KeyError

[e-coral]

Describe the bug
During plotting, towards the end of the pipeline, I am running into KeyError: 'Chromosome not found: 17'. This is occurring at line 339 in plotting.py, when trying to fetch bigwig intervals.

I have double checked my input files, and they are all using "chr17" naming, not "17". Also, I do not run into any chromosome key errors before this point in the pipeline, suggesting there are no naming issues in my input files.

I suspect the 'chr' part of the chromosome name is somehow being lost during the creation of the genomeRange object (gr). However, I can't find where this happens to test it.

Could this possibly be related to a pyranges/pandas bug from last year, #281?

To Reproduce
I am running capcruncher for a single viewpoint:

• viewpoint: chr17 3469 3916 17p-tel
• T2T reference files

Expected behavior
There should not be key errors affecting plotting

Screenshots
[text of error messages copied below]

Additional context
Removing temporary output capcruncher_output/interim/comparisons/summaries_and_subtractions/Late.mean-summary.17p-tel.bedgraph. /home/emmon/miniconda3/lib/python3.10/site-packages/iced/normalization/_ca_utils.py:8: UserWarning: The API of this module is likely to change. Use only for testing purposes warnings.warn( 2025-03-25 13:21:43.558 | INFO | __main__:<module>:21 - Checking if we can group tracks by condition 2025-03-25 13:21:43.559 | INFO | __main__:<module>:26 - Setting up tracks 2025-03-25 13:21:43.559 | INFO | __main__:<module>:35 - Adding bigwig tracks 2025-03-25 13:21:43.561 | INFO | __main__:<module>:62 - Added Early bigwig track 2025-03-25 13:21:43.561 | INFO | __main__:<module>:62 - Added Late bigwig track 2025-03-25 13:21:43.562 | INFO | __main__:<module>:78 - Adding subtraction tracks 2025-03-25 13:21:43.562 | INFO | __main__:<module>:81 - Adding Early-Late.mean-subtraction.17p-tel subtraction track 2025-03-25 13:21:43.562 | INFO | __main__:<module>:81 - Adding Late-Early.mean-subtraction.17p-tel subtraction track 2025-03-25 13:21:43.562 | INFO | __main__:<module>:139 - Adding genes track 2025-03-25 13:21:43.562 | INFO | __main__:<module>:149 - Making figure cat: PATH_TO_GENES_IN_BED12_FORMAT: No such file or directory 2025-03-25 13:21:43.615 | INFO | __main__:<module>:152 - Saving figure to: capcruncher_output/results/figures/17p-tel.pdf [ERROR:frame.py:224 - plot()] Error occured when plot track: track name: BigWigCollection.Early track type:<class 'capcruncher.api.plotting.CCBigWigCollection'> Error: <class 'KeyError'> 'Chromosome not found: 17' occurred in "/home/emmon/miniconda3/lib/python3.10/site-packages/coolbox/core/frame/frame.py", line 218 [ERROR:frame.py:231 - plot()] 'Chromosome not found: 17' Traceback (most recent call last): File "/home/emmon/miniconda3/lib/python3.10/site-packages/coolbox/core/frame/frame.py", line 218, in plot track.plot(ax, copy(gr), gr2=copy(gr2)) File "/home/emmon/miniconda3/lib/python3.10/site-packages/capcruncher/api/plotting.py", line 400, in plot data = self.fetch_data(gr, **kwargs) File "/home/emmon/miniconda3/lib/python3.10/site-packages/capcruncher/api/plotting.py", line 338, in fetch_data datasets = [ File "/home/emmon/miniconda3/lib/python3.10/site-packages/capcruncher/api/plotting.py", line 339, in <listcomp> bw.bw.fetch_intervals(gr.chrom, gr.start, gr.end) File "bbi/cbbi.pyx", line 677, in bbi.cbbi.BBIFile.fetch_intervals KeyError: 'Chromosome not found: 17' [ERROR:frame.py:224 - plot()] Error occured when plot track: track name: BigWigCollection.Late track type:<class 'capcruncher.api.plotting.CCBigWigCollection'> Error: <class 'KeyError'> 'Chromosome not found: 17' occurred in "/home/emmon/miniconda3/lib/python3.10/site-packages/coolbox/core/frame/frame.py", line 218 [ERROR:frame.py:231 - plot()] 'Chromosome not found: 17' Traceback (most recent call last): File "/home/emmon/miniconda3/lib/python3.10/site-packages/coolbox/core/frame/frame.py", line 218, in plot track.plot(ax, copy(gr), gr2=copy(gr2)) File "/home/emmon/miniconda3/lib/python3.10/site-packages/capcruncher/api/plotting.py", line 400, in plot data = self.fetch_data(gr, **kwargs) File "/home/emmon/miniconda3/lib/python3.10/site-packages/capcruncher/api/plotting.py", line 338, in fetch_data datasets = [ File "/home/emmon/miniconda3/lib/python3.10/site-packages/capcruncher/api/plotting.py", line 339, in <listcomp> bw.bw.fetch_intervals(gr.chrom, gr.start, gr.end) File "bbi/cbbi.pyx", line 677, in bbi.cbbi.BBIFile.fetch_intervals KeyError: 'Chromosome not found: 17'

[e-coral]

In my case, this seems to be caused by errors occurring in the differential interactions section, which don't make it into the main log. If you encounter the above issue, I would suggest checking capcruncher_output/logs/differential_interactions/[name].log to see if you have any errors in there.
Next week, I'll have a look into the error message I discovered there, and will update this issue if I mange to fully resolve it.

File "path/to/miniconda3/lib/python3.10/site-packages/cooler/util.py", line 112, in _check_token
    raise ValueError(f'Unexpected token "{token}"')
ValueError: Unexpected token "-"

[e-coral]

I have also now identified and resolved
ValueError: Unexpected token "-"

In cooler_to_bedgraph (pileup.py), the viewpoint distance is subtracted from the viewpoint coordinate, regardless of the values of the two variables. This means it's possible for the distance to be larger than the viewpoint, resulting in a negative coordinate, which causes the above error. I have added a few lines to check for this issue, and set the start coordinate to 1 if it would otherwise be less than 0.
None of our viewpoints are very close to the ends of chromosomes, and I have therefore not investigated whether other problems could arise from potential extension of a region beyond the full chromosome size. A similar capping mechanism may need to be implemented here for the end coordinate, if so.
I'll make a pull request with my bug fix once I've tested it.

[alsmith151]

These should hopefully be fixed by #324 and #322