From 0ac37c7c6001e112ccc108b48a74fc24a8aa0b61 Mon Sep 17 00:00:00 2001 From: Daniel Himmelstein Date: Wed, 5 Oct 2016 12:57:49 -0400 Subject: [PATCH] Create sample lookup JSON objects for frontend --- 5.data-to-JSON.ipynb | 264 ++ data/.gitignore | 1 + data/json/disease_to_samples.json | 7372 +++++++++++++++++++++++++++++ scripts/5.data-to-JSON.py | 66 + 4 files changed, 7703 insertions(+) create mode 100644 5.data-to-JSON.ipynb create mode 100644 data/json/disease_to_samples.json create mode 100644 scripts/5.data-to-JSON.py diff --git a/5.data-to-JSON.ipynb b/5.data-to-JSON.ipynb new file mode 100644 index 0000000..8b7b488 --- /dev/null +++ b/5.data-to-JSON.ipynb @@ -0,0 +1,264 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Export cancer-data to JSON for frontend" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "import os\n", + "import json\n", + "import gzip\n", + "\n", + "import pandas" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## gene_to_mutated_samples" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "path = os.path.join('data', 'mutation-matrix.tsv.bz2')\n", + "mutation_mat_df = pandas.read_table(path, index_col=0)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "gene_to_mutated_samples = dict()\n", + "for entrez_gene_id, series in mutation_mat_df.iteritems():\n", + " gene_to_mutated_samples[int(entrez_gene_id)] = list(series.index[series == 1])" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'20.68 MB'" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "path = os.path.join('data', 'json', 'gene_to_mutated_samples.json')\n", + "with open(path, 'w') as write_file:\n", + " json.dump(gene_to_mutated_samples, write_file, indent=2, sort_keys=True)\n", + "'{:.2f} MB'.format(1e-6 * os.path.getsize(path))" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'2.97 MB'" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "path = os.path.join('data', 'json', 'gene_to_mutated_samples.json.gz')\n", + "with gzip.open(path, 'wt') as write_file:\n", + " json.dump(gene_to_mutated_samples, write_file, indent=2, sort_keys=True)\n", + "'{:.2f} MB'.format(1e-6 * os.path.getsize(path))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## disease_to_samples" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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sample_idpatient_idsample_typediseaseacronymorgan_of_origingenderage_diagnoseddeaddays_survivedrecurreddays_recurrence_freen_mutations
0TCGA-02-0047-01TCGA-02-0047Primary Tumorglioblastoma multiformeGBMBrainMale78.01.0448.0NaNNaN39
1TCGA-02-0055-01TCGA-02-0055Primary Tumorglioblastoma multiformeGBMBrainFemale62.01.076.0NaNNaN33
\n", + "
" + ], + "text/plain": [ + " sample_id patient_id sample_type disease \\\n", + "0 TCGA-02-0047-01 TCGA-02-0047 Primary Tumor glioblastoma multiforme \n", + "1 TCGA-02-0055-01 TCGA-02-0055 Primary Tumor glioblastoma multiforme \n", + "\n", + " acronym organ_of_origin gender age_diagnosed dead days_survived \\\n", + "0 GBM Brain Male 78.0 1.0 448.0 \n", + "1 GBM Brain Female 62.0 1.0 76.0 \n", + "\n", + " recurred days_recurrence_free n_mutations \n", + "0 NaN NaN 39 \n", + "1 NaN NaN 33 " + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "path = os.path.join('data', 'samples.tsv')\n", + "sample_df = pandas.read_table(path)\n", + "sample_df.head(2)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "disease_to_samples = {acronym: sorted(sample_ids) for acronym, sample_ids in sample_df.groupby('acronym').sample_id}" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'0.17 MB'" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "path = os.path.join('data', 'json', 'disease_to_samples.json')\n", + "with open(path, 'w') as write_file:\n", + " json.dump(disease_to_samples, write_file, indent=2, sort_keys=True)\n", + "'{:.2f} MB'.format(1e-6 * os.path.getsize(path))" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python [default]", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.5.2" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +} diff --git a/data/.gitignore b/data/.gitignore index 2a3abb1..99875de 100644 --- a/data/.gitignore +++ b/data/.gitignore @@ -1,2 +1,3 @@ # Ignore compressed files in this directory due to file size *.bz2 +*.gz diff --git a/data/json/disease_to_samples.json b/data/json/disease_to_samples.json new file mode 100644 index 0000000..19bdd71 --- /dev/null +++ b/data/json/disease_to_samples.json @@ -0,0 +1,7372 @@ +{ + "ACC": [ + "TCGA-OR-A5J1-01", + "TCGA-OR-A5J2-01", + "TCGA-OR-A5J3-01", + "TCGA-OR-A5J5-01", + "TCGA-OR-A5J6-01", + "TCGA-OR-A5J7-01", + "TCGA-OR-A5J8-01", + "TCGA-OR-A5J9-01", + "TCGA-OR-A5JA-01", + "TCGA-OR-A5JB-01", + "TCGA-OR-A5JC-01", + "TCGA-OR-A5JD-01", + "TCGA-OR-A5JE-01", + "TCGA-OR-A5JF-01", + "TCGA-OR-A5JG-01", + "TCGA-OR-A5JI-01", + "TCGA-OR-A5JJ-01", + "TCGA-OR-A5JK-01", + "TCGA-OR-A5JL-01", + "TCGA-OR-A5JM-01", + "TCGA-OR-A5JO-01", + "TCGA-OR-A5JP-01", + "TCGA-OR-A5JQ-01", + "TCGA-OR-A5JR-01", + "TCGA-OR-A5JS-01", + "TCGA-OR-A5JT-01", + "TCGA-OR-A5JV-01", + "TCGA-OR-A5JW-01", + "TCGA-OR-A5JX-01", + "TCGA-OR-A5JY-01", + "TCGA-OR-A5JZ-01", + "TCGA-OR-A5K0-01", + "TCGA-OR-A5K1-01", + "TCGA-OR-A5K2-01", + "TCGA-OR-A5K3-01", + "TCGA-OR-A5K4-01", + "TCGA-OR-A5K5-01", + "TCGA-OR-A5K6-01", + "TCGA-OR-A5K8-01", + "TCGA-OR-A5K9-01", + "TCGA-OR-A5KO-01", + "TCGA-OR-A5KT-01", + "TCGA-OR-A5KU-01", + "TCGA-OR-A5KV-01", + "TCGA-OR-A5KW-01", + "TCGA-OR-A5KX-01", + "TCGA-OR-A5KY-01", + "TCGA-OR-A5KZ-01", + "TCGA-OR-A5L3-01", + "TCGA-OR-A5L4-01", + "TCGA-OR-A5L5-01", + "TCGA-OR-A5L6-01", + "TCGA-OR-A5L8-01", + "TCGA-OR-A5L9-01", + "TCGA-OR-A5LA-01", + "TCGA-OR-A5LB-01", + "TCGA-OR-A5LC-01", + "TCGA-OR-A5LD-01", + "TCGA-OR-A5LE-01", + "TCGA-OR-A5LG-01", + "TCGA-OR-A5LH-01", + "TCGA-OR-A5LJ-01", + "TCGA-OR-A5LK-01", + "TCGA-OR-A5LL-01", + "TCGA-OR-A5LN-01", + "TCGA-OR-A5LO-01", + "TCGA-OR-A5LP-01", + "TCGA-OR-A5LR-01", + "TCGA-OR-A5LS-01", + "TCGA-OR-A5LT-01", + "TCGA-OU-A5PI-01", + "TCGA-P6-A5OF-01", + "TCGA-P6-A5OG-01", + "TCGA-PA-A5YG-01", + "TCGA-PK-A5H8-01", + "TCGA-PK-A5H9-01", + "TCGA-PK-A5HA-01", + "TCGA-PK-A5HB-01" + ], + "BLCA": [ 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"TCGA-EM-A2CP-01", + "TCGA-EM-A2CQ-01", + "TCGA-EM-A2CR-01", + "TCGA-EM-A2CS-01", + "TCGA-EM-A2CT-01", + "TCGA-EM-A2CU-01", + "TCGA-EM-A2OV-01", + "TCGA-EM-A2OW-01", + "TCGA-EM-A2OX-01", + "TCGA-EM-A2OY-01", + "TCGA-EM-A2OZ-01", + "TCGA-EM-A2P0-01", + "TCGA-EM-A2P1-01", + "TCGA-EM-A2P2-01", + "TCGA-EM-A2P3-01", + "TCGA-EM-A3AI-01", + "TCGA-EM-A3AJ-01", + "TCGA-EM-A3AK-01", + "TCGA-EM-A3AL-01", + "TCGA-EM-A3AN-01", + "TCGA-EM-A3AO-01", + "TCGA-EM-A3AP-01", + "TCGA-EM-A3AQ-01", + "TCGA-EM-A3AR-01", + "TCGA-EM-A3FJ-01", + "TCGA-EM-A3FK-01", + "TCGA-EM-A3FL-01", + "TCGA-EM-A3FM-01", + "TCGA-EM-A3FN-01", + "TCGA-EM-A3FO-01", + "TCGA-EM-A3FP-01", + "TCGA-EM-A3FQ-01", + "TCGA-EM-A3FR-01", + "TCGA-EM-A3O3-01", + "TCGA-EM-A3O6-01", + "TCGA-EM-A3O7-01", + "TCGA-EM-A3O8-01", + "TCGA-EM-A3O9-01", + "TCGA-EM-A3OA-01", + "TCGA-EM-A3OB-01", + "TCGA-EM-A3ST-01", + "TCGA-EM-A3SU-01", + "TCGA-EM-A3SX-01", + "TCGA-EM-A3SY-01", + "TCGA-EM-A3SZ-01", + "TCGA-EM-A4FF-01", + "TCGA-EM-A4FH-01", + "TCGA-EM-A4FK-01", + "TCGA-EM-A4FM-01", + "TCGA-EM-A4FN-01", + "TCGA-EM-A4FO-01", + "TCGA-EM-A4FQ-01", + "TCGA-EM-A4FR-01", + "TCGA-EM-A4FU-01", + "TCGA-EM-A4FV-01", + "TCGA-EM-A4G1-01", + "TCGA-ET-A25G-01", + "TCGA-ET-A25I-01", + "TCGA-ET-A25J-01", + "TCGA-ET-A25K-01", + "TCGA-ET-A25O-01", + "TCGA-ET-A25R-01", + "TCGA-ET-A2MX-01", + "TCGA-ET-A2MY-01", + "TCGA-ET-A2MZ-01", + "TCGA-ET-A2N0-01", + "TCGA-ET-A2N3-01", + "TCGA-ET-A2N4-01", + "TCGA-ET-A2N5-01", + "TCGA-ET-A39I-01", + "TCGA-ET-A39J-01", + "TCGA-ET-A39K-01", + "TCGA-ET-A39L-01", + "TCGA-ET-A39M-01", + "TCGA-ET-A39N-01", + "TCGA-ET-A39O-01", + "TCGA-ET-A39P-01", + "TCGA-ET-A39R-01", + "TCGA-ET-A39S-01", + "TCGA-ET-A39T-01", + "TCGA-ET-A3BN-01", + "TCGA-ET-A3BO-01", + "TCGA-ET-A3BP-01", + "TCGA-ET-A3BQ-01", + "TCGA-ET-A3BS-01", + "TCGA-ET-A3BT-01", + "TCGA-ET-A3BU-01", + "TCGA-ET-A3BV-01", + "TCGA-ET-A3BW-01", + "TCGA-ET-A3BX-01", + "TCGA-ET-A3DO-01", + "TCGA-ET-A3DP-01", + "TCGA-ET-A3DQ-01", + "TCGA-ET-A3DR-01", + "TCGA-ET-A3DS-01", + "TCGA-ET-A3DT-01", + "TCGA-ET-A3DU-01", + "TCGA-ET-A3DV-01", + "TCGA-ET-A3DW-01", + "TCGA-ET-A40P-01", + "TCGA-ET-A40Q-01", + "TCGA-ET-A40R-01", + "TCGA-ET-A40S-01", + "TCGA-ET-A40T-01", + "TCGA-ET-A4KN-01", + "TCGA-ET-A4KQ-01", + "TCGA-FE-A22Z-01", + "TCGA-FE-A230-01", + "TCGA-FE-A231-01", + "TCGA-FE-A232-01", + "TCGA-FE-A233-01", + "TCGA-FE-A234-01", + "TCGA-FE-A235-01", + "TCGA-FE-A236-01", + "TCGA-FE-A237-01", + "TCGA-FE-A23A-01", + "TCGA-FE-A3PA-01", + "TCGA-FE-A3PB-01", + "TCGA-FE-A3PC-01", + "TCGA-FE-A3PD-01", + "TCGA-FK-A3S3-01", + "TCGA-FK-A3SB-01", + "TCGA-FK-A3SD-01", + "TCGA-FK-A3SE-01", + "TCGA-FK-A3SG-01", + "TCGA-FK-A3SH-01", + "TCGA-FK-A4UB-01", + "TCGA-FY-A2QD-01", + "TCGA-FY-A3BL-01", + "TCGA-FY-A3I4-01", + "TCGA-FY-A3I5-01", + "TCGA-FY-A3NM-01", + "TCGA-FY-A3NN-01", + "TCGA-FY-A3NP-01", + "TCGA-FY-A3ON-01", + "TCGA-FY-A3R6-01", + "TCGA-FY-A3R7-01", + "TCGA-FY-A3R8-01", + "TCGA-FY-A3R9-01", + "TCGA-FY-A3RA-01", + "TCGA-FY-A3TY-01", + "TCGA-FY-A3W9-01", + "TCGA-FY-A3WA-01", + "TCGA-FY-A3YR-01", + "TCGA-FY-A40K-01", + "TCGA-FY-A40L-01", + "TCGA-FY-A40M-01", + "TCGA-FY-A40N-01", + "TCGA-FY-A4B0-01", + "TCGA-FY-A4B3-01", + "TCGA-FY-A4B4-01", + "TCGA-FY-A76V-01", + "TCGA-GE-A2C6-01", + "TCGA-H2-A26U-01", + "TCGA-H2-A2K9-01", + "TCGA-H2-A3RH-01", + "TCGA-H2-A3RI-01", + "TCGA-H2-A421-01", + "TCGA-H2-A422-01", + "TCGA-IM-A3EB-01", + "TCGA-IM-A3ED-01", + "TCGA-IM-A3U2-01", + "TCGA-IM-A3U3-01", + "TCGA-IM-A41Y-01", + "TCGA-IM-A41Z-01", + "TCGA-IM-A420-01", + "TCGA-IM-A4EB-01", + "TCGA-J8-A3NZ-01", + "TCGA-J8-A3O0-01", + "TCGA-J8-A3O1-01", + "TCGA-J8-A3O2-01", + "TCGA-J8-A3YD-01", + "TCGA-J8-A3YE-01", + "TCGA-J8-A3YF-01", + "TCGA-J8-A3YG-01", + "TCGA-J8-A3YH-01", + "TCGA-J8-A42S-01", + "TCGA-J8-A4HW-01", + "TCGA-J8-A4HY-01", + "TCGA-KS-A41F-01", + "TCGA-KS-A41I-01", + "TCGA-KS-A41J-01", + "TCGA-KS-A41L-01", + "TCGA-KS-A4I1-01", + "TCGA-KS-A4I3-01", + "TCGA-KS-A4I5-01", + "TCGA-KS-A4I7-01", + "TCGA-KS-A4I9-01", + "TCGA-KS-A4IB-01", + "TCGA-KS-A4IC-01", + "TCGA-KS-A4ID-01", + "TCGA-L6-A4EP-01", + "TCGA-L6-A4EQ-01", + "TCGA-L6-A4ET-01", + "TCGA-L6-A4EU-01", + "TCGA-MK-A4N6-01", + "TCGA-MK-A4N7-01", + "TCGA-MK-A4N9-01", + "TCGA-MK-A84Z-01", + "TCGA-QD-A8IV-01" + ], + "THYM": [ + "TCGA-3G-AB0O-01", + "TCGA-3G-AB0Q-01", + "TCGA-3G-AB0T-01", + "TCGA-3G-AB14-01", + "TCGA-3G-AB19-01", + "TCGA-3Q-A9WF-01", + "TCGA-3S-A8YW-01", + "TCGA-3S-AAYX-01", + "TCGA-3T-AA9L-01", + "TCGA-4V-A9QI-01", + "TCGA-4V-A9QJ-01", + "TCGA-4V-A9QL-01", + "TCGA-4V-A9QM-01", + "TCGA-4V-A9QN-01", + "TCGA-4V-A9QR-01", + "TCGA-4V-A9QS-01", + "TCGA-4V-A9QT-01", + "TCGA-4V-A9QU-01", + "TCGA-4V-A9QW-01", + "TCGA-4V-A9QX-01", + "TCGA-4X-A9F9-01", + "TCGA-4X-A9FA-01", + "TCGA-4X-A9FB-01", + "TCGA-4X-A9FC-01", + "TCGA-4X-A9FD-01", + "TCGA-5G-A9ZZ-01", + "TCGA-5K-AAAP-01", + "TCGA-5U-AB0D-01", + "TCGA-5U-AB0E-01", + "TCGA-5U-AB0F-01", + "TCGA-5V-A9RR-01", + "TCGA-X7-A8D6-01", + "TCGA-X7-A8D7-01", + "TCGA-X7-A8D8-01", + "TCGA-X7-A8D9-01", + "TCGA-X7-A8DB-01", + "TCGA-X7-A8DD-01", + "TCGA-X7-A8DE-01", + "TCGA-X7-A8DF-01", + "TCGA-X7-A8DG-01", + "TCGA-X7-A8DJ-01", + "TCGA-X7-A8M0-01", + "TCGA-X7-A8M1-01", + "TCGA-X7-A8M3-01", + "TCGA-X7-A8M4-01", + "TCGA-X7-A8M5-01", + "TCGA-X7-A8M6-01", + "TCGA-X7-A8M7-01", + "TCGA-X7-A8M8-01", + "TCGA-XH-A853-01", + "TCGA-XM-A8R8-01", + "TCGA-XM-A8R9-01", + "TCGA-XM-A8RB-01", + "TCGA-XM-A8RC-01", + "TCGA-XM-A8RD-01", + "TCGA-XM-A8RE-01", + "TCGA-XM-A8RF-01", + "TCGA-XM-A8RG-01", + "TCGA-XM-A8RH-01", + "TCGA-XM-A8RI-01", + "TCGA-XM-A8RL-01", + "TCGA-XM-AAZ1-01", + "TCGA-XM-AAZ2-01", + "TCGA-XM-AAZ3-01", + "TCGA-XU-A92O-01", + "TCGA-XU-A92Q-01", + "TCGA-XU-A92T-01", + "TCGA-XU-A92U-01", + "TCGA-XU-A92V-01", + "TCGA-XU-A92W-01", + "TCGA-XU-A92X-01", + "TCGA-XU-A92Y-01", + "TCGA-XU-A92Z-01", + "TCGA-XU-A930-01", + "TCGA-XU-A931-01", + "TCGA-XU-A932-01", + "TCGA-XU-A933-01", + "TCGA-XU-A936-01", + "TCGA-XU-AAXW-01", + "TCGA-XU-AAXX-01", + "TCGA-XU-AAXY-01", + "TCGA-XU-AAXZ-01", + "TCGA-XU-AAY0-01", + "TCGA-XU-AAY1-01", + "TCGA-YT-A95D-01", + "TCGA-YT-A95E-01", + "TCGA-YT-A95F-01", + "TCGA-YT-A95G-01", + "TCGA-YT-A95H-01", + "TCGA-ZB-A961-01", + "TCGA-ZB-A962-01", + "TCGA-ZB-A963-01", + "TCGA-ZB-A964-01", + "TCGA-ZB-A965-01", + "TCGA-ZB-A966-01", + "TCGA-ZB-A969-01", + "TCGA-ZB-A96A-01", + "TCGA-ZB-A96B-01", + "TCGA-ZB-A96C-01", + "TCGA-ZB-A96D-01", + "TCGA-ZB-A96E-01", + "TCGA-ZB-A96F-01", + "TCGA-ZB-A96G-01", + "TCGA-ZB-A96H-01", + "TCGA-ZB-A96I-01", + "TCGA-ZB-A96K-01", + "TCGA-ZB-A96L-01", + "TCGA-ZB-A96M-01", + "TCGA-ZB-A96O-01", + "TCGA-ZB-A96P-01", + "TCGA-ZB-A96Q-01", + "TCGA-ZB-A96R-01", + "TCGA-ZB-A96V-01", + "TCGA-ZC-AAA7-01", + "TCGA-ZC-AAAA-01", + "TCGA-ZC-AAAF-01", + "TCGA-ZC-AAAH-01", + "TCGA-ZL-A9V6-01", + "TCGA-ZT-A8OM-01" + ], + "UCEC": [ + "TCGA-AX-A05W-01", + "TCGA-AX-A1C7-01", + "TCGA-B5-A0JN-01", + "TCGA-B5-A0JR-01", + "TCGA-B5-A0K9-01", + "TCGA-B5-A11R-01", + "TCGA-BS-A0V7-01" + ], + "UCS": [ + "TCGA-N5-A4R8-01", + "TCGA-N5-A4RA-01", + "TCGA-N5-A4RD-01", + "TCGA-N5-A4RF-01", + "TCGA-N5-A4RJ-01", + "TCGA-N5-A4RM-01", + "TCGA-N5-A4RN-01", + "TCGA-N5-A4RO-01", + "TCGA-N5-A4RS-01", + "TCGA-N5-A4RT-01", + "TCGA-N5-A4RU-01", + "TCGA-N5-A4RV-01", + "TCGA-N5-A59E-01", + "TCGA-N5-A59F-01", + "TCGA-N6-A4V9-01", + "TCGA-N6-A4VC-01", + "TCGA-N6-A4VD-01", + "TCGA-N6-A4VE-01", + "TCGA-N6-A4VF-01", + "TCGA-N6-A4VG-01", + "TCGA-N7-A4Y0-01", + "TCGA-N7-A4Y5-01", + "TCGA-N7-A4Y8-01", + "TCGA-N7-A59B-01", + "TCGA-N8-A4PI-01", + "TCGA-N8-A4PL-01", + "TCGA-N8-A4PM-01", + "TCGA-N8-A4PN-01", + "TCGA-N8-A4PO-01", + "TCGA-N8-A4PP-01", + "TCGA-N8-A4PQ-01", + "TCGA-N8-A56S-01", + "TCGA-N9-A4PZ-01", + "TCGA-N9-A4Q1-01", + "TCGA-N9-A4Q3-01", + "TCGA-N9-A4Q4-01", + "TCGA-N9-A4Q7-01", + "TCGA-N9-A4Q8-01", + "TCGA-NA-A4QV-01", + "TCGA-NA-A4QW-01", + "TCGA-NA-A4QX-01", + "TCGA-NA-A4QY-01", + "TCGA-NA-A4R0-01", + "TCGA-NA-A4R1-01", + "TCGA-NA-A5I1-01", + "TCGA-ND-A4W6-01", + "TCGA-ND-A4WA-01", + "TCGA-ND-A4WC-01", + "TCGA-ND-A4WF-01", + "TCGA-NF-A4WU-01", + "TCGA-NF-A4WX-01", + "TCGA-NF-A4X2-01", + "TCGA-NF-A5CP-01", + "TCGA-NG-A4VU-01", + "TCGA-NG-A4VW-01", + "TCGA-QM-A5NM-01", + "TCGA-QN-A5NN-01" + ], + "UVM": [ + "TCGA-RZ-AB0B-01", + "TCGA-V3-A9ZX-01", + "TCGA-V3-A9ZY-01", + "TCGA-V4-A9E5-01", + "TCGA-V4-A9E7-01", + "TCGA-V4-A9E8-01", + "TCGA-V4-A9E9-01", + "TCGA-V4-A9EA-01", + "TCGA-V4-A9EC-01", + "TCGA-V4-A9ED-01", + "TCGA-V4-A9EE-01", + "TCGA-V4-A9EF-01", + "TCGA-V4-A9EH-01", + "TCGA-V4-A9EI-01", + "TCGA-V4-A9EJ-01", + "TCGA-V4-A9EK-01", + "TCGA-V4-A9EL-01", + "TCGA-V4-A9EM-01", + "TCGA-V4-A9EO-01", + "TCGA-V4-A9EQ-01", + "TCGA-V4-A9ES-01", + "TCGA-V4-A9ET-01", + "TCGA-V4-A9EU-01", + "TCGA-V4-A9EV-01", + "TCGA-V4-A9EW-01", + "TCGA-V4-A9EX-01", + "TCGA-V4-A9EY-01", + "TCGA-V4-A9EZ-01", + "TCGA-V4-A9F0-01", + "TCGA-V4-A9F1-01", + "TCGA-V4-A9F2-01", + "TCGA-V4-A9F3-01", + "TCGA-V4-A9F4-01", + "TCGA-V4-A9F5-01", + "TCGA-V4-A9F7-01", + "TCGA-V4-A9F8-01", + "TCGA-VD-A8K7-01", + "TCGA-VD-A8K8-01", + "TCGA-VD-A8K9-01", + "TCGA-VD-A8KA-01", + "TCGA-VD-A8KB-01", + "TCGA-VD-A8KD-01", + "TCGA-VD-A8KE-01", + "TCGA-VD-A8KF-01", + "TCGA-VD-A8KG-01", + "TCGA-VD-A8KH-01", + "TCGA-VD-A8KI-01", + "TCGA-VD-A8KJ-01", + "TCGA-VD-A8KK-01", + "TCGA-VD-A8KL-01", + "TCGA-VD-A8KM-01", + "TCGA-VD-A8KN-01", + "TCGA-VD-A8KO-01", + "TCGA-VD-AA8M-01", + "TCGA-VD-AA8N-01", + "TCGA-VD-AA8O-01", + "TCGA-VD-AA8P-01", + "TCGA-VD-AA8Q-01", + "TCGA-VD-AA8R-01", + "TCGA-VD-AA8S-01", + "TCGA-VD-AA8T-01", + "TCGA-WC-A87T-01", + "TCGA-WC-A87U-01", + "TCGA-WC-A87W-01", + "TCGA-WC-A87Y-01", + "TCGA-WC-A880-01", + "TCGA-WC-A881-01", + "TCGA-WC-A882-01", + "TCGA-WC-A883-01", + "TCGA-WC-A884-01", + "TCGA-WC-A885-01", + "TCGA-WC-A888-01", + "TCGA-WC-A88A-01", + "TCGA-WC-AA9A-01", + "TCGA-WC-AA9E-01", + "TCGA-YZ-A980-01", + "TCGA-YZ-A982-01", + "TCGA-YZ-A983-01", + "TCGA-YZ-A984-01", + "TCGA-YZ-A985-01" + ] +} \ No newline at end of file diff --git a/scripts/5.data-to-JSON.py b/scripts/5.data-to-JSON.py new file mode 100644 index 0000000..61f0901 --- /dev/null +++ b/scripts/5.data-to-JSON.py @@ -0,0 +1,66 @@ + +# coding: utf-8 + +# # Export cancer-data to JSON for frontend + +# In[1]: + +import os +import json +import gzip + +import pandas + + +# ## gene_to_mutated_samples + +# In[2]: + +path = os.path.join('data', 'mutation-matrix.tsv.bz2') +mutation_mat_df = pandas.read_table(path, index_col=0) + + +# In[3]: + +gene_to_mutated_samples = dict() +for entrez_gene_id, series in mutation_mat_df.iteritems(): + gene_to_mutated_samples[int(entrez_gene_id)] = list(series.index[series == 1]) + + +# In[4]: + +path = os.path.join('data', 'json', 'gene_to_mutated_samples.json') +with open(path, 'w') as write_file: + json.dump(gene_to_mutated_samples, write_file, indent=2, sort_keys=True) +'{:.2f} MB'.format(1e-6 * os.path.getsize(path)) + + +# In[5]: + +path = os.path.join('data', 'json', 'gene_to_mutated_samples.json.gz') +with gzip.open(path, 'wt') as write_file: + json.dump(gene_to_mutated_samples, write_file, indent=2, sort_keys=True) +'{:.2f} MB'.format(1e-6 * os.path.getsize(path)) + + +# ## disease_to_samples + +# In[6]: + +path = os.path.join('data', 'samples.tsv') +sample_df = pandas.read_table(path) +sample_df.head(2) + + +# In[7]: + +disease_to_samples = {acronym: sorted(sample_ids) for acronym, sample_ids in sample_df.groupby('acronym').sample_id} + + +# In[8]: + +path = os.path.join('data', 'json', 'disease_to_samples.json') +with open(path, 'w') as write_file: + json.dump(disease_to_samples, write_file, indent=2, sort_keys=True) +'{:.2f} MB'.format(1e-6 * os.path.getsize(path)) +