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 https://github.com/XiaoTaoWang/NeoLoopFinder/issues/34#issuecomment-1249998579, 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.plotgenes(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.plotgenes(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.plotgenes(self, species, release, filter, color, border_color, fontsize, labels, style, global_max_row, label_aligns) 481 def plotgenes(self, species='human', release=97, filter=None, 482 color='#999999', border_color='#999999', fontsize=7, labels='auto', 483 style='flybase', global_max_row=False, labelaligns={}): 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_fileh = 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 https://github.com/XiaoTaoWang/NeoLoopFinder/issues/34#issuecomment-1300765880, 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 https://github.com/XiaoTaoWang/NeoLoopFinder/issues/34#issuecomment-1301010862, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANEBFVSZW4NKSYGAYMWZ63DWGKSTTANCNFSM54GBYVIQ . You are receiving this because you authored the thread.Message ID: @.***>