download pre-trained Peakachu models

[Bo-UT]

Hi Xiaotao,

Our sever is offline. Would be possible to download all pre-trained Peakachu models for neoloop-caller locally? I tried the https://dl.dropboxusercontent.com, but it seems not accessible.

Thank you.

Bo

[XiaoTaoWang]

Hi Bo, all the pre-trained models can be found at https://github.com/tariks/peakachu#using-peakachu-as-a-standard-loop-caller.

[XiaoTaoWang]

Hi Bo, I recently released a new version (https://github.com/XiaoTaoWang/NeoLoopFinder#release-notes). All the reference data and models were moved to a new server. Can you upgrade your NeoLoopFinder and try again? Note that the dependent packages need to be re-installed as well. Thanks!

[Bo-UT]

Hi Xiaotao, Thanks a lot! Will try the new version. Best, Bo

…

On Fri, Sep 16, 2022 at 11:41 PM Xiaotao Wang ***@***.***> wrote: Hi Bo, I recently released a new version ( https://github.com/XiaoTaoWang/NeoLoopFinder#release-notes). All the reference data and models were moved to a new server. Can you upgrade your NeoLoopFinder and try again? Note that the dependent packages need to be re-installed as well. Thanks! — Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANEBFVRWUINFOXVMTYY4NSDV6VDXTANCNFSM54GBYVIQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Bo-UT]

Hi Xiaotao,

I tried the new version of NeoLoopFinder and it works well. Thanks!

I tried to plot genes with the sample codes:
vis = Triangle(clr, assembly, n_rows=5, figsize=(7, 6), track_partition=[5, 0.8, 0.8, 0.2, 0.5], correct='weight', span=300000, space=0.08)
vis.matrix_plot(vmin=0, cbr_fontsize=9)
vis.plot_chromosome_bounds(linewidth=2)
vis.plot_signal('RNA-Seq', 'sample_blacklistfiltered.CPM.bw', label_size=10, data_range_size=9, max_value=0.01, color='#E31A1C')
vis.plot_signal('H3K27ac', 'H3K27acChIPseq/sample_h3k27ac_CPM_extendReads200.bw', label_size=10, data_range_size=9, max_value=1, color='#6A3D9A')
vis.plot_genes(filter_=List, fontsize=10)
vis.plot_chromosome_bar(name_size=12, coord_size=10)

but constantly got the error. Do you have an idea what the problem? Thanks a lot!

----> 6 vis.plot_genes(filter_=List, fontsize=10)
7 vis.plot_chromosome_bar(name_size=12, coord_size=10)
8 # vis.outfig('SCaBER.NFIB.png', dpi=300)

File ~/miniconda3/envs/neoloop/lib/python3.10/site-packages/neoloop/visualize/core.py:487, in Triangle.plot_genes(self, species, release, filter_, color, border_color, fontsize, labels, style, global_max_row, label_aligns)
481 def plot_genes(self, species='human', release=97, filter_=None,
482 color='#999999', border_color='#999999', fontsize=7, labels='auto',
483 style='flybase', global_max_row=False, label_aligns={}):
485 genes = Genes(self.bounds, self.orients, self.res, species=species, release=release,
486 filter_=filter_)
--> 487 _wk = plotGenes(genes.file_handler, color=color, fontsize=fontsize, labels=labels,
488 style=style, global_max_row=global_max_row)
490 ax = self.fig.add_subplot(self.grid[self.track_count])
491 self.track_count += 1

File ~/miniconda3/envs/neoloop/lib/python3.10/site-packages/neoloop/visualize/bed.py:319, in plotGenes.init(self, file_, **kwargs)
316 # to set the distance between rows
317 self.row_scale = self.properties['interval_height'] * 2.3
--> 319 self.interval_tree, min_score, max_score = self._process_bed()

File ~/miniconda3/envs/neoloop/lib/python3.10/site-packages/neoloop/visualize/bed.py:324, in plotGenes._process_bed(self)
322 def process_bed(self):
--> 324 bed_file_h = ReadBed(self.properties['file'])
325 self.bed_type = bed_file_h.file_type
327 if 'color' in self.properties and self.properties['color'] == 'bed_rgb' and
328 self.bed_type not in ['bed12', 'bed9']:

File ~/miniconda3/envs/neoloop/lib/python3.10/site-packages/neoloop/visualize/base.py:258, in ReadBed.init(self, file_handle)
256 self.line_number = 0
257 # guess file type
--> 258 fields = self.get_no_comment_line()
259 fields = to_string(fields)
260 fields = fields.split()

File ~/miniconda3/envs/neoloop/lib/python3.10/site-packages/neoloop/visualize/base.py:290, in ReadBed.get_no_comment_line(self)
285 def get_no_comment_line(self):
286 """
287 Skips comment lines starting with '#'
288 "track" or "browser" in the bed files
289 """
--> 290 line = next(self.file_handle)
291 line = to_string(line)
292 if line.startswith("#") or line.startswith("track") or
293 line.startswith("browser") or line.strip() == '':

StopIteration:

[XiaoTaoWang]

Hi Bo, it seems that no genes were left after filtering by List. Can you check to make sure at least one genes in the List are located in the current region?

[Bo-UT]

Hi Xiaotao, Thanks so much for your prompt response! I put one gene located in the current region to the list and it works. Many thanks! I have one more question, is there any way to make the plot window wider? Take the assembly "C24 inversion,6,164305000,+,6,169035000,+ 6,162710000 6,168820000" for example, I want to plot the range of *[160M, 180M]* instead of [164305000, 168820000]. Thanks in advance. Regards, Bo

…

On Wed, Nov 2, 2022 at 11:01 AM Xiaotao Wang ***@***.***> wrote: Hi Bo, it seems that no genes were left after filtering by List. Can you check to make sure at least one genes in the List are located in the current region? — Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANEBFVW6CDKMT7TATEPS23DWGKF6RANCNFSM54GBYVIQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[XiaoTaoWang]

Probably the easiest way to do this is to increase the value of span when you construct a Triangle object. For example, the following command will extend the region by 1Mb on both sides of the local assembly::

>>> vis = Triangle(clr, assembly, n_rows=5, figsize=(7, 6), track_partition=[5, 0.8, 0.8, 0.2, 0.5], correct='weight', span=1000000, space=0.08)

[Bo-UT]

That works. Thanks so much!

…

On Wed, Nov 2, 2022 at 12:49 PM Xiaotao Wang ***@***.***> wrote: Probably the easiest way to do this is to increase the value of span when you construct a Triangle object. For example, the following command will extend the region by 1Mb on both sides of the local assembly:: >>> vis = Triangle(clr, assembly, n_rows=5, figsize=(7, 6), track_partition=[5, 0.8, 0.8, 0.2, 0.5], correct='weight', span=1000000, space=0.08) — Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANEBFVSZW4NKSYGAYMWZ63DWGKSTTANCNFSM54GBYVIQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>