Bug report [BUG] list index out of error when running get_consensus_peaks

[midichlorianrich]

Describe the bug list index out of error when running get_consensus_peaks

To Reproduce

from pycisTopic.iterative_peak_calling import *
# Other param
peak_half_width=250
path_to_blacklist='/Users/M258140/scenicplus/notebooks/Kylie_tutorial/data/mm10-blacklist.v2.bed'
# Get consensus peaks
consensus_peaks=get_consensus_peaks(narrow_peaks_dict, peak_half_width, chromsizes=chromsizes, path_to_blacklist=path_to_blacklist)

Error output

2023-04-06 10:40:11,398 cisTopic     INFO     Extending and merging peaks per class
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[160], line 6
      4 path_to_blacklist='/Users/M258140/scenicplus/notebooks/Kylie_tutorial/data/mm10-blacklist.v2.bed'
      5 # Get consensus peaks
----> 6 consensus_peaks=get_consensus_peaks(narrow_peaks_dict, peak_half_width, chromsizes=chromsizes, path_to_blacklist=path_to_blacklist)

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/pycisTopic/iterative_peak_calling.py:65, in get_consensus_peaks(narrow_peaks_dict, peak_half_width, chromsizes, path_to_blacklist)
     62     chromsizes = pr.PyRanges(chromsizes)
     64 log.info("Extending and merging peaks per class")
---> 65 center_extended_peaks = [
     66     iterative_peak_filtering(
     67         calculate_peaks_and_extend(
     68             narrow_peaks_dict[x], peak_half_width, chromsizes, path_to_blacklist
     69         )
     70     ).df
     71     for x in list(narrow_peaks_dict.keys())
     72 ]
     73 log.info("Normalizing peak scores")
     74 center_extended_peaks_norm = [cpm(x, "Score") for x in center_extended_peaks]

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/pycisTopic/iterative_peak_calling.py:67, in <listcomp>(.0)
     62     chromsizes = pr.PyRanges(chromsizes)
     64 log.info("Extending and merging peaks per class")
     65 center_extended_peaks = [
     66     iterative_peak_filtering(
---> 67         calculate_peaks_and_extend(
     68             narrow_peaks_dict[x], peak_half_width, chromsizes, path_to_blacklist
     69         )
     70     ).df
     71     for x in list(narrow_peaks_dict.keys())
     72 ]
     73 log.info("Normalizing peak scores")
     74 center_extended_peaks_norm = [cpm(x, "Score") for x in center_extended_peaks]

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/pycisTopic/iterative_peak_calling.py:142, in calculate_peaks_and_extend(narrow_peaks, peak_half_width, chromsizes, path_to_blacklist)
    138     center_extended_peaks = center_extended_peaks.intersect(
    139         chromsizes, how="containment"
    140     )
    141 if isinstance(path_to_blacklist, str):
--> 142     blacklist = pr.read_bed(path_to_blacklist)
    143     center_extended_peaks = center_extended_peaks.overlap(blacklist, invert=True)
    144 return center_extended_peaks

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/pyranges/readers.py:80, in read_bed(f, as_df, nrows)
     78     first_start = gzip.open(f).readline().split()[1]
     79 else:
---> 80     first_start = open(f).readline().split()[1]
     82 header = None
     84 try:

IndexError: list index out of range

**Version (please complete the following information):**
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tifffile                  2023.3.21                pypi_0    pypi
tinycss2                  1.2.1                    pypi_0    pypi
tk                        8.6.12               h5dbffcc_0    conda-forge
tktable                   2.10                 h49f0cf7_3    conda-forge
tmtoolkit                 0.11.2                   pypi_0    pypi
toolz                     0.12.0                   pypi_0    pypi
tornado                   6.2                      pypi_0    pypi
toyplot                   1.0.3                    pypi_0    pypi
toytree                   2.0.1                    pypi_0    pypi
tqdm                      4.64.1                   pypi_0    pypi
traitlets                 5.9.0                    pypi_0    pypi
tspex                     0.6.2                    pypi_0    pypi
typing                    3.7.4.3                  pypi_0    pypi
typing-extensions         4.4.0                    pypi_0    pypi
typing-inspect            0.8.0                    pypi_0    pypi
tzdata                    2022g                h191b570_0    conda-forge
umap-learn                0.5.3                    pypi_0    pypi
upsetplot                 0.8.0                    pypi_0    pypi
url-normalize             1.4.3                    pypi_0    pypi
urllib3                   1.26.14                  pypi_0    pypi
virtualenv                20.21.0                  pypi_0    pypi
wcwidth                   0.2.6                    pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
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wrapt                     1.15.0                   pypi_0    pypi
xarray                    2023.1.0                 pypi_0    pypi
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zope-interface            5.5.2                    pypi_0    pypi
zstd                      1.5.2                hbc0c0cd_6    conda-forge

Additional context Add any other context about the problem here.

[SeppeDeWinter]

Hi @midichlorianrich

There seems to be an issue reading the blacklist bed file.

Can you try reading it like this to see if you still have the same error?

import pyranges as pr
path_to_blacklist = '/Users/M258140/scenicplus/notebooks/Kylie_tutorial/data/mm10-blacklist.v2.bed'
blacklist = pr.read_bed(path_to_blacklist)

If you still have an error try reading it with pandas (and please report back the output).

import pandas as pd
blacklist = pd.read_csv(path_to_blacklist, sep = '\t')

If that fails, can you please show

head /Users/M258140/scenicplus/notebooks/Kylie_tutorial/data/mm10-blacklist.v2.bed

Best,

Seppe