,121,112,80,64,147,34,196,123,168,112,143,189,94,95,181,108,93,130,137,170,157,110,202,125,118,82,107,129,2716, 0,20200,24306,25162,25590,28499,28767,29799,31314,32207,33632,34949,38806,39489,40925,42176,43954,44159,44669,45549,46260,47644,48686,52619,53141,53593,54713,55318,56268,57341,57789,58975,59961, +chr1 135027742 135036377 NM_133819 0 + 135028323 135033464 0 2 2450,3138, 0,5497, +chr1 135142673 135200012 NM_001160268 0 + 135156631 135195612 0 23 46,81,115,105,73,101,203,483,517,69,81,150,96,112,140,130,107,177,168,134,146,124,3727, 0,12912,13945,17700,18564,20469,23903,26112,27761,34242,35686,36020,37174,38783,39150,41373,41677,46255,47609,47857,48466,52823,53612, +chr1 135142673 135200012 NM_182930 0 + 135156631 135195612 0 27 46,81,115,105,73,101,143,483,517,87,54,81,69,81,150,96,112,140,150,130,107,177,168,134,146,124,3727, 0,12912,13945,17700,18564,20469,23963,26112,27761,28696,29715,33276,34242,35686,36020,37174,38783,39150,40150,41373,41677,46255,47609,47857,48466,52823,53612, +chr1 135146428 135166385 NR_037984 0 - 135166385 135166385 0 4 1565,1052,110,385, 0,6256,8593,19572, +chr1 135206399 135219603 NM_026680 0 + 135206463 135218227 0 5 89,92,179,64,1418, 0,9458,10330,11168,11786, +chr1 135223788 135226299 NM_178260 0 + 135223826 135226222 0 2 129,367, 0,2144, +chr1 135247142 135256900 NM_031193 0 + 135247213 135256715 0 9 232,151,124,119,197,120,136,99,347, 0,3561,4236,4929,5819,7838,8372,8768,9411, +chr1 135247250 135256896 NM_031192 0 + 135247282 135256715 0 9 124,151,124,119,197,120,145,99,343, 0,3453,4128,4821,5711,7730,8264,8660,9303, +chr1 135260148 135276895 NM_175443 0 + 135260340 135275966 0 8 447,260,123,143,84,146,74,1002, 0,2004,5178,9563,10955,13334,14877,15745, +chr1 135278876 135320789 NM_011439 0 - 135280227 135289847 0 14 1625,217,144,97,110,163,83,115,69,173,87,112,199,337, 0,2157,3166,3694,3885,4466,4784,6149,6629,7024,8259,8429,10773,41576, +chr1 135500447 135506857 NM_009227 0 - 135500597 135506794 0 5 206,79,63,27,117, 0,2630,5026,5847,6293, +chr1 135516438 135557976 NM_001357228 0 - 135518119 135543966 0 17 1940,68,167,328,83,504,99,60,111,81,117,204,124,120,194,466,163, 0,2255,3122,4621,5986,6905,13900,16135,17487,18671,18971,19178,20750,25865,27474,34111,41375, +chr1 135516447 135557976 NM_001276767 0 - 135518119 135543966 0 18 1931,68,167,328,83,504,99,60,111,81,117,204,124,120,194,60,54,163, 0,2246,3113,4612,5977,6896,13891,16126,17478,18662,18962,19169,20741,25856,27465,34102,35474,41366, +chr1 135516447 135557976 NM_144530 0 - 135518119 135543966 0 17 1931,68,167,328,83,504,99,60,111,81,117,204,124,120,194,60,163, 0,2246,3113,4612,5977,6896,13891,16126,17478,18662,18962,19169,20741,25856,27465,34102,41366, +chr1 135552455 135557462 NM_001166552 0 - 135553231 135556174 0 1 5007, 0, +chr1 135575605 135586685 NM_001159649 0 - 135576354 135585483 0 6 1607,71,105,104,184,300, 0,3954,4509,4977,9792,10780, +chr1 135575605 135586593 NM_172842 0 - 135576354 135585483 0 6 1607,71,105,104,184,202, 0,3954,4509,4977,9792,10786, +chr1 135599250 135650324 NM_213616 0 - 135603267 135649858 0 20 4323,177,108,212,214,192,107,88,180,232,242,243,215,162,36,129,126,258,198,659, 0,12380,13831,15114,16026,16650,23783,25049,26023,27043,27695,28989,29552,32374,33942,35316,35864,36489,37240,50415, +chr1 135599250 135650324 NM_001167949 0 - 135608210 135649858 0 21 4323,191,177,108,212,214,192,107,88,180,232,242,243,215,162,36,129,126,258,198,659, 0,8958,12380,13831,15114,16026,16650,23783,25049,26023,27043,27695,28989,29552,32374,33942,35316,35864,36489,37240,50415, +chr1 135623134 135623222 NR_105868 0 - 135623222 135623222 0 1 88, 0, +chr1 135793770 135803750 NM_054076 0 - 135794376 135803611 0 7 777,96,203,159,133,280,243, 0,1148,3794,4801,6456,7783,9737, +chr1 135793770 135804576 NM_001160420 0 - 135794376 135803611 0 7 777,96,203,133,280,104,28, 0,1148,3794,6456,7783,9737,10778, +chr1 135793770 135803750 NM_001160421 0 - 135794376 135803611 0 6 777,96,203,133,280,243, 0,1148,3794,6456,7783,9737, +chr1 135797412 135803750 NM_001160422 0 - 135797510 135803611 0 5 355,159,133,280,243, 0,1159,2814,4141,6095, +chr1 135806881 135817978 NM_054077 0 - 135809182 135811982 0 3 2477,977,147, 0,4140,10950, +chr1 135933830 135944857 NM_021355 0 + 135936800 135943202 0 3 329,987,1807, 0,2962,9220, +chr1 135971441 135975732 NM_007570 0 - 135973945 135975630 0 2 2839,244, 0,4047, +chr1 136007818 136048117 NM_001284524 0 + 136035324 136047956 0 11 121,132,30,202,57,166,125,124,186,108,329, 0,27399,29018,31998,32769,34010,34349,35320,37094,38134,39970, +chr1 136007818 136048117 NM_027979 0 + 136035324 136047925 0 12 121,132,30,202,57,166,125,124,186,108,127,437, 0,27399,29018,31998,32769,34010,34349,35320,37094,38134,39237,39862, +chr1 136007818 136048117 NM_001284525 0 + 136035324 136047925 0 12 121,168,30,202,57,166,125,124,186,108,127,437, 0,27363,29018,31998,32769,34010,34349,35320,37094,38134,39237,39862, +chr1 136078732 136086608 NM_001374626 0 + 136078833 136086189 0 10 120,30,205,57,151,122,124,183,117,551, 0,624,1341,1968,2993,4349,5714,6339,7041,7325, +chr1 136078980 136086608 NM_007695 0 + 136079080 136086189 0 10 149,30,205,57,151,122,124,183,117,551, 0,376,1093,1720,2745,4101,5466,6091,6793,7077, +chr1 136090024 136097809 NM_016749 0 + 136090080 136096988 0 11 279,135,168,89,196,140,160,137,187,53,285, 0,366,1129,3522,3903,4282,4953,6266,6502,6947,7500, +chr1 136090024 136097814 NM_001357515 0 + 136090080 136096988 0 11 279,135,168,89,196,140,160,137,187,53,293, 0,366,1129,3522,3903,4282,4953,6266,6502,6947,7497, +chr1 136095791 136132034 NM_001282945 0 - 136099527 136130932 0 3 4376,432,230, 0,34800,36013, +chr1 136095791 136131433 NM_001291928 0 - 136099527 136131310 0 2 4376,194, 0,35448, +chr1 136095791 136132034 NM_001291930 0 - 136099527 136100082 0 2 4376,230, 0,36013, +chr1 136095791 136132034 NM_001008533 0 - 136099527 136130932 0 2 4376,1443, 0,34800, +chr1 136095791 136132034 NM_001039510 0 - 136099527 136130932 0 3 4376,398,230, 0,34800,36013, +chr1 136185171 136186338 NR_160520 0 - 136186338 136186338 0 1 1167, 0, +chr1 136186580 136189125 NM_031189 0 + 136186632 136188372 0 3 523,82,875, 0,1089,1670, +chr1 136193359 136229505 NM_001144855 0 - 136195654 136229100 0 29 2046,111,178,69,176,98,176,27,63,201,82,94,164,134,36,241,209,109,92,132,84,135,147,192,90,75,165,102,639, 0,2243,2508,3687,6822,7504,12793,14746,15274,15753,16304,16847,19832,20280,20655,21025,22432,24278,26219,27296,27728,29701,30033,30475,31217,31510,31861,32363,35507, +chr1 136193359 136241293 NM_001374777 0 - 136195355 136229100 0 29 2046,178,69,176,98,176,27,63,201,82,94,164,134,36,241,209,109,92,132,84,135,147,192,90,75,165,102,639,124, 0,2508,3687,6822,7504,12793,14746,15274,15753,16304,16847,19832,20280,20655,21025,22432,24278,26219,27296,27728,29701,30033,30475,31217,31510,31861,32363,35507,47810, +chr1 136242672 136258583 NR_151737 0 - 136258583 136258583 0 9 2099,156,81,163,181,157,168,90,245, 0,3987,6259,6879,8565,9464,14661,15438,15666, +chr1 136242673 136258576 NM_020588 0 - 136244585 136258447 0 8 2098,156,81,181,157,168,90,238, 0,3986,6258,8564,9463,14660,15437,15665, +chr1 136242673 136258576 NM_001042485 0 - 136244585 136258447 0 8 2098,156,81,181,154,168,90,238, 0,3986,6258,8564,9463,14660,15437,15665, +chr1 136282516 136287560 NM_173771 0 + 136282794 136287508 0 4 288,131,157,1194, 0,1935,2744,3850, +chr1 136302357 136308315 NM_001355133 0 + 136302615 136307656 0 9 273,54,73,107,130,84,86,100,832, 0,628,818,1265,1793,2623,3820,4712,5126, +chr1 136302357 136308315 NM_028057 0 + 136302615 136307656 0 9 273,150,73,107,130,84,86,100,832, 0,532,818,1265,1793,2623,3820,4712,5126, +chr1 136302357 136308315 NR_149307 0 + 136308315 136308315 0 9 273,150,73,107,130,671,86,100,832, 0,532,818,1265,1793,2036,3820,4712,5126, +chr1 136311954 136329927 NM_028320 0 + 136319591 136328235 0 8 208,235,117,172,187,188,194,1821, 0,7543,8580,9373,10531,12704,15679,16152, +chr1 136312240 136329927 NM_001306069 0 + 136319591 136328235 0 8 326,235,117,172,187,188,194,1821, 0,7257,8294,9087,10245,12418,15393,15866, +chr1 136352107 136387450 NM_153128 0 + 136355048 136386035 0 12 135,201,154,218,150,115,107,196,159,99,106,1542, 0,2935,8296,12120,16863,20257,28216,30187,31479,32113,33485,33801, +chr1 136352107 136387450 NM_001311136 0 + 136355048 136386035 0 12 135,201,154,218,150,115,107,196,159,99,187,1542, 0,2935,8296,12120,16863,20257,28216,30187,31479,32113,33404,33801, +chr1 136391215 136404466 NM_145510 0 + 136391260 136402898 0 2 171,1814, 0,11437, +chr1 136437517 136446259 NM_001291015 0 - 136437561 136438635 0 4 1225,97,300,210, 0,5685,5943,8532, +chr1 136437517 136446259 NM_001145300 0 - 136437561 136443599 0 3 1225,300,210, 0,5943,8532, +chr1 136456754 136529455 NM_152895 0 + 136456915 136527951 0 27 365,78,123,171,135,97,110,159,120,159,182,163,120,195,182,125,151,115,356,139,180,159,486,112,155,321,1642, 0,24976,27744,28599,33151,35622,37405,38882,40456,42272,44264,45535,47510,48687,53010,53709,55740,56011,57514,59382,60665,61757,64533,67087,68420,70255,71059, +chr1 136543188 136649726 NM_009307 0 + 136637428 136644258 0 10 224,209,204,167,120,168,168,118,134,5675, 0,17178,94223,95198,96898,97348,97772,99118,100142,100863, +chr1 136605876 136649726 NM_001355726 0 + 136637428 136644258 0 9 125,204,167,120,168,168,118,134,5675, 0,31535,32510,34210,34660,35084,36430,37454,38175, +chr1 136651242 136852517 NM_001368827 0 - 136656985 136852359 0 24 5830,51,54,105,145,17,42,113,190,189,91,183,126,83,201,113,140,80,75,145,160,119,131,449, 0,17332,18760,21710,22649,27485,79769,81119,81312,83187,87977,111112,118141,119273,121299,124967,131757,132609,136090,137492,138684,141677,147712,200826, +chr1 136651242 136852517 NM_001368829 0 - 136656985 136792956 0 23 5830,51,54,105,145,17,42,113,190,189,91,183,126,83,201,113,140,80,75,145,160,119,449, 0,17332,18760,21710,22649,27485,79769,81119,81312,83187,87977,111112,118141,119273,121299,124967,131757,132609,136090,137492,138684,141677,200826, +chr1 136651242 136852517 NM_001081307 0 - 136662519 136852359 0 25 5830,181,51,54,105,145,17,42,113,190,189,91,183,126,83,201,113,140,80,75,145,160,119,131,449, 0,11231,17332,18760,21710,22649,27485,79769,81119,81312,83187,87977,111112,118141,119273,121299,124967,131757,132609,136090,137492,138684,141677,147712,200826, +chr1 136676299 136700419 NR_015606 0 - 136700419 136700419 0 2 2445,741, 0,23379, +chr1 136842810 136842876 NR_162775 0 - 136842876 136842876 0 1 66, 0, +chr1 136859141 136870756 NM_001278115 0 + 136864366 136870523 0 7 45,172,70,106,99,84,380, 0,5162,6676,8685,9336,9541,11235, +chr1 136859141 136870756 NM_026024 0 + 136864366 136870523 0 7 222,172,70,106,99,84,380, 0,5162,6676,8685,9336,9541,11235, +chr1 136882929 137001853 NM_001033409 0 - 136883512 137001717 0 18 1839,81,161,126,72,72,66,72,69,72,72,69,72,216,72,72,72,348, 0,4252,7516,9631,11300,11832,12961,14125,15347,16847,17105,19338,35422,40699,77268,86532,88874,118576, +chr1 137005074 137029152 NR_153383 0 - 137029152 137029152 0 37 198,136,164,117,129,77,79,88,68,136,161,123,135,77,91,94,48,127,68,211,141,282,267,264,273,276,246,255,264,270,273,49,67,77,68,634,56, 0,421,788,1065,1311,1587,1754,1915,2152,2548,2804,3692,4392,5612,5803,6044,7886,8021,9616,10164,10731,11168,11759,12204,13834,15041,15450,15797,16745,17207,17638,18079,18518,19539,20156,20619,24022, +chr1 137005074 137029152 NM_007955 0 - 137005200 137023649 0 38 198,136,164,117,129,77,79,88,68,136,161,123,135,77,91,94,48,127,68,211,141,282,267,264,273,276,246,255,264,270,273,49,67,43,25,68,634,56, 0,421,788,1065,1311,1587,1754,1915,2152,2548,2804,3692,4392,5612,5803,6044,7886,8021,9616,10164,10731,11168,11759,12204,13834,15041,15450,15797,16745,17207,17638,18079,18518,19539,19591,20156,20619,24022, +chr1 137029276 137041903 NM_177081 0 + 137030378 137039831 0 10 91,174,184,85,77,138,111,155,114,2166, 0,1050,1740,2131,3399,4624,5068,6424,9243,10461, +chr1 137029885 137041903 NM_001356382 0 + 137030378 137039831 0 10 147,174,184,85,77,138,111,155,114,2166, 0,441,1131,1522,2790,4015,4459,5815,8634,9852, +chr1 137043410 137052845 NM_026823 0 + 137043554 137051848 0 7 267,81,74,94,68,71,1047, 0,5637,5959,7342,7574,7879,8388, +chr1 137056826 137064258 NM_134438 0 - 137057456 137064081 0 2 1446,807, 0,6625, +chr1 137150150 137155049 NM_007921 0 - 137150842 137154351 0 9 807,196,117,90,120,96,222,168,124, 0,1351,2401,2660,2897,3205,3431,4041,4775, +chr1 137150150 137155049 NM_001163131 0 - 137150842 137154351 0 9 807,196,117,90,120,96,282,168,124, 0,1351,2401,2660,2897,3205,3431,4041,4775, +chr1 137159275 137180661 NM_001159624 0 - 137159547 137180585 0 10 431,143,225,109,113,114,236,149,141,523, 0,1354,2484,4171,4471,5384,8830,14690,16068,20863, +chr1 137159275 137180661 NM_145417 0 - 137159547 137180585 0 11 431,143,225,109,113,114,236,117,149,141,523, 0,1354,2484,4171,4471,5384,8830,9663,14690,16068,20863, +chr1 137198111 137210314 NM_001360858 0 - 137198494 137202747 0 6 469,111,129,64,104,44, 0,2895,4554,7600,8232,12159, +chr1 137198111 137210314 NM_011590 0 - 137198494 137210296 0 6 469,111,129,64,100,44, 0,2895,4554,7600,8236,12159, +chr1 137198111 137210314 NM_001360857 0 - 137198494 137206407 0 6 469,111,129,64,100,183, 0,2895,4554,7600,8236,12020, +chr1 137221389 137264642 NM_053106 0 + 137221586 137262685 0 3 458,1500,1984, 0,38857,41269, +chr1 137268032 137271640 NM_175259 0 - 137268526 137271538 0 5 541,168,134,172,175, 0,741,1696,2922,3433, +chr1 137278888 137327076 NM_001357577 0 - 137281943 137315874 0 26 3166,77,102,123,134,167,276,129,149,227,160,140,107,99,152,59,101,120,87,89,202,87,62,60,111,232, 0,3615,3907,4372,5062,6199,7001,8226,9184,11824,17732,19921,20976,21912,23509,24205,24447,24640,25676,27081,36925,37679,37980,43612,44619,47956, +chr1 137278888 137327076 NR_151727 0 - 137327076 137327076 0 25 3166,77,102,123,134,167,276,129,149,181,227,160,140,107,99,152,59,101,120,87,89,202,87,62,232, 0,3615,3907,4372,5062,6199,7001,8226,9184,9443,11824,17732,19921,20976,21912,23509,24205,24447,24640,25676,27081,36925,37679,37980,47956, +chr1 137278888 137327076 NM_001357575 0 - 137281943 137323555 0 25 3166,77,102,123,134,167,276,129,149,227,160,140,107,99,152,59,101,120,87,89,202,87,62,118,232, 0,3615,3907,4372,5062,6199,7001,8226,9184,11824,17732,19921,20976,21912,23509,24205,24447,24640,25676,27081,36925,37679,37980,44612,47956, +chr1 137278888 137327076 NM_001357578 0 - 137281943 137303400 0 25 3166,77,102,123,134,167,276,129,149,227,160,140,107,99,152,59,97,120,87,89,202,87,62,118,232, 0,3615,3907,4372,5062,6199,7001,8226,9184,11824,17732,19921,20976,21912,23509,24205,24447,24640,25676,27081,36925,37679,37980,44612,47956, +chr1 137278888 137327076 NM_001357576 0 - 137281943 137315874 0 25 3166,77,102,123,134,167,276,129,149,227,160,140,107,99,152,59,101,120,87,89,202,87,62,111,232, 0,3615,3907,4372,5062,6199,7001,8226,9184,11824,17732,19921,20976,21912,23509,24205,24447,24640,25676,27081,36925,37679,37980,44619,47956, +chr1 137278891 137327068 NM_153774 0 - 137281943 137327007 0 24 3163,77,102,123,134,167,276,129,149,227,160,140,107,99,152,59,101,120,87,89,202,87,62,224, 0,3612,3904,4369,5059,6196,6998,8223,9181,11821,17729,19918,20973,21909,23506,24202,24444,24637,25673,27078,36922,37676,37977,47953, +chr1 137331156 137481932 NM_173437 0 - 137338260 137481897 0 29 7200,198,119,197,72,155,236,160,96,98,169,193,197,131,112,84,78,24,53,171,149,42,435,691,298,139,366,103,801, 0,9054,14351,15315,15990,16206,17592,18225,18613,19465,19854,20111,20554,24067,25764,26111,29142,29335,30126,31259,33061,34276,35052,35900,37579,38153,97769,102617,149975, +chr1 137351179 137351260 NR_049188 0 - 137351260 137351260 0 1 81, 0, +chr1 137494352 137496511 NR_151586 0 + 137496511 137496511 0 2 206,523, 0,1636, +chr1 137616639 137648806 NM_001360782 0 + 137635977 137647697 0 6 131,113,169,130,94,1186, 0,19337,25196,26657,30502,30981, +chr1 137625743 137648806 NR_153810 0 + 137648806 137648806 0 4 108,113,94,1186, 0,10233,21398,21877, +chr1 137625743 137648806 NM_007791 0 + 137635977 137647697 0 6 108,113,169,130,94,1186, 0,10233,16092,17553,21398,21877, +chr1 137662661 137665711 NM_013750 0 + 137663025 137663403 0 2 810,657, 0,2393, +chr1 137695997 137707566 NM_021467 0 + 137699189 137706310 0 9 76,48,32,44,132,90,177,110,377, 0,552,3173,5630,6078,8100,9212,10205,11192, +chr1 137696087 137707566 NM_001112702 0 + 137699189 137706310 0 9 28,48,32,44,132,90,177,110,377, 0,462,3083,5540,5988,8010,9122,10115,11102, +chr1 137715174 137729918 NM_133664 0 + 137715555 137728894 0 10 419,138,883,105,44,73,138,87,75,1030, 0,7157,8566,10117,11091,12302,12485,12927,13276,13714, +chr1 137732910 137748845 NM_011619 0 + 137737451 137748649 0 14 113,52,11,90,36,34,64,117,78,111,110,91,41,242, 0,4527,5567,9221,9564,10388,11375,11647,12477,13016,14377,15018,15362,15693, +chr1 137732910 137748845 NM_001130178 0 + 137737451 137748649 0 15 113,52,11,12,90,36,34,64,117,78,111,119,91,41,242, 0,4527,5567,5681,9221,9564,10388,11375,11647,12477,13016,14368,15018,15362,15693, +chr1 137732910 137748845 NM_001130175 0 + 137732949 137748649 0 14 113,49,35,90,36,34,64,117,78,111,110,91,41,242, 0,4531,7446,9221,9564,10388,11375,11647,12477,13016,14377,15018,15362,15693, +chr1 137732910 137748845 NM_001130181 0 + 137732949 137748649 0 14 113,48,11,90,36,34,64,117,78,111,119,91,41,242, 0,4531,5567,9221,9564,10388,11375,11647,12477,13016,14368,15018,15362,15693, +chr1 137732910 137748845 NM_001130180 0 + 137737451 137748649 0 14 113,52,11,90,36,34,64,117,78,111,119,91,41,242, 0,4527,5567,9221,9564,10388,11375,11647,12477,13016,14368,15018,15362,15693, +chr1 137732910 137748845 NM_001130179 0 + 137732949 137748649 0 15 113,48,11,12,90,36,34,64,117,78,111,119,91,41,242, 0,4531,5567,5681,9221,9564,10388,11375,11647,12477,13016,14368,15018,15362,15693, +chr1 137732910 137748845 NM_001130177 0 + 137737451 137748649 0 14 113,56,37,90,36,34,64,117,78,111,110,91,41,242, 0,4527,7444,9221,9564,10388,11375,11647,12477,13016,14377,15018,15362,15693, +chr1 137732910 137748845 NM_001130174 0 + 137737451 137748649 0 14 113,53,35,90,36,34,64,117,78,111,110,91,41,242, 0,4527,7446,9221,9564,10388,11375,11647,12477,13016,14377,15018,15362,15693, +chr1 137737437 137748838 NM_001130176 0 + 137737451 137748649 0 13 56,37,90,36,34,64,117,78,111,119,91,41,235, 0,2917,4694,5037,5861,6848,7120,7950,8489,9841,10491,10835,11166, +chr1 137767970 137815784 NM_019645 0 - 137772206 137815589 0 14 2256,107,88,187,154,177,156,115,178,208,145,395,107,397, 0,4204,5677,6279,6728,8452,9328,11087,12503,13511,15339,18298,37482,47417, +chr1 137767970 137815784 NM_001313701 0 - 137772206 137815589 0 14 2252,107,88,187,154,177,156,115,178,208,145,395,107,397, 0,4204,5677,6279,6728,8452,9328,11087,12503,13511,15339,18298,37482,47417, +chr1 137850154 137902919 NM_177642 0 - 137850600 137902919 0 27 460,327,300,196,89,303,129,174,300,300,142,125,4485,273,169,114,178,46,45,100,140,123,134,96,125,101,22, 0,992,1980,3120,5361,6123,8409,9491,10180,11085,11714,12487,13098,18328,19768,21156,22311,23093,23340,24650,26287,28254,28789,30636,44189,45010,52743, +chr1 137904795 137931607 NM_001160145 0 + 137915118 137930797 0 6 197,102,92,109,132,963, 0,10287,11439,16399,19178,25849, +chr1 137914577 137931607 NM_025439 0 + 137915118 137930797 0 6 62,102,92,109,132,963, 0,505,1657,6617,9396,16067, +chr1 137914732 137931607 NM_001160146 0 + 137915118 137930797 0 6 93,102,92,109,132,963, 0,350,1502,6462,9241,15912, +chr1 137947380 137947947 NM_001270609 0 + 137947380 137947947 0 1 567, 0, +chr1 137949387 138016399 NM_001081023 0 + 137949477 138015707 0 44 242,106,140,143,153,206,104,146,82,161,226,208,121,115,94,70,133,130,60,107,88,108,53,147,202,159,111,84,57,129,66,92,160,128,97,103,102,125,129,251,86,107,144,866, 0,1768,16110,17823,18099,20696,22256,23916,24818,26668,31404,32481,33873,34513,35492,36209,38887,39776,40449,42070,42652,42959,44267,44554,45361,45721,47789,48668,51759,52637,52973,53591,54206,55269,58055,59167,60099,60472,62337,63114,64796,65525,65859,66146, +chr1 137949387 138016399 NM_014193 0 + 137949477 138015707 0 43 242,106,140,143,153,206,104,146,82,161,226,208,121,115,94,70,133,130,60,107,88,108,53,147,202,159,111,84,129,66,92,160,128,97,103,102,125,129,251,86,92,153,866, 0,1768,16110,17823,18099,20696,22256,23916,24818,26668,31404,32481,33873,34513,35492,36209,38887,39776,40449,42070,42652,42959,44267,44554,45361,45721,47789,48668,52637,52973,53591,54206,55269,58055,59167,60099,60472,62337,63114,64796,65525,65850,66146, +chr1 138024295 138027760 NR_046168 0 - 138027760 138027760 0 4 65,113,164,163, 0,1674,2507,3302, +chr1 138024295 138027760 NR_046167 0 - 138027760 138027760 0 4 68,113,164,163, 0,1674,2507,3302, +chr1 138024295 138027760 NR_046169 0 - 138027760 138027760 0 3 68,113,163, 0,1674,3302, +chr1 138024295 138027760 NR_046170 0 - 138027760 138027760 0 3 65,113,163, 0,1674,3302, +chr1 138027966 138074578 NR_153829 0 + 138074578 138074578 0 36 373,223,183,150,135,171,116,196,190,64,219,82,118,192,200,108,69,233,148,195,102,166,52,58,206,78,114,39,137,181,165,118,171,200,180,3965, 0,13209,13740,16108,16344,16817,17236,17871,19741,20653,20807,21368,21803,22714,24707,26073,26891,27854,28248,28623,28914,30016,30339,30574,31397,31683,33628,35772,37797,38599,39752,40198,40769,41413,42082,42647, +chr1 138027966 138074578 NM_001039472 0 + 138028298 138070668 0 35 373,223,183,150,135,171,116,196,190,64,219,82,118,192,200,108,69,233,148,195,102,166,52,58,206,78,114,39,137,181,165,118,171,200,3965, 0,13209,13740,16108,16344,16817,17236,17871,19741,20653,20807,21368,21803,22714,24707,26073,26891,27854,28248,28623,28914,30016,30339,30574,31397,31683,33628,35772,37797,38599,39752,40198,40769,41413,42647, +chr1 138078362 138109405 NM_001329610 0 - 138078362 138107953 0 23 155,60,103,102,159,177,141,115,138,173,148,155,150,89,136,108,87,130,80,123,65,115,224, 0,932,1534,2479,3667,4161,4875,8913,9122,9726,10317,14482,16312,17737,18557,19155,25131,25967,26462,26627,27059,29503,30819, +chr1 138110098 138130857 NM_028872 0 - 138110902 138130682 0 10 897,685,174,211,54,223,117,125,149,378, 0,2234,6201,6609,7550,11814,12630,13258,13992,20381, +chr1 138155490 138157503 NM_001101516 0 - 138156373 138157450 0 1 2013, 0, +chr1 138164699 138242681 NM_001347109 0 - 138167418 138242014 0 18 3025,119,116,73,221,137,2194,70,35,94,94,140,142,33,84,162,260,806, 0,3408,5627,6678,8415,9071,12183,14689,15744,17786,19777,24757,25157,29161,29619,36172,56614,77176, +chr1 138164699 138242681 NM_001347110 0 - 138167418 138242014 0 17 3025,119,116,73,221,137,2194,70,35,94,94,140,142,84,162,260,806, 0,3408,5627,6678,8415,9071,12183,14689,15744,17786,19777,24757,25157,29619,36172,56614,77176, +chr1 138308492 138312096 NR_024328 0 - 138312096 138312096 0 3 912,514,671, 0,1248,2933, +chr1 138311847 138336797 NM_026500 0 + 138313169 138336593 0 8 153,815,168,90,252,153,129,468, 0,1311,4139,9524,17041,18442,19235,24482, +chr1 138364424 138427396 NM_001287179 0 + 138364534 138424193 0 29 1327,255,88,99,53,31,108,117,116,173,148,64,185,103,164,148,153,127,94,130,101,89,225,182,156,120,75,133,3574, 0,3472,5537,8492,10511,11296,11960,14540,15076,18424,19187,19556,22352,26780,28008,28722,29515,32169,34799,35462,42297,45886,48006,48412,51781,53342,57934,58927,59398, +chr1 138521477 138526968 NM_001160251 0 + 138521862 138524544 0 2 151,5124, 0,367, +chr1 138521477 138526968 NM_177643 0 + 138521862 138524544 0 2 151,5120, 0,371, +chr1 138579972 138587382 NR_045324 0 + 138587382 138587382 0 3 78,67,269, 0,5348,7141, +chr1 138580205 138587382 NR_045325 0 + 138587382 138587382 0 3 75,67,269, 0,5115,6908, +chr1 138592787 138622305 NR_037986 0 + 138622305 138622305 0 5 181,104,108,48,758, 0,9328,28360,28581,28760, +chr1 138740160 138850207 NM_001159769 0 - 138742039 138845380 0 9 2127,148,120,641,142,119,138,63,137, 0,38680,47099,96825,99703,101375,105138,108518,109910, +chr1 138740160 138857025 NM_030676 0 - 138742039 138856867 0 9 2127,148,120,641,142,119,138,63,222, 0,38680,47099,96825,99703,101375,105138,108518,116643, +chr1 139863031 139863118 NR_029795 0 + 139863118 139863118 0 1 87, 0, +chr1 139863215 139863295 NR_029820 0 + 139863295 139863295 0 1 80, 0, +chr1 139959435 140071882 NM_011210 0 - 139961082 140071664 0 30 1920,136,176,123,135,134,91,150,136,158,126,98,37,77,91,110,35,109,61,209,156,135,159,141,216,24,72,24,112,98, 0,3229,5027,5453,8278,9398,10745,15587,17276,17978,19777,20704,20888,25644,25808,26636,29340,30037,31383,36624,38183,44916,48293,49332,50705,52760,54095,63444,112156,112349, +chr1 139959435 140071882 NM_001268286 0 - 139961082 140071664 0 29 1920,136,176,123,135,134,91,150,136,158,126,98,37,77,91,110,35,109,61,209,156,135,159,141,216,24,24,112,98, 0,3229,5027,5453,8278,9398,10745,15587,17276,17978,19777,20704,20888,25644,25808,26636,29340,30037,31383,36624,38183,44916,48293,49332,50705,52760,63444,112156,112349, +chr1 139959435 140071703 NM_001111316 0 - 139961082 140071664 0 32 1920,136,176,123,135,134,91,150,136,158,126,98,37,77,91,110,35,109,61,209,156,135,159,141,216,24,72,141,147,129,24,112, 0,3229,5027,5453,8278,9398,10745,15587,17276,17978,19777,20704,20888,25644,25808,26636,29340,30037,31383,36624,38183,44916,48293,49332,50705,52760,54095,54895,57161,59597,63444,112156, +chr1 140170314 140186039 NM_177397 0 + 140170342 140184537 0 3 110,101,1676, 0,9928,14049, +chr1 140380413 140516334 NM_021605 0 - 140383576 140458336 0 10 3274,114,95,108,109,111,63,141,83,206, 0,14739,18734,31788,32691,48900,50527,60366,77866,135715, +chr1 140380413 140516334 NM_001311148 0 - 140383670 140458336 0 8 3274,108,109,111,63,141,83,206, 0,31788,32691,48900,50527,60366,77866,135715, +chr1 140536671 140578652 NR_040304 0 - 140578652 140578652 0 5 486,66,1160,115,103, 0,13560,16717,37721,41878, +chr1 140721762 140739021 NM_001025565 0 - 140725230 140738558 0 5 3525,203,356,203,637, 0,7516,13157,14687,16622, +chr1 140721762 140744156 NM_010714 0 - 140725230 140743780 0 7 3525,203,356,203,119,72,73, 0,7516,13157,14687,16622,21990,22321, +chr1 140727523 140739021 NM_001042577 0 - 140727943 140738558 0 5 678,203,356,203,637, 0,1755,7396,8926,10861, +chr1 140748555 140753431 NM_001081226 0 - 140748678 140753394 0 3 195,102,274, 0,1592,4602, +chr1 140772848 140773527 NR_138576 0 - 140773527 140773527 0 2 374,36, 0,643, +chr1 140860285 141072619 NM_001166501 0 + 140860445 141066875 0 22 177,65,44,50,120,70,81,54,111,101,46,102,126,102,91,41,69,57,108,86,217,6287, 0,2457,59396,76291,78215,89637,90832,96566,99152,117464,122174,126745,138259,146675,169962,175672,176743,179125,180184,203962,205123,206047, +chr1 140864297 141072619 NM_181347 0 + 140938549 141066875 0 21 108,44,50,120,70,81,54,111,101,46,102,126,102,91,41,69,57,108,86,217,6287, 0,55384,72279,74203,85625,86820,92554,95140,113452,118162,122733,134247,142663,165950,171660,172731,175113,176172,199950,201111,202035, +chr1 140874233 140875823 NR_108103 0 + 140875823 140875823 0 3 226,149,85, 0,435,1505, +chr1 141094830 141273653 NM_133239 0 - 141095148 141273487 0 12 534,127,129,907,166,548,957,183,140,196,579,236, 0,33410,36473,38568,42869,44724,49865,116317,124973,129897,138776,178587, +chr1 141276028 141299429 NR_040455 0 + 141299429 141299429 0 9 72,116,149,61,100,70,126,56,361, 0,1001,1388,12351,18586,19067,19673,22424,23040, +chr1 141304856 141310441 NR_151522 0 + 141310441 141310441 0 3 179,102,219, 0,2200,5366, +chr1 141318959 141349584 NM_172643 0 + 141319727 141344107 0 11 41,1234,208,70,148,130,96,107,106,89,6133, 0,651,6743,7898,9546,15058,16575,17962,19380,20426,24492, +chr1 141351349 141390665 NM_009791 0 + 141351508 141390327 0 28 432,144,1408,105,147,246,68,142,131,176,146,86,222,208,143,129,195,3795,167,88,210,150,192,193,155,177,170,441, 0,1967,2264,6653,6999,8283,9463,13145,13845,14563,15665,15899,16798,18765,19065,19472,21935,22573,27565,30927,32434,33615,34873,35191,35526,36745,37934,38875, +chr1 141398283 141420333 NM_031164 0 + 141398322 141420004 0 12 106,201,186,177,177,180,186,183,201,183,214,384, 0,2054,5059,5866,6382,8750,9141,11275,14580,15465,20636,21666, +chr1 141443640 141456799 NM_015780 0 - 141444276 141456735 0 6 857,183,183,177,195,137, 0,3756,6449,9268,10375,13022, +chr1 141480870 141557583 NM_001374101 0 - 141481353 141557476 0 7 680,183,177,177,195,174,165, 0,9460,13262,37761,38310,43842,76548, +chr1 141480870 141557583 NM_001374102 0 - 141481353 141557476 0 6 680,183,177,195,174,165, 0,9460,37761,38310,43842,76548, +chr1 141594495 141677816 NM_001160303 0 - 141594671 141677745 0 15 373,183,177,174,210,177,177,180,183,174,177,183,177,195,144, 0,3880,33611,34384,35121,35492,38879,41272,41538,42496,55055,56310,76011,76558,83177, +chr1 141594495 141677816 NM_001029977 0 - 141594671 141677745 0 15 373,183,177,174,210,177,177,180,186,174,177,183,177,195,144, 0,3880,33611,34384,35121,35492,38879,41272,41538,42496,55055,56310,76011,76558,83177, +chr1 141594495 141677816 NM_001160304 0 - 141594671 141677745 0 14 373,183,174,210,177,177,180,186,174,177,183,177,195,144, 0,3880,34384,35121,35492,38879,41272,41538,42496,55055,56310,76011,76558,83177, +chr1 141706868 141755276 NM_001025575 0 - 141707399 141755204 0 6 728,183,177,195,174,145, 0,3142,11332,11880,20772,48263, +chr1 141982431 142079988 NM_009888 0 - 141982902 142079853 0 22 668,183,177,177,174,210,177,177,180,183,174,177,183,177,195,174,171,192,77,106,186,247, 0,2803,13015,14953,15730,16482,16853,19540,22637,22903,26578,32732,34016,50292,50841,58076,61800,68614,71405,76691,77096,97310, +chr1 142142294 142510622 NM_001081027 0 + 142142833 142506289 0 28 634,80,100,49,60,75,84,95,181,165,137,64,109,109,150,230,214,106,173,72,135,112,102,84,129,301,85,4445, 0,105490,108736,117231,119807,129390,130635,137283,179475,181110,183091,185652,204478,238407,261982,263666,267103,273148,277370,285035,288143,307242,324664,327877,329011,338301,350257,363883, +chr1 142466752 142552979 NR_040604 0 - 142552979 142552979 0 4 356,47,73,75, 0,24752,51218,86152, +chr1 145450405 145550023 NM_145991 0 - 145455650 145549754 0 17 5282,142,101,162,88,36,58,65,79,99,217,89,53,63,70,106,400, 0,6094,12027,14003,24226,24570,31756,64349,66714,68054,74363,82647,87999,88138,92117,95941,99218, +chr1 145487826 145497067 NM_020025 0 + 145493257 145494526 0 2 646,3932, 0,5309, +chr1 145586478 145596808 NM_001038593 0 + 145588778 145593769 0 4 94,64,177,3171, 0,2299,5698,7159, +chr1 145586697 145596808 NM_001038592 0 + 145586790 145593769 0 4 191,64,177,3171, 0,2080,5479,6940, +chr1 145586744 145596808 NM_023505 0 + 145588778 145593769 0 4 70,64,177,3171, 0,2033,5432,6893, +chr1 145587576 145596808 NM_001038594 0 + 145588778 145593769 0 4 33,64,177,3171, 0,1201,4600,6061, +chr1 145597920 145624181 NM_013835 0 - 145604871 145618135 0 9 7104,147,114,117,138,147,221,601,131, 0,9152,9562,10479,14642,14983,15799,19635,26130, +chr1 145624407 145654596 NM_019562 0 + 145624530 145653858 0 11 199,64,106,126,62,131,64,103,114,99,783, 0,6688,8852,16999,17205,17402,19484,21113,22643,24857,29406, +chr1 145624407 145654596 NM_001159866 0 + 145624530 145653858 0 11 199,64,106,126,62,131,64,103,111,99,783, 0,6688,8852,16999,17205,17402,19484,21113,22646,24857,29406, +chr1 145846467 145851279 NM_009061 0 - 145848809 145851248 0 5 2537,167,62,102,141, 0,2778,3442,3614,4671, +chr1 145985796 146024502 NM_153171 0 - 145986630 146018611 0 6 1017,167,62,70,69,112, 0,2043,28620,32750,37159,38594, +chr1 146091798 146096234 NM_015811 0 - 146092431 146096167 0 5 819,164,62,81,204, 0,1521,3237,3810,4232, +chr1 146366819 146414797 NR_110891 0 - 146414797 146414797 0 4 204,167,73,306, 0,17140,25620,47672, +chr1 146366819 146414797 NM_001290269 0 - 146366819 146392450 0 5 204,167,77,73,306, 0,17140,21535,25620,47672, +chr1 146599812 146622557 NM_022881 0 - 146600941 146622371 0 5 1387,167,62,102,305, 0,3240,20838,21884,22440, +chr1 148342758 148749601 NM_001357571 0 + 148361847 148749247 0 9 449,73,286,191,191,106,237,223,1471, 0,3134,19039,186947,206027,250851,256126,335932,405372, +chr1 148342795 148749602 NM_153539 0 + 148361847 148749247 0 8 412,286,191,191,106,237,223,1472, 0,19002,186910,205990,250814,256089,335895,405335, +chr1 148344816 148749602 NM_001145807 0 + 148361847 148749247 0 8 54,286,191,191,106,237,223,1472, 0,16981,184889,203969,248793,254068,333874,403314, +chr1 148344816 148749601 NM_001357572 0 + 148599039 148749247 0 9 54,286,66,191,191,106,237,223,1471, 0,16981,66778,184889,203969,248793,254068,333874,403314, +chr1 151676748 151808420 NM_008869 0 - 151677190 151779820 0 18 574,158,196,185,240,72,93,138,115,223,137,142,38,114,149,82,99,100, 0,10999,12545,21648,27826,31436,35292,35497,41782,42919,50371,56528,57988,71481,72675,92436,103039,131572, +chr1 151676748 151769569 NM_001305632 0 - 151677190 151769382 0 17 574,158,196,185,240,72,93,138,115,223,137,142,38,114,149,82,196, 0,10999,12545,21648,27826,31436,35292,35497,41782,42919,50371,56528,57988,71481,72675,92436,92625, +chr1 151922002 151947004 NR_015466 0 - 151947004 151947004 0 5 2173,60,226,88,447, 0,9707,12247,16731,24555, +chr1 151947160 151955364 NM_011198 0 + 151947353 151952912 0 10 245,117,144,144,182,84,247,287,148,2862, 0,943,1182,1960,2565,3644,3838,4252,4911,5342, +chr1 152006172 152012078 NR_110420 0 - 152012078 152012078 0 2 1610,135, 0,5771, +chr1 152166546 152181036 NM_001159730 0 + 152175469 152180632 0 4 84,85,146,932, 0,8899,11309,13558, +chr1 152166546 152181036 NM_024458 0 + 152175469 152180632 0 4 72,85,146,932, 0,8899,11309,13558, +chr1 152167810 152193901 NR_040603 0 - 152193901 152193901 0 4 240,188,72,110, 0,1962,24216,25981, +chr1 152208434 152240210 NM_001357579 0 - 152209950 152233574 0 14 1584,108,171,91,129,66,96,141,37,107,96,97,121,391, 0,2186,10724,13490,14191,19007,20194,20963,21753,23124,25053,27218,28931,31385, +chr1 152208440 152240185 NM_001077237 0 - 152209950 152237464 0 13 1578,108,171,91,129,66,141,37,107,96,135,121,366, 0,2180,10718,13484,14185,19001,20957,21747,23118,25047,27212,28925,31379, +chr1 152208440 152240185 NM_145511 0 - 152209950 152237464 0 14 1578,108,171,91,129,66,96,141,37,107,96,135,121,366, 0,2180,10718,13484,14185,19001,20188,20957,21747,23118,25047,27212,28925,31379, +chr1 152239967 152297065 NM_133780 0 + 152240073 152296917 0 52 176,303,105,74,97,104,165,93,81,88,141,92,198,108,227,164,134,149,163,135,141,166,167,153,117,204,185,148,138,132,131,211,144,187,206,62,209,273,149,84,195,132,91,185,69,95,107,96,157,119,96,204, 0,518,2361,5762,9417,10760,11037,13624,14491,14652,15906,16365,17142,19063,20053,20806,21578,21828,23231,24544,25110,27000,28798,29690,30219,30648,30959,31825,32799,34025,35282,36497,37723,38324,39573,39981,40840,42805,43880,44565,46244,47229,47601,49221,50346,50497,51530,53030,53247,54674,56305,56894, +chr1 152296541 152313295 NM_001110146 0 - 152297113 152312703 0 12 670,126,201,157,137,78,69,87,120,123,99,17, 0,1351,1837,2442,2811,4051,4640,6839,11240,12685,16086,16737, +chr1 152296541 152313295 NM_021400 0 - 152297113 152312703 0 13 670,126,201,157,137,78,2286,120,144,120,123,99,17, 0,1351,1837,2442,2811,4051,4640,8076,8737,11240,12685,16086,16737, +chr1 152409631 152840565 NM_001024720 0 - 152410656 152840181 0 107 1392,127,120,351,129,126,114,135,120,63,238,122,138,150,171,171,171,171,171,171,270,82,191,135,214,191,270,135,138,108,165,122,157,128,145,142,137,82,197,279,98,184,125,160,150,132,82,203,114,162,97,188,114,195,151,146,114,174,192,87,114,168,282,162,123,97,176,124,152,177,102,124,155,170,109,282,279,155,127,148,131,195,96,270,128,169,160,113,145,128,96,195,159,114,128,142,276,122,145,264,121,107,172,123,159,71,652, 0,2815,10974,14770,17726,19721,20665,23853,24447,25710,30454,31410,32617,33345,35434,35754,36370,36979,41289,41594,42343,44787,47121,48116,50125,52608,56339,60399,60662,61985,64528,64871,67714,68152,68665,69904,71108,72620,76351,84076,86385,87077,87460,90010,93291,93952,94191,94569,94876,95977,101356,102271,105325,106871,109410,111794,113011,113474,114734,117007,118109,121088,124163,127014,128052,132335,134918,137935,139330,140667,141635,153199,156593,158115,159111,159860,160756,170301,171943,174680,174976,176086,179762,181085,182451,185670,186443,188149,191068,192754,194021,195766,202855,207732,209934,211262,236220,240315,243866,246031,247185,254519,256857,296637,297717,313923,430282, +chr1 152985163 152991225 NR_038011 0 + 152991225 152991225 0 7 601,126,52,179,144,157,1381, 0,870,1668,3493,4168,4425,4681, +chr1 153051250 153052926 NM_001372355 0 + 153051292 153052195 0 1 1676, 0, +chr1 153191615 153211574 NM_001359263 0 + 153206829 153210495 0 14 270,228,170,76,174,126,1070,130,225,122,127,132,174,1333, 0,4890,7068,7344,9434,10148,10681,15136,15467,16232,16446,16657,16976,18626, +chr1 153191615 153211574 NM_001359262 0 + 153198698 153210495 0 14 270,228,170,76,174,126,108,130,225,122,127,132,174,1333, 0,4890,7068,7344,9434,10148,11643,15136,15467,16232,16446,16657,16976,18626, +chr1 153191627 153211575 NM_054102 0 + 153198128 153210495 0 15 258,228,129,170,76,174,126,108,130,225,122,127,132,174,1334, 0,4878,6483,7056,7332,9422,10136,11631,15124,15455,16220,16434,16645,16964,18614, +chr1 153191627 153211575 NM_001039512 0 + 153198128 153210495 0 14 258,228,129,170,76,174,108,130,225,122,127,132,174,1334, 0,4878,6483,7056,7332,9422,11631,15124,15455,16220,16434,16645,16964,18614, +chr1 153191627 153203928 NM_001039511 0 + 153198128 153202305 0 8 258,228,129,170,76,174,126,1632, 0,4878,6483,7056,7332,9422,10136,10669, +chr1 153214828 153275565 NM_025819 0 - 153215588 153270690 0 20 890,65,67,132,188,149,139,164,146,94,189,102,130,60,688,56,84,87,99,139, 0,2880,4609,11684,16618,20921,23737,26910,29507,33381,35256,36096,37717,39877,43072,45092,52401,54335,55808,60598, +chr1 153275671 153305313 NM_001357570 0 + 153290438 153305064 0 15 389,111,114,65,130,124,80,272,213,191,79,167,63,127,502, 0,5252,7186,10974,12264,14045,14705,19684,21358,23506,24535,25343,26436,28921,29140, +chr1 153275671 153305313 NM_026876 0 + 153276006 153305064 0 15 561,111,114,65,130,124,80,244,213,191,79,167,63,127,502, 0,5252,7186,10974,12264,14045,14705,19712,21358,23506,24535,25343,26436,28921,29140, +chr1 153275671 153305313 NM_001357569 0 + 153276006 153305064 0 14 561,111,114,65,130,124,80,244,213,191,79,167,127,502, 0,5252,7186,10974,12264,14045,14705,19712,21358,23506,24535,25343,28921,29140, +chr1 153289522 153289580 NR_106150 0 + 153289580 153289580 0 1 58, 0, +chr1 153316527 153348121 NM_001360845 0 - 153318445 153325753 0 8 2020,172,273,216,161,89,185,273, 0,2240,3674,6742,7474,9139,11557,31321, +chr1 153316527 153348121 NM_001360844 0 - 153318445 153330885 0 9 2020,172,273,216,161,89,135,237,273, 0,2240,3674,6742,7474,9139,14333,29856,31321, +chr1 153316527 153348121 NM_001360847 0 - 153318445 153325753 0 8 2020,172,273,216,161,89,184,273, 0,2240,3674,6742,7474,9139,17874,31321, +chr1 153316527 153348121 NM_011277 0 - 153318445 153325753 0 7 2020,172,273,216,161,89,273, 0,2240,3674,6742,7474,9139,31321, +chr1 153418502 153566477 NM_022018 0 + 153418659 153565476 0 14 212,131,132,115,165,116,105,163,188,162,111,108,112,2119, 0,65031,70055,73502,77906,118146,124317,124752,128736,132329,134614,137724,144287,145856, +chr1 153596079 153602148 NR_151475 0 - 153602148 153602148 0 2 1279,176, 0,5893, +chr1 153596079 153602148 NR_151473 0 - 153602148 153602148 0 2 1279,101, 0,5968, +chr1 153596079 153601857 NR_151474 0 - 153601857 153601857 0 2 1279,13, 0,5765, +chr1 153602503 153669458 NM_001311166 0 + 153602696 153665843 0 20 354,46,101,40,113,154,135,106,98,126,84,84,125,166,155,100,192,166,186,4019, 0,4364,15458,16036,20483,22032,26999,29365,36954,39302,39606,40692,41409,48904,49291,50473,51992,52830,56145,62936, +chr1 153602503 153669458 NM_001311165 0 + 153602696 153665843 0 21 354,46,101,40,113,154,135,106,98,126,84,84,125,166,155,97,192,166,186,15,4019, 0,4364,15458,16036,20483,22032,26999,29365,36954,39302,39606,40692,41409,48904,49291,50476,51992,52830,56145,57380,62936, +chr1 153602503 153669458 NM_001039644 0 + 153602696 153665843 0 20 354,46,101,40,113,154,135,106,98,126,84,84,125,166,155,154,192,166,186,4019, 0,4364,15458,16036,20483,22032,26999,29365,36954,39302,39606,40692,41409,48904,49291,50476,51992,52830,56145,62936, +chr1 153731653 153937450 NM_197990 0 - 153740523 153853768 0 6 8909,61,77,95,223,389, 0,30958,36523,95902,122021,205408, +chr1 154217865 154233812 NM_025677 0 - 154218392 154233714 0 5 548,142,136,82,224, 0,1018,12526,12963,15723, +chr1 154246996 154357825 NM_177756 0 + 154247267 154355918 0 12 531,111,118,135,205,120,77,107,133,128,207,2184, 0,68582,71821,73228,84971,89913,95935,100038,103091,104211,106926,108645, +chr1 154363892 154472347 NM_016846 0 - 154366138 154472140 0 18 2434,115,255,187,90,122,33,87,90,85,104,216,125,185,78,209,111,234, 0,4532,7882,11510,14743,16743,19504,20968,23174,27588,32304,35658,37533,40640,54835,69644,107055,108221, +chr1 154363892 154613435 NM_001346119 0 - 154366138 154522121 0 18 2434,115,255,187,90,122,33,87,90,85,104,216,125,185,78,209,164,399, 0,4532,7882,11510,14743,16743,19504,20968,23174,27588,32304,35658,37533,40640,54835,69644,158097,249144, +chr1 154363892 154613435 NM_001346117 0 - 154366138 154522121 0 19 2434,115,255,187,90,122,33,87,90,85,104,216,125,185,78,209,111,167,399, 0,4532,7882,11510,14743,16743,19504,20968,23174,27588,32304,35658,37533,40640,54835,69644,107055,158097,249144, +chr1 154363892 154613435 NM_001346118 0 - 154366138 154522121 0 19 2434,115,255,187,90,122,33,87,90,85,104,216,125,185,78,209,111,164,399, 0,4532,7882,11510,14743,16743,19504,20968,23174,27588,32304,35658,37533,40640,54835,69644,107055,158097,249144, +chr1 154597680 154604674 NM_001081197 0 + 154603352 154604477 0 2 214,1352, 0,5642, +chr1 154613671 154622710 NM_026369 0 + 154613854 154621452 0 4 326,73,177,1321, 0,2319,4822,7718, +chr1 154647282 154684120 NM_010877 0 + 154655161 154683244 0 16 361,949,83,109,135,108,60,44,142,69,76,23,152,112,178,989, 0,7104,10765,16838,21363,24064,25729,27265,30199,30540,31461,33170,33624,33916,34874,35849, +chr1 154684124 154749775 NM_001160257 0 - 154686401 154725223 0 24 2391,146,171,160,81,150,372,383,145,283,120,61,71,154,163,136,151,72,172,133,118,32,137,137, 0,3040,3307,4030,4518,6235,7041,8218,9124,11739,12880,15603,17315,18854,19454,21884,22357,23455,24686,29586,31257,33765,41046,65514, +chr1 154684124 154749775 NM_001359257 0 - 154686401 154703579 0 24 2391,146,171,160,81,150,372,383,145,283,120,61,71,154,163,136,151,72,103,172,133,118,32,137, 0,3040,3307,4030,4518,6235,7041,8218,9124,11739,12880,15603,17315,18854,19454,21884,22357,23455,23768,24686,29586,31257,33765,65514, +chr1 154684124 154749776 NM_001160256 0 - 154686401 154749667 0 23 2391,146,171,160,81,150,372,383,145,283,120,61,71,154,163,136,151,72,172,133,118,32,138, 0,3040,3307,4030,4518,6235,7041,8218,9124,11739,12880,15603,17315,18854,19454,21884,22357,23455,24686,29586,31257,33765,65514, +chr1 154684124 154749776 NM_001005507 0 - 154686401 154749667 0 22 2391,146,171,160,81,372,383,145,421,120,61,71,154,163,136,151,72,172,133,118,32,138, 0,3040,3307,4030,4518,7041,8218,9124,11601,12880,15603,17315,18854,19454,21884,22357,23455,24686,29586,31257,33765,65514, +chr1 154802230 154966391 NM_175460 0 + 154802238 154962800 0 11 93,89,68,79,127,81,45,77,102,68,3694, 0,118696,119572,121808,131236,133683,135396,138936,157041,157279,160467, +chr1 154969885 155033577 NM_008485 0 - 154971159 155033117 0 24 1528,100,159,200,115,150,145,150,80,206,163,146,246,183,219,113,190,123,137,99,136,189,193,194, 0,4060,4250,6201,7280,7894,9067,10843,12021,13942,14435,16970,18770,20970,21758,22883,26172,27988,29281,31636,36096,43363,63153,63498, +chr1 155066051 155179916 NM_010683 0 - 155068602 155179669 0 28 2808,100,159,200,115,150,145,138,80,206,157,179,143,154,246,189,222,113,190,123,137,99,118,189,167,131,305,659, 0,4737,7462,8589,9813,10120,11800,12812,14563,15526,20333,21395,22955,23707,24309,28016,28315,30118,30643,30923,31465,31690,32155,33030,36267,39154,43468,113206, +chr1 155251315 155261363 NR_033736 0 - 155261363 155261363 0 4 2416,88,234,89, 0,3416,4151,9959, +chr1 155272338 155299704 NM_001033162 0 + 155272353 155299594 0 10 378,150,215,87,219,106,154,251,123,362, 0,3351,7966,10554,10709,12316,20589,22515,23692,27004, +chr1 155302887 155334790 NM_007842 0 - 155303198 155330980 0 28 996,201,116,230,128,162,112,161,153,74,95,214,101,157,83,142,192,78,162,90,137,47,149,113,118,141,133,128, 0,1773,2295,2502,3580,3800,4520,5224,6794,8582,8860,9097,9919,11274,13116,13842,15862,16468,16643,16914,17389,19905,22283,23108,25374,26984,27982,31775, +chr1 155350145 155396844 NM_028749 0 - 155350502 155392460 0 12 542,40,85,47,149,93,76,58,88,74,84,67, 0,6096,9530,12224,12386,15867,21331,25049,32856,34412,42247,46632, +chr1 155500166 155544795 NM_026380 0 + 155515057 155540037 0 7 319,81,129,102,65,167,4941, 0,12799,14788,17746,18717,37861,39688, +chr1 155512403 155544797 NM_001357525 0 + 155515057 155540037 0 7 265,81,129,102,65,167,4943, 0,562,2551,5509,6480,25624,27451, +chr1 155512802 155544795 NM_001347115 0 + 155513026 155540037 0 6 41,81,102,65,167,4941, 0,163,5110,6081,25225,27052, +chr1 155568369 155584959 NR_046171 0 - 155584959 155584959 0 3 2858,125,354, 0,10630,16236, +chr1 155587482 155592598 NM_011267 0 + 155587598 155590985 0 5 160,111,62,167,1835, 0,510,1267,1610,3281, +chr1 155596555 155611351 NM_011882 0 + 155600869 155609420 0 9 182,201,103,1607,86,206,133,137,2103, 0,2433,3419,4181,6525,8957,10118,11349,12693, +chr1 155626516 155691271 NM_001368270 0 - 155628818 155691244 0 22 291,192,96,110,125,139,175,130,115,118,194,103,108,223,63,968,162,105,130,75,83,40, 0,2202,5756,10842,14368,14701,20407,22849,24627,25223,28294,32827,38117,41964,42922,45889,48054,49168,58668,60335,62379,64715, +chr1 155626516 155691271 NM_001243223 0 - 155628818 155691244 0 21 291,192,96,110,125,139,175,130,115,118,194,103,108,223,63,968,162,130,75,83,40, 0,2202,5756,10842,14368,14701,20407,22849,24627,25223,28294,32827,38117,41964,42922,45889,48054,58668,60335,62379,64715, +chr1 155696671 155698325 NM_178243 0 - 155697473 155698256 0 1 1654, 0, +chr1 155721474 155724001 NM_001008426 0 + 155721576 155722497 0 1 2527, 0, +chr1 155738775 155740190 NM_178244 0 + 155738921 155739839 0 1 1415, 0, +chr1 155747055 155747166 NR_106194 0 + 155747166 155747166 0 1 111, 0, +chr1 155747058 155756853 NM_008131 0 + 155750076 155755312 0 7 131,179,162,147,128,200,1860, 0,3005,4608,6420,7091,7357,7935, +chr1 156048316 156053968 NM_001204908 0 + 156051226 156052804 0 2 242,2799, 0,2853, +chr1 156088650 156104036 NR_040629 0 - 156104036 156104036 0 4 180,56,73,304, 0,12755,14519,15082, +chr1 156102818 156117546 NR_108050 0 + 156117546 156117546 0 3 73,83,325, 0,7365,14403, +chr1 156239648 156573050 NM_009782 0 - 156245522 156573049 0 47 6417,191,181,112,107,101,108,106,97,128,166,92,66,126,84,111,165,202,138,161,97,12,107,60,130,163,314,654,57,98,68,118,73,132,113,113,210,90,54,116,104,182,153,104,140,106,270, 0,9464,11159,15193,19545,19924,20532,21457,23542,28509,33318,34007,39912,43899,44748,48976,49613,51282,52353,52981,56327,58327,73200,74427,75165,76427,78819,79541,81338,85247,86732,89033,90032,90556,90998,93144,93979,95525,96266,100783,169212,241035,242321,243238,307852,308756,333132, +chr1 156910576 156930394 NR_151545 0 - 156930394 156930394 0 7 412,141,180,188,141,144,2073, 0,1433,1769,2275,16256,17193,17745, +chr1 156943496 156946766 NM_010500 0 - 156945633 156946560 0 1 3270, 0, +chr1 156975003 156993944 NM_008209 0 - 156976396 156993816 0 6 1452,99,276,276,261,183, 0,2759,4486,8701,9640,18758, +chr1 156975003 156993944 NM_001355063 0 - 156976396 156983960 0 6 1452,99,276,276,76,183, 0,2759,4486,8701,9825,18758, +chr1 156975003 156993944 NM_001355062 0 - 156976396 156984826 0 6 1452,99,276,276,181,183, 0,2759,4486,8701,9720,18758, +chr1 157005832 157050647 NM_021433 0 + 157006022 157049146 0 8 225,170,95,63,126,107,95,1578, 0,15283,19151,29075,32726,34516,38638,43237, +chr1 157059600 157091662 NM_001370865 0 - 157060649 157091359 0 10 1243,185,128,253,157,1538,144,64,902,347, 0,4911,5789,8864,10804,12440,19975,28265,28954,31715, +chr1 157122786 157264574 NM_011273 0 - 157128139 157264364 0 15 5414,222,137,167,195,172,180,191,82,84,150,224,102,52,279, 0,7556,14538,17452,31965,33294,37102,37514,48657,52942,54681,56506,69896,108954,141509, +chr1 157367302 157374241 NR_132128 0 - 157374241 157374241 0 2 1665,86, 0,6853, +chr1 157405249 157434924 NM_001145781 0 + 157405767 157434605 0 4 740,65,97,355, 0,6537,9465,29320, +chr1 157405249 157534363 NM_028250 0 + 157405767 157534233 0 8 740,65,97,83,106,90,31,285, 0,6537,9465,43334,57747,66749,119084,128829, +chr1 157405249 157419417 NM_026683 0 + 157405767 157419357 0 4 740,65,97,90, 0,6537,9465,14078, +chr1 157548823 157589157 NM_010712 0 - 157549351 157589007 0 6 923,172,155,203,172,226, 0,3007,3478,8419,23096,40108, +chr1 157625284 157660029 NM_023268 0 - 157625972 157659929 0 13 697,221,180,148,123,130,135,146,91,103,46,101,374, 0,1563,3120,4370,5248,8639,11143,12826,14039,16391,17196,25542,34371, +chr1 157625284 157660029 NM_001024945 0 - 157626298 157659929 0 12 1784,180,148,123,130,135,146,91,103,46,101,374, 0,3120,4370,5248,8639,11143,12826,14039,16391,17196,25542,34371, +chr1 157692093 157820385 NM_001039184 0 - 157695692 157809677 0 38 3764,123,147,405,1964,83,137,161,145,209,200,161,147,88,185,197,164,126,137,141,111,164,203,187,173,142,1061,122,662,147,114,114,614,160,112,44,86,407, 0,13059,15205,15472,16684,21076,23707,26945,30358,33946,40943,49630,52471,55822,56476,57623,61525,64240,65654,66172,66924,69752,70485,77350,79601,81450,83149,86544,87825,90851,95753,99135,108190,113597,114756,116180,117511,127885, +chr1 157851728 157883610 NM_001160018 0 - 157854054 157883365 0 10 3111,57,69,42,81,39,45,60,75,723, 0,8719,12912,13619,17701,18550,25788,26815,29127,31159, +chr1 157851728 157881947 NM_001160019 0 - 157854054 157878601 0 10 3111,57,69,42,81,39,45,60,75,137, 0,8719,12912,13619,17701,18550,25788,26815,29127,30082, +chr1 157851728 157883610 NM_144791 0 - 157854054 157883365 0 7 3111,81,39,45,60,75,723, 0,17701,18550,25788,26815,29127,31159, +chr1 157882793 157915989 NM_172843 0 + 157906650 157912588 0 7 445,60,330,177,582,102,4159, 0,5411,15630,23747,25924,27929,29037, +chr1 157882856 157900866 NM_001160180 0 + 157899007 157899403 0 3 194,60,2443, 0,5348,15567, +chr1 157883165 157900866 NM_001160182 0 + 157899007 157899403 0 3 73,60,2443, 0,5039,15258, +chr1 157887969 157915989 NM_001358627 0 + 157906650 157912588 0 6 163,330,177,582,102,4159, 0,10454,18571,20748,22753,23861, +chr1 157887969 157915989 NM_001358626 0 + 157906650 157912588 0 5 163,177,582,102,4159, 0,18571,20748,22753,23861, +chr1 157887990 157900866 NM_001160181 0 + 157899007 157899403 0 3 142,60,2443, 0,214,10433, +chr1 157887990 157900866 NM_022329 0 + 157899007 157899403 0 2 142,2443, 0,10433, +chr1 157923085 158135156 NM_177838 0 - 157926026 157927174 0 5 3355,220,22,98,197, 0,3996,5436,11833,211874, +chr1 158185425 158233479 NM_001134741 0 - 158185703 158232729 0 19 550,205,144,183,159,135,201,67,213,221,209,154,57,84,194,393,57,179,38, 0,4435,7533,8110,11917,15270,15903,21266,22002,28969,30090,32932,38031,39139,45301,46218,47071,47129,48016, +chr1 158185425 158233737 NM_001277730 0 - 158185703 158232729 0 19 550,205,144,183,159,135,201,67,213,221,209,154,57,84,140,162,57,179,29, 0,4435,7533,8110,11917,15270,15903,21266,22002,28969,30090,32932,38031,39139,45301,46449,47071,47129,48283, +chr1 158240849 158258166 NM_130456 0 + 158240918 158256269 0 8 349,104,73,83,204,56,79,2176, 0,2256,6093,7969,10165,13018,14218,15141, +chr1 158260545 158351046 NM_001346967 0 - 158260773 158350559 0 26 296,239,83,102,333,111,97,209,94,202,235,76,164,102,121,105,141,122,103,57,86,115,104,173,196,70, 0,1072,2770,4928,8330,11369,16281,18486,20943,35201,46072,47967,50365,51961,57576,61498,62234,65017,67025,68077,69767,72416,87819,88824,89920,90431, +chr1 158358238 158404459 NM_009230 0 - 158361189 158396899 0 16 3008,146,136,99,98,130,46,82,79,283,108,60,152,59,118,181, 0,4096,4739,6045,7685,9596,11180,11593,12399,13121,14273,16447,18433,29838,38573,46040, +chr1 158488917 158579750 NM_001136104 0 + 158489179 158572847 0 13 419,63,171,296,273,85,178,185,153,90,174,237,8078, 0,62052,63698,66501,71066,72558,74293,74966,76278,78031,81652,82206,82755, +chr1 158488917 158579750 NM_009595 0 + 158489179 158572847 0 12 419,63,171,296,273,85,178,185,153,90,174,8627, 0,62052,63698,66501,71066,72558,74293,74966,76278,78031,81652,82206, +chr1 158583747 158604470 NM_023141 0 - 158585823 158604436 0 6 2327,125,179,266,117,254, 0,2855,12982,15754,19913,20469, +chr1 158608701 158649041 NM_145413 0 - 158611541 158636175 0 8 3072,60,192,172,110,87,500,45, 0,7620,8785,11906,20156,23828,27097,40295, +chr1 158734296 158869757 NM_001357391 0 - 158739294 158814723 0 20 5028,92,106,93,106,55,152,157,68,91,138,127,93,90,84,105,51,105,140,138, 0,7279,9272,13575,15647,19825,23974,24806,26219,28499,28729,65275,80367,82925,83781,88742,96420,97620,103473,135323, +chr1 158734296 158869518 NM_001159966 0 - 158739294 158837826 0 20 5028,92,106,93,106,78,55,152,157,68,91,138,127,93,90,84,51,105,140,36, 0,7279,9272,13575,15647,17221,19825,23974,24806,26219,28499,28729,65275,80367,82925,83781,96420,97620,103473,135186, +chr1 158734296 158869757 NM_001159968 0 - 158739294 158837826 0 19 5028,92,106,93,106,78,55,152,157,68,91,138,127,93,90,84,51,140,138, 0,7279,9272,13575,15647,17221,19825,23974,24806,26219,28499,28729,65275,80367,82925,83781,96420,103473,135323, +chr1 158734296 158869757 NM_001159965 0 - 158739294 158837826 0 20 5028,92,106,93,106,78,55,152,157,68,91,138,127,93,90,84,51,105,140,138, 0,7279,9272,13575,15647,17221,19825,23974,24806,26219,28499,28729,65275,80367,82925,83781,96420,97620,103473,135323, +chr1 158734296 158869757 NM_001159967 0 - 158739294 158837826 0 19 5028,92,106,93,106,55,152,157,68,91,138,127,93,90,84,51,105,140,138, 0,7279,9272,13575,15647,19825,23974,24806,26219,28499,28729,65275,80367,82925,83781,96420,97620,103473,135323, +chr1 158734296 158869518 NM_001357392 0 - 158739294 158814723 0 20 5028,92,106,93,106,55,152,157,68,91,138,127,93,90,84,105,51,105,140,36, 0,7279,9272,13575,15647,19825,23974,24806,26219,28499,28729,65275,80367,82925,83781,88742,96420,97620,103473,135186, +chr1 158734296 158869757 NM_023884 0 - 158739294 158837826 0 20 5028,92,106,93,106,78,55,152,157,68,91,138,127,93,90,84,51,105,80,138, 0,7279,9272,13575,15647,17221,19825,23974,24806,26219,28499,28729,65275,80367,82925,83781,96420,97620,103473,135323, +chr1 158769153 158791209 NM_028333 0 + 158774736 158790733 0 5 215,846,194,271,664, 0,5557,18060,19337,21392, +chr1 159029275 159038789 NM_001374637 0 - 159029423 159038700 0 8 259,184,65,60,57,69,45,128, 0,935,1315,5199,5886,8045,8698,9386, +chr1 159029277 159038781 NM_001305059 0 - 159029473 159038700 0 9 257,44,184,65,60,57,69,45,120, 0,557,933,1313,5197,5884,8043,8696,9384, +chr1 159029277 159038811 NM_001305063 0 - 159029473 159037994 0 9 257,44,184,65,60,57,69,45,28, 0,557,933,1313,5197,5884,8043,8696,9506, +chr1 159029277 159038811 NM_001305062 0 - 159029473 159037994 0 9 260,44,184,65,60,57,69,45,28, 0,557,933,1313,5197,5884,8043,8696,9506, +chr1 159029277 159038781 NM_001305061 0 - 159029473 159037994 0 9 260,44,184,65,60,57,69,45,209, 0,557,933,1313,5197,5884,8043,8696,9295, +chr1 159029277 159038781 NM_028540 0 - 159029473 159038700 0 9 260,44,184,65,60,57,69,45,120, 0,557,933,1313,5197,5884,8043,8696,9384, +chr1 159065313 159342726 NM_177644 0 - 159070841 159342069 0 18 5693,88,203,135,862,200,202,237,145,145,555,99,154,110,107,124,128,859, 0,11007,12447,14590,21723,23476,25942,28520,29424,38960,40480,42463,43916,57564,94856,151548,163954,276554, +chr1 159342482 159350367 NR_027984 0 + 159350367 159350367 0 3 774,52,368, 0,1392,7517, +chr1 159388698 159419193 NM_001356418 0 + 159388726 159418642 0 8 78,109,97,59,66,110,82,620, 0,176,3385,5841,6397,7144,8598,29875, +chr1 159388698 159419193 NM_001356419 0 + 159388726 159418598 0 7 78,109,97,59,66,110,620, 0,176,3385,5841,6397,7144,29875, +chr1 159388698 159419193 NM_001033284 0 + 159388726 159418642 0 10 78,109,97,59,66,110,82,182,229,620, 0,176,3385,5841,6397,7144,8598,12048,13620,29875, +chr1 159428132 159441854 NR_151610 0 - 159441854 159441854 0 3 384,77,74, 0,4180,13648, +chr1 159436926 159498555 NR_027641 0 + 159498555 159498555 0 27 65,69,341,113,121,100,145,152,62,136,231,98,82,118,112,106,141,114,73,294,68,150,99,109,80,99,1149, 0,17989,22368,24484,25257,26283,27833,28565,29056,30722,31317,37070,39403,44211,46137,47951,49969,51239,52653,53887,54720,57651,57965,58625,58857,59832,60480, +chr1 159436926 159498555 NM_033354 0 + 159459354 159497478 0 28 65,168,69,341,113,121,100,145,152,62,136,231,98,82,118,112,106,141,114,73,294,68,150,99,109,80,99,1149, 0,590,17989,22368,24484,25257,26283,27833,28565,29056,30722,31317,37070,39403,44211,46137,47951,49969,51239,52653,53887,54720,57651,57965,58625,58857,59832,60480, +chr1 159456300 159498555 NM_001159986 0 + 159459354 159497478 0 26 55,341,113,121,100,145,152,62,136,231,98,82,118,112,106,141,114,73,294,68,150,99,109,80,99,1149, 0,2994,5110,5883,6909,8459,9191,9682,11348,11943,17696,20029,24837,26763,28577,30595,31865,33279,34513,35346,38277,38591,39251,39483,40458,41106, +chr1 160175399 160286391 NM_207583 0 - 160176328 160225825 0 8 2046,223,237,106,209,191,345,744, 0,4020,5971,9705,21193,22561,50157,110248, +chr1 160292434 160621917 NM_001205204 0 + 160292713 160618881 0 23 562,188,394,147,108,150,192,85,75,138,151,167,195,128,105,189,269,134,152,136,101,184,3274, 0,110071,139744,141899,143058,147542,148651,158140,210648,217277,217907,234853,238011,239633,246947,250042,294736,301691,305178,306324,312276,321773,326209, +chr1 160292434 160621917 NM_007495 0 + 160292713 160618881 0 23 562,188,394,147,108,150,168,85,75,138,151,167,195,128,105,189,269,134,152,136,101,184,3274, 0,110071,139744,141899,143058,147542,148651,158140,210648,217277,217907,234853,238011,239633,246947,250042,294736,301691,305178,306324,312276,321773,326209, +chr1 160435755 160435864 NR_030441 0 + 160435864 160435864 0 1 109, 0, +chr1 160641865 160888306 NM_001085376 0 - 160645076 160887569 0 23 3286,99,72,110,136,169,214,178,172,208,136,147,194,92,129,490,122,193,294,146,1072,1265,49, 0,5227,38795,49795,51334,53193,70446,72162,75855,102605,103002,120974,123015,126814,133269,136201,139361,143115,145399,159667,224211,244782,246392, +chr1 160897831 160910593 NR_163823 0 - 160910593 160910593 0 3 2165,157,152, 0,11977,12610, +chr1 161162330 161285003 NM_001360878 0 + 161162568 161274969 0 20 651,60,98,65,120,69,60,77,58,115,136,144,109,82,117,118,125,161,45,10052, 0,7362,12389,17002,17823,20348,34557,35909,45889,52348,56705,74373,76210,76683,87524,92717,94877,96402,110607,112621, +chr1 161162330 161285003 NM_011931 0 + 161162568 161274969 0 20 651,60,98,77,120,69,60,77,58,115,136,144,109,82,117,118,125,161,45,10052, 0,7362,12389,17002,17823,20348,34557,35909,45889,52348,56705,74373,76210,76683,87524,92717,94877,96402,110607,112621, +chr1 161223903 161224296 NR_144489 0 + 161224296 161224296 0 1 393, 0, +chr1 161270437 161270555 NR_028518 0 + 161270555 161270555 0 1 118, 0, +chr1 161270488 161270554 NR_039543 0 + 161270554 161270554 0 1 66, 0, +chr1 161453899 161855053 NM_022312 0 + 161780177 161854344 0 23 447,101,560,477,264,116,151,270,186,90,264,270,120,147,120,144,131,133,152,97,162,164,829, 0,213742,326217,328188,334408,337441,339869,344247,350339,361002,362288,363101,364488,365515,368240,371192,371931,373221,388871,390767,395175,399495,400325, +chr1 161974510 162008717 NM_001162896 0 + 162005292 162005592 0 3 374,104,3556, 0,26320,30651, +chr1 161974510 162002913 NR_028111 0 + 162002913 162002913 0 3 374,104,1356, 0,26320,27047, +chr1 162004865 162008049 NR_038030 0 - 162008049 162008049 0 3 593,108,129, 0,2648,3055, +chr1 162004865 162008116 NR_038031 0 - 162008116 162008116 0 3 593,108,57, 0,2648,3194, +chr1 162015162 162083706 NM_177839 0 - 162016161 162077986 0 22 1137,164,168,97,152,133,131,264,264,264,264,264,264,264,264,264,90,186,264,375,442,94, 0,3361,12162,13181,19795,20366,21979,25214,29459,31038,33307,35466,37623,40321,41300,45652,54217,55555,59951,60980,62415,68450, +chr1 162125345 162131317 NM_025474 0 + 162125397 162129741 0 3 97,159,1759, 0,1731,4213, +chr1 162125462 162131317 NM_001347121 0 + 162125649 162129741 0 3 214,159,1759, 0,1614,4096, +chr1 162132497 162143023 NM_009786 0 - 162133697 162142798 0 6 1357,98,100,97,217,246, 0,2601,3729,4246,6012,10280, +chr1 162149304 162281702 NM_001038621 0 - 162154346 162281519 0 9 5195,198,72,84,105,111,93,129,351, 0,7311,12622,17452,19357,28285,38269,122862,132047, +chr1 162186702 162723069 NM_013862 0 - 162187382 162671020 0 21 695,93,129,42,144,126,75,114,151,94,142,167,103,67,111,158,175,211,193,180,203, 0,871,85464,135610,185251,186619,197179,215426,370643,388736,425469,444140,445786,453575,465561,467460,476957,478976,482324,484180,536164, +chr1 162225994 162226103 NR_035448 0 - 162226103 162226103 0 1 109, 0, +chr1 162504847 162509835 NM_001146330 0 - 162506798 162507884 0 2 3256,540, 0,4448, +chr1 162504847 162509835 NM_001368668 0 - 162506798 162507884 0 2 3256,678, 0,4310, +chr1 162836541 162905107 NM_001024952 0 + 162860244 162897928 0 20 289,381,121,240,176,201,133,119,113,282,215,368,165,153,214,91,133,171,116,7330, 0,23553,31701,33584,34408,36117,40123,41896,43811,44430,45204,48373,49404,52990,55860,57068,57297,58539,59262,61236, +chr1 162908736 162933145 NM_080844 0 + 162917673 162932594 0 8 110,143,370,216,138,391,65,728, 0,8835,10773,14790,16712,18744,21383,23681, +chr1 162938922 162964980 NR_151478 0 - 162964980 162964980 0 7 700,137,923,100,957,197,72, 0,4093,10692,20850,23013,25296,25986, +chr1 162938922 162964980 NR_151479 0 - 162964980 162964980 0 6 700,923,100,960,197,72, 0,10692,20850,23013,25296,25986, +chr1 162947886 162964980 NM_001356489 0 - 162950051 162962864 0 5 2651,100,957,197,72, 0,11886,14049,16332,17022, +chr1 162947886 162964980 NM_173424 0 - 162950051 162962864 0 5 2651,100,960,197,72, 0,11886,14049,16332,17022, +chr1 162965046 162968670 NR_153815 0 + 162968670 162968670 0 9 279,53,32,37,31,33,43,48,83, 0,836,1067,1292,1633,1904,3079,3309,3541, +chr1 162965046 162968670 NR_153814 0 + 162968670 162968670 0 10 279,53,32,31,33,28,43,43,48,83, 0,836,1067,1633,1904,2372,2589,3079,3309,3541, +chr1 162965046 162968670 NR_153812 0 + 162968670 162968670 0 12 279,53,32,37,31,33,41,28,43,43,48,83, 0,836,1067,1292,1633,1904,2208,2372,2589,3079,3309,3541, +chr1 162965046 162968670 NR_153813 0 + 162968670 162968670 0 11 279,53,32,37,31,33,28,43,43,48,83, 0,836,1067,1292,1633,1904,2372,2589,3079,3309,3541, +chr1 162968222 162968287 NR_028543 0 + 162968287 162968287 0 1 65, 0, +chr1 162970731 163000791 NM_172644 0 - 162971846 163000247 0 17 1330,76,111,219,153,63,108,180,70,107,47,124,96,102,67,100,668, 0,3012,4358,4657,6176,9337,10730,13340,15860,16846,19444,20135,22181,22646,24624,28479,29392, +chr1 163000897 163016856 NR_131029 0 + 163016856 163016856 0 6 590,174,152,143,543,738, 0,3990,7562,9101,12141,15221, +chr1 163000897 163016856 NM_001159930 0 + 163004890 163016190 0 5 590,174,252,543,738, 0,3990,7462,12141,15221, +chr1 163000897 163016856 NR_131028 0 + 163016856 163016856 0 6 590,174,252,143,543,738, 0,3990,7462,9101,12141,15221, +chr1 163000897 163016856 NR_131030 0 + 163016856 163016856 0 5 590,174,152,543,738, 0,3990,7562,12141,15221, +chr1 163018508 163061610 NM_001039482 0 - 163020557 163060527 0 12 2134,107,209,134,144,184,116,95,159,574,64,117, 0,5303,7151,9885,10764,13073,14601,17023,18329,20844,42011,42985, +chr1 163072827 163100638 NM_001368766 0 + 163081123 163094322 0 8 22,55,353,168,95,139,43,2796, 0,1613,8268,12549,17970,20570,21475,25015, +chr1 163072842 163100638 NM_028664 0 + 163072897 163094322 0 7 129,353,168,95,139,43,2796, 0,8253,12534,17955,20555,21460,25000, +chr1 163086973 163089445 NM_001195189 0 - 163087229 163089317 0 2 502,452, 0,2020, +chr1 163170242 163181341 NM_001303408 0 - 163171851 163179512 0 6 1738,147,147,157,111,189, 0,3463,4084,7145,9247,10910, +chr1 163170242 163181341 NM_007453 0 - 163171851 163181247 0 5 1738,147,147,157,189, 0,3463,4084,7145,10910, +chr1 163170242 163181341 NR_130150 0 - 163181341 163181341 0 4 1738,147,147,189, 0,3463,4084,10910, +chr1 163325568 163348337 NM_009452 0 + 163325712 163347469 0 3 306,43,1260, 0,19530,21509, +chr1 163424787 163435421 NM_183391 0 + 163424843 163433935 0 3 191,34,1839, 0,5814,8795, +chr1 163710822 163718626 NM_001205243 0 - 163713081 163718416 0 3 1279,57,552, 0,2256,7252, +chr1 163710822 163718626 NM_010177 0 - 163711706 163718416 0 4 1279,57,46,552, 0,2256,6413,7252, +chr1 163746242 163806813 NM_001357402 0 - 163748496 163806503 0 24 2698,56,92,155,105,88,1158,91,69,66,92,56,21,106,108,68,125,124,151,138,155,111,112,372, 0,4283,11545,12044,13124,17304,17924,21607,22642,27890,28677,29191,29448,31093,32530,36163,36699,37603,40709,41232,43238,46080,47802,60199, +chr1 163746242 163806813 NR_151684 0 - 163806813 163806813 0 25 2698,53,98,92,155,105,88,1158,91,69,66,92,56,21,106,108,68,125,124,151,138,155,111,112,372, 0,4283,11188,11545,12044,13124,17304,17924,21607,22642,27890,28677,29191,29448,31093,32530,36163,36699,37603,40709,41232,43238,46080,47802,60199, +chr1 163746242 163806813 NR_151683 0 - 163806813 163806813 0 25 2698,56,98,92,155,105,88,1158,91,69,66,92,56,21,106,108,68,125,124,151,138,155,111,112,372, 0,4283,11188,11545,12044,13124,17304,17924,21607,22642,27890,28677,29191,29448,31093,32530,36163,36699,37603,40709,41232,43238,46080,47802,60199, +chr1 163746242 163806813 NM_001357401 0 - 163748496 163806503 0 24 2698,53,92,155,105,88,1158,91,69,66,92,56,21,106,108,68,137,124,151,138,155,111,112,372, 0,4283,11545,12044,13124,17304,17924,21607,22642,27890,28677,29191,29448,31093,32530,36163,36699,37603,40709,41232,43238,46080,47802,60199, +chr1 163746242 163806813 NM_172645 0 - 163748496 163806503 0 24 2698,56,92,155,105,88,1158,91,69,66,92,56,21,106,108,68,137,124,151,138,155,111,112,372, 0,4283,11545,12044,13124,17304,17924,21607,22642,27890,28677,29191,29448,31093,32530,36163,36699,37603,40709,41232,43238,46080,47802,60199, +chr1 163872219 163909767 NM_001204904 0 - 163872520 163909637 0 7 447,59,68,84,85,86,151, 0,7495,10511,15004,22733,25822,37397, +chr1 163872219 163899279 NM_001204905 0 - 163872520 163894997 0 7 447,59,68,84,85,86,184, 0,7495,10511,15004,22733,25822,26876, +chr1 163899318 163903566 NM_001039045 0 + 163900581 163901475 0 2 92,3196, 0,1052, +chr1 163899318 163903566 NM_026078 0 + 163900581 163901475 0 2 92,3209, 0,1039, +chr1 163917432 164408165 NM_001038619 0 - 163922152 164407954 0 21 4790,237,227,165,12,112,110,114,52,71,87,139,68,136,143,161,99,204,150,74,372, 0,23566,24399,32526,88473,96731,147155,244352,287186,298695,308250,320566,324090,326259,331279,333650,334385,366218,368058,420033,490361, +chr1 163917432 164408165 NM_172646 0 - 163922152 164407954 0 20 4790,237,227,165,112,110,114,52,71,87,139,68,136,143,161,99,204,150,74,372, 0,23566,24399,32526,96731,147155,244352,287186,298695,308250,320566,324090,326259,331279,333650,334385,366218,368058,420033,490361, +chr1 163935099 163946616 NR_040562 0 + 163946616 163946616 0 3 366,387,166, 0,467,11351, +chr1 164147753 164155681 NR_002870 0 + 164155681 164155681 0 1 7928, 0, +chr1 164147944 164148054 NR_029810 0 + 164148054 164148054 0 1 110, 0, +chr1 164153498 164153608 NR_029796 0 + 164153608 164153608 0 1 110, 0, +chr1 164463802 164478476 NM_144877 0 - 164464406 164478387 0 8 879,132,213,168,196,200,760,242, 0,2170,3447,5160,8586,10514,12096,14432, +chr1 164500645 164529211 NM_001356527 0 + 164504481 164524705 0 8 266,119,47,51,101,80,52,4535, 0,3783,7357,11304,17681,18950,22111,24031, +chr1 164500645 164529211 NM_001356526 0 + 164504481 164527208 0 8 266,119,47,51,101,80,52,2032, 0,3783,7357,11304,17681,18950,22111,26534, +chr1 164500958 164529211 NM_001347125 0 + 164504481 164524705 0 8 52,119,47,51,101,80,52,4535, 0,3470,7044,10991,17368,18637,21798,23718, +chr1 164500958 164529209 NM_016796 0 + 164504481 164527208 0 8 52,119,47,51,101,80,52,2030, 0,3470,7044,10991,17368,18637,21798,26221, +chr1 164569280 164579825 NM_010865 0 + 164569394 164579332 0 3 676,126,1278, 0,8294,9267, +chr1 164577373 164588350 NM_001177581 0 - 164577578 164588246 0 4 294,140,133,174, 0,7215,9793,10803, +chr1 164601915 164670687 NM_001081290 0 - 164603532 164654946 0 35 1872,237,127,104,219,108,232,137,113,204,202,102,93,252,189,86,841,155,209,2253,208,259,158,547,54,145,88,134,83,221,126,110,178,166,232, 0,3820,4906,5570,6225,7715,8041,8975,9436,10533,12270,16331,19356,20588,20951,24493,25648,27094,30397,32584,35981,37068,37744,38498,41519,42458,43607,43801,44494,46905,48696,49645,51325,52919,68540, +chr1 164724013 164742680 NM_144878 0 - 164724088 164740052 0 9 511,70,353,197,143,163,189,140,21, 0,1169,4916,9690,11271,13638,14378,15907,18646, +chr1 164759691 164796741 NM_010231 0 - 164760102 164789687 0 9 754,73,356,200,143,163,189,138,372, 0,3402,3969,6571,10057,20501,21794,29864,36678, +chr1 164759691 164790131 NM_001330291 0 - 164760102 164789687 0 9 754,73,356,200,143,163,189,138,200, 0,3402,3969,6571,10057,20501,21794,29864,30240, +chr1 164770348 164790131 NM_001330318 0 - 164771130 164789687 0 5 847,163,189,138,200, 0,9844,11137,19207,19583, +chr1 164804448 164828624 NM_001360914 0 - 164806858 164828436 0 9 2762,73,356,200,143,163,189,138,100, 0,3695,6064,7672,11991,13250,14378,23856,24076, +chr1 164804448 164828624 NM_001360913 0 - 164806858 164828436 0 8 2762,73,356,200,143,163,189,320, 0,3695,6064,7672,11991,13250,14378,23856, +chr1 164804448 164828889 NM_018881 0 - 164806858 164828436 0 9 2762,73,356,200,143,163,189,138,87, 0,3695,6064,7672,11991,13250,14378,23856,24354, +chr1 164846681 164867356 NM_001178038 0 - 164846853 164867257 0 8 515,73,356,200,143,163,189,231, 0,1646,3760,6108,7741,9537,13331,20444, +chr1 164883929 164914659 NM_008030 0 - 164884308 164913250 0 9 728,73,356,200,143,163,189,138,58, 0,1392,4438,10081,13074,13982,14882,29189,30672, +chr1 164954432 165015801 NM_030071 0 - 164954573 165010710 0 22 452,63,103,117,153,177,138,121,138,146,166,155,150,122,136,105,87,136,80,47,55,109, 0,2163,13681,14572,14782,19682,21348,21669,23534,31252,32457,33717,36315,38127,41687,47616,50366,51243,51988,55178,56253,61260, +chr1 165175249 165243781 NM_175686 0 - 165184124 165242766 0 5 3278,72,182,176,1256, 0,8858,12642,16721,67276, +chr1 165175249 165243781 NM_011127 0 - 165178388 165242766 0 4 3278,182,176,1256, 0,12642,16721,67276, +chr1 165185407 165243781 NM_001025570 0 - 165187887 165242766 0 3 2666,176,1256, 0,6563,57118, +chr1 165315033 165333800 NM_178883 0 - 165316383 165333714 0 5 1795,141,102,358,147, 0,7507,9688,11909,18620, +chr1 165315033 165333800 NM_001313738 0 - 165316383 165324777 0 5 1795,141,102,362,147, 0,7507,9688,11905,18620, +chr1 165315033 165333800 NR_132627 0 - 165333800 165333800 0 6 1795,141,138,102,362,147, 0,7507,8686,9688,11905,18620, +chr1 165633123 165655363 NM_001143956 0 - 165633147 165655186 0 4 296,250,176,331, 0,1010,14090,21909, +chr1 165709713 165847238 NM_010629 0 + 165710001 165842248 0 21 320,132,155,56,142,100,125,99,179,163,101,109,113,166,126,99,86,190,100,66,1383, 0,3402,14366,16402,17669,34786,36242,38250,46105,49550,69078,76453,77889,82372,83128,85856,89118,103800,108623,132489,136142, +chr1 165709713 165847238 NM_001305643 0 + 165710001 165845964 0 20 320,132,155,56,142,100,125,99,179,163,101,109,113,166,126,99,86,190,100,1383, 0,3402,14366,16402,17669,34786,36242,38250,46105,49550,69078,76453,77889,82372,83128,85856,89118,103800,108623,136142, +chr1 165859230 165885257 NM_001286002 0 + 165863659 165883569 0 14 235,215,186,114,57,103,112,78,140,146,172,159,680,1745, 0,4379,5532,7318,9640,10781,12007,14724,15696,17103,20042,21468,22837,24282, +chr1 165859895 165885257 NM_028776 0 + 165863659 165883569 0 14 422,215,186,114,57,103,112,78,140,185,172,159,680,1745, 0,3714,4867,6653,8975,10116,11342,14059,15031,16399,19377,20803,22172,23617, +chr1 165859895 165885257 NM_001286003 0 + 165871296 165883569 0 14 422,215,125,114,57,103,198,78,140,185,172,159,680,1745, 0,3714,4928,6653,8975,10116,11256,14059,15031,16399,19377,20803,22172,23617, +chr1 165859895 165885257 NM_001357426 0 + 165871296 165883569 0 14 422,215,186,114,57,103,198,78,140,185,172,159,680,1745, 0,3714,4867,6653,8975,10116,11256,14059,15031,16399,19377,20803,22172,23617, +chr1 165876123 165924927 NM_001357049 0 - 165876480 165924851 0 25 433,191,120,81,105,114,96,123,186,90,52,83,187,115,146,65,81,139,85,163,141,105,89,40,187, 0,8156,9344,10835,11500,13295,14584,15971,18477,18742,20415,21081,22161,25854,26214,30751,32087,36672,38331,40012,40894,41613,43712,44727,48617, +chr1 165884138 165924927 NM_201364 0 - 165884275 165924851 0 24 332,120,81,105,114,96,123,186,90,52,83,187,115,146,65,81,139,85,163,141,105,89,40,187, 0,1329,2820,3485,5280,6569,7956,10462,10727,12400,13066,14146,17839,18199,22736,24072,28657,30316,31997,32879,33598,35697,36712,40602, +chr1 165925019 165927376 NM_001355132 0 + 165926242 165927331 0 2 89,1332, 0,1025, +chr1 165925019 165927376 NM_027279 0 + 165926242 165927331 0 2 183,1332, 0,1025, +chr1 165978364 165987808 NM_011345 0 + 165978816 165985865 0 14 89,84,384,108,189,186,189,189,189,177,111,22,73,922, 0,426,981,1846,2410,3303,3591,4731,5302,5584,6383,7320,7443,8522, +chr1 165992206 166010916 NM_011346 0 + 165992319 166009827 0 9 116,82,387,108,186,186,129,19,1108, 0,977,3226,4134,4535,6797,10037,14066,17602, +chr1 165992206 166010916 NM_001164059 0 + 165992319 166009827 0 8 116,82,387,186,186,129,19,1108, 0,977,3226,4535,6797,10037,14066,17602, +chr1 166045394 166080157 NM_011347 0 + 166045517 166078661 0 16 126,91,387,108,186,186,186,186,186,186,210,186,120,31,56,1007, 0,8438,10963,11933,12899,14815,16874,18603,21840,26088,27410,28630,29631,32055,33212,33756, +chr1 166078706 166082348 NR_037987 0 - 166082348 166082348 0 3 557,325,359, 0,744,3283, +chr1 166081965 166150408 NM_007976 0 + 166082093 166149655 0 25 286,89,123,213,144,222,166,178,100,212,151,213,2707,175,237,208,180,117,72,104,156,145,152,183,900, 0,2491,9943,22265,24386,27521,29777,30982,32673,33077,34932,38277,40092,43716,46877,49687,52947,55175,56017,57102,57628,59913,62540,65532,67543, +chr1 166147808 166147871 NR_162776 0 + 166147871 166147871 0 1 63, 0, +chr1 166179176 166195516 NM_001276455 0 + 166179383 166193649 0 6 411,489,226,193,142,1996, 0,7701,11746,13001,13574,14344, +chr1 166179176 166195516 NM_054087 0 + 166179383 166193649 0 6 411,603,226,193,142,1996, 0,7701,11746,13001,13574,14344, +chr1 166205728 166217978 NM_029115 0 + 166208328 166217800 0 6 164,141,948,147,155,341, 0,2576,4269,6793,10643,11909, +chr1 166219929 166237618 NM_001357052 0 - 166222356 166232810 0 8 2613,220,129,200,437,77,78,341, 0,5911,8440,9746,12485,14049,16640,17348, +chr1 166219930 166237615 NM_025505 0 - 166222356 166236609 0 9 2612,220,129,200,437,21,78,208,43, 0,5910,8439,9745,12484,14104,16639,17347,17642, +chr1 166219930 166237615 NM_001160209 0 - 166222356 166236609 0 7 2612,220,129,200,437,78,338, 0,5910,8439,9745,12484,16639,17347, +chr1 166219930 166237615 NM_001160208 0 - 166222356 166236609 0 8 2612,220,129,200,437,78,208,43, 0,5910,8439,9745,12484,16639,17347,17642, +chr1 166237802 166279566 NM_178071 0 + 166243009 166278312 0 10 83,191,83,108,167,111,51,208,106,1277, 0,388,5184,20621,24940,33057,35542,37547,40102,40487, +chr1 166237802 166367431 NM_001293313 0 + 166243009 166367179 0 14 83,191,83,108,167,111,51,208,106,65,69,102,108,285, 0,388,5184,20621,24940,33057,35542,37547,40102,71687,72969,78028,95298,129344, +chr1 166237802 166367431 NM_138314 0 + 166243009 166367179 0 14 83,191,86,108,167,111,51,208,106,65,69,102,108,285, 0,388,5181,20621,24940,33057,35542,37547,40102,71687,72969,78028,95298,129344, +chr1 166367229 166388486 NM_009721 0 - 166368406 166387988 0 6 1441,84,185,156,129,595, 0,2200,4358,6096,16390,20662, +chr1 166433437 166445013 NR_151593 0 + 166445013 166445013 0 3 238,131,1656, 0,4898,9920, +chr1 166726793 166754404 NM_019759 0 + 166726862 166753367 0 4 374,126,108,1104, 0,12243,22232,26507, +chr1 166793251 166801569 NR_040303 0 + 166801569 166801569 0 5 355,117,102,129,885, 0,1406,3117,7017,7433, +chr1 166861774 166865653 NM_008510 0 - 166861915 166865621 0 3 310,115,93, 0,1251,3786, +chr1 166996747 167022061 NR_040480 0 - 167022061 167022061 0 5 540,63,251,99,45, 0,1413,1841,2769,25269, +chr1 167067983 167090904 NM_032005 0 - 167069093 167090693 0 8 1405,136,189,62,62,135,265,408, 0,2278,4556,7203,9782,14149,15609,22513, +chr1 167104471 167124569 NR_151712 0 - 167124569 167124569 0 9 4955,30,56,36,82,167,86,87,199, 0,7711,9486,9629,10667,12381,13628,13907,19899, +chr1 167104471 167124569 NR_151711 0 - 167124569 167124569 0 7 4955,30,56,36,82,87,199, 0,7711,9486,9629,10667,13907,19899, +chr1 167104471 167124564 NM_145512 0 - 167109386 167124433 0 8 4955,30,56,36,82,86,87,194, 0,7711,9486,9629,10667,13628,13907,19899, +chr1 167142416 167167089 NM_145513 0 - 167145870 167166964 0 7 3595,63,96,132,100,180,229, 0,5497,7813,10243,15219,15982,24444, +chr1 167145048 167167091 NM_001357410 0 - 167145870 167166870 0 7 963,63,96,132,100,180,289, 0,2865,5181,7611,12587,13350,21754, +chr1 167145048 167167091 NM_001357411 0 - 167145870 167158559 0 7 963,63,96,132,100,180,583, 0,2865,5181,7611,12587,13350,21460, +chr1 167225896 167256876 NM_001310429 0 + 167226012 167251832 0 6 123,415,725,105,120,5310, 0,10412,14503,21474,22983,25670, +chr1 167225896 167256876 NM_001081126 0 + 167226012 167251832 0 7 123,39,415,725,105,120,5310, 0,6101,10412,14503,21474,22983,25670, +chr1 167232753 167256876 NM_001310430 0 + 167236352 167251832 0 6 187,415,725,105,120,5310, 0,3555,7646,14617,16126,18813, +chr1 167259631 167390594 NM_028759 0 - 167260069 167390358 0 19 503,106,89,157,139,397,69,116,118,258,120,94,215,136,114,186,93,62,333, 0,3788,7244,8687,10384,21383,21971,22460,27928,59157,60913,62638,70153,81963,90610,93355,94801,99753,130630, +chr1 167391390 167411349 NM_027430 0 + 167391533 167411070 0 5 252,41,85,112,316, 0,13694,16961,18207,19643, +chr1 167415313 167506904 NM_001357427 0 + 167468534 167506753 0 34 153,122,208,105,39,144,206,97,89,192,119,77,190,157,193,87,275,137,126,279,291,70,232,108,176,154,205,97,116,118,196,189,93,235, 0,2022,17927,18765,21151,21389,25072,27887,30123,33029,34253,34674,36595,53195,54599,56391,57870,61335,62933,65898,66704,71048,71566,73371,73944,76495,78740,79022,80083,82444,85436,87320,90420,91356, +chr1 167415313 167506904 NM_173029 0 + 167433300 167506753 0 34 153,208,105,39,144,206,97,89,192,119,77,190,56,157,193,87,275,137,126,279,291,70,232,108,176,154,205,97,116,118,196,189,93,235, 0,17927,18765,21151,21389,25072,27887,30123,33029,34253,34674,36595,39822,53195,54599,56391,57870,61335,62933,65898,66704,71048,71566,73371,73944,76495,78740,79022,80083,82444,85436,87320,90420,91356, +chr1 167522306 167564672 NM_001347128 0 - 167523706 167564524 0 3 1502,167,239, 0,16262,42127, +chr1 167522311 167564672 NM_001001880 0 - 167523783 167564524 0 5 1497,133,214,167,239, 0,12429,13428,16257,42122, +chr1 167522311 167564672 NM_001083897 0 - 167523706 167564524 0 6 1497,106,133,214,167,239, 0,9569,12429,13428,16257,42122, +chr1 167579075 167638225 NM_001038846 0 - 167580308 167638027 0 6 1266,732,204,72,102,204, 0,6360,8554,10428,16004,58946, +chr1 167579075 167638225 NM_178593 0 - 167580308 167638027 0 7 1266,732,204,72,90,102,204, 0,6360,8554,10428,14621,16004,58946, +chr1 167693888 167705440 NM_011804 0 + 167693915 167703978 0 4 381,120,185,1466, 0,6055,6874,10086, +chr1 167693888 167705440 NR_149310 0 + 167705440 167705440 0 5 381,154,120,185,1466, 0,843,6055,6874,10086, +chr1 167718811 167792243 NM_001113391 0 + 167718959 167791200 0 8 206,104,57,81,36,57,36,1109, 0,66485,67719,68735,69762,70538,71108,72323, +chr1 167718811 167797567 NM_031162 0 + 167718959 167796977 0 8 206,104,57,81,36,57,36,782, 0,66485,67719,68735,69762,70538,71108,77974, +chr1 167718811 167801284 NM_001113393 0 + 167718959 167799195 0 9 206,104,57,81,33,57,36,94,2136, 0,66485,67719,68735,69765,70538,71108,77974,80337, +chr1 167718811 167801284 NM_001113392 0 + 167718959 167799253 0 8 206,104,57,81,36,57,36,2136, 0,66485,67719,68735,69762,70538,71108,80337, +chr1 167718811 167801284 NR_103716 0 + 167801284 167801284 0 9 206,104,57,81,36,57,36,244,2136, 0,66485,67719,68735,69762,70538,71108,77974,80337, +chr1 167795284 167932765 NM_198932 0 - 167805868 167932753 0 16 10895,89,346,106,180,146,142,174,95,127,189,123,54,101,66,73, 0,11823,14976,26656,29751,31283,32471,36986,41531,43726,46134,48073,49956,51768,66508,137408, +chr1 167795284 167865079 NM_198934 0 - 167805868 167864962 0 17 10895,89,346,72,106,180,146,142,174,95,127,189,123,54,101,66,145, 0,11823,14976,17893,26656,29751,31283,32471,36986,41531,43726,46134,48073,49956,51768,66508,69650, +chr1 167795284 167883202 NM_001368808 0 - 167805868 167861850 0 17 10895,89,346,72,106,180,146,142,174,95,127,189,123,54,101,66,291, 0,11823,14976,17893,26656,29751,31283,32471,36986,41531,43726,46134,48073,49956,51768,66508,87627, +chr1 167795284 167932765 NM_011137 0 - 167805868 167932753 0 17 10895,89,346,72,106,180,146,142,174,95,127,189,123,54,101,66,73, 0,11823,14976,17893,26656,29751,31283,32471,36986,41531,43726,46134,48073,49956,51768,66508,137408, +chr1 167795284 167865079 NM_198933 0 - 167805868 167864962 0 16 10895,89,346,106,180,146,142,174,95,127,189,123,54,101,66,145, 0,11823,14976,26656,29751,31283,32471,36986,41531,43726,46134,48073,49956,51768,66508,69650, +chr1 168028278 168058029 NM_001160049 0 - 168028755 168057310 0 6 3239,218,232,95,130,107, 0,9825,11904,13883,28922,29644, +chr1 168028278 168058029 NM_001033344 0 - 168028755 168057310 0 6 3239,218,232,95,134,107, 0,9825,11904,13883,28922,29644, +chr1 168060351 168096641 NM_021610 0 + 168060692 168095410 0 7 384,155,217,156,120,136,1364, 0,16418,22347,27292,33552,34359,34926, +chr1 168060351 168096641 NM_001360925 0 + 168082824 168095410 0 6 384,217,156,120,136,1364, 0,22347,27292,33552,34359,34926, +chr1 168060351 168084267 NM_001360926 0 + 168060692 168084171 0 4 384,155,217,227, 0,16418,22347,23689, +chr1 168131515 168168875 NM_175296 0 - 168131678 168168797 0 12 351,76,133,63,142,55,125,42,156,100,93,210, 0,890,3405,4468,24205,24452,25181,32780,34016,35488,36878,37150, +chr1 168184269 168246963 NM_001357428 0 + 168184506 168240926 0 9 328,333,120,57,147,114,214,697,6073, 0,15166,16360,37277,40452,49363,53581,54708,56621, +chr1 168184269 168246963 NM_001164528 0 + 168184506 168240926 0 10 328,333,120,57,147,177,114,214,697,6073, 0,15166,16360,37277,40452,41613,49363,53581,54708,56621, +chr1 168184269 168246963 NM_001357432 0 + 168184506 168240921 0 9 328,333,120,57,147,177,114,214,6073, 0,15166,16360,37277,40452,41613,49363,53581,56621, +chr1 168184269 168246963 NM_001357431 0 + 168184506 168240926 0 8 328,333,120,57,114,214,697,6073, 0,15166,16360,37277,49363,53581,54708,56621, +chr1 168184269 168246963 NM_001357429 0 + 168184506 168240926 0 7 328,333,120,114,214,697,6073, 0,15166,16360,49363,53581,54708,56621, +chr1 168184269 168246963 NM_001357430 0 + 168184506 168240926 0 9 328,333,120,147,177,114,214,697,6073, 0,15166,16360,40452,41613,49363,53581,54708,56621, +chr1 168309297 168323751 NM_030245 0 + 168309533 168322851 0 8 310,92,66,98,210,152,163,1053, 0,2960,3230,7499,9395,10669,12656,13401, +chr1 168323741 168339959 NM_001142948 0 - 168328830 168339892 0 5 6555,99,127,134,122, 0,8255,9887,14788,16096, +chr1 168323741 168339959 NM_175170 0 - 168328830 168339147 0 6 6555,99,127,134,334,122, 0,8255,9887,14788,15387,16096, +chr1 168378382 168385619 NR_151518 0 - 168385619 168385619 0 3 904,84,285, 0,5131,6952, +chr1 168413743 168427719 NM_001164306 0 - 168413802 168427651 0 8 423,73,350,200,143,163,189,203, 0,2020,3280,6403,7925,10897,12216,13773, +chr1 168559101 168577824 NM_001164312 0 - 168560299 168573610 0 9 1556,76,350,200,143,163,189,140,195, 0,3689,5769,9218,11025,12636,13208,14374,18528, +chr1 168592185 168611976 NM_172844 0 - 168593418 168610415 0 10 1597,73,353,200,143,163,189,145,116,86, 0,2542,5093,11492,12370,14450,15444,18095,19050,19705, +chr1 168592185 168611976 NM_001347135 0 - 168593418 168607800 0 8 1597,73,353,200,143,163,189,86, 0,2542,5093,11492,12370,14450,15444,19705, +chr1 168904153 168929861 NR_037988 0 - 168929861 168929861 0 3 711,47,178, 0,8387,25530, +chr1 168931547 169021433 NM_001160261 0 + 168931696 169009190 0 3 412,929,3325, 0,77120,86561, +chr1 168931547 169021433 NM_175461 0 + 168931696 169009190 0 3 412,931,3325, 0,77120,86561, +chr1 168931547 169021433 NM_001160262 0 + 168931696 169009190 0 3 412,1249,3325, 0,77120,86561, +chr1 169156216 169215258 NM_030724 0 - 169156512 169215005 0 7 436,49,98,143,97,160,352, 0,1646,3807,8606,10517,11403,58690, +chr1 169220255 169220356 NR_105765 0 + 169220356 169220356 0 1 101, 0, +chr1 169238800 169264109 NM_001039483 0 + 169238994 169260396 0 7 264,78,60,47,68,145,3812, 0,636,5437,7573,10592,17206,21497, +chr1 169280121 169298661 NM_019993 0 + 169280366 169297630 0 11 426,146,130,135,197,141,189,88,142,113,1126, 0,2529,4436,5681,6539,7319,11412,11813,14517,15784,17414, +chr1 169302097 169323972 NM_025569 0 - 169302633 169308539 0 6 676,73,58,74,124,91, 0,1826,3485,5294,6325,21784, +chr1 169375805 169396911 NM_001013382 0 - 169375931 169396845 0 2 449,688, 0,20418, +chr1 169528492 169569754 NM_009107 0 + 169528882 169569404 0 10 439,248,145,180,161,130,133,92,106,498, 0,15342,26566,28930,32600,32868,34153,36073,37338,40764, +chr1 169548395 169569754 NM_001159731 0 + 169555130 169569404 0 9 231,145,180,161,130,133,92,106,498, 0,6663,9027,12697,12965,14250,16170,17435,20861, +chr1 169619688 169778864 NM_033652 0 + 169619905 169776892 0 8 293,187,233,173,78,70,171,2133, 0,2423,101779,140988,143259,151345,155074,157043, +chr1 170049494 170362300 NM_008783 0 - 170113703 170361635 0 8 2117,90,160,136,191,245,74,856, 0,64166,71914,76384,83983,89987,308505,311950, +chr1 170083657 170362300 NM_001291509 0 - 170088862 170361635 0 7 5298,90,136,191,245,74,856, 0,30003,42221,49820,55824,274342,277787, +chr1 170083657 170362300 NM_183355 0 - 170088862 170361635 0 9 5298,90,113,160,136,191,245,74,856, 0,30003,31429,37751,42221,49820,55824,274342,277787, +chr1 170083657 170362300 NM_001291508 0 - 170113703 170361635 0 8 5298,90,160,136,191,245,74,856, 0,30003,37751,42221,49820,55824,274342,277787, +chr1 170420773 170420893 NR_105766 0 + 170420893 170420893 0 1 120, 0, +chr1 170949104 170949220 NR_105772 0 - 170949220 170949220 0 1 116, 0, +chr1 171428064 171461595 NM_001355159 0 - 171428919 171455565 0 15 987,136,176,141,138,63,97,74,98,62,77,75,138,76,143, 0,6531,8048,9310,12466,14233,15511,16978,18627,24437,24921,25970,27378,30802,33388, +chr1 171428064 171461595 NM_023284 0 - 171428919 171455565 0 14 987,136,176,141,138,63,97,74,98,62,77,75,138,143, 0,6531,8048,9310,12466,14233,15511,16978,18627,24437,24921,25970,27378,33388, +chr1 171585631 171614077 NM_001313705 0 + 171585708 171613635 0 4 121,111,62,450, 0,21326,27254,27996, +chr1 171585631 171625944 NM_009063 0 + 171585708 171622471 0 5 121,111,62,167,3635, 0,21326,27254,34915,36678, +chr1 171671607 171677773 NM_009062 0 - 171673811 171677654 0 5 2444,167,62,105,163, 0,2874,3198,3740,6003, +chr1 171859069 171864784 NM_001033185 0 + 171860104 171864331 0 4 65,242,121,1012, 0,980,4056,4703, +chr1 171860049 171864784 NM_001347138 0 + 171860104 171864331 0 3 242,124,1012, 0,3073,3723, +chr1 171879667 171899336 NM_010476 0 - 171883163 171899263 0 9 3598,99,57,105,195,115,93,204,108, 0,6398,9886,10150,11468,14854,16150,17693,19561, +chr1 171899539 171902527 NR_040438 0 + 171902527 171902527 0 3 167,353,615, 0,1041,2373, +chr1 171902437 172019075 NM_022563 0 - 171907985 171966125 0 17 5683,150,235,189,128,224,211,131,63,244,184,106,148,232,103,109,150, 0,9670,12065,12570,14710,16102,18126,22278,23245,25624,29522,31857,32348,32766,34455,63606,116488, +chr1 172071353 172105095 NM_133806 0 - 172072610 172097036 0 11 1350,67,48,189,141,194,173,176,205,323,215, 0,2174,6773,8048,9089,9720,15701,17528,20144,25403,33527, +chr1 172071353 172105095 NM_001305045 0 - 172072610 172097036 0 11 1350,67,51,189,141,194,173,176,205,323,215, 0,2174,6773,8048,9089,9720,15701,17528,20144,25403,33527, +chr1 172071353 172105095 NM_001305046 0 - 172072610 172097036 0 10 1350,67,189,141,194,173,176,205,323,215, 0,2174,8048,9089,9720,15701,17528,20144,25403,33527, +chr1 172123552 172144865 NM_001360809 0 - 172129997 172144629 0 8 6592,89,99,77,95,192,293,237, 0,11693,13692,13924,15233,17609,18814,21076, +chr1 172123552 172145538 NM_010633 0 - 172129997 172145371 0 8 6592,89,99,77,95,192,293,435, 0,11693,13692,13924,15233,17609,18814,21551, +chr1 172163001 172181718 NM_001033499 0 + 172163001 172181718 0 4 134,64,163,38, 0,15262,17158,18679, +chr1 172184179 172185870 NR_151590 0 - 172185870 172185870 0 1 1691, 0, +chr1 172207448 172216900 NR_153837 0 + 172216900 172216900 0 3 192,163,2127, 0,5817,7325, +chr1 172207448 172216900 NM_012009 0 + 172207506 172214811 0 4 192,64,163,2127, 0,2466,5817,7325, +chr1 172228323 172236463 NM_001198955 0 - 172231276 172232958 0 3 3449,328,56, 0,4318,8084, +chr1 172238949 172242256 NM_001039593 0 + 172239012 172242179 0 2 166,589, 0,2718, +chr1 172245597 172487241 NR_154593 0 - 172487241 172487241 0 10 3424,166,3787,167,142,109,59,93,72,407, 0,4955,8444,13674,22646,33928,59781,75264,199148,241237, +chr1 172245597 172519980 NM_001109985 0 - 172248602 172519495 0 10 3424,166,180,167,142,109,59,93,72,590, 0,4955,12051,13674,22646,33928,59781,75264,199148,273793, +chr1 172574662 172612920 NM_177068 0 + 172575052 172612456 0 8 564,264,108,177,226,513,177,1066, 0,3150,5204,17827,22040,24219,36505,37192, +chr1 172634587 172797902 NM_001081304 0 - 172640009 172797832 0 16 5631,85,115,68,100,114,132,92,186,221,204,127,101,88,77,122, 0,42649,82889,84151,89500,90200,95157,110966,114790,130363,136224,137229,144660,148448,150656,163193, +chr1 172780692 172781112 NM_001372466 0 - 172780842 172781061 0 1 420, 0, +chr1 172804317 172815671 NR_151476 0 - 172815671 172815671 0 5 384,187,97,114,474, 0,5473,5943,6728,10880, +chr1 172804317 172815671 NM_001356485 0 - 172804622 172815538 0 5 384,97,119,114,474, 0,5943,6386,6728,10880, +chr1 172804317 172815671 NM_001356486 0 - 172804539 172811125 0 6 384,187,97,119,127,474, 0,5473,5943,6386,6728,10880, +chr1 172804317 172815671 NR_151477 0 - 172815671 172815671 0 5 384,187,97,127,474, 0,5473,5943,6728,10880, +chr1 172804318 172815671 NM_023173 0 - 172804539 172815538 0 6 383,187,97,119,114,474, 0,5472,5942,6385,6727,10879, +chr1 172837403 172843072 NM_001029984 0 - 172837403 172843072 0 6 431,279,267,255,21,31, 0,578,1359,4752,5349,5638, +chr1 172847724 172857714 NR_027666 0 - 172857714 172857714 0 5 801,285,267,186,188, 0,3240,3924,4628,9802, +chr1 172847724 172857714 NM_001160215 0 - 172848280 172857671 0 5 801,285,267,186,122, 0,3240,3924,4628,9868, +chr1 172847724 172857714 NM_145141 0 - 172848280 172857671 0 5 801,285,267,183,122, 0,3240,3924,4628,9868, +chr1 172890688 172906202 NM_010187 0 - 172891144 172906134 0 7 543,38,123,255,255,21,171, 0,638,5144,5888,7422,8916,15343, +chr1 172890688 172906202 NM_001077189 0 - 172891144 172906134 0 8 543,38,141,123,255,255,21,171, 0,638,2767,5144,5888,7422,8916,15343, +chr1 172949056 172959892 NM_144559 0 + 172949110 172959446 0 5 94,21,255,255,625, 0,602,970,6618,10211, +chr1 172981299 172989534 NM_010188 0 - 172981798 172989484 0 5 684,255,258,21,135, 0,2770,6522,7417,8100, +chr1 172981299 172989525 NM_001356511 0 - 172981798 172989484 0 5 684,255,255,21,126, 0,2770,6522,7417,8100, +chr1 172994721 172994783 NR_106103 0 - 172994783 172994783 0 1 62, 0, +chr1 173051791 173057098 NM_001081275 0 + 173053297 173056916 0 6 161,148,63,81,177,404, 0,1385,3373,3609,4373,4903, +chr1 173059287 173080734 NM_025321 0 - 173059931 173080709 0 6 749,164,62,102,57,45, 0,6836,9537,14401,16599,21402, +chr1 173080843 173091261 NM_008623 0 + 173085712 173090174 0 8 22,115,96,167,214,136,61,1189, 0,1109,4840,7648,8040,8785,9061,9229, +chr1 173085648 173091261 NM_001315500 0 + 173085712 173090366 0 6 131,167,214,136,61,1189, 0,2843,3235,3980,4256,4424, +chr1 173085648 173091261 NM_001315499 0 + 173085712 173090174 0 6 131,167,214,136,61,1189, 0,2843,3235,3980,4256,4424, +chr1 173103394 173126399 NM_025557 0 - 173104513 173126150 0 3 1262,55,258, 0,2306,22747, +chr1 173144100 173148976 NM_001243062 0 + 173144479 173148739 0 8 204,143,131,170,140,146,117,257, 0,373,974,2409,2776,3106,3344,4619, +chr1 173144100 173148976 NM_009803 0 + 173144479 173148849 0 9 204,143,131,170,140,146,117,106,257, 0,373,974,2409,2776,3106,3344,3656,4619, +chr1 173144100 173148976 NM_001243063 0 + 173144479 173148849 0 9 204,143,131,170,140,146,114,106,257, 0,373,974,2409,2776,3106,3347,3656,4619, +chr1 173147933 173152645 NM_001037170 0 - 173149651 173152149 0 10 1858,103,77,123,106,102,93,68,250,140, 0,1991,2306,2498,2744,3002,3365,3769,4101,4572, +chr1 173151694 173156510 NM_001305585 0 + 173155445 173156397 0 4 415,80,133,237, 0,3723,4102,4579, +chr1 173155184 173156510 NM_013474 0 + 173155445 173156397 0 4 68,83,133,237, 0,230,612,1089, +chr1 173155184 173156510 NM_001305549 0 + 173155445 173156397 0 4 68,80,133,237, 0,233,612,1089, +chr1 173155184 173156510 NR_131173 0 + 173156510 173156510 0 3 68,80,237, 0,233,1089, +chr1 173155184 173156510 NM_001305550 0 + 173155445 173156397 0 4 68,68,133,237, 0,245,612,1089, +chr1 173159702 173164480 NM_010185 0 - 173159995 173164376 0 5 356,21,36,92,153, 0,495,1424,1605,4625, +chr1 173164983 173177253 NM_153064 0 - 173165180 173177219 0 13 235,58,84,96,130,120,86,78,188,121,191,107,129, 0,420,1504,1753,2287,3092,3434,3662,3857,4421,6094,11238,12141, +chr1 173180259 173192398 NM_172845 0 + 173180979 173189309 0 9 1341,324,133,171,287,187,176,176,3516, 0,2408,2958,3764,6019,6399,6826,7590,8623, +chr1 173200458 173207026 NM_020579 0 + 173201873 173206510 0 8 87,171,295,236,191,123,105,790, 0,875,1379,2193,3625,3938,5554,5778, +chr1 173207122 173211317 NM_008911 0 - 173207187 173210891 0 13 208,43,150,111,119,61,191,145,133,116,135,95,314, 0,294,455,702,890,1143,2131,2438,2877,3148,3396,3682,3881, +chr1 173212083 173218092 NM_013919 0 - 173212342 173217080 0 13 350,115,108,79,87,104,65,159,112,121,60,621,200, 0,544,742,1062,1402,1685,2009,2625,2974,3302,3589,4397,5809, +chr1 173218694 173225133 NM_001360931 0 - 173219021 173224887 0 7 408,91,77,64,68,194,86, 0,607,954,1320,1585,6070,6353, +chr1 173218694 173225133 NM_025388 0 - 173219021 173224887 0 7 408,91,77,64,68,194,82, 0,607,954,1320,1585,6070,6357, +chr1 173218694 173225133 NM_001360932 0 - 173219021 173224887 0 7 408,91,77,64,68,189,82, 0,607,954,1320,1585,6070,6357, +chr1 173218694 173225133 NM_001360933 0 - 173219021 173220000 0 7 408,91,77,93,68,194,82, 0,607,954,1291,1585,6070,6357, +chr1 173258938 173272483 NM_001357550 0 + 173268446 173271335 0 5 91,389,108,147,1525, 0,9444,10015,11385,12020, +chr1 173259031 173272483 NM_001357551 0 + 173268446 173271335 0 5 63,389,108,147,1525, 0,9351,9922,11292,11927, +chr1 173259275 173272632 NM_011615 0 + 173268446 173271335 0 5 382,389,108,147,1674, 0,9107,9678,11048,11683, +chr1 173259275 173272632 NM_001128609 0 + 173268446 173271335 0 6 382,33,389,108,147,1674, 0,2108,9107,9678,11048,11683, +chr1 173259699 173272483 NM_001357553 0 + 173268446 173271335 0 5 124,389,108,147,1525, 0,8683,9254,10624,11259, +chr1 173259699 173272483 NM_001357552 0 + 173268446 173271335 0 6 124,33,389,108,147,1525, 0,1684,8683,9254,10624,11259, +chr1 173272367 173275776 NM_001242580 0 - 173272661 173274660 0 7 561,126,134,104,252,87,110, 0,1201,1457,1827,2051,2677,3299, +chr1 173272367 173275776 NM_012049 0 - 173272661 173275700 0 7 561,126,134,104,252,87,78, 0,1201,1457,1827,2051,2677,3331, +chr1 173275084 173289385 NM_001360825 0 + 173286729 173288157 0 4 91,89,124,1405, 0,11576,11751,12896, +chr1 173275805 173289385 NM_011070 0 + 173275842 173288157 0 4 112,89,124,1405, 0,10855,11030,12175, +chr1 173275805 173289385 NM_001360824 0 + 173275842 173288038 0 4 112,89,124,1467, 0,10855,11030,12113, +chr1 173288579 173290929 NM_001033039 0 - 173288944 173290792 0 4 532,199,160,664, 0,1006,1293,1686, +chr1 173300303 173318418 NM_001122680 0 + 173300798 173316936 0 8 571,360,291,121,149,154,76,1707, 0,9945,12205,13464,14511,14925,15490,16408, +chr1 173300303 173318418 NM_027893 0 + 173300798 173316936 0 9 571,360,291,121,149,154,76,75,1707, 0,9945,12205,13464,14511,14925,15490,15987,16408, +chr1 173319090 173340370 NM_001005508 0 + 173319397 173339472 0 12 404,103,145,83,108,128,175,104,78,369,278,2512, 0,8515,11596,12965,13197,14253,14821,15074,15261,15850,18398,18768, +chr1 173341443 173348890 NM_001305676 0 + 173344652 173348252 0 10 128,93,50,116,102,196,88,59,224,728, 0,3124,4192,4402,4822,5497,5929,6160,6328,6719, +chr1 173341443 173348890 NM_001305677 0 + 173344652 173348252 0 10 128,157,50,116,102,196,88,59,224,728, 0,3060,4192,4402,4822,5497,5929,6160,6328,6719, +chr1 173341443 173348890 NM_001305678 0 + 173346268 173348252 0 10 128,93,50,85,102,196,88,59,224,728, 0,3124,4192,4402,4822,5497,5929,6160,6328,6719, +chr1 173341811 173348890 NM_009480 0 + 173344652 173348252 0 10 182,93,50,116,102,196,88,59,224,728, 0,2756,3824,4034,4454,5129,5561,5792,5960,6351, +chr1 173349163 173350483 NM_001164525 0 + 173349202 173350373 0 4 103,123,163,162, 0,305,905,1158, +chr1 173353315 173367453 NR_151523 0 - 173367453 173367453 0 2 877,81, 0,14057, +chr1 173367691 173394724 NM_172647 0 + 173367771 173393225 0 10 141,69,108,147,206,103,108,13,52,1535, 0,22802,22977,23268,23640,24002,24244,25042,25328,25498, +chr1 173433608 173434881 NM_019484 0 + 173433787 173434444 0 1 1273, 0, +chr1 173448254 173465425 NM_010584 0 - 173448371 173464942 0 8 270,104,121,159,248,99,64,74, 0,10997,12370,12910,13382,15242,16630,17097, +chr1 173489323 173515447 NM_018729 0 + 173489455 173513015 0 9 193,324,276,105,155,72,63,57,2513, 0,14488,14900,18050,18622,19906,21565,22450,23611, +chr1 173518743 173537541 NM_001277968 0 - 173519190 173537454 0 9 513,72,335,54,99,270,339,276,211, 0,4810,5242,7877,9071,11034,12369,13174,18587, +chr1 173518743 173537465 NR_102726 0 - 173537465 173537465 0 10 513,72,335,54,99,270,339,276,330,227, 0,4810,5242,7877,9071,11034,12369,13174,16377,18495, +chr1 173518743 173537541 NM_008534 0 - 173519190 173537454 0 10 513,72,335,54,99,270,339,276,330,211, 0,4810,5242,7877,9071,11034,12369,13174,16377,18587, +chr1 173562533 173583168 NM_144539 0 - 173565055 173579058 0 8 2594,63,104,123,273,312,127,381, 0,3909,4894,6260,6593,8553,16470,20254, +chr1 173562535 173579130 NM_001347184 0 - 173565068 173579058 0 6 2592,63,123,273,312,127, 0,3907,6258,6591,8551,16468, +chr1 173571970 173572031 NR_106151 0 - 173572031 173572031 0 1 61, 0, +chr1 173612122 173635388 NM_001360767 0 + 173612224 173635008 0 3 175,303,460, 0,13672,22806, +chr1 173612122 173635388 NM_007649 0 + 173612224 173635008 0 4 175,303,267,460, 0,13672,17392,22806, +chr1 173641200 173641660 NM_001372440 0 + 173641218 173641413 0 1 460, 0, +chr1 173697262 173723260 NM_001360898 0 + 173697357 173722595 0 5 171,342,297,96,835, 0,7651,9950,20808,25163, +chr1 173697262 173731315 NM_013730 0 + 173697357 173729754 0 7 171,342,297,96,74,96,1612, 0,7651,9950,20808,25163,31011,32441, +chr1 173769827 173785228 NM_001252472 0 + 173770788 173782310 0 3 102,124,3295, 0,883,12106, +chr1 173769827 173820849 NM_001289470 0 + 173770788 173816557 0 9 102,124,333,252,135,92,63,66,2121, 0,883,12106,33000,33608,44891,45874,46664,48901, +chr1 173769827 173820849 NM_013489 0 + 173770788 173816557 0 9 102,124,333,252,135,95,63,66,2121, 0,883,12106,33000,33608,44888,45874,46664,48901, +chr1 173843662 173849487 NR_151536 0 - 173849487 173849487 0 3 92,243,105, 0,1268,5720, +chr1 173843662 173849487 NR_151535 0 - 173849487 173849487 0 3 92,333,105, 0,1178,5720, +chr1 173847592 173879089 NM_001347187 0 + 173847838 173878204 0 8 331,342,264,114,30,74,77,266, 0,16637,19007,20540,20990,21934,30537,31231, +chr1 173847592 173879089 NM_001347186 0 + 173847838 173878204 0 9 331,342,264,114,30,74,72,77,266, 0,16637,19007,20540,20990,21934,24163,30537,31231, +chr1 173847592 173874041 NM_030710 0 + 173847838 173872723 0 8 331,342,264,114,30,74,72,1333, 0,16637,19007,20540,20990,21934,24163,25116, +chr1 173931090 173957426 NM_033509 0 - 173934732 173943284 0 8 3903,232,136,137,608,121,263,298, 0,5130,6951,7547,8481,11868,12123,26038, +chr1 173982422 173987727 NM_010916 0 - 173984026 173984428 0 2 2177,310, 0,4995, +chr1 173996143 174012880 NM_021607 0 - 173996804 174012813 0 17 784,213,155,88,96,103,173,78,105,153,110,151,146,122,124,105,149, 0,1318,1776,2173,2549,2749,3963,5238,5452,6108,6453,6764,8260,8902,9392,15199,16588, +chr1 174012659 174052463 NM_009938 0 + 174013040 174051890 0 33 421,114,74,81,77,110,110,100,136,83,151,67,76,83,140,86,139,163,147,190,96,89,124,90,110,78,69,137,187,111,162,195,633, 0,5023,6568,8410,8635,9716,15145,17139,18850,19681,21580,22657,23588,25783,27257,27960,28148,29336,29595,30497,30805,32216,32494,34397,34658,35486,35724,36312,36658,36929,37348,38701,39171, +chr1 174056885 174066628 NM_001356514 0 + 174056909 174064421 0 7 94,110,166,86,162,177,2291, 0,1876,2400,3147,3857,6375,7452, +chr1 174056885 174066628 NM_001356513 0 + 174056909 174064413 0 8 94,110,166,86,162,177,45,2239, 0,1876,2400,3147,3857,6375,7245,7504, +chr1 174056885 174066628 NM_023041 0 + 174056909 174064421 0 8 94,110,166,86,162,177,45,2291, 0,1876,2400,3147,3857,6375,7245,7452, +chr1 174056885 174066628 NM_001159525 0 + 174056909 174064421 0 6 94,86,162,177,45,2291, 0,3147,3857,6375,7245,7452, +chr1 174078145 174126524 NM_153555 0 + 174095997 174124803 0 14 154,73,71,653,141,95,111,73,58,108,131,120,117,1838, 0,1234,17833,24314,25928,27468,31892,38281,38840,39338,40924,44503,45770,46541, +chr1 174078145 174126524 NR_151641 0 + 174126524 174126524 0 14 154,73,71,653,141,95,111,73,108,131,236,120,117,1838, 0,1234,17833,24314,25928,27468,31892,38281,39338,40924,42829,44503,45770,46541, +chr1 174078145 174126524 NM_001357204 0 + 174095997 174124803 0 14 324,73,71,653,141,95,111,73,58,108,131,120,117,1838, 0,1234,17833,24314,25928,27468,31892,38281,38840,39338,40924,44503,45770,46541, +chr1 174126858 174136935 NM_011063 0 - 174128756 174130710 0 4 1963,156,174,208, 0,2383,3680,9869, +chr1 174126858 174136935 NM_001329871 0 - 174128756 174130710 0 4 1963,156,108,208, 0,2383,3746,9869, +chr1 174126858 174136935 NM_001329869 0 - 174128756 174130710 0 4 1963,156,174,246, 0,2383,3680,9831, +chr1 174140024 174150026 NM_009813 0 - 174140475 174149821 0 11 610,75,101,55,46,131,74,112,101,85,484, 0,2054,3134,3443,3912,5118,5583,6015,6900,7996,9518, +chr1 174153638 174188555 NM_013734 0 - 174153928 174188165 0 23 319,92,102,131,146,124,155,169,151,137,173,190,135,110,202,269,118,135,114,207,60,176,70, 0,589,3575,3792,7624,8417,8678,10445,10898,11431,16193,16497,20519,20830,21323,23124,27378,27776,30545,31349,34135,34377,34847, +chr1 174201839 174228195 NM_178405 0 - 174204831 174228023 0 23 3021,92,102,131,146,124,155,169,151,137,176,190,135,110,199,269,118,135,114,204,60,105,184, 0,4209,4412,6548,6826,7162,7604,7959,8227,8860,12791,13060,13945,14255,14489,15491,17592,18544,18902,19484,21618,21863,26172, +chr1 174242497 174249974 NM_080419 0 + 174242666 174249539 0 7 227,378,462,408,414,131,260, 0,3784,4988,5670,6187,6926,7217, +chr1 174250638 174259453 NM_001360808 0 - 174252993 174256686 0 4 2687,878,131,188, 0,5198,7490,8627, +chr1 174250638 174259453 NM_008429 0 - 174252993 174256686 0 4 2687,878,101,188, 0,5198,7490,8627, +chr1 174271340 174304216 NM_001039484 0 + 174299051 174300191 0 2 242,5165, 0,27711, +chr1 174306661 174314230 NM_026234 0 + 174306829 174308101 0 1 7569, 0, +chr1 174405490 174408540 NM_029612 0 + 174405627 174408390 0 4 180,342,273,350, 0,773,1846,2700, +chr1 174412343 174429008 NM_001145800 0 + 174414619 174428669 0 21 48,266,189,153,155,118,142,146,143,141,117,151,124,176,251,85,177,43,861,128,521, 0,2068,2569,7300,8076,8442,9402,9652,9888,11274,11885,12193,12540,12895,13321,13770,13938,14385,14673,15784,16144, +chr1 174412447 174429008 NM_033608 0 + 174414619 174428669 0 21 114,266,189,153,155,118,142,146,143,141,117,151,124,176,251,85,177,43,861,128,521, 0,1964,2465,7196,7972,8338,9298,9548,9784,11170,11781,12089,12436,12791,13217,13666,13834,14281,14569,15680,16040, +chr1 174430376 174437506 NM_178598 0 + 174435278 174436839 0 5 87,208,175,103,809, 0,4874,5515,5940,6321, +chr1 174451260 174476001 NM_027972 0 + 174451309 174475884 0 12 52,126,143,145,171,179,130,147,114,194,225,196, 0,6660,8680,10951,11401,12816,14081,17349,19357,20055,23962,24545, +chr1 174471750 174480937 NR_040558 0 - 174480937 174480937 0 3 554,97,290, 0,1287,8897, +chr1 174486068 174493848 NM_177723 0 + 174486202 174493435 0 7 183,176,202,222,120,199,699, 0,3670,4296,4620,5558,6021,7081, +chr1 174490036 174493848 NR_027644 0 + 174493848 174493848 0 6 78,202,222,120,199,699, 0,328,652,1590,2053,3113, +chr1 174511507 174520699 NM_029084 0 - 174512574 174520563 0 5 1129,108,306,327,170, 0,2775,2963,6532,9022, +chr1 174526770 174532682 NM_001164725 0 - 174527786 174532591 0 7 1061,32,123,282,273,21,122, 0,1143,1563,1982,2413,3397,5790, +chr1 174560899 174563105 NM_026725 0 - 174561771 174563013 0 2 1058,359, 0,1847, +chr1 174628186 174630097 NM_007768 0 + 174628267 174629158 0 2 145,1553, 0,358, +chr1 174824091 174825185 NM_011318 0 - 174824233 174825018 0 2 750,234, 0,860, +chr1 174886898 174887948 NM_008763 0 + 174886927 174887857 0 1 1050, 0, +chr1 175060330 175067465 NM_146764 0 - 175060413 175061346 0 2 1037,225, 0,6910, +chr1 175113572 175114635 NM_146763 0 - 175113630 175114563 0 1 1063, 0, +chr1 175133488 175134430 NM_001001809 0 + 175133488 175134430 0 1 942, 0, +chr1 175145737 175146771 NM_146881 0 + 175145783 175146725 0 1 1034, 0, +chr1 175151401 175157360 NM_010184 0 - 175151620 175157306 0 5 389,255,258,21,103, 0,1268,4029,5456,5856, +chr1 175200277 175201268 NM_146651 0 + 175200307 175201240 0 1 991, 0, +chr1 175204591 175207887 NM_001205011 0 - 175204591 175207853 0 2 596,98, 0,3198, +chr1 175262016 175263634 NM_010045 0 - 175262076 175263541 0 2 1044,114, 0,1504, +chr1 175264384 175297826 NM_053199 0 - 175267151 175297625 0 9 2886,126,170,91,171,138,153,141,283, 0,3766,6800,7415,10066,10666,11491,12168,33159, +chr1 175350734 175396167 NM_001013779 0 + 175385484 175395149 0 9 83,140,121,90,282,152,414,189,1066, 0,7155,32224,33620,34730,39094,41303,43255,44367, +chr1 175398615 175421449 NM_001372437 0 - 175398821 175417003 0 8 308,189,417,1686,107,285,52,332, 0,2890,5151,11886,17044,18123,20436,22502, +chr1 175398615 175421068 NM_001372436 0 - 175398821 175417003 0 8 308,189,417,1686,107,285,52,186, 0,2890,5151,11886,17044,18123,20436,22267, +chr1 175451441 175466088 NM_001024721 0 - 175451769 175459666 0 5 349,240,137,282,286, 0,5153,6531,7963,14361, +chr1 175496413 175529403 NR_160907 0 - 175529403 175529403 0 9 987,292,107,125,68,954,107,285,253, 0,2526,4764,8511,15848,23224,27655,28738,32737, +chr1 175504086 175529403 NM_001368798 0 - 175504916 175525428 0 6 963,68,954,107,285,253, 0,8175,15551,19982,21065,25064, +chr1 175510487 175529403 NR_160908 0 - 175529403 175529403 0 4 1842,954,285,253, 0,9150,14664,18663, +chr1 175510487 175529403 NM_001368799 0 - 175512257 175525428 0 5 1842,954,107,285,253, 0,9150,13581,14664,18663, +chr1 175522087 175529403 NM_001177350 0 - 175524044 175525428 0 3 2088,285,253, 0,3064,7063, +chr1 175522087 175529403 NM_001177349 0 - 175524044 175525428 0 4 2088,285,52,253, 0,3064,4999,7063, +chr1 175560989 175578059 NM_175026 0 + 175567436 175576142 0 7 297,282,137,240,414,189,1938, 0,6427,8007,10146,11628,13789,15132, +chr1 175603810 175628523 NM_001162938 0 + 175607816 175627598 0 7 287,285,107,954,68,298,988, 0,3998,5250,8985,16987,21892,23725, +chr1 175653558 175671940 NM_001204910 0 - 175653862 175666582 0 8 325,189,417,1659,168,218,285,222, 0,1506,3981,5454,8847,11668,12759,18160, +chr1 175677424 175697050 NM_008329 0 - 175677730 175691994 0 9 327,189,417,189,423,159,197,285,109, 0,1901,4334,5416,8313,12175,12836,14305,19517, +chr1 175787350 175810318 NM_001170853 0 - 175787515 175805968 0 10 291,189,423,159,168,168,122,285,66,37, 0,2956,5241,8179,14158,15632,17131,18356,22705,22931, +chr1 175787352 175810089 NM_001374640 0 - 175787515 175805968 0 8 289,189,423,168,168,122,313,34, 0,2954,5239,14156,15630,17129,18354,22703, +chr1 175826471 175843177 NM_001301745 0 - 175826729 175837992 0 7 303,189,423,159,191,285,233, 0,3003,5279,9132,9791,11256,16473, +chr1 175826471 175843177 NM_001033450 0 - 175826729 175837992 0 7 303,189,423,159,197,285,233, 0,3003,5279,9132,9791,11256,16473, +chr1 175850530 175872623 NM_001302649 0 - 175852666 175868137 0 10 2205,189,417,1242,144,168,122,285,65,38, 0,3549,6406,7875,13383,14610,16118,17342,21830,22055, +chr1 175850530 175872803 NM_001302650 0 - 175852666 175868137 0 9 2205,189,417,144,168,122,285,65,17, 0,3549,6406,13383,14610,16118,17342,21830,22256, +chr1 175850530 175872623 NM_001302651 0 - 175852666 175868137 0 8 2205,189,417,168,122,285,65,38, 0,3549,6406,14610,16118,17342,21830,22055, +chr1 175892699 175912975 NM_011940 0 - 175892933 175907515 0 7 255,189,405,189,414,170,171, 0,1225,8784,9622,12164,14696,20105, +chr1 175892699 175912975 NM_008327 0 - 175892933 175907515 0 7 255,189,405,189,414,173,171, 0,1225,8784,9622,12164,14696,20105, +chr1 175942128 175961886 NM_172648 0 - 175942374 175958593 0 7 291,189,423,159,134,285,132, 0,2961,5236,14530,15195,16200,19626, +chr1 175972063 175973067 NM_146717 0 + 175972082 175973027 0 1 1004, 0, +chr1 175980505 175981444 NM_146716 0 + 175980505 175981444 0 1 939, 0, +chr1 175999430 176000384 NM_146718 0 + 175999430 176000384 0 1 954, 0, +chr1 176019168 176020111 NM_146722 0 + 176019172 176020111 0 1 943, 0, +chr1 176029590 176030539 NM_207158 0 + 176029590 176030538 0 1 949, 0, +chr1 176029590 176030541 NM_001206926 0 + 176029590 176030541 0 2 926,23, 0,928, +chr1 176047221 176048145 NM_001005520 0 - 176047221 176048145 0 1 924, 0, +chr1 176066876 176067824 NM_146721 0 + 176066876 176067824 0 1 948, 0, +chr1 176081611 176082661 NR_047667 0 + 176082661 176082661 0 1 1050, 0, +chr1 176081611 176082661 NM_146720 0 + 176081648 176082596 0 1 1050, 0, +chr1 176088852 176089898 NM_146305 0 + 176088905 176089871 0 1 1046, 0, +chr1 176102906 176178580 NM_011465 0 + 176103071 176177588 0 52 186,237,126,141,147,134,145,155,136,102,138,111,78,156,205,182,244,123,218,93,138,152,187,102,92,145,182,100,198,144,104,163,132,138,105,209,121,122,133,99,163,77,210,297,113,18,52,188,54,147,145,1118, 0,1551,2987,5882,6955,8228,8929,11805,12855,14422,17320,18172,20144,20753,23080,24827,25586,26645,29475,30477,32495,34261,35536,36518,38788,39762,40568,41086,41280,42702,44356,44749,45101,45627,45948,46990,49803,50485,51652,56466,57850,58546,65009,67341,68265,69452,70372,71268,72363,72871,73698,74556, +chr1 176180019 176181107 NM_146715 0 - 176180114 176181056 0 1 1088, 0, +chr1 176260648 176263008 NM_025470 0 + 176260703 176262920 0 2 119,684, 0,1676, +chr1 176299049 176299979 NM_207137 0 + 176299049 176299979 0 1 930, 0, +chr1 176321176 176322186 NM_146714 0 + 176321201 176322131 0 1 1010, 0, +chr1 176360560 176361515 NM_146761 0 + 176360560 176361514 0 1 955, 0, +chr1 176378755 176379733 NM_207694 0 + 176378755 176379733 0 1 978, 0, +chr1 176431955 176752860 NM_019445 0 + 176432176 176751376 0 18 1767,167,148,56,1571,145,88,62,92,130,147,60,121,93,52,150,82,1511, 0,35220,80091,91236,106557,110682,145281,164818,192362,192607,193761,196944,197731,218020,242430,289433,318129,319394, +chr1 176763915 176851950 NM_011825 0 - 176766905 176767412 0 2 3498,247, 0,87788, +chr1 176989206 177422676 NM_011880 0 - 176989874 177421261 0 17 719,90,187,126,111,62,99,75,82,77,65,52,107,51,97,124,285, 0,19113,20329,24896,27040,30343,31918,34728,62652,62819,63855,90576,94048,130101,211741,431977,433185, +chr1 176989206 177422676 NM_001347195 0 - 177006153 177421261 0 18 719,81,90,187,126,111,62,99,75,82,77,65,52,107,51,97,124,285, 0,16941,19113,20329,24896,27040,30343,31918,34728,62652,62819,63855,90576,94048,130101,211741,431977,433185, +chr1 176989206 177422676 NM_001199003 0 - 176996771 177421261 0 18 719,78,90,187,126,111,62,99,75,82,77,65,52,107,51,97,124,285, 0,7541,19113,20329,24896,27040,30343,31918,34728,62652,62819,63855,90576,94048,130101,211741,431977,433185, +chr1 176989206 177422676 NM_001357129 0 - 176996771 177421261 0 16 719,78,90,187,126,111,62,99,75,82,77,65,51,97,124,285, 0,7541,19113,20329,24896,27040,30343,31918,34728,62652,62819,63855,130101,211741,431977,433185, +chr1 177531508 177555766 NM_010209 0 - 177531554 177555704 0 10 189,154,128,204,166,183,177,111,135,185, 0,2560,4677,6439,8259,10769,13359,15151,17673,24073, +chr1 177562323 177590984 NM_133809 0 + 177562350 177589953 0 15 81,70,98,90,49,88,166,72,122,148,58,83,102,60,1211, 0,5316,5694,6907,11365,14920,16959,18372,19394,21334,22876,24528,26128,26320,27450, +chr1 177592552 177622763 NM_010098 0 - 177593021 177622667 0 4 733,252,320,463, 0,1105,2888,29748, +chr1 177612368 177618484 NM_021350 0 - 177616618 177618484 0 1 6116, 0, +chr1 177628723 177745864 NM_029453 0 + 177628917 177745497 0 28 339,131,103,104,30,111,215,135,80,140,127,149,124,176,177,131,102,70,37,137,106,59,110,189,106,81,99,448, 0,7352,18686,21685,26074,27796,30190,32889,44953,56931,65349,68413,70913,73580,76982,86885,91311,92600,93524,94368,96490,100624,101708,107261,110083,111935,113419,116693, +chr1 177810908 177841527 NM_012012 0 + 177813038 177838696 0 15 79,69,174,120,124,138,213,188,94,226,244,574,102,194,2967, 0,354,2117,5912,6800,7946,11156,12096,12963,15350,18611,20102,23558,25018,27652, +chr1 177850459 177852356 NM_001290692 0 + 177850500 177851952 0 2 1360,429, 0,1468, +chr1 177892436 178144073 NM_001357847 0 - 177893958 177975076 0 9 1779,115,169,137,198,128,87,144,323, 0,8172,13153,22141,31546,82529,112133,177649,251314, +chr1 177892436 178144073 NM_001357845 0 - 177893958 178070135 0 10 1779,115,169,137,198,128,112,169,144,323, 0,8172,13153,22141,31546,82529,112108,127565,177649,251314, +chr1 177892436 178205443 NM_001357846 0 - 177893958 177975076 0 9 1779,115,169,137,198,128,87,144,627, 0,8172,13153,22141,31546,82529,112133,177649,312380, +chr1 177892436 178205443 NM_001357844 0 - 177893958 178070135 0 10 1779,115,169,137,198,128,112,169,144,627, 0,8172,13153,22141,31546,82529,112108,127565,177649,312380, +chr1 177892436 178144073 NM_001195816 0 - 177893958 178143753 0 10 1779,115,169,137,198,128,112,169,137,323, 0,8172,13153,22141,31546,82529,112108,127565,177656,251314, +chr1 177892436 178205443 NM_176916 0 - 177893958 178205005 0 10 1779,115,169,137,198,128,112,169,137,627, 0,8172,13153,22141,31546,82529,112108,127565,177656,312380, +chr1 178360241 178457400 NR_151528 0 - 178457400 178457400 0 4 682,56,83,134, 0,23955,88055,97025, +chr1 178663783 178727439 NM_001368873 0 - 178665810 178723740 0 19 2329,52,94,89,171,178,235,1818,121,150,158,477,135,160,57,81,90,145,1699, 0,3191,3875,5428,6266,8818,16273,21513,24744,27698,36060,40781,46608,48598,48844,54812,58883,59852,61957, +chr1 178663783 178744084 NM_001368872 0 - 178665810 178723740 0 18 2329,52,94,89,171,97,235,1818,121,158,477,135,160,57,81,90,145,58, 0,3191,3875,5428,6266,8899,16273,21513,24744,36060,40781,46608,48598,48844,54812,58883,59852,80243, +chr1 178663783 178737255 NM_001099637 0 - 178665810 178723740 0 20 2329,52,94,89,171,148,235,1818,121,150,294,158,477,135,160,57,81,90,145,126, 0,3191,3875,5428,6266,8848,16273,21513,24744,27698,35580,36060,40781,46608,48598,48844,54812,58883,59852,73346, +chr1 178702455 178702554 NR_029775 0 - 178702554 178702554 0 1 99, 0, +chr1 178744790 178886491 NR_151682 0 + 178886491 178886491 0 17 396,153,86,114,126,141,65,189,139,153,208,135,117,143,128,109,569, 0,10092,11539,14210,16397,25625,30164,30521,39104,53552,57393,59904,63330,104884,131448,133621,141132, +chr1 178744790 178950569 NM_001357390 0 + 178745119 178950275 0 19 396,153,86,114,126,141,65,189,139,153,135,117,27,143,128,109,132,127,324, 0,10092,11539,14210,16397,25625,30164,30521,39104,53552,59904,63330,74101,104884,131448,133621,141132,197229,205455, +chr1 178744790 178950563 NM_029756 0 + 178745119 178950275 0 18 396,153,86,114,126,141,65,189,139,153,135,117,143,128,109,132,127,318, 0,10092,11539,14210,16397,25625,30164,30521,39104,53552,59904,63330,104884,131448,133621,141132,197229,205455, +chr1 178764754 178766264 NR_037996 0 - 178766264 178766264 0 1 1510, 0, +chr1 178950206 179178898 NM_011785 0 - 178955494 179178852 0 13 5374,103,88,215,129,123,69,66,132,145,112,126,92, 0,11574,23699,29962,39258,47135,58698,60125,76891,82886,89551,110895,228600, +chr1 179372481 179380896 NM_001355099 0 + 179377233 179378802 0 2 245,3677, 0,4738, +chr1 179372481 179380895 NM_001355098 0 + 179374940 179378802 0 4 245,118,84,3676, 0,873,2388,4738, +chr1 179372481 179380895 NM_001355100 0 + 179377233 179378802 0 3 245,118,3676, 0,873,4738, +chr1 179372481 179380895 NM_001355101 0 + 179377233 179378802 0 4 245,118,108,3676, 0,873,1634,4738, +chr1 179374783 179380896 NM_001355103 0 + 179374940 179378029 0 3 170,688,2877, 0,2436,3236, +chr1 179374791 179380897 NM_001012330 0 + 179374940 179378802 0 2 162,3678, 0,2428, +chr1 179375068 179380896 NM_001355102 0 + 179377233 179378802 0 2 118,3677, 0,2151, +chr1 179375951 179380897 NM_013915 0 + 179377233 179378802 0 1 4946, 0, +chr1 179509582 179509660 NR_162777 0 - 179509660 179509660 0 1 78, 0, +chr1 179571672 179573074 NR_037994 0 - 179573074 179573074 0 3 356,105,237, 0,468,1165, +chr1 179659944 179683436 NM_027077 0 + 179663627 179683159 0 6 148,78,96,173,120,134, 0,3661,11181,13440,23102,23358, +chr1 179693308 179726640 NM_007422 0 - 179694375 179726525 0 13 1120,150,98,125,155,127,82,108,67,51,69,103,298, 0,4477,6747,7963,8894,10397,12403,13279,13635,19665,20871,21718,33034, +chr1 179738549 179892384 NM_001368823 0 + 179738680 179892364 0 22 199,49,74,70,65,25,78,107,493,481,455,59,76,53,51,34,80,100,87,158,54,174, 0,11280,16900,17722,20261,34424,41811,49011,51419,63413,71322,73134,78146,99306,128182,129228,129330,134436,139815,143344,151402,153661, +chr1 179921528 180102836 NM_001368822 0 + 179921647 180102436 0 23 187,49,74,70,65,25,78,78,107,493,478,455,59,76,53,51,34,80,100,87,158,54,554, 0,11597,23730,24517,26279,48911,55522,86057,105192,106986,112226,119750,121716,124800,131362,148979,150011,150113,157485,163064,165246,178436,180754, +chr1 179921528 180102836 NR_160909 0 + 180102836 180102836 0 24 187,49,74,70,65,25,78,25,78,107,493,478,455,59,76,53,51,34,80,100,87,158,54,554, 0,11597,23730,24517,26279,48911,55522,79131,86057,105192,106986,112226,119750,121716,124800,131362,148979,150011,150113,157485,163064,165246,178436,180754, +chr1 179921528 180102836 NR_155538 0 + 180102836 180102836 0 22 187,49,74,70,65,25,78,78,107,493,478,455,59,76,53,51,182,100,87,158,54,554, 0,11597,23730,24517,26279,48911,55522,86057,105192,106986,112226,119750,121716,124800,131362,148979,150011,157485,163064,165246,178436,180754, +chr1 179921565 179978422 NM_001034899 0 + 179921647 179977279 0 8 150,49,74,70,65,25,78,1152, 0,11560,23693,24480,26242,48874,55485,55705, +chr1 180117547 180182728 NM_024282 0 + 180118046 180179599 0 5 541,73,94,142,3363, 0,50495,55195,56924,61818, +chr1 180249283 180252824 NM_025511 0 + 180249300 180252747 0 4 56,115,64,213, 0,2592,2789,3328, +chr1 180251238 180267946 NR_149827 0 - 180267946 180267946 0 17 2088,94,51,71,72,182,255,169,129,120,264,113,100,140,74,112,863, 0,2512,2858,4135,8760,9057,9484,9985,10241,10727,10985,11889,12439,12779,14774,14939,15845, +chr1 180256864 180267946 NM_016805 0 - 180259484 180267702 0 14 2674,72,182,255,169,129,120,264,113,100,140,74,112,863, 0,3134,3431,3858,4359,4615,5101,5359,6263,6813,7153,9148,9313,10219, +chr1 180336148 180414644 NM_026626 0 + 180336233 180411559 0 7 116,85,73,80,43,67,3201, 0,31384,49798,68864,69667,69807,75295, +chr1 180459255 180862988 NM_001161665 0 + 180459693 180862359 0 15 501,402,534,167,184,207,94,263,184,160,163,3415,203,151,778, 0,1264,149701,186678,292358,335721,340221,341472,344847,354790,384564,385637,399034,399719,402955, +chr1 180882090 181448172 NM_027188 0 - 180887591 181448082 0 12 5603,109,175,88,111,103,68,137,58,108,64,254, 0,20228,91777,98331,134364,140906,142375,453323,458447,459718,471395,565828, +chr1 181458184 181476407 NM_008249 0 - 181459307 181476262 0 8 1301,161,63,90,149,151,89,455, 0,3250,4011,5579,9645,14253,16844,17768, +chr1 181458184 181476407 NM_001331054 0 - 181459307 181476262 0 7 1301,161,90,149,151,89,455, 0,3250,5579,9645,14253,16844,17768, +chr1 181458184 181476407 NM_001331055 0 - 181459307 181472573 0 7 1301,161,63,90,149,151,455, 0,3250,4011,5579,9645,14253,17768, +chr1 181476659 181557604 NM_146105 0 + 181509520 181555335 0 11 88,431,182,31,87,115,22,97,881,136,2475, 0,32809,46156,55173,57990,58424,59719,59908,63257,76238,78470, +chr1 181598361 181617315 NM_178653 0 + 181598486 181616808 0 12 315,113,81,130,50,131,118,120,57,112,82,613, 0,2352,8160,9810,10649,11354,12261,13202,13420,15974,17465,18341, +chr1 181625167 181675331 NM_001370897 0 - 181625789 181675331 0 23 778,176,148,107,167,135,275,108,119,145,124,55,91,113,107,68,112,155,225,36,204,192,84, 0,2740,3571,3942,4257,5200,7345,10073,10712,13360,14314,16254,17415,17791,18836,21675,33172,36209,37961,39326,40893,44891,50080, +chr1 181675034 181734146 NM_026375 0 - 181676463 181729462 0 36 1625,77,134,1762,206,95,100,418,204,193,108,151,151,132,145,188,147,57,124,94,105,141,90,91,129,62,182,133,151,85,117,208,181,254,128,663, 0,2276,3653,7407,10545,13031,15358,17641,18566,20974,23391,24085,24405,25685,25895,30428,31104,32599,32796,34700,35952,36739,38043,39186,40104,41166,41791,42064,43285,44745,45395,47442,48739,50773,54307,58449, +chr1 181890890 182095734 NM_001359548 0 + 181961677 182092297 0 38 528,92,158,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,48,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,63885,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,157976,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001359543 0 + 181891240 182092297 0 37 528,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,48,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,157976,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001359547 0 + 181961677 182092297 0 39 528,92,158,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,48,39,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,63885,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,157976,163164,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001346805 0 + 181891240 182092297 0 35 528,92,84,96,149,94,201,249,80,167,123,134,111,248,106,125,106,149,92,77,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133621,140265,145287,148394,150504,150985,153263,156907,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001359544 0 + 181891240 182092297 0 36 528,92,84,96,149,94,201,249,80,167,123,134,111,248,106,125,106,149,92,77,84,106,137,140,82,217,63,594,98,85,124,118,186,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133621,140265,145287,148394,150504,150985,153263,156907,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,195035,198846,200780,201275, +chr1 181890890 182095734 NM_001359542 0 + 181891240 182092297 0 38 528,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,48,39,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,157976,163164,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001359549 0 + 181961677 182092297 0 37 528,92,158,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,17,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,63885,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,163186,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NR_153194 0 + 182095734 182095734 0 36 528,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,48,84,106,137,140,82,217,63,594,98,85,124,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,157976,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,198846,200780,201275, +chr1 181890890 182095734 NM_001359546 0 + 181929521 182092297 0 38 528,73,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,39,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,10122,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,163164,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001359545 0 + 181891240 182092297 0 36 528,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,17,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,163186,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001346804 0 + 181891240 182092297 0 36 528,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,198846,200780,201275, +chr1 181890890 182095734 NM_001359541 0 + 181891240 182092297 0 37 528,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,84,106,137,140,82,217,63,594,98,85,124,118,186,118,158,3569, 0,38602,70745,76069,79292,101030,104206,106391,108537,111585,113810,123612,133184,133621,140265,145287,148394,150504,150985,153263,156907,173537,175892,176970,177672,178963,180582,181517,183647,186185,188393,189375,190400,195035,198846,200780,201275, +chr1 181891219 182095733 NM_001033285 0 + 181891240 182092297 0 37 199,92,84,96,149,94,201,249,80,167,123,134,243,111,248,106,125,106,149,92,77,39,84,106,137,140,82,217,63,594,98,85,124,118,118,158,3568, 0,38273,70416,75740,78963,100701,103877,106062,108208,111256,113481,123283,132855,133292,139936,144958,148065,150175,150656,152934,156578,162835,173208,175563,176641,177343,178634,180253,181188,183318,185856,188064,189046,190071,198517,200451,200946, +chr1 182095368 182123616 NM_001163290 0 - 182097299 182112369 0 15 2219,87,66,108,142,94,82,141,86,123,75,67,402,186,50, 0,3084,3333,3535,3842,4178,4395,4824,5105,6326,9013,13339,13645,16824,28198, +chr1 182095368 182126151 NM_023341 0 - 182097299 182112369 0 15 2219,87,66,108,142,94,82,141,86,123,75,67,402,186,148, 0,3084,3333,3535,3842,4178,4395,4824,5105,6326,9013,13339,13645,16824,30635, +chr1 182096744 182126151 NM_001359268 0 - 182097299 182109687 0 16 843,87,66,108,142,94,82,141,86,123,75,67,402,93,186,148, 0,1708,1957,2159,2466,2802,3019,3448,3729,4950,7637,11963,12269,12886,15448,29259, +chr1 182096744 182126151 NM_001359269 0 - 182097299 182109190 0 14 843,87,66,108,142,94,82,141,86,123,75,67,402,148, 0,1708,1957,2159,2466,2802,3019,3448,3729,4950,7637,11963,12269,29259, +chr1 182157134 182186431 NM_001128605 0 - 182157703 182175885 0 11 725,119,102,84,99,221,68,142,215,144,78, 0,1839,2382,2838,6607,7985,8907,11869,13727,18610,29219, +chr1 182157134 182176081 NM_011183 0 - 182157703 182175885 0 11 725,119,102,84,99,221,68,142,215,144,87, 0,1839,2382,2838,6607,7985,8907,11869,13727,18610,18860, +chr1 182257099 182260680 NR_003623 0 - 182260680 182260680 0 1 3581, 0, +chr1 182260606 182353790 NM_001081175 0 + 182262441 182352021 0 8 304,2119,100,214,205,102,72,1985, 0,1636,82198,83311,87678,89782,90799,91199, +chr1 182362503 182413635 NM_001081227 0 - 182368459 182413460 0 4 5991,9,180,377, 0,6733,10171,50755, +chr1 182499021 182531130 NM_007415 0 + 182499164 182530662 0 23 263,166,116,215,103,117,177,148,141,240,69,133,196,129,84,123,129,99,153,128,62,115,550, 0,4761,8692,10263,11642,13867,14839,16952,18370,19030,19468,19759,20507,22327,23957,25152,25764,28399,29320,30062,30702,31205,31559, +chr1 182517331 182517398 NR_105869 0 + 182517398 182517398 0 1 67, 0, +chr1 182571280 182620818 NR_120498 0 + 182620818 182620818 0 15 248,33,95,105,134,126,158,134,118,102,81,126,180,98,1420, 0,7151,9592,10712,17913,20327,24633,26175,27616,27982,32914,39950,46810,47113,48118, +chr1 182571280 182620818 NM_001103182 0 + 182571449 182619504 0 15 248,33,95,105,134,126,158,134,120,102,81,126,180,98,1420, 0,7151,9592,10712,17913,20327,24633,26175,27614,27982,32914,39950,46810,47113,48118, +chr1 182623178 182627165 NM_013729 0 - 182624749 182627143 0 2 1874,415, 0,3572, +chr1 182656173 182684335 NM_133225 0 + 182656232 182682501 0 8 336,142,141,159,175,187,285,2046, 0,7123,8334,10649,12420,19028,20751,26116, +chr1 182732690 182743736 NM_008210 0 - 182733207 182742057 0 4 646,154,151,135, 0,7557,9239,10911, +chr1 182781281 182798245 NM_145943 0 + 182781303 182796424 0 7 142,118,112,170,121,484,2043, 0,4652,6972,8750,9947,11207,14921, +chr1 182823238 182829238 NM_177099 0 + 182823314 182827944 0 4 326,247,246,1658, 0,1027,1488,4342, +chr1 182834404 182838219 NM_133705 0 + 182834594 182837773 0 7 257,71,180,222,93,164,612, 0,470,1600,1889,2321,2516,3203, +chr1 182865152 182868532 NM_010094 0 + 182865240 182868106 0 4 338,247,246,790, 0,1525,1987,2590, +chr1 182872648 182905235 NM_144794 0 + 182876710 182904467 0 23 42,200,80,64,38,143,52,109,71,81,124,134,138,154,107,87,63,163,106,168,116,63,936, 0,4048,6295,9614,10463,12290,13475,13902,15459,17908,18217,18530,19829,20481,23022,23226,23950,26227,27662,29449,30198,30622,31651, +chr1 182919686 182947700 NM_010145 0 - 182919909 182932112 0 9 425,126,109,209,130,228,181,188,143, 0,837,2377,4323,5072,6393,10167,12243,27871, +chr1 182919686 182947700 NM_001312918 0 - 182919909 182932112 0 9 425,126,109,167,130,228,181,188,143, 0,837,2377,4323,5072,6393,10167,12243,27871, +chr1 182981367 182990798 NM_001033819 0 + 182981449 182989945 0 3 164,743,991, 0,3520,8440, +chr1 183017268 183074335 NM_026171 0 - 183023995 183074238 0 23 6772,71,89,77,107,100,120,63,105,219,250,145,118,102,135,77,133,273,58,97,53,74,154, 0,7846,9998,11989,14391,17934,19722,22022,25150,26945,30298,33217,36729,39800,42371,43256,43600,47654,49735,51933,52116,55188,56913, +chr1 183081061 183099125 NM_030131 0 + 183081123 183096339 0 5 131,69,113,141,2814, 0,2804,4928,11144,15250, +chr1 183103356 183142109 NM_145514 0 - 183107936 183141568 0 14 4606,186,130,79,146,120,141,139,157,98,137,105,100,903, 0,8078,9543,10501,11025,12722,14380,18535,24349,25621,29798,35777,35987,37850, +chr1 183282758 183390772 NM_028408 0 + 183283556 183389383 0 6 879,69,105,113,144,1417, 0,53839,57001,97342,101967,106597, +chr1 183282758 183390772 NM_001160212 0 + 183283556 183389383 0 5 879,69,48,113,1417, 0,53839,57001,97342,106597, +chr1 183282758 183390772 NM_001160211 0 + 183283556 183389383 0 6 879,69,48,113,144,1417, 0,53839,57001,97342,101967,106597, +chr1 183439763 183441582 NM_207280 0 - 183440544 183441516 0 1 1819, 0, +chr1 183745445 183772532 NM_133815 0 - 183746988 183768673 0 14 1704,123,81,169,126,104,192,55,197,193,84,231,179,114, 0,1950,2174,3525,4549,5359,6121,10307,13397,16227,16834,20743,23063,26973, +chr1 183826515 183950111 NM_001083120 0 - 183835990 183949665 0 14 9513,58,79,67,49,58,146,305,843,281,85,178,166,451, 0,10002,11913,16922,20814,21873,22053,22940,25273,27175,34293,60009,65369,123145, +chr1 183826515 183950111 NM_001083121 0 - 183835990 183949665 0 14 9513,58,79,67,49,58,146,305,111,281,85,178,166,451, 0,10002,11913,16922,20814,21873,22053,22940,25273,27175,34293,60009,65369,123145, +chr1 183826515 183950111 NM_008680 0 - 183835990 183949665 0 15 9513,58,79,67,49,58,146,305,843,281,85,12,178,166,451, 0,10002,11913,16922,20814,21873,22053,22940,25273,27175,34293,34789,60009,65369,123145, +chr1 183826515 183950111 NM_010135 0 - 183835990 183949665 0 15 9513,58,79,67,49,58,146,305,843,281,85,57,178,166,451, 0,10002,11913,16922,20814,21873,22053,22940,25273,27175,34293,39275,60009,65369,123145, +chr1 184054867 184062546 NM_012058 0 + 184055034 184061586 0 3 239,69,1080, 0,3947,6599, +chr1 184087308 184088229 NM_001166728 0 - 184087308 184088229 0 1 921, 0, +chr1 184187921 184196163 NM_001372438 0 + 184193574 184195500 0 2 88,2878, 0,5364, +chr1 184206094 184212932 NM_007853 0 - 184206877 184212834 0 3 930,743,180, 0,3012,6658, +chr1 184206094 184212326 NM_001360783 0 - 184206877 184209823 0 3 930,743,35, 0,3012,6197, +chr1 184230964 184233420 NR_015458 0 + 184233420 184233420 0 2 365,321, 0,2135, +chr1 184243232 184271737 NM_175127 0 - 184247021 184271720 0 5 4184,196,139,110,284, 0,4708,13152,16772,28221, +chr1 184339297 184392567 NM_173378 0 + 184339554 184391859 0 18 284,148,114,83,102,175,182,165,229,108,149,463,779,138,134,167,200,750, 0,19727,22392,26185,27731,31670,32455,32966,33466,35158,35494,37107,39234,43488,44531,46530,49593,52520, +chr1 184397383 184447741 NM_009794 0 - 184398342 184447485 0 21 983,59,117,79,69,65,58,66,37,212,12,170,161,75,86,84,169,134,119,70,493, 0,2926,3426,5268,5671,6629,9998,11295,12453,14194,15283,16950,19291,20462,21741,22712,23614,24809,25499,44954,49865, +chr1 184495137 184536657 NM_001145806 0 + 184495191 184535374 0 10 291,70,119,134,169,84,86,75,161,1294, 0,6926,31940,32568,33655,34535,37022,38640,39433,40226, +chr1 184495137 184562483 NM_130890 0 + 184495191 184562238 0 21 291,70,119,134,169,84,86,75,161,176,12,212,37,69,58,65,69,79,117,59,269, 0,6926,31940,32568,33655,34535,37022,38640,39433,42587,46082,48319,49782,55143,57454,58912,62529,62971,63592,65095,67077, +chr1 184677256 184679311 NM_001033547 0 - 184677387 184679253 0 1 2055, 0, +chr1 184694174 184826720 NM_001356462 0 + 184695171 184825358 0 9 70,183,213,174,189,192,145,383,1391, 0,962,69019,89913,94378,123296,124724,127839,131155, +chr1 184694346 184826720 NM_001356464 0 + 184695171 184825358 0 9 181,183,213,174,189,198,145,383,1391, 0,790,68847,89741,94206,123118,124552,127667,130983, +chr1 184694346 184826720 NM_001356461 0 + 184695171 184825358 0 9 181,183,213,174,189,192,145,383,1391, 0,790,68847,89741,94206,123124,124552,127667,130983, +chr1 184695026 184826720 NM_144796 0 + 184695171 184825358 0 8 293,213,174,189,192,145,383,1391, 0,68167,89061,93526,122444,123872,126987,130303, +chr1 184695026 184826720 NM_001356463 0 + 184695171 184825358 0 8 293,213,174,189,198,145,383,1391, 0,68167,89061,93526,122438,123872,126987,130303, +chr1 184884918 184906175 NM_016928 0 + 184902565 184905885 0 4 95,128,102,2874, 0,14226,17583,18383, +chr1 185572855 185633625 NR_151520 0 + 185633625 185633625 0 3 160,138,334, 0,33160,60436, +chr1 185856910 185857877 NM_028516 0 - 185857034 185857739 0 1 967, 0, +chr1 185858259 185899515 NM_022019 0 + 185860717 185898402 0 4 189,852,372,1379, 0,2420,34471,39877, +chr1 186351719 186381570 NR_040472 0 - 186381570 186381570 0 6 230,232,81,111,45,79, 0,996,2244,3863,26528,29772, +chr1 186536375 186542868 NR_040627 0 + 186542868 186542868 0 3 798,113,811, 0,909,5682, +chr1 186551023 186556372 NM_008250 0 - 186551387 186556020 0 4 847,185,180,935, 0,2715,3546,4414, +chr1 186610645 186635179 NM_001290273 0 - 186611593 186635008 0 7 1075,72,62,141,163,174,455, 0,8467,8665,15135,17161,20248,24079, +chr1 186636944 186669787 NM_133684 0 - 186643099 186669696 0 8 818,147,72,62,141,169,174,363, 0,6135,9269,9423,19510,20794,28188,32480, +chr1 186636944 186669787 NM_001368285 0 - 186643099 186669696 0 7 818,147,72,62,141,169,363, 0,6135,9269,9423,19510,20794,32480, +chr1 186636944 186670330 NM_001368286 0 - 186643099 186665299 0 8 818,147,72,62,141,169,174,109, 0,6135,9269,9423,19510,20794,28188,33277, +chr1 186646285 186646367 NR_035502 0 - 186646367 186646367 0 1 82, 0, +chr1 186695804 186706915 NM_178692 0 - 186698186 186706870 0 2 2502,351, 0,10760, +chr1 186720302 186823428 NM_145515 0 - 186722402 186823351 0 18 2455,45,252,165,101,194,154,113,100,120,237,57,71,66,49,54,204,128, 0,4385,8979,10659,11905,15572,16058,18093,19655,22886,23094,25128,29392,31610,32898,46782,48373,102998, +chr1 187028046 187110625 NM_001163754 0 + 187028120 187107875 0 35 186,65,124,82,48,76,102,100,99,149,80,90,140,217,144,83,65,91,128,214,98,106,161,229,174,107,67,71,36,75,219,90,213,159,2900, 0,17677,28793,29953,31136,31263,31792,34611,36494,42468,43676,43845,45712,46765,47496,47863,48148,51577,54330,55146,56233,57162,58511,59463,62733,63005,67266,68404,71744,72979,73980,77483,78130,79214,79679, +chr1 187066804 187066917 NR_034044 0 + 187066917 187066917 0 1 113, 0, +chr1 187066853 187066922 NR_035529 0 + 187066922 187066922 0 1 69, 0, +chr1 187110520 187153280 NM_198653 0 - 187110927 187153166 0 23 550,145,191,146,107,132,126,103,109,94,103,161,152,91,170,116,91,110,50,149,160,123,381, 0,1398,2711,3844,4677,8102,8913,9769,10831,16066,16657,29252,31165,31922,34195,35758,36179,36351,36544,37025,38861,40978,42379, +chr1 187137197 187137264 NR_029580 0 + 187137264 187137264 0 1 67, 0, +chr1 187137459 187137570 NR_029908 0 + 187137570 187137570 0 1 111, 0, +chr1 187156037 187181656 NM_001347212 0 + 187165146 187180505 0 8 105,105,108,49,92,198,106,1300, 0,9064,13156,14516,16585,20023,21798,24319, +chr1 187156037 187181648 NM_011794 0 + 187161991 187180505 0 9 105,127,105,108,49,92,198,106,1292, 0,5947,9064,13156,14516,16585,20023,21798,24319, +chr1 187156037 187181656 NM_001347210 0 + 187161991 187180505 0 10 105,127,105,108,49,92,45,198,106,1300, 0,5947,9064,13156,14516,16585,17678,20023,21798,24319, +chr1 187186922 187252239 NM_029735 0 + 187187076 187252026 0 32 200,85,100,157,140,95,127,193,172,234,85,60,111,137,208,113,118,360,234,263,52,210,73,80,102,156,198,174,161,79,65,364, 0,4487,6533,7845,9874,11074,15731,16501,18756,21833,23202,24015,31319,32986,34016,35350,36178,38265,43917,44447,47141,48114,48659,50111,50405,51286,52710,55168,57083,61267,64808,64953, +chr1 187186922 187252239 NM_001357474 0 + 187187076 187252026 0 33 200,85,100,157,140,95,127,193,172,234,85,60,21,111,137,208,113,118,360,234,263,52,210,73,80,102,156,198,174,161,79,65,364, 0,4487,6533,7845,9874,11074,15731,16501,18756,21833,23202,24015,24313,31319,32986,34016,35350,36178,38265,43917,44447,47141,48114,48659,50111,50405,51286,52710,55168,57083,61267,64808,64953, +chr1 187253235 187265698 NR_038006 0 - 187265698 187265698 0 2 3252,154, 0,12309, +chr1 187270994 187279447 NR_040305 0 - 187279447 187279447 0 3 2099,129,533, 0,6889,7920, +chr1 187278726 187292640 NM_001033286 0 + 187278942 187288434 0 4 832,78,240,4685, 0,1504,7839,9229, +chr1 187321184 187321893 NR_033600 0 + 187321893 187321893 0 1 709, 0, +chr1 187911610 187941189 NM_146106 0 - 187912407 187941129 0 5 1037,116,170,100,154, 0,1712,12461,26532,29425, +chr1 188335716 188382560 NR_131158 0 - 188382560 188382560 0 2 1056,314, 0,46530, +chr1 188335716 188382560 NR_131124 0 - 188382560 188382560 0 3 1247,187,314, 0,7303,46530, +chr1 188446670 188529868 NM_001329107 0 - 188449326 188528653 0 8 2815,154,178,111,133,164,84,1561, 0,6091,7818,9666,9886,26943,67929,81637, +chr1 188446670 188529868 NM_009367 0 - 188449326 188528653 0 7 2815,154,178,111,133,164,1561, 0,6091,7818,9666,9886,26943,81637, +chr1 188544964 188573237 NM_026041 0 - 188545281 188573187 0 5 461,199,98,260,195, 0,15030,16502,18518,28078, +chr1 188791294 188794506 NM_033077 0 + 188791754 188793737 0 1 3212, 0, +chr1 188872285 189039325 NM_028848 0 - 188872287 189039164 0 10 83,136,149,207,124,104,51,82,90,277, 0,49370,64071,68856,91966,125968,134813,144532,145519,166763, +chr1 188944747 188948244 NR_151534 0 - 188948244 188948244 0 3 182,95,1885, 0,1097,1612, +chr1 188949016 188951731 NR_040554 0 + 188951731 188951731 0 3 178,354,291, 0,492,2424, +chr1 188959171 189039325 NM_029067 0 - 188959501 189039164 0 7 342,124,104,51,82,90,277, 0,5080,39082,47927,57646,58633,79877, +chr1 189039389 189175308 NM_001357646 0 + 189039502 189172456 0 8 166,717,62,183,80,68,89,3073, 0,9992,15273,17620,18236,88819,125976,132846, +chr1 189039389 189175308 NM_026367 0 + 189039502 189172456 0 10 166,717,62,183,80,68,40,71,89,3073, 0,9992,15273,17620,18236,88819,101013,106773,125976,132846, +chr1 189039389 189062617 NM_001357647 0 + 189039502 189058618 0 6 166,717,62,183,80,4107, 0,9992,15273,17620,18236,19121, +chr1 189039389 189058220 NM_001357648 0 + 189039502 189057865 0 6 166,717,62,183,80,388, 0,9992,15273,17620,18236,18443, +chr1 189039389 189175308 NR_151741 0 + 189175308 189175308 0 11 166,717,62,183,80,68,120,40,71,89,3073, 0,9992,15273,17620,18236,88819,99848,101013,106773,125976,132846, +chr1 189039621 189175308 NM_001357645 0 + 189049397 189172456 0 10 164,717,62,183,80,68,40,71,89,3073, 0,9760,15041,17388,18004,88587,100781,106541,125744,132614, +chr1 189432884 190038763 NM_001243792 0 + 189867225 190035018 0 8 200,88,416,117,111,162,270,3990, 0,184319,434328,457335,537307,541173,589570,601889, +chr1 189475636 190038764 NM_001357534 0 + 189867225 190035018 0 8 198,88,416,117,111,162,270,3991, 0,141567,391576,414583,494555,498421,546818,559137, +chr1 189476119 190038764 NM_001357535 0 + 189867225 190035018 0 8 32,88,416,117,111,162,270,3991, 0,141084,391093,414100,494072,497938,546335,558654, +chr1 189821705 190038764 NM_001357536 0 + 189846357 190035018 0 8 226,122,416,117,111,162,270,3991, 0,24535,45507,68514,148486,152352,200749,213068, +chr1 189821705 190038763 NM_011935 0 + 189821875 190035018 0 7 226,416,117,111,162,270,3990, 0,45507,68514,148486,152352,200749,213068, +chr1 189830454 189832869 NR_038007 0 - 189832869 189832869 0 3 1277,396,539, 0,1388,1876, +chr1 190086716 190788918 NM_021408 0 + 190086912 190788807 0 71 672,166,133,64,295,185,222,94,196,131,196,642,184,164,159,495,261,170,145,222,131,127,102,180,131,274,204,81,192,114,162,160,172,148,152,163,180,151,143,629,335,123,164,210,203,113,199,169,222,224,205,198,155,199,108,184,158,159,163,355,228,1517,322,207,239,209,177,84,245,222,201, 0,4133,56123,88199,93851,95018,95655,96977,116078,118579,132917,136903,152840,167869,173974,180176,181605,183859,188896,203281,260490,268821,270301,273471,274860,279765,286997,287327,290261,313340,315527,363739,365705,370743,385436,391722,415412,451466,452203,465273,470595,471834,480684,490675,492227,496909,519482,521800,534890,547335,551349,558841,559750,563454,578659,586110,587111,599900,601751,611759,643599,647875,653149,681764,684075,685544,688552,690906,694430,699880,702001, +chr1 190794974 190831719 NM_001359578 0 - 190796003 190819645 0 17 1588,139,185,97,156,171,117,88,116,91,141,81,59,74,46,54,311, 0,2970,3191,5515,7401,10129,11914,12111,16420,24646,25304,25866,26181,29157,30247,30809,36434, +chr1 190794974 190831719 NM_001359577 0 - 190796003 190831491 0 16 1588,139,185,97,156,171,117,116,91,141,81,59,74,46,54,311, 0,2970,3191,5515,7401,10129,11914,16420,24646,25304,25866,26181,29157,30247,30809,36434, +chr1 190794974 190831719 NM_001359576 0 - 190796003 190831491 0 18 1588,133,185,97,156,171,117,88,116,191,91,141,81,59,74,46,54,311, 0,2970,3191,5515,7401,10129,11914,12111,16420,21467,24646,25304,25866,26181,29157,30247,30809,36434, +chr1 190794974 190831719 NR_153196 0 - 190831719 190831719 0 18 1588,139,185,337,156,171,128,88,116,191,91,141,81,59,74,46,54,311, 0,2970,3191,5275,7401,10129,11903,12111,16420,21467,24646,25304,25866,26181,29157,30247,30809,36434, +chr1 190794976 190831719 NM_172650 0 - 190796003 190831491 0 18 1586,139,185,97,156,171,117,88,116,191,91,141,81,59,74,46,54,311, 0,2968,3189,5513,7399,10127,11912,12109,16418,21465,24644,25302,25864,26179,29155,30245,30807,36432, +chr1 191031808 191167232 NM_001159850 0 - 191033668 191166967 0 7 2178,140,187,161,118,311,311, 0,34957,48638,50808,87664,131855,135113, +chr1 191031808 191226152 NM_001281848 0 - 191033668 191163847 0 6 2178,140,187,161,311,161, 0,34957,48638,50808,131855,194183, +chr1 191031808 191167232 NM_001357119 0 - 191033668 191163847 0 6 2178,140,187,161,311,311, 0,34957,48638,50808,131855,135113, +chr1 191031808 191168071 NM_001281847 0 - 191033668 191167879 0 7 2178,140,187,161,118,311,202, 0,34957,48638,50808,87664,131855,136061, +chr1 191031808 191167586 NM_010607 0 - 191033668 191167180 0 7 2178,140,187,161,118,311,407, 0,34957,48638,50808,87664,131855,135371, +chr1 191464492 191511965 NM_001081363 0 - 191466477 191508985 0 18 2189,179,477,160,153,2832,3428,136,123,129,126,203,286,92,107,197,194,111, 0,6188,7997,9948,10534,11647,16031,21383,27902,30434,31895,38325,39607,41747,42231,43154,44331,47362, +chr1 191552146 191700572 NM_008976 0 + 191610653 191693934 0 19 397,313,170,98,68,71,88,89,88,83,58,79,1484,144,219,129,235,164,6767, 0,58368,70244,94321,96762,104460,105050,108073,111204,112194,114894,118066,121756,126657,128366,132190,134936,137104,141659, +chr1 191704370 191746170 NM_026796 0 - 191704664 191746158 0 12 375,109,175,121,111,103,68,125,61,111,64,185, 0,1617,3332,4807,6029,8323,10908,16079,16931,19326,29359,41615, +chr1 191941913 191993394 NM_001360827 0 - 191947098 191986125 0 5 5371,195,106,1794,353, 0,28917,35381,42485,51128, +chr1 191941913 191994706 NM_008937 0 - 191947098 191986125 0 5 5371,195,106,1794,560, 0,28917,35381,42485,52233, +chr1 191994174 192041158 NR_151620 0 + 192041158 192041158 0 2 133,698, 0,46286, +chr1 192227526 192241024 NR_151624 0 + 192241024 192241024 0 3 93,138,900, 0,12378,12598, +chr1 192596757 192735649 NM_178775 0 - 192597471 192735539 0 15 825,96,83,90,1569,133,48,93,116,360,94,116,121,36,215, 0,9656,10685,25773,26134,36004,37195,61127,71608,98713,112455,115770,126572,132204,138677, +chr1 192748986 192770370 NM_001199020 0 + 192756752 192768970 0 10 72,47,326,257,70,422,127,58,164,1552, 0,1580,7759,12336,13979,15766,17013,17722,18669,19832, +chr1 192752368 192770842 NM_001357134 0 + 192761444 192768970 0 8 228,257,70,422,127,58,164,2024, 0,8954,10597,12384,13631,14340,15287,16450, +chr1 192752368 192770842 NR_151630 0 + 192770842 192770842 0 7 269,257,70,422,58,164,2024, 0,8954,10597,12384,14340,15287,16450, +chr1 192752368 192770842 NM_001357131 0 + 192756752 192768970 0 9 228,326,257,70,422,127,58,164,2024, 0,4377,8954,10597,12384,13631,14340,15287,16450, +chr1 192752368 192770842 NM_001357132 0 + 192761444 192768970 0 8 269,257,70,422,127,58,164,2024, 0,8954,10597,12384,13631,14340,15287,16450, +chr1 192752383 192770370 NM_021421 0 + 192752578 192768970 0 9 254,326,257,70,422,127,58,164,1552, 0,4362,8939,10582,12369,13616,14325,15272,16435, +chr1 192752700 192770842 NM_001357133 0 + 192756752 192768970 0 9 83,326,257,70,422,127,58,164,2024, 0,4045,8622,10265,12052,13299,14008,14955,16118, +chr1 192771524 192803175 NR_027352 0 - 192803175 192803175 0 8 2611,116,382,75,57,89,407,160, 0,10968,12452,18557,19283,22758,30535,31491, +chr1 192771524 192802877 NM_144879 0 - 192774062 192802335 0 8 2611,116,382,75,57,89,407,293, 0,10968,12452,18557,19283,22758,30535,31060, +chr1 192829710 192850069 NM_001313747 0 - 192832017 192849715 0 9 2379,68,115,106,111,104,68,141,814, 0,2536,3717,5356,5704,6307,7532,9526,19545, +chr1 192829710 192850069 NM_001081259 0 - 192832017 192849972 0 10 2379,68,115,106,111,104,68,141,181,814, 0,2536,3717,5356,5704,6307,7532,9526,15244,19545, +chr1 192848787 192850069 NM_198025 0 - 192849231 192849972 0 1 1282, 0, +chr1 192849229 192853660 NR_027298 0 + 192853660 192853660 0 2 1219,430, 0,4001, +chr1 192860700 192866820 NM_029336 0 + 192863461 192866777 0 3 53,312,63, 0,2723,6057, +chr1 192869708 192886811 NM_026895 0 - 192869986 192886736 0 10 491,81,113,56,110,63,85,74,33,132, 0,3452,7030,9026,9432,10533,12997,14283,15395,16971, +chr1 192869708 192886789 NM_001357166 0 - 192869986 192886736 0 10 491,78,113,56,110,63,85,74,33,110, 0,3452,7030,9026,9432,10533,12997,14283,15395,16971, +chr1 192869708 192886811 NM_001163421 0 - 192870188 192886736 0 10 507,81,113,56,110,63,85,74,33,132, 0,3452,7030,9026,9432,10533,12997,14283,15395,16971, +chr1 192869708 192886811 NM_001163422 0 - 192870188 192886736 0 9 491,81,56,110,63,85,74,33,132, 0,3452,9026,9432,10533,12997,14283,15395,16971, +chr1 192886899 192908437 NM_198654 0 + 192886917 192906328 0 6 252,79,131,55,68,2388, 0,2154,6969,8157,17468,19150, +chr1 192922292 192932822 NM_030060 0 + 192922337 192932512 0 3 114,105,493, 0,2314,10037, +chr1 192986462 192988696 NM_001109759 0 - 192986565 192988323 0 1 2234, 0, +chr1 192994175 193007212 NM_007498 0 - 192995360 193001349 0 4 1383,108,244,241, 0,2078,6934,12796, +chr1 193048332 193049566 NR_151547 0 + 193049566 193049566 0 2 89,479, 0,755, +chr1 193130665 193142010 NM_025424 0 - 193130791 193141971 0 4 303,104,61,213, 0,3132,4673,11132, +chr1 193149780 193175163 NM_025864 0 + 193149919 193173729 0 8 175,97,210,152,143,145,108,1596, 0,2281,12880,14825,19075,20858,22466,23787, +chr1 193175859 193220920 NM_144880 0 - 193176855 193220295 0 13 1129,102,128,120,51,54,109,60,131,93,102,197,806, 0,1893,2550,2761,3042,4353,4906,5811,6944,10268,16660,20489,44255, +chr1 193260218 193288927 NR_151615 0 - 193288927 193288927 0 6 1641,157,262,21,79,225, 0,5311,6172,9226,27963,28484, +chr1 193361234 193399423 NM_029766 0 - 193363121 193399279 0 15 1986,833,133,90,113,105,104,74,113,66,121,62,99,126,196, 0,3348,9135,10940,15632,19085,19428,20705,24069,25755,30935,31139,32311,33223,37993, +chr1 193361234 193399423 NM_001305233 0 - 193363121 193392225 0 16 1986,833,133,90,113,105,104,74,113,66,32,121,62,99,126,196, 0,3348,9135,10940,15632,19085,19428,20705,24069,25755,27963,30935,31139,32311,33223,37993, +chr1 193399514 193447569 NM_001306203 0 + 193410403 193445343 0 19 316,147,138,47,200,123,118,135,98,240,138,207,195,104,69,133,99,186,2526, 0,7543,10888,18791,20537,21251,26609,29171,30485,32184,34728,36222,37379,38003,38943,40065,42176,43960,45529, +chr1 193399514 193447569 NM_178632 0 + 193399736 193445343 0 20 316,130,147,138,47,200,123,118,135,98,240,138,207,195,104,69,133,99,186,2526, 0,6763,7543,10888,18791,20537,21251,26609,29171,30485,32184,34728,36222,37379,38003,38943,40065,42176,43960,45529, +chr1 193399514 193447569 NM_001306204 0 + 193410403 193445343 0 18 316,138,47,200,123,118,135,98,240,138,207,195,104,69,133,99,186,2526, 0,10888,18791,20537,21251,26609,29171,30485,32184,34728,36222,37379,38003,38943,40065,42176,43960,45529, +chr1 193541902 193608134 NM_172266 0 + 193543259 193602413 0 8 182,265,119,96,274,127,107,5873, 0,1330,31516,37908,41950,45521,58299,60359, +chr1 193542273 193608134 NM_001134829 0 + 193542386 193602413 0 8 203,265,119,96,274,127,107,5873, 0,959,31145,37537,41579,45150,57928,59988, +chr1 193645351 193656928 NM_010892 0 + 193645524 193655236 0 8 269,218,241,83,127,220,126,1913, 0,674,1019,4010,4750,5677,7919,9664, +chr1 193717950 193731406 NR_030669 0 - 193731406 193731406 0 5 3057,554,239,44,468, 0,4201,6608,9470,12988, +chr1 193730659 193737126 NM_009579 0 + 193730885 193733634 0 2 833,4397, 0,2070, +chr1 193801250 193812163 NM_023727 0 + 193807146 193809384 0 3 340,312,3071, 0,5880,7842, +chr1 193801250 193812163 NM_001177900 0 + 193807146 193809184 0 3 340,239,3071, 0,5883,7842, +chr1 193802134 193812163 NM_001303132 0 + 193807146 193809184 0 3 544,242,3071, 0,4996,6958, +chr1 193821083 193916480 NM_011633 0 - 193821310 193894515 0 10 805,171,93,75,78,165,102,58,219,344, 0,2595,57147,59937,60772,61792,65439,69691,73214,95053, +chr1 193822434 193822515 NR_039566 0 - 193822515 193822515 0 1 81, 0, +chr1 193922428 193961922 NM_144814 0 - 193924691 193961780 0 10 2608,78,219,79,125,162,53,78,57,302, 0,17721,21367,24991,25695,27318,29428,31835,38886,39192, +chr1 193922428 193961922 NM_001290278 0 - 193924800 193961780 0 11 2608,58,78,219,79,125,162,53,78,57,302, 0,10096,17721,21367,24991,25695,27318,29428,31835,38886,39192, +chr1 193922428 193961922 NM_001346740 0 - 193924691 193961780 0 12 2608,242,58,78,219,79,125,162,53,78,57,302, 0,3078,10096,17721,21367,24991,25695,27318,29428,31835,38886,39192, +chr1 193922428 193961922 NM_001290282 0 - 193924691 193949899 0 11 2608,78,219,79,125,162,53,114,78,57,302, 0,17721,21367,24991,25695,27318,29428,31276,31835,38886,39192, +chr1 193925264 193961922 NM_001290280 0 - 193925473 193961780 0 11 484,58,78,219,79,125,162,53,78,57,302, 0,7260,14885,18531,22155,22859,24482,26592,28999,36050,36356, +chr1 193925264 193961922 NM_001290279 0 - 193925703 193961780 0 10 484,78,219,79,125,162,53,78,57,302, 0,14885,18531,22155,22859,24482,26592,28999,36050,36356, +chr1 193960779 193974907 NR_033536 0 + 193974907 193974907 0 4 164,103,234,2111, 0,7539,8319,12017, +chr1 194014658 194334041 NM_001038607 0 + 194014889 194330003 0 11 310,124,107,129,119,393,430,200,253,197,4896, 0,30556,34068,47948,51142,85921,146623,222240,227906,243946,314487, +chr1 194014658 194334041 NM_010600 0 + 194014889 194330003 0 11 310,124,107,129,119,474,430,200,253,197,4896, 0,30556,34068,47948,51142,85921,146623,222240,227906,243946,314487, +chr1 194336709 194597413 NM_144881 0 - 194337765 194585955 0 12 1148,145,202,36,151,172,234,195,114,68,130,240, 0,40111,82059,148628,183283,206441,215604,216768,230994,238365,249155,260464, +chr1 194659312 194661407 NR_155503 0 - 194661407 194661407 0 1 2095, 0, +chr1 194667898 194668933 NR_040468 0 + 194668933 194668933 0 3 33,83,288, 0,598,747, +chr1 194670681 194681946 NM_198247 0 - 194672566 194677320 0 4 2728,116,192,310, 0,5263,6464,10955, +chr1 194670681 194677941 NM_001177794 0 - 194672566 194677320 0 4 2728,116,192,55, 0,5263,6464,7205, +chr1 194681121 194683049 NR_131748 0 + 194683049 194683049 0 2 151,841, 0,1087, +chr1 194717427 194861969 NM_181546 0 - 194723500 194861829 0 8 6387,190,450,272,216,165,48,153, 0,10518,39244,41880,89112,95484,135736,144389, +chr1 194717427 194861969 NM_001301370 0 - 194723500 194861829 0 9 6387,57,190,450,272,216,165,48,153, 0,7617,10518,39244,41880,89112,95484,135736,144389, +chr1 194930593 194956464 NR_151719 0 - 194956464 194956464 0 12 3387,224,113,183,203,220,411,89,171,280,40,227, 0,9357,10205,10439,13101,13793,15910,17606,19238,23867,25091,25644, +chr1 194930596 194956445 NM_145415 0 - 194933736 194956344 0 12 3384,246,113,183,203,220,411,89,171,280,40,208, 0,9354,10202,10436,13098,13790,15907,17603,19235,23864,25088,25641, +chr1 194930596 194956177 NM_001368818 0 - 194933736 194954548 0 12 3384,246,113,183,203,220,411,89,171,280,40,132, 0,9354,10202,10436,13098,13790,15907,17603,19235,23864,25088,25449, +chr1 194941849 194956445 NM_001368819 0 - 194943601 194956344 0 8 2048,220,411,89,171,280,40,208, 0,2537,4654,6350,7982,12611,13835,14388, +chr1 194979305 194998229 NM_016851 0 + 194983412 194995700 0 8 188,177,205,129,159,393,119,2754, 0,4104,8501,9490,12654,14327,15405,16170, +chr1 194999662 195004026 NM_001160360 0 + 195000535 195001327 0 2 42,3588, 0,776, +chr1 194999770 195004026 NM_001160359 0 + 195000535 195001327 0 2 194,3588, 0,668, +chr1 194999770 195004026 NM_181048 0 + 195000535 195001327 0 2 204,3588, 0,668, +chr1 195001697 195027740 NM_153137 0 - 195001860 195024213 0 16 256,137,57,63,136,138,141,72,96,30,25,64,148,400,106,252, 0,2660,3989,5802,6378,8963,9290,11595,18785,19016,19321,19569,19771,22174,25389,25791, +chr1 195047834 195068554 NM_001044751 0 - 195048204 195068456 0 6 588,144,186,112,131,186, 0,1981,18590,18886,19691,20534, +chr1 195047834 195090239 NM_008288 0 - 195048204 195068456 0 7 588,144,186,112,131,114,98, 0,1981,18590,18886,19691,20534,42307, +chr1 195098353 195099382 NM_008059 0 - 195098656 195098968 0 2 643,200, 0,829, +chr1 195128187 195170072 NM_008484 0 + 195129713 195169704 0 23 148,60,155,115,74,192,64,185,121,189,156,197,112,379,161,218,198,145,208,142,177,154,505, 0,1494,2442,18438,19059,21743,23566,23895,25900,26641,28046,28754,29302,30129,32186,32422,32855,33363,36812,37395,37891,38754,41380, +chr1 195128436 195170072 NM_001277928 0 + 195129713 195169704 0 23 109,60,155,115,74,192,64,185,121,189,156,197,112,379,161,218,198,145,208,142,177,154,505, 0,1245,2193,18189,18810,21494,23317,23646,25651,26392,27797,28505,29053,29880,31937,32173,32606,33114,36563,37146,37642,38505,41131, +chr1 195172539 195196476 NM_144817 0 - 195173550 195188298 0 13 857,116,428,88,79,113,76,124,139,75,129,121,108, 0,986,1711,2373,3929,4644,6022,7646,8610,9971,13373,15667,23829, +chr1 195333656 195333724 NR_029592 0 - 195333724 195333724 0 1 68, 0, +chr1 196038380 196048953 NR_040477 0 - 196048953 196048953 0 3 150,97,331, 0,2824,10242, +chr1 196446022 196643062 NM_008882 0 + 196469953 196638355 0 32 569,1262,183,135,101,124,154,97,115,201,97,191,152,118,137,168,94,240,144,235,143,269,67,147,160,104,100,191,170,213,151,4803, 0,23857,29627,92355,126301,129483,131547,132224,134491,142570,144653,147542,160684,166738,168950,169892,170282,173900,174544,174994,177078,177711,179681,179946,180672,181214,185074,186453,187673,190233,191028,192237, +chr1 196648194 196648258 NR_039539 0 + 196648258 196648258 0 1 64, 0, +chr1 196765014 196787486 NM_001111059 0 + 196765159 196785988 0 8 224,168,260,81,157,53,165,1513, 0,9018,10484,12118,19596,19989,20245,20959, +chr1 196765014 196787486 NM_133654 0 + 196765159 196786315 0 8 224,168,260,81,157,53,165,1357, 0,9018,10484,12118,19596,19989,20245,21115, +chr1 196781952 196803153 NR_033564 0 - 196803153 196803153 0 5 1020,329,121,165,856, 0,3126,3619,19095,20345, +chr1 196843592 196864102 NR_015566 0 + 196864102 196864102 0 8 153,340,179,108,167,110,52,4086, 0,1202,3987,4289,6151,6898,14488,16424, +chr1 196863233 196863314 NR_029809 0 + 196863314 196863314 0 1 81, 0, +chr1 196863740 196863828 NR_029745 0 + 196863828 196863828 0 1 88, 0, +chr1 196867431 196918442 NM_010778 0 - 196868185 196918419 0 11 776,61,36,42,48,183,198,89,103,189,150, 0,21115,23450,26889,34272,36416,41344,42310,44095,44854,50861, +chr1 196867431 196918442 NR_132621 0 - 196918442 196918442 0 12 776,61,36,42,48,73,183,198,89,103,189,150, 0,21115,23450,26889,34272,35293,36416,41344,42310,44095,44854,50861, +chr1 196924904 196957764 NM_001355061 0 - 196925022 196957257 0 9 131,76,24,186,402,86,100,180,511, 0,12369,13663,15945,18768,24979,30436,31119,32349, +chr1 196924904 196957764 NM_001355060 0 - 196925022 196957499 0 10 131,105,76,24,186,402,86,100,180,383, 0,8107,12369,13663,15945,18768,24979,30436,31119,32477, +chr1 196929981 196957764 NM_013499 0 - 196930055 196957499 0 10 120,105,76,24,186,402,86,100,180,383, 0,3030,7292,8586,10868,13691,19902,25359,26042,27400, +chr1 196963005 197002913 NM_001368765 0 - 196967383 197002804 0 26 2987,105,73,24,186,186,393,83,79,408,77,91,177,408,83,100,189,390,86,103,174,399,86,100,180,167, 0,4367,13160,14111,14760,17320,18313,19072,19468,20325,21248,21600,21766,22604,23458,23784,23967,26386,28227,28937,29405,31522,32447,32890,34179,39741, +chr1 196963005 197002913 NM_007758 0 - 196967383 197002804 0 19 2987,109,73,24,186,186,393,83,79,408,77,91,177,408,83,100,189,390,167, 0,4363,13160,14111,14760,17320,18313,19072,19468,20325,21248,21600,21766,22604,23458,23784,23967,26386,39741, +chr10 3134303 3227479 NM_172546 0 + 3134857 3226253 0 13 606,164,203,88,42,120,60,69,147,125,209,90,1525, 0,51430,57752,59286,69235,71799,73823,77121,77569,83090,85394,86053,91651, +chr10 3308331 3587948 NM_001302795 0 - 3309379 3587930 0 6 1052,66,89,521,353,98, 0,24103,58505,207712,208972,279519, +chr10 3308331 3557965 NM_001039652 0 - 3309379 3557666 0 6 1052,66,89,521,353,583, 0,24103,58505,207712,208972,249051, +chr10 3308331 3587948 NM_001302796 0 - 3332476 3587930 0 5 1052,66,521,353,98, 0,24103,207712,208972,279519, +chr10 3308331 3557971 NM_001304950 0 - 3332476 3557666 0 5 1052,66,521,353,589, 0,24103,207712,208972,249051, +chr10 3308331 3557971 NM_001304955 0 - 3309379 3557666 0 7 1052,66,108,89,521,353,589, 0,24103,52424,58505,207712,208972,249051, +chr10 3323355 3434998 NM_001033391 0 + 3349993 3434626 0 8 44,47,74,72,59,89,373,416, 0,26609,67053,68444,86026,87910,103099,111227, +chr10 3366075 3428987 NM_001170802 0 + 3366868 3426898 0 7 219,170,74,72,59,89,2533, 0,782,24333,25724,43306,45190,60379, +chr10 3366075 3428987 NM_001170801 0 + 3366868 3426898 0 7 219,170,74,72,59,101,2533, 0,782,24333,25724,43306,45190,60379, +chr10 3366075 3460176 NM_001170800 0 + 3366868 3456066 0 9 219,170,74,72,59,89,373,194,4311, 0,782,24333,25724,43306,45190,60379,79702,89790, +chr10 3366259 3460739 NM_001347225 0 + 3366868 3456066 0 9 35,170,74,72,59,101,373,194,4874, 0,598,24149,25540,43122,45006,60195,79518,89606, +chr10 3495968 3557971 NM_001302793 0 - 3496696 3557666 0 4 767,521,353,589, 0,20075,21335,61414, +chr10 3495968 3587948 NM_001302794 0 - 3496696 3587930 0 4 767,521,353,98, 0,20075,21335,91882, +chr10 3505160 3557971 NM_001304938 0 - 3505264 3557666 0 4 122,521,353,589, 0,10883,12143,52222, +chr10 3505160 3557971 NM_001304948 0 - 3505903 3557666 0 4 815,521,353,589, 0,10883,12143,52222, +chr10 3515901 3557971 NM_001304937 0 - 3516028 3557666 0 3 663,353,589, 0,1402,41481, diff --git a/hicexplorer/test/test_data/hicPCA/mm9_reduced_chr1.cool b/hicexplorer/test/test_data/hicPCA/mm9_reduced_chr1.cool new file mode 100644 index 00000000..f3ccbad1 Binary files /dev/null and b/hicexplorer/test/test_data/hicPCA/mm9_reduced_chr1.cool differ diff --git a/hicexplorer/test/test_data/hicPCA/pca1.bedgraph b/hicexplorer/test/test_data/hicPCA/pca1.bedgraph index b5bd786d..79f1e48d 100644 --- a/hicexplorer/test/test_data/hicPCA/pca1.bedgraph +++ b/hicexplorer/test/test_data/hicPCA/pca1.bedgraph @@ -1,2655 +1,2794 @@ -chr2RHet 0 50000 0.016528988354 -chr2RHet 50000 100000 -0.440112486575 -chr2RHet 100000 150000 -0.210846065912 -chr2RHet 150000 200000 -0.102898084853 -chr2RHet 200000 250000 -0.383343043254 -chr2RHet 300000 350000 -0.190173244086 -chr2RHet 350000 400000 0.117131713686 -chr2RHet 400000 450000 -0.102838177167 -chr2RHet 450000 500000 -0.129732286270 -chr2RHet 500000 550000 -0.013990964737 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00000000..61f98f13 Binary files /dev/null and b/hicexplorer/test/test_data/hicPCA/pca_reduced_mm9_1.bw differ diff --git a/hicexplorer/test/test_data/hicPCA/pca_reduced_mm9_2.bw b/hicexplorer/test/test_data/hicPCA/pca_reduced_mm9_2.bw new file mode 100644 index 00000000..fe659c02 Binary files /dev/null and b/hicexplorer/test/test_data/hicPCA/pca_reduced_mm9_2.bw differ diff --git a/hicexplorer/test/test_data/hicPlotMatrix/plot_tads.png b/hicexplorer/test/test_data/hicPlotMatrix/plot_tads.png new file mode 100644 index 00000000..29410ffa Binary files /dev/null and b/hicexplorer/test/test_data/hicPlotMatrix/plot_tads.png differ diff --git a/hicexplorer/test/test_data/hicQuickQC/QC.log b/hicexplorer/test/test_data/hicQuickQC/QC.log index 91e402c5..7fa2db54 100644 --- a/hicexplorer/test/test_data/hicQuickQC/QC.log +++ b/hicexplorer/test/test_data/hicQuickQC/QC.log @@ -1,5 +1,5 @@ -File /tmp/tmpriojfa68.h5 +File /tmp/tmpjo4ushzb.h5 Sequenced reads 3494 Min rest. site distance 300 Max library insert size 1000 @@ -12,7 +12,7 @@ One mate not unique 68 (1.95) Low mapping quality 634 (18.15) # count (percentage w.r.t. mappable, unique and high quality pairs) -dangling end GATC 1 (0.10) +dangling end GATC (restriction sequence GATC) 1 (0.10) self ligation (removed) 104 (10.40) One mate not close to rest site 0 (0.00) same fragment 198 (19.80) diff --git a/hicexplorer/test/test_data/hicTADClassifier/X_unittest.csv b/hicexplorer/test/test_data/hicTADClassifier/X_unittest.csv new file mode 100644 index 00000000..eaaa34a8 --- /dev/null +++ b/hicexplorer/test/test_data/hicTADClassifier/X_unittest.csv @@ -0,0 +1,6 @@ +0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0 +10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0 +20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0 +30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0 +40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0 +50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0 diff --git a/hicexplorer/test/test_data/hicTADClassifier/gm12878_chr1.cool b/hicexplorer/test/test_data/hicTADClassifier/gm12878_chr1.cool new file mode 100644 index 00000000..84f43176 Binary files /dev/null and b/hicexplorer/test/test_data/hicTADClassifier/gm12878_chr1.cool differ diff --git a/hicexplorer/test/test_data/hicTADClassifier/positions_unittest.csv b/hicexplorer/test/test_data/hicTADClassifier/positions_unittest.csv new file mode 100644 index 00000000..5133a65a --- /dev/null +++ b/hicexplorer/test/test_data/hicTADClassifier/positions_unittest.csv @@ -0,0 +1,6 @@ +chr1,10000,20000 +chr1,20000,30000 +chr1,30000,40000 +chr1,40000,50000 +chr1,50000,60000 +chr1,60000,70000 diff --git a/hicexplorer/test/test_data/hicTADClassifier/trained_model.bin.BIN b/hicexplorer/test/test_data/hicTADClassifier/trained_model.bin.BIN new file mode 100644 index 00000000..383a1743 Binary files /dev/null and b/hicexplorer/test/test_data/hicTADClassifier/trained_model.bin.BIN differ diff --git a/hicexplorer/test/test_data/hicTADClassifier/unittest.regionPeak b/hicexplorer/test/test_data/hicTADClassifier/unittest.regionPeak new file mode 100644 index 00000000..1b4455c4 --- /dev/null +++ b/hicexplorer/test/test_data/hicTADClassifier/unittest.regionPeak @@ -0,0 +1,28 @@ +chr14 106873443 106873898 . 0 . 236.506270365299 -1 4.87017557727929 238 +chr14 50328789 50329090 . 0 . 195.780738251541 -1 4.87017557727929 147 +chr14 106765077 106765577 . 0 . 191.934976032859 -1 4.87017557727929 264 +chr1 114889153 114889464 . 0 . 189.113611860423 -1 4.87017557727929 138 +chr6 41336636 41336925 . 0 . 184.525551510734 -1 4.87017557727929 155 +chr10 6130652 6130984 . 0 . 176.870974744313 -1 4.87017557727929 190 +chr16 4304053 4304347 . 0 . 174.119300036933 -1 4.87017557727929 157 +chr15 56538265 56538529 . 0 . 172.720096288972 -1 4.87017557727929 137 +chr14 107119933 107120289 . 0 . 169.059639259099 -1 4.87017557727929 178 +chr7 150869662 150869951 . 0 . 166.512341204918 -1 4.87017557727929 145 +chr8 22431911 22432208 . 0 . 164.26854088224 -1 4.87017557727929 151 +chr9 130879921 130880229 . 0 . 164.019544166973 -1 4.87017557727929 146 +chr3 48477461 48477721 . 0 . 163.446221496378 -1 4.87017557727929 121 +chr16 86597433 86597717 . 0 . 162.624745692983 -1 4.87017557727929 151 +chr21 27173882 27174168 . 0 . 158.199689532744 -1 4.87017557727929 167 +chr5 137688066 137688358 . 0 . 157.972412831718 -1 4.87017557727929 147 +chr16 50058788 50059056 . 0 . 157.438713431924 -1 4.87017557727929 141 +chr6 53036668 53036990 . 0 . 156.865297515623 -1 4.87017557727929 150 +chr17 41561005 41561299 . 0 . 156.734537638411 -1 4.87017557727929 129 +chr14 104544327 104544592 . 0 . 156.33328619469 -1 4.87017557727929 143 +chr17 39818980 39819279 . 0 . 154.565001724799 -1 4.87017557727929 147 +chr19 41140448 41140713 . 0 . 153.396829317026 -1 4.87017557727929 151 +chr17 79075560 79075836 . 0 . 152.245617184307 -1 4.87017557727929 126 +chr1 9687039 9687332 . 0 . 152.242543086672 -1 4.87017557727929 153 +chr1 155220534 155220784 . 0 . 149.257835121156 -1 4.87017557727929 122 +chr1 90228582 90228795 . 0 . 102.735213401916 -1 4.87017557727929 127 +chr1 999287 999434 . 0 . 85.9604955475794 -1 4.87017557727929 104 +chr1 3540000 3650000 . 0 . 102.735213401916 -1 4.87017557727929 127 diff --git a/hicexplorer/test/test_data/hicTADClassifier/unittest_classifier.BIN b/hicexplorer/test/test_data/hicTADClassifier/unittest_classifier.BIN new file mode 100644 index 00000000..522958e9 Binary files /dev/null and b/hicexplorer/test/test_data/hicTADClassifier/unittest_classifier.BIN differ diff --git a/hicexplorer/test/test_data/hicTADClassifier/unittest_domains.bed b/hicexplorer/test/test_data/hicTADClassifier/unittest_domains.bed new file mode 100644 index 00000000..aa22258b --- /dev/null +++ b/hicexplorer/test/test_data/hicTADClassifier/unittest_domains.bed @@ -0,0 +1,34 @@ +1 160150000 160400000 ID_0.001_1 0.747332738471 . 160150000 160400000 31,120,180 +1 160400000 160590000 ID_0.001_2 -0.740064848867 . 160400000 160590000 51,160,44 +1 160590000 160800000 ID_0.001_3 -0.819849692308 . 160590000 160800000 31,120,180 +1 160800000 161440000 ID_0.001_4 0.237820777683 . 160800000 161440000 51,160,44 +1 161440000 161930000 ID_0.001_5 -1.877349023761 . 161440000 161930000 31,120,180 +1 161930000 162790000 ID_0.001_6 0.004116446031 . 161930000 162790000 51,160,44 +1 162790000 165340000 ID_0.001_7 -1.846473638473 . 162790000 165340000 31,120,180 +1 165340000 165570000 ID_0.001_8 -0.684240526925 . 165340000 165570000 51,160,44 +1 165570000 166140000 ID_0.001_9 -1.099825883078 . 165570000 166140000 31,120,180 +1 166140000 167030000 ID_0.001_10 -0.496719433598 . 166140000 167030000 51,160,44 +1 167030000 167190000 ID_0.001_11 -0.639574553208 . 167030000 167190000 31,120,180 +1 167190000 167520000 ID_0.001_12 -0.841807234239 . 167190000 167520000 51,160,44 +1 167520000 167680000 ID_0.001_13 -0.681806673357 . 167520000 167680000 31,120,180 +1 167680000 169570000 ID_0.001_14 -0.794102918610 . 167680000 169570000 51,160,44 +1 169570000 169680000 ID_0.001_15 -0.173278231729 . 169570000 169680000 31,120,180 +1 169680000 169770000 ID_0.001_16 -0.661214069089 . 169680000 169770000 51,160,44 +1 169770000 170500000 ID_0.001_17 -0.455026698609 . 169770000 170500000 31,120,180 +1 170500000 171450000 ID_0.001_18 -0.552532348223 . 170500000 171450000 51,160,44 +1 171450000 172150000 ID_0.001_19 -0.910653216972 . 171450000 172150000 31,120,180 +1 172150000 172410000 ID_0.001_20 -0.148016433655 . 172150000 172410000 51,160,44 +1 172410000 172710000 ID_0.001_21 -0.942283074669 . 172410000 172710000 31,120,180 +1 172710000 173170000 ID_0.001_22 -1.132074005451 . 172710000 173170000 51,160,44 +1 173170000 173390000 ID_0.001_23 -0.962053079874 . 173170000 173390000 31,120,180 +1 173390000 173840000 ID_0.001_24 -1.186912820387 . 173390000 173840000 51,160,44 +1 173840000 173900000 ID_0.001_25 -0.006618477894 . 173840000 173900000 31,120,180 +1 173900000 175000000 ID_0.001_26 0.168865207165 . 173900000 175000000 51,160,44 +1 175000000 175120000 ID_0.001_27 -1.148661341851 . 175000000 175120000 31,120,180 +1 175120000 175730000 ID_0.001_28 -0.970965227179 . 175120000 175730000 51,160,44 +1 175730000 175980000 ID_0.001_29 -0.461134190427 . 175730000 175980000 31,120,180 +1 175980000 176180000 ID_0.001_30 -1.211531806856 . 175980000 176180000 51,160,44 +1 176180000 178510000 ID_0.001_31 -0.808791791125 . 176180000 178510000 31,120,180 +1 178510000 179050000 ID_0.001_32 -1.244434555379 . 178510000 179050000 51,160,44 +1 179050000 179340000 ID_0.001_33 -0.686168727622 . 179050000 179340000 31,120,180 +1 179340000 179790000 ID_0.001_34 -1.118004943244 . 179340000 179790000 51,160,44 diff --git a/hicexplorer/test/test_data/hicTADClassifier/unittest_matrix.cool b/hicexplorer/test/test_data/hicTADClassifier/unittest_matrix.cool new file mode 100644 index 00000000..a654ae90 Binary files /dev/null and b/hicexplorer/test/test_data/hicTADClassifier/unittest_matrix.cool differ diff --git a/hicexplorer/test/test_data/hicTADClassifier/unittest_matrix_2.cool b/hicexplorer/test/test_data/hicTADClassifier/unittest_matrix_2.cool new file mode 100644 index 00000000..22cf9b83 Binary files /dev/null and b/hicexplorer/test/test_data/hicTADClassifier/unittest_matrix_2.cool differ diff --git a/hicexplorer/test/test_data/hicTADClassifier/unittest_tads.bed b/hicexplorer/test/test_data/hicTADClassifier/unittest_tads.bed new file mode 100644 index 00000000..d0af9d74 --- /dev/null +++ b/hicexplorer/test/test_data/hicTADClassifier/unittest_tads.bed @@ -0,0 +1,11 @@ +chr1 900000 1060000 ID_0.03_1 0.490582574999 . 900000 1060000 31,120,180 +chr1 1060000 1240000 ID_0.03_2 0.187649376784 . 1060000 1240000 51,160,44 +chr1 1240000 1440000 ID_0.03_3 0.199248276714 . 1240000 1440000 31,120,180 +chr1 1440000 1850000 ID_0.03_4 0.161240236933 . 1440000 1850000 51,160,44 +chr1 1850000 2120000 ID_0.03_5 -1.243685923789 . 1850000 2120000 31,120,180 +chr1 2120000 2250000 ID_0.03_6 -0.743593419486 . 2120000 2250000 51,160,44 +chr1 2250000 2340000 ID_0.03_7 0.034041385680 . 2250000 2340000 31,120,180 +chr1 2340000 2520000 ID_0.03_8 -0.777315422750 . 2340000 2520000 51,160,44 +chr1 2520000 3330000 ID_0.03_9 -0.277242546117 . 2520000 3330000 31,120,180 +chr1 3330000 3540000 ID_0.03_10 -0.573527560267 . 3330000 3540000 51,160,44 +chr1 3540000 3650000 ID_0.03_11 -0.279406156684 . 3540000 3650000 31,120,180 diff --git a/hicexplorer/test/test_data/hicTADClassifier/unittest_tads_2.bed b/hicexplorer/test/test_data/hicTADClassifier/unittest_tads_2.bed new file mode 100644 index 00000000..e3d3933d --- /dev/null +++ b/hicexplorer/test/test_data/hicTADClassifier/unittest_tads_2.bed @@ -0,0 +1,62 @@ +chr1 160150000 160400000 ID_0.03_1 0.747332738471 . 160150000 160400000 31,120,180 +chr1 160400000 160590000 ID_0.03_2 -0.740064848867 . 160400000 160590000 51,160,44 +chr1 160590000 160800000 ID_0.03_3 -0.819849692308 . 160590000 160800000 31,120,180 +chr1 160800000 160960000 ID_0.03_4 0.237820777683 . 160800000 160960000 51,160,44 +chr1 160960000 161190000 ID_0.03_5 -0.193749722805 . 160960000 161190000 31,120,180 +chr1 161190000 161440000 ID_0.03_6 0.367964847548 . 161190000 161440000 51,160,44 +chr1 161440000 161520000 ID_0.03_7 -1.877349023761 . 161440000 161520000 31,120,180 +chr1 161520000 161730000 ID_0.03_8 -1.873704312426 . 161520000 161730000 51,160,44 +chr1 161730000 161930000 ID_0.03_9 -0.551866730658 . 161730000 161930000 31,120,180 +chr1 161930000 162470000 ID_0.03_10 0.004116446031 . 161930000 162470000 51,160,44 +chr1 162470000 162790000 ID_0.03_11 -0.551536932286 . 162470000 162790000 31,120,180 +chr1 162790000 164790000 ID_0.03_12 -1.846473638473 . 162790000 164790000 51,160,44 +chr1 164790000 165210000 ID_0.03_13 -0.674366686693 . 164790000 165210000 31,120,180 +chr1 165210000 165340000 ID_0.03_14 -0.333040128383 . 165210000 165340000 51,160,44 +chr1 165340000 165570000 ID_0.03_15 -0.684240526925 . 165340000 165570000 31,120,180 +chr1 165570000 165900000 ID_0.03_16 -1.099825883078 . 165570000 165900000 51,160,44 +chr1 165900000 166140000 ID_0.03_17 -1.231503583498 . 165900000 166140000 31,120,180 +chr1 166140000 167030000 ID_0.03_18 -0.496719433598 . 166140000 167030000 51,160,44 +chr1 167030000 167190000 ID_0.03_19 -0.639574553208 . 167030000 167190000 31,120,180 +chr1 167190000 167320000 ID_0.03_20 -0.841807234239 . 167190000 167320000 51,160,44 +chr1 167320000 167520000 ID_0.03_21 0.197536239768 . 167320000 167520000 31,120,180 +chr1 167520000 167680000 ID_0.03_22 -0.681806673357 . 167520000 167680000 51,160,44 +chr1 167680000 167780000 ID_0.03_23 -0.794102918610 . 167680000 167780000 31,120,180 +chr1 167780000 168150000 ID_0.03_24 -0.138702915915 . 167780000 168150000 51,160,44 +chr1 168150000 168290000 ID_0.03_25 -0.158316155383 . 168150000 168290000 31,120,180 +chr1 168290000 168410000 ID_0.03_26 -0.253377267708 . 168290000 168410000 51,160,44 +chr1 168410000 169570000 ID_0.03_27 -0.249995761226 . 168410000 169570000 31,120,180 +chr1 169570000 169680000 ID_0.03_28 -0.173278231729 . 169570000 169680000 51,160,44 +chr1 169680000 169770000 ID_0.03_29 -0.661214069089 . 169680000 169770000 31,120,180 +chr1 169770000 169860000 ID_0.03_30 -0.455026698609 . 169770000 169860000 51,160,44 +chr1 169860000 170500000 ID_0.03_31 -0.350733192888 . 169860000 170500000 31,120,180 +chr1 170500000 171450000 ID_0.03_32 -0.552532348223 . 170500000 171450000 51,160,44 +chr1 171450000 171570000 ID_0.03_33 -0.910653216972 . 171450000 171570000 31,120,180 +chr1 171570000 171620000 ID_0.03_34 0.191504935103 . 171570000 171620000 51,160,44 +chr1 171620000 171750000 ID_0.03_35 0.060804982655 . 171620000 171750000 31,120,180 +chr1 171750000 172150000 ID_0.03_36 -0.435014042694 . 171750000 172150000 51,160,44 +chr1 172150000 172300000 ID_0.03_37 -0.148016433655 . 172150000 172300000 31,120,180 +chr1 172300000 172410000 ID_0.03_38 0.277505386377 . 172300000 172410000 51,160,44 +chr1 172410000 172500000 ID_0.03_39 -0.942283074669 . 172410000 172500000 31,120,180 +chr1 172500000 172710000 ID_0.03_40 -0.326918992820 . 172500000 172710000 51,160,44 +chr1 172710000 173170000 ID_0.03_41 -1.132074005451 . 172710000 173170000 31,120,180 +chr1 173170000 173270000 ID_0.03_42 -0.962053079874 . 173170000 173270000 51,160,44 +chr1 173270000 173390000 ID_0.03_43 -0.031952730550 . 173270000 173390000 31,120,180 +chr1 173390000 173680000 ID_0.03_44 -1.186912820387 . 173390000 173680000 51,160,44 +chr1 173680000 173840000 ID_0.03_45 -0.501001084739 . 173680000 173840000 31,120,180 +chr1 173840000 173900000 ID_0.03_46 -0.006618477894 . 173840000 173900000 51,160,44 +chr1 173900000 173990000 ID_0.03_47 0.168865207165 . 173900000 173990000 31,120,180 +chr1 173990000 175000000 ID_0.03_48 -0.530859452559 . 173990000 175000000 51,160,44 +chr1 175000000 175120000 ID_0.03_49 -1.148661341851 . 175000000 175120000 31,120,180 +chr1 175120000 175560000 ID_0.03_50 -0.970965227179 . 175120000 175560000 51,160,44 +chr1 175560000 175730000 ID_0.03_51 0.024550257654 . 175560000 175730000 31,120,180 +chr1 175730000 175980000 ID_0.03_52 -0.461134190427 . 175730000 175980000 51,160,44 +chr1 175980000 176180000 ID_0.03_53 -1.211531806856 . 175980000 176180000 31,120,180 +chr1 176180000 176250000 ID_0.03_54 -0.808791791125 . 176180000 176250000 51,160,44 +chr1 176250000 176860000 ID_0.03_55 -0.341635925294 . 176250000 176860000 31,120,180 +chr1 176860000 177520000 ID_0.03_56 -0.720403722150 . 176860000 177520000 51,160,44 +chr1 177520000 178510000 ID_0.03_57 -0.163313868176 . 177520000 178510000 31,120,180 +chr1 178510000 178730000 ID_0.03_58 -1.244434555379 . 178510000 178730000 51,160,44 +chr1 178730000 179050000 ID_0.03_59 -0.646088361265 . 178730000 179050000 31,120,180 +chr1 179050000 179260000 ID_0.03_60 -0.686168727622 . 179050000 179260000 51,160,44 +chr1 179260000 179340000 ID_0.03_61 -0.039332513177 . 179260000 179340000 31,120,180 +chr1 179340000 179790000 ID_0.03_62 -1.118004943244 . 179340000 179790000 51,160,44 diff --git a/hicexplorer/test/test_data/hicTADClassifier/y_unittest.csv b/hicexplorer/test/test_data/hicTADClassifier/y_unittest.csv new file mode 100644 index 00000000..36637c9c --- /dev/null +++ b/hicexplorer/test/test_data/hicTADClassifier/y_unittest.csv @@ -0,0 +1,6 @@ +False +True +False +False +True +False diff --git a/hicexplorer/test/test_data/hicValidateLocations/GSM1436265_RAD21_ENCFF002EMQ_10kb.cool b/hicexplorer/test/test_data/hicValidateLocations/GSM1436265_RAD21_ENCFF002EMQ_10kb.cool new file mode 100644 index 00000000..5673295c Binary files /dev/null and b/hicexplorer/test/test_data/hicValidateLocations/GSM1436265_RAD21_ENCFF002EMQ_10kb.cool differ diff --git a/hicexplorer/test/test_data/hicValidateLocations/overlap_ctcf_matched_locations b/hicexplorer/test/test_data/hicValidateLocations/overlap_ctcf_matched_locations index 304d1e15..dc141ce9 100644 --- a/hicexplorer/test/test_data/hicValidateLocations/overlap_ctcf_matched_locations +++ b/hicexplorer/test/test_data/hicValidateLocations/overlap_ctcf_matched_locations @@ -1,6615 +1,6615 @@ -chr1 720000 730000 chr1 224200000 224210000 0.001 -chr1 1050000 1060000 chr1 1180000 1190000 0.001 -chr1 1710000 1720000 chr1 1830000 1840000 0.001 -chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407133 -chr1 2120000 2130000 chr1 2310000 2320000 0.001 -chr1 2120000 2130000 chr1 2480000 2490000 0.001 -chr1 2340000 2350000 chr1 3340000 3350000 0.001 -chr1 2340000 2350000 chr1 2480000 2490000 0.001 -chr1 2480000 2490000 chr1 3570000 3580000 0.001 -chr1 3400000 3410000 chr1 3530000 3540000 0.001 -chr1 3820000 3830000 chr1 5800000 5810000 0.001 -chr1 3820000 3830000 chr1 4880000 4890000 0.001 -chr1 4710000 4720000 chr1 4880000 4890000 0.001 -chr1 5570000 5580000 chr1 5970000 5980000 0.001 -chr1 6540000 6550000 chr1 6700000 6710000 0.001 -chr1 6770000 6780000 chr1 7700000 7710000 0.001 -chr1 6770000 6780000 chr1 7270000 7280000 0.001 -chr1 6780000 6790000 chr1 7130000 7140000 0.001 -chr1 6850000 6860000 chr1 6950000 6960000 0.001 -chr1 7100000 7110000 chr1 7700000 7710000 0.001 -chr1 8620000 8630000 chr1 8730000 8740000 0.001 -chr1 9340000 9350000 chr1 9510000 9520000 0.001 -chr1 9680000 9690000 chr1 9780000 9790000 0.001 -chr1 10270000 10280000 chr1 10390000 10400000 0.001 -chr1 10560000 10570000 chr1 11700000 11710000 0.001 -chr1 10560000 10570000 chr1 10920000 10930000 0.001 -chr1 11090000 11100000 chr1 11700000 11710000 0.001 -chr1 11390000 11400000 chr1 11700000 11710000 0.001 -chr1 12370000 12380000 chr1 12670000 12680000 0.001 -chr1 13990000 14000000 chr1 14280000 14290000 0.001 -chr1 13990000 14000000 chr1 14130000 14140000 0.001 -chr1 14150000 14160000 chr1 14280000 14290000 0.001 -chr1 14280000 14290000 chr1 15370000 15380000 0.001 -chr1 14720000 14730000 chr1 15380000 15390000 0.001 -chr1 15450000 15460000 chr1 15590000 15600000 0.001 -chr1 15650000 15660000 chr1 15750000 15760000 0.001 -chr1 15920000 15930000 chr1 16060000 16070000 0.001 -chr1 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/home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/hicValidateLocations/loops_1.bedgraph with protein file /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/hicValidateLocations/GSM1436265_RAD21_ENCFF002EMQ_10kb.cool +# +Protein peaks: 7987 +Matched Loops: 2164 +Total Loops: 11723 +Loops match protein: 0.18459438710227757 diff --git a/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_matched_locations b/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_matched_locations index 9f0044a9..b7fa8405 100644 --- a/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_matched_locations +++ b/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_matched_locations @@ -1,6 +1,6 @@ chr1 1050000 1060000 chr1 1180000 1190000 0.001 chr1 1710000 1720000 chr1 1830000 1840000 0.001 -chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407133 +chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407 chr1 2120000 2130000 chr1 2310000 2320000 0.001 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chr2 75100000 75110000 0.001 chr2 75140000 75150000 chr2 75830000 75840000 0.001 @@ -2969,7 +2969,7 @@ chr2 103770000 103780000 chr2 105460000 105470000 0.001 chr2 104650000 104660000 chr2 105460000 105470000 0.001 chr2 105730000 105740000 chr2 105850000 105860000 0.001 chr2 105980000 105990000 chr2 106130000 106140000 0.001 -chr2 106190000 106200000 chr2 106580000 106590000 0.001980875213302446 +chr2 106190000 106200000 chr2 106580000 106590000 0.0019808752133024 chr2 108960000 108970000 chr2 109200000 109210000 0.001 chr2 109740000 109750000 chr2 110260000 110270000 0.001 chr2 109760000 109770000 chr2 109870000 109880000 0.001 @@ -3006,7 +3006,7 @@ chr2 129490000 129500000 chr2 130150000 130160000 0.001 chr2 129490000 129500000 chr2 130600000 130610000 0.001 chr2 129490000 129500000 chr2 130050000 130060000 0.001 chr2 129950000 129960000 chr2 130600000 130610000 0.001 -chr2 130690000 130700000 chr2 131900000 131910000 0.0011104422626731726 +chr2 130690000 130700000 chr2 131900000 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chr3 46110000 46120000 0.001 chr3 45980000 45990000 chr3 46410000 46420000 0.001 -chr3 45980000 45990000 chr3 46250000 46260000 0.001110147831339191 +chr3 45980000 45990000 chr3 46250000 46260000 0.0011101478313391 chr3 46120000 46130000 chr3 46410000 46420000 0.001 chr3 46130000 46140000 chr3 46240000 46250000 0.001 chr3 46250000 46260000 chr3 46410000 46420000 0.001 @@ -3998,7 +3998,7 @@ chr3 167920000 167930000 chr3 168560000 168570000 0.001 chr3 168220000 168230000 chr3 168560000 168570000 0.001 chr3 168220000 168230000 chr3 168330000 168340000 0.001 chr3 168860000 168870000 chr3 169380000 169390000 0.001 -chr3 169580000 169590000 chr3 169680000 169690000 0.00634766181541061 +chr3 169580000 169590000 chr3 169680000 169690000 0.0063476618154106 chr3 170020000 170030000 chr3 170120000 170130000 0.001 chr3 170130000 170140000 chr3 170520000 170530000 0.001 chr3 170760000 170770000 chr3 171280000 171290000 0.001 @@ -4035,7 +4035,7 @@ chr3 185700000 185710000 chr3 185960000 185970000 0.001 chr3 185700000 185710000 chr3 186250000 186260000 0.001 chr3 185970000 185980000 chr3 186250000 186260000 0.001 chr3 186330000 186340000 chr3 186530000 186540000 0.001 -chr3 186650000 186660000 chr3 186750000 186760000 0.003680233551586256 +chr3 186650000 186660000 chr3 186750000 186760000 0.0036802335515862 chr3 187030000 187040000 chr3 187390000 187400000 0.001 chr3 187450000 187460000 chr3 188670000 188680000 0.001 chr3 187450000 187460000 chr3 188860000 188870000 0.001 @@ -4052,7 +4052,7 @@ chr3 191130000 191140000 chr3 192160000 192170000 0.001 chr3 192280000 192290000 chr3 192750000 192760000 0.001 chr3 192520000 192530000 chr3 193290000 193300000 0.001 chr3 192530000 192540000 chr3 192750000 192760000 0.001 -chr3 192530000 192540000 chr3 192630000 192640000 0.002327483393010536 +chr3 192530000 192540000 chr3 192630000 192640000 0.0023274833930105 chr3 193170000 193180000 chr3 193290000 193300000 0.001 chr3 193500000 193510000 chr3 194030000 194040000 0.001 chr3 193500000 193510000 chr3 193850000 193860000 0.001 @@ -4245,7 +4245,7 @@ chr4 83380000 83390000 chr4 83660000 83670000 0.001 chr4 83380000 83390000 chr4 84200000 84210000 0.001 chr4 83990000 84000000 chr4 84180000 84190000 0.001 chr4 84560000 84570000 chr4 85420000 85430000 0.001 -chr4 84690000 84700000 chr4 85180000 85190000 0.0021024744898931573 +chr4 84690000 84700000 chr4 85180000 85190000 0.0021024744898931 chr4 84820000 84830000 chr4 85420000 85430000 0.001 chr4 85670000 85680000 chr4 85890000 85900000 0.001 chr4 86060000 86070000 chr4 86660000 86670000 0.001 @@ -4389,7 +4389,7 @@ chr4 155900000 155910000 chr4 156700000 156710000 0.001 chr4 156360000 156370000 chr4 156700000 156710000 0.001 chr4 156580000 156590000 chr4 156680000 156690000 0.001 chr4 156730000 156740000 chr4 156870000 156880000 0.001 -chr4 156870000 156880000 chr4 157890000 157900000 0.006394624397006017 +chr4 156870000 156880000 chr4 157890000 157900000 0.006394624397006 chr4 158910000 158920000 chr4 159090000 159100000 0.001 chr4 159170000 159180000 chr4 159540000 159550000 0.001 chr4 159650000 159660000 chr4 159770000 159780000 0.001 @@ -4420,7 +4420,7 @@ chr4 167940000 167950000 chr4 168990000 169000000 0.001 chr4 169100000 169110000 chr4 169830000 169840000 0.001 chr4 169500000 169510000 chr4 169830000 169840000 0.001 chr4 169940000 169950000 chr4 170400000 170410000 0.001 -chr4 170210000 170220000 chr4 170320000 170330000 0.0012104580545098693 +chr4 170210000 170220000 chr4 170320000 170330000 0.0012104580545098 chr4 170530000 170540000 chr4 170960000 170970000 0.001 chr4 170530000 170540000 chr4 170670000 170680000 0.001 chr4 170730000 170740000 chr4 170960000 170970000 0.001 @@ -4469,7 +4469,7 @@ chr5 5490000 5500000 chr5 5880000 5890000 0.001 chr5 5750000 5760000 chr5 6490000 6500000 0.001 chr5 5750000 5760000 chr5 6730000 6740000 0.001 chr5 5880000 5890000 chr5 6570000 6580000 0.001 -chr5 6370000 6380000 chr5 6480000 6490000 0.0011675004466256823 +chr5 6370000 6380000 chr5 6480000 6490000 0.0011675004466256 chr5 6630000 6640000 chr5 6730000 6740000 0.001 chr5 7260000 7270000 chr5 7740000 7750000 0.001 chr5 7920000 7930000 chr5 9200000 9210000 0.001 @@ -4762,7 +4762,7 @@ chr5 153450000 153460000 chr5 153550000 153560000 0.001 chr5 153560000 153570000 chr5 153780000 153790000 0.001 chr5 153840000 153850000 chr5 153990000 154000000 0.001 chr5 154030000 154040000 chr5 154190000 154200000 0.001 -chr5 155370000 155380000 chr5 156360000 156370000 0.00957529346434801 +chr5 155370000 155380000 chr5 156360000 156370000 0.009575293464348 chr5 155370000 155380000 chr5 156240000 156250000 0.001 chr5 156260000 156270000 chr5 156360000 156370000 0.001 chr5 156360000 156370000 chr5 156550000 156560000 0.001 @@ -4888,7 +4888,7 @@ chr6 17150000 17160000 chr6 18500000 18510000 0.001 chr6 17150000 17160000 chr6 17580000 17590000 0.001 chr6 17150000 17160000 chr6 18300000 18310000 0.001 chr6 17580000 17590000 chr6 17810000 17820000 0.001 -chr6 17600000 17610000 chr6 17700000 17710000 0.007486699089923394 +chr6 17600000 17610000 chr6 17700000 17710000 0.0074866990899233 chr6 18150000 18160000 chr6 18260000 18270000 0.001 chr6 18320000 18330000 chr6 18500000 18510000 0.001 chr6 18590000 18600000 chr6 20050000 20060000 0.001 @@ -4930,7 +4930,7 @@ chr6 30580000 30590000 chr6 30690000 30700000 0.001 chr6 30710000 30720000 chr6 30840000 30850000 0.001 chr6 30880000 30890000 chr6 31040000 31050000 0.001 chr6 31160000 31170000 chr6 31330000 31340000 0.001 -chr6 31460000 31470000 chr6 31560000 31570000 0.0036013103293332845 +chr6 31460000 31470000 chr6 31560000 31570000 0.0036013103293332 chr6 31690000 31700000 chr6 31790000 31800000 0.001 chr6 32160000 32170000 chr6 33170000 33180000 0.001 chr6 32390000 32400000 chr6 32660000 32670000 0.001 @@ -5146,7 +5146,7 @@ chr6 125630000 125640000 chr6 126080000 126090000 0.001 chr6 125630000 125640000 chr6 126290000 126300000 0.001 chr6 126100000 126110000 chr6 126290000 126300000 0.001 chr6 126310000 126320000 chr6 127440000 127450000 0.001 -chr6 126310000 126320000 chr6 126970000 126980000 0.0015915274608644205 +chr6 126310000 126320000 chr6 126970000 126980000 0.0015915274608644 chr6 126680000 126690000 chr6 127440000 127450000 0.001 chr6 127120000 127130000 chr6 127440000 127450000 0.001 chr6 127620000 127630000 chr6 127740000 127750000 0.001 @@ -5220,7 +5220,7 @@ chr6 154990000 155000000 chr6 155490000 155500000 0.001 chr6 155640000 155650000 chr6 156880000 156890000 0.001 chr6 155640000 155650000 chr6 155850000 155860000 0.001 chr6 155660000 155670000 chr6 157000000 157010000 0.001 -chr6 156880000 156890000 chr6 157340000 157350000 0.0017143704279680516 +chr6 156880000 156890000 chr6 157340000 157350000 0.001714370427968 chr6 157000000 157010000 chr6 157100000 157110000 0.001 chr6 157740000 157750000 chr6 158080000 158090000 0.001 chr6 157880000 157890000 chr6 157980000 157990000 0.001 @@ -5315,7 +5315,7 @@ chr7 25930000 25940000 chr7 26100000 26110000 0.001 chr7 25930000 25940000 chr7 26700000 26710000 0.001 chr7 26100000 26110000 chr7 27200000 27210000 0.001 chr7 26110000 26120000 chr7 26700000 26710000 0.001 -chr7 26130000 26140000 chr7 26230000 26240000 0.0015562709572580814 +chr7 26130000 26140000 chr7 26230000 26240000 0.001556270957258 chr7 26410000 26420000 chr7 27190000 27200000 0.001 chr7 26410000 26420000 chr7 26700000 26710000 0.001 chr7 26540000 26550000 chr7 27200000 27210000 0.001 @@ -5336,7 +5336,7 @@ chr7 31480000 31490000 chr7 32240000 32250000 0.001 chr7 31780000 31790000 chr7 32240000 32250000 0.001 chr7 31780000 31790000 chr7 32390000 32400000 0.001 chr7 32250000 32260000 chr7 32380000 32390000 0.001 -chr7 32530000 32540000 chr7 33100000 33110000 0.003383275768225125 +chr7 32530000 32540000 chr7 33100000 33110000 0.0033832757682251 chr7 33220000 33230000 chr7 33970000 33980000 0.001 chr7 33460000 33470000 chr7 33970000 33980000 0.001 chr7 35110000 35120000 chr7 35570000 35580000 0.001 @@ -5581,7 +5581,7 @@ chr7 149000000 149010000 chr7 149100000 149110000 0.001 chr7 149190000 149200000 chr7 149310000 149320000 0.001 chr7 149580000 149590000 chr7 149970000 149980000 0.001 chr7 149750000 149760000 chr7 149970000 149980000 0.001 -chr7 149980000 149990000 chr7 150450000 150460000 0.0060197557875710786 +chr7 149980000 149990000 chr7 150450000 150460000 0.006019755787571 chr7 150140000 150150000 chr7 150450000 150460000 0.001 chr7 150310000 150320000 chr7 150410000 150420000 0.001 chr7 151060000 151070000 chr7 151450000 151460000 0.001 @@ -5600,7 +5600,7 @@ chr8 6280000 6290000 chr8 6630000 6640000 0.001 chr8 6280000 6290000 chr8 6420000 6430000 0.001 chr8 6430000 6440000 chr8 6630000 6640000 0.001 chr8 8100000 8110000 chr8 8840000 8850000 0.001 -chr8 8240000 8250000 chr8 8350000 8360000 0.002535254874021222 +chr8 8240000 8250000 chr8 8350000 8360000 0.0025352548740212 chr8 8420000 8430000 chr8 8520000 8530000 0.001 chr8 8600000 8610000 chr8 8840000 8850000 0.001 chr8 8880000 8890000 chr8 9190000 9200000 0.001 @@ -5657,7 +5657,7 @@ chr8 27170000 27180000 chr8 27450000 27460000 0.001 chr8 27180000 27190000 chr8 27280000 27290000 0.001 chr8 27320000 27330000 chr8 27450000 27460000 0.001 chr8 27720000 27730000 chr8 27840000 27850000 0.001 -chr8 27940000 27950000 chr8 28040000 28050000 0.00878578486350742 +chr8 27940000 27950000 chr8 28040000 28050000 0.0087857848635074 chr8 28480000 28490000 chr8 28640000 28650000 0.001 chr8 28740000 28750000 chr8 29900000 29910000 0.001 chr8 28990000 29000000 chr8 29170000 29180000 0.001 @@ -5822,7 +5822,7 @@ chr8 102340000 102350000 chr8 103820000 103830000 0.001 chr8 102340000 102350000 chr8 102530000 102540000 0.001 chr8 102510000 102520000 chr8 103200000 103210000 0.001 chr8 102650000 102660000 chr8 103210000 103220000 0.001 -chr8 102800000 102810000 chr8 102910000 102920000 0.0013374941729332056 +chr8 102800000 102810000 chr8 102910000 102920000 0.0013374941729332 chr8 102990000 103000000 chr8 103100000 103110000 0.001 chr8 103660000 103670000 chr8 103820000 103830000 0.001 chr8 103870000 103880000 chr8 104030000 104040000 0.001 @@ -5871,7 +5871,7 @@ chr8 123090000 123100000 chr8 123580000 123590000 0.001 chr8 123470000 123480000 chr8 123580000 123590000 0.001 chr8 123680000 123690000 chr8 124770000 124780000 0.001 chr8 123740000 123750000 chr8 124030000 124040000 0.001 -chr8 124170000 124180000 chr8 124700000 124710000 0.02045736118875823 +chr8 124170000 124180000 chr8 124700000 124710000 0.0204573611887582 chr8 124250000 124260000 chr8 125480000 125490000 0.001 chr8 124280000 124290000 chr8 124390000 124400000 0.001 chr8 124400000 124410000 chr8 125480000 125490000 0.001 @@ -6054,7 +6054,7 @@ chr9 90560000 90570000 chr9 91190000 91200000 0.001 chr9 91200000 91210000 chr9 91610000 91620000 0.001 chr9 92040000 92050000 chr9 92160000 92170000 0.001 chr9 92210000 92220000 chr9 93510000 93520000 0.001 -chr9 92210000 92220000 chr9 92680000 92690000 0.00945560619719485 +chr9 92210000 92220000 chr9 92680000 92690000 0.0094556061971948 chr9 92210000 92220000 chr9 92860000 92870000 0.001 chr9 92980000 92990000 chr9 93630000 93640000 0.001 chr9 93670000 93680000 chr9 94440000 94450000 0.001 @@ -6253,7 +6253,7 @@ chrX 43200000 43210000 chrX 43410000 43420000 0.001 chrX 43810000 43820000 chrX 45040000 45050000 0.001 chrX 45370000 45380000 chrX 46260000 46270000 0.001 chrX 45680000 45690000 chrX 46260000 46270000 0.001 -chrX 46410000 46420000 chrX 46510000 46520000 0.009352380652948585 +chrX 46410000 46420000 chrX 46510000 46520000 0.0093523806529485 chrX 47050000 47060000 chrX 47380000 47390000 0.001 chrX 47050000 47060000 chrX 47240000 47250000 0.001 chrX 47240000 47250000 chrX 47350000 47360000 0.001 diff --git a/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_statistics b/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_statistics index 7abd04ac..aee8d74b 100644 --- a/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_statistics +++ b/hicexplorer/test/test_data/hicValidateLocations/overlap_smc3_statistics @@ -1,5 +1,5 @@ -# HiCExplorer hicValidateLocations 3.0 -# Overlap of loop file loops_1.bedgraph with protein file proteins/GSM935376_hg19_Gm12878_Smc3.narrowPeak +# HiCExplorer hicValidateLocations 3.7-dev +# Overlap of loop file /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/hicValidateLocations/loops_1.bedgraph with protein file /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak # Protein peaks: 34474 Matched Loops: 6379 diff --git a/hicexplorer/test/test_data/number_of_tests.txt b/hicexplorer/test/test_data/number_of_tests.txt index 266217da..5ae48373 100644 --- a/hicexplorer/test/test_data/number_of_tests.txt +++ b/hicexplorer/test/test_data/number_of_tests.txt @@ -1 +1 @@ -493 \ No newline at end of file +585 \ No newline at end of file diff --git a/hicexplorer/test/test_data/small_test_matrix_parallel_two_rc_chr3R.h5 b/hicexplorer/test/test_data/small_test_matrix_parallel_two_rc_chr3R.h5 new file mode 100644 index 00000000..556d43fe Binary files /dev/null and b/hicexplorer/test/test_data/small_test_matrix_parallel_two_rc_chr3R.h5 differ diff --git a/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs.py b/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs.py index d132f43b..813e706d 100644 --- a/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs.py +++ b/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs.py @@ -54,14 +54,13 @@ @pytest.mark.parametrize("restrictionSequence", ['GATC']) @pytest.mark.parametrize("danglingSequence", ['GATC']) @pytest.mark.parametrize("region", ["ChrX"]) # region does not work!! -@pytest.mark.parametrize("removeSelfLigation", [True]) @pytest.mark.parametrize("minMappingQuality", [15]) @pytest.mark.parametrize("threads", [4]) @pytest.mark.parametrize("inputBufferSize", [400000]) def test_build_matrix_restrictionCutFile_two(sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile, minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence, - danglingSequence, region, removeSelfLigation, + danglingSequence, region, minMappingQuality, threads, inputBufferSize): # test more args for restrictionCutFile option region = genomicRegion(region) @@ -71,15 +70,15 @@ def test_build_matrix_restrictionCutFile_two(sam1, sam2, outFile, qcFolder, outB "--danglingSequence {} " \ "--minDistance {} " \ "--maxLibraryInsertSize {} --threads {} " \ - "--region {} --removeSelfLigation {} ".format(bam_R1, bam_R2, - restrictionCutFile, outFile.name, - qcFolder, - restrictionSequence, - danglingSequence, - minDistance, - maxLibraryInsertSize, - threads, region, - removeSelfLigation).split() + "--region {} ".format(bam_R1, bam_R2, + restrictionCutFile, outFile.name, + qcFolder, + restrictionSequence, + danglingSequence, + minDistance, + maxLibraryInsertSize, + threads, region + ).split() # hicBuildMatrix.main(args) compute(hicBuildMatrix.main, args, 5) @@ -101,14 +100,13 @@ def test_build_matrix_restrictionCutFile_two(sam1, sam2, outFile, qcFolder, outB @pytest.mark.parametrize("restrictionSequence", ['GATC']) @pytest.mark.parametrize("danglingSequence", ['GATC']) @pytest.mark.parametrize("region", ["ChrX"]) # region does not work!! -@pytest.mark.parametrize("removeSelfLigation", [True]) @pytest.mark.parametrize("minMappingQuality", [15]) @pytest.mark.parametrize("threads", [4]) @pytest.mark.parametrize("inputBufferSize", [400000]) def test_build_matrix_restrictionCutFile_three(sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile, minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence, - danglingSequence, region, removeSelfLigation, + danglingSequence, region, minMappingQuality, threads, inputBufferSize): # test more params with restrictionCutFile (now without region param) args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \ @@ -116,11 +114,11 @@ def test_build_matrix_restrictionCutFile_three(sam1, sam2, outFile, qcFolder, ou "--danglingSequence {} " \ "--minDistance {} " \ "--maxLibraryInsertSize {} --threads {} " \ - "--removeSelfLigation {} ".format(bam_R1, bam_R2, - restrictionCutFile, outFile.name, qcFolder, - restrictionSequence, danglingSequence, - minDistance, maxLibraryInsertSize, threads, - removeSelfLigation).split() + " ".format(bam_R1, bam_R2, + restrictionCutFile, outFile.name, qcFolder, + restrictionSequence, danglingSequence, + minDistance, maxLibraryInsertSize, threads + ).split() # hicBuildMatrix.main(args) compute(hicBuildMatrix.main, args, 5) @@ -143,14 +141,13 @@ def test_build_matrix_restrictionCutFile_three(sam1, sam2, outFile, qcFolder, ou @pytest.mark.parametrize("restrictionSequence", ['GATC']) @pytest.mark.parametrize("danglingSequence", ['GATC']) @pytest.mark.parametrize("region", ["ChrX"]) # region does not work!! -@pytest.mark.parametrize("removeSelfLigation", [True]) @pytest.mark.parametrize("minMappingQuality", [15]) @pytest.mark.parametrize("threads", [4]) @pytest.mark.parametrize("inputBufferSize", [400000]) def test_build_matrix_restrictionCutFile_four(sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile, minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence, - danglingSequence, region, removeSelfLigation, + danglingSequence, region, minMappingQuality, threads, inputBufferSize): # test more params with restrictionCutFile (now without region param) args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \ @@ -158,15 +155,15 @@ def test_build_matrix_restrictionCutFile_four(sam1, sam2, outFile, qcFolder, out "--danglingSequence {} " \ "--minDistance {} " \ "--maxLibraryInsertSize {} --threads {} " \ - "--removeSelfLigation {} --keepSelfCircles ".format(bam_R1, bam_R2, - restrictionCutFile, - outFile.name, qcFolder, - restrictionSequence, - danglingSequence, - minDistance, - maxLibraryInsertSize, - threads, - removeSelfLigation).split() + " --keepSelfCircles ".format(bam_R1, bam_R2, + restrictionCutFile, + outFile.name, qcFolder, + restrictionSequence, + danglingSequence, + minDistance, + maxLibraryInsertSize, + threads + ).split() # hicBuildMatrix.main(args) compute(hicBuildMatrix.main, args, 5) diff --git a/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs_2.py b/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs_2.py index d030c447..a3fb3ab1 100644 --- a/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs_2.py +++ b/hicexplorer/test/trivial_runs/test_hicBuildMatrix_trivial_runs_2.py @@ -53,14 +53,13 @@ @pytest.mark.parametrize("restrictionSequence", ['GATC']) @pytest.mark.parametrize("danglingSequence", ['GATC']) @pytest.mark.parametrize("region", ["ChrX"]) # region does not work!! -@pytest.mark.parametrize("removeSelfLigation", [True]) @pytest.mark.parametrize("minMappingQuality", [15]) @pytest.mark.parametrize("threads", [4]) @pytest.mark.parametrize("inputBufferSize", [400000]) def test_build_matrix_restrictionCutFile_five(sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile, minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence, - danglingSequence, region, removeSelfLigation, + danglingSequence, region, minMappingQuality, threads, inputBufferSize): # added minMappingQuality args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \ @@ -68,12 +67,12 @@ def test_build_matrix_restrictionCutFile_five(sam1, sam2, outFile, qcFolder, out "--danglingSequence {} " \ "--minDistance {} " \ "--maxLibraryInsertSize {} --threads {} " \ - "--removeSelfLigation {} --keepSelfCircles " \ + " --keepSelfCircles " \ "--minMappingQuality {} ".format(bam_R1, bam_R2, restrictionCutFile, outFile.name, qcFolder, restrictionSequence, danglingSequence, minDistance, maxLibraryInsertSize, threads, - removeSelfLigation, minMappingQuality).split() + minMappingQuality).split() # hicBuildMatrix.main(args) compute(hicBuildMatrix.main, args, 5) @@ -96,14 +95,13 @@ def test_build_matrix_restrictionCutFile_five(sam1, sam2, outFile, qcFolder, out @pytest.mark.parametrize("restrictionSequence", ['GATC']) @pytest.mark.parametrize("danglingSequence", ['GATC']) @pytest.mark.parametrize("region", ["ChrX"]) # region does not work!! -@pytest.mark.parametrize("removeSelfLigation", [True]) @pytest.mark.parametrize("minMappingQuality", [15]) @pytest.mark.parametrize("threads", [4]) @pytest.mark.parametrize("inputBufferSize", [400000]) def test_build_matrix_restrictionCutFile_six(sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile, minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence, - danglingSequence, region, removeSelfLigation, + danglingSequence, region, keepSelfLigation, minMappingQuality, threads, inputBufferSize): # added inputBufferSize args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \ @@ -111,7 +109,7 @@ def test_build_matrix_restrictionCutFile_six(sam1, sam2, outFile, qcFolder, outB "--danglingSequence {} " \ "--minDistance {} " \ "--maxLibraryInsertSize {} --threads {} " \ - "--removeSelfLigation {} --keepSelfCircles " \ + "--keepSelfCircles " \ "--minMappingQuality {} --inputBufferSize {} ".format(bam_R1, bam_R2, restrictionCutFile, outFile.name, qcFolder, @@ -120,7 +118,6 @@ def test_build_matrix_restrictionCutFile_six(sam1, sam2, outFile, qcFolder, outB minDistance, maxLibraryInsertSize, threads, - removeSelfLigation, minMappingQuality, inputBufferSize).split() @@ -145,14 +142,13 @@ def test_build_matrix_restrictionCutFile_six(sam1, sam2, outFile, qcFolder, outB @pytest.mark.parametrize("restrictionSequence", ['GATC']) @pytest.mark.parametrize("danglingSequence", ['GATC']) @pytest.mark.parametrize("region", ["ChrX"]) # region does not work!! -@pytest.mark.parametrize("removeSelfLigation", [True]) @pytest.mark.parametrize("minMappingQuality", [15]) @pytest.mark.parametrize("threads", [4]) @pytest.mark.parametrize("inputBufferSize", [400000]) def test_build_matrix_restrictionCutFile_seven(sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile, minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence, - danglingSequence, region, removeSelfLigation, + danglingSequence, region, minMappingQuality, threads, inputBufferSize): # added doTestRun args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \ @@ -160,13 +156,13 @@ def test_build_matrix_restrictionCutFile_seven(sam1, sam2, outFile, qcFolder, ou "--danglingSequence {} " \ "--minDistance {} " \ "--maxLibraryInsertSize {} --threads {} " \ - "--removeSelfLigation {} --keepSelfCircles " \ + " --keepSelfCircles " \ "--minMappingQuality {} --inputBufferSize {} " \ "--doTestRun ".format(bam_R1, bam_R2, restrictionCutFile, outFile.name, qcFolder, restrictionSequence, danglingSequence, minDistance, maxLibraryInsertSize, threads, - removeSelfLigation, minMappingQuality, + minMappingQuality, inputBufferSize).split() # hicBuildMatrix.main(args) @@ -190,14 +186,13 @@ def test_build_matrix_restrictionCutFile_seven(sam1, sam2, outFile, qcFolder, ou @pytest.mark.parametrize("restrictionSequence", ['GATC']) @pytest.mark.parametrize("danglingSequence", ['GATC']) @pytest.mark.parametrize("region", ["ChrX"]) # region does not work!! -@pytest.mark.parametrize("removeSelfLigation", [True]) @pytest.mark.parametrize("minMappingQuality", [15]) @pytest.mark.parametrize("threads", [4]) @pytest.mark.parametrize("inputBufferSize", [400000]) def test_build_matrix_restrictionCutFile_eight(sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile, minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence, - danglingSequence, region, removeSelfLigation, + danglingSequence, region, minMappingQuality, threads, inputBufferSize): # added skipDuplicationCheck args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \ @@ -205,14 +200,14 @@ def test_build_matrix_restrictionCutFile_eight(sam1, sam2, outFile, qcFolder, ou "--danglingSequence {} " \ "--minDistance {} " \ "--maxLibraryInsertSize {} --threads {} " \ - "--removeSelfLigation {} --keepSelfCircles " \ + "--keepSelfCircles " \ "--minMappingQuality {} --inputBufferSize {} " \ "--doTestRun --skipDuplicationCheck ".format(bam_R1, bam_R2, restrictionCutFile, outFile.name, qcFolder, restrictionSequence, danglingSequence, minDistance, maxLibraryInsertSize, threads, - removeSelfLigation, + minMappingQuality, inputBufferSize).split() diff --git a/hicexplorer/trained_models/100kb_model_cleanlab_proteins_obs_exp.BIN b/hicexplorer/trained_models/100kb_model_cleanlab_proteins_obs_exp.BIN new file mode 100644 index 00000000..f2103758 Binary files /dev/null and b/hicexplorer/trained_models/100kb_model_cleanlab_proteins_obs_exp.BIN differ diff --git a/hicexplorer/trained_models/100kb_model_cleanlab_proteins_range.BIN b/hicexplorer/trained_models/100kb_model_cleanlab_proteins_range.BIN new file mode 100644 index 00000000..4eaef076 Binary files /dev/null and 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a/hicexplorer/trained_models/25kb_model_cleanlab_proteins_range.BIN b/hicexplorer/trained_models/25kb_model_cleanlab_proteins_range.BIN new file mode 100644 index 00000000..d5f23fab Binary files /dev/null and b/hicexplorer/trained_models/25kb_model_cleanlab_proteins_range.BIN differ diff --git a/hicexplorer/trained_models/50kb_model_cleanlab_proteins_obs_exp.BIN b/hicexplorer/trained_models/50kb_model_cleanlab_proteins_obs_exp.BIN new file mode 100644 index 00000000..b719ab66 Binary files /dev/null and b/hicexplorer/trained_models/50kb_model_cleanlab_proteins_obs_exp.BIN differ diff --git a/hicexplorer/trained_models/50kb_model_cleanlab_proteins_range.BIN b/hicexplorer/trained_models/50kb_model_cleanlab_proteins_range.BIN new file mode 100644 index 00000000..6c8c2bb4 Binary files /dev/null and b/hicexplorer/trained_models/50kb_model_cleanlab_proteins_range.BIN differ diff --git a/hicexplorer/utilities.py b/hicexplorer/utilities.py index 1a816ef1..54e56670 100644 --- a/hicexplorer/utilities.py +++ b/hicexplorer/utilities.py @@ -25,8 +25,11 @@ def readBed(pBedFile): _line = line.strip().split('\t') if len(line) == 0: continue - - chrom, start, end = _line[:3] + try: + chrom, start, end = _line[:3] + except ValueError: + _line = line.strip().split() + chrom, start, end = _line[:3] viewpoints.append((chrom, start, end)) return viewpoints @@ -415,6 +418,34 @@ def expected_interactions(pSubmatrix, pThreads=None): # return sum_per_distance / binary_interactions_per_distance +def compute_zscore(pSubmatrix, pDepth, pThreads): + # depth is to be expected in matrix units + # indice == distance + + expected_interactions_array = expected_interactions(pSubmatrix, pThreads=pThreads) + occurrences = np.arange(pSubmatrix.shape[0] + 1, 1, -1) + row, col = pSubmatrix.nonzero() + distance = np.absolute(row - col) + if pDepth is not None: + max_distance = min(pSubmatrix.shape[0], pDepth) + mask = distance > pDepth + pSubmatrix.data[mask] = 0 + else: + max_distance = pSubmatrix.shape[0] + + x_minus_mu = np.zeros(len(pSubmatrix.data)) + # sum_for_sigma = np.zeros(len(expected_interactions_array)) + for distance_index in range(max_distance): + mask = distance == distance_index + x_minus_mu[mask] -= expected_interactions_array[distance_index] + sum_for_sigma = np.sum(np.square(x_minus_mu[mask])) + + sum_for_sigma += np.square((0 - expected_interactions_array[distance_index]) * (occurrences[distance_index] - np.sum(mask))) + pSubmatrix.data[mask] = x_minus_mu[mask] / np.sqrt(sum_for_sigma / occurrences[distance_index]) + + return pSubmatrix + + def obs_exp_matrix_lieberman(pSubmatrix, pLength_chromosome, pChromosome_count): """ Creates normalized contact matrix M* by @@ -481,7 +512,7 @@ def obs_exp_matrix_non_zero(pSubmatrix, ligation_factor=False, pInplace=True, pT return submatrix -def obs_exp_matrix(pSubmatrix, pInplace=True, pToEpsilon=False, pThreads=None): +def obs_exp_matrix(pSubmatrix, pInplace=True, pToEpsilon=False, pThreads=None, pDistance=None): """ Creates normalized contact matrix M* by dividing each entry by the gnome-wide @@ -491,6 +522,13 @@ def obs_exp_matrix(pSubmatrix, pInplace=True, pToEpsilon=False, pThreads=None): interactions at abs(i-j) """ # time_start = time.time() + if pDistance is not None: + row, col = pSubmatrix.nonzero() + distance = np.absolute(row - col) + mask = distance >= pDistance + pSubmatrix.data[mask] = 0 + pSubmatrix.eliminate_zeros() + expected_interactions_in_distance_ = expected_interactions(pSubmatrix, pThreads) if expected_interactions_in_distance_ is None: return None diff --git a/requirements.txt b/requirements.txt index d2508a3d..66559064 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,13 +5,13 @@ matplotlib-base >= 3.1.* ipykernel >= 5.3.0 pysam >= 0.16.* intervaltree >= 3.1.* -biopython < 1.77 +biopython pytables >= 3.6.* pandas >= 1.1.* pybigwig >= 0.3.* jinja2 >= 2.11 unidecode >= 1.1.* -hicmatrix >= 15 +hicmatrix >= 16 hic2cool >= 0.8.3 psutil >= 5.7.* pygenometracks >= 3.5 @@ -24,3 +24,5 @@ tqdm >= 4.50 hyperopt >= 0.2.4 python-graphviz >= 0.14 scikit-learn >= 0.23.2 +imbalanced-learn >= 0.7.* +cleanlab >= 0.1.* diff --git a/setup.py b/setup.py index 46c65cc5..c8657a47 100755 --- a/setup.py +++ b/setup.py @@ -94,18 +94,18 @@ def checkProgramIsInstalled(self, program, args, where_to_download, install_requires_py = ["numpy >= 1.19.*", "scipy >= 1.5.*", - "matplotlib-base >= 3.1.*", + "matplotlib >= 3.1.*", "ipykernel >= 5.3.0", "pysam >= 0.16", "intervaltree >= 3.1.*", - "biopython < 1.77", + "biopython", "tables >= 3.6.*", "pandas >= 1.1.*", "pyBigWig >= 0.3.*", "cooler >= 0.8.10", "jinja2 >= 2.11.*", "unidecode >= 1.1.*", - "hicmatrix >= 15", + "hicmatrix >= 16", "pygenometracks >= 3.5", "psutil >= 5.7.*", "fit_nbinom >= 1.1", @@ -116,7 +116,9 @@ def checkProgramIsInstalled(self, program, args, where_to_download, "tqdm >= 4.50", "hyperopt >= 0.2.4", "graphviz >= 0.14", - "scikit-learn >= 0.23.2" + "scikit-learn >= 0.23.2", + "imbalanced-learn >= 0.7.*", + "cleanlab >= 0.1.*" ] @@ -135,7 +137,8 @@ def checkProgramIsInstalled(self, program, args, where_to_download, 'bin/hicConvertFormat', 'bin/hicAdjustMatrix', 'bin/hicNormalize', 'bin/hicAverageRegions', 'bin/hicPlotAverageRegions', 'bin/hicDetectLoops', 'bin/hicValidateLocations', 'bin/hicMergeLoops', 'bin/hicCompartmentalization', 'bin/hicQuickQC', 'bin/hicPlotSVL', 'bin/hicCreateThresholdFile', 'bin/hicHyperoptDetectLoops', - 'bin/hicHyperoptDetectLoopsHiCCUPS', 'bin/hicMergeDomains', 'bin/hicDifferentialTAD' + 'bin/hicHyperoptDetectLoopsHiCCUPS', 'bin/hicMergeDomains', 'bin/hicDifferentialTAD', 'bin/chicExportData', 'bin/hicInterIntraTAD', + 'bin/hicTADClassifier', 'bin/hicTrainTADClassifier' ], include_package_data=True, package_dir={'hicexplorer': 'hicexplorer'},