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aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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get_consensus_peaks: 'PyRanges object has no attribute', 'Count' Bug report [BUG] #19

Closed IrinaMate closed 3 years ago

IrinaMate commented 3 years ago

Describe the bug

AttributeError                            Traceback (most recent call last)
/tmp/ipykernel_20438/870027147.py in <module>
      4 path_to_blacklist='/staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/pycisTopic/blacklist/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)

/opt/venv/lib/python3.8/site-packages/pycisTopic/iterative_peak_calling.py in get_consensus_peaks(narrow_peaks_dict, peak_half_width, chromsizes, path_to_blacklist)
     60 
     61     log.info('Extending and merging peaks per class')
---> 62     center_extended_peaks = [
     63         iterative_peak_filtering(
     64             calculate_peaks_and_extend(

/opt/venv/lib/python3.8/site-packages/pycisTopic/iterative_peak_calling.py in <listcomp>(.0)
     61     log.info('Extending and merging peaks per class')
     62     center_extended_peaks = [
---> 63         iterative_peak_filtering(
     64             calculate_peaks_and_extend(
     65                 narrow_peaks_dict[x],

/opt/venv/lib/python3.8/site-packages/pycisTopic/iterative_peak_calling.py in iterative_peak_filtering(center_extended_peaks)
    188     # equal to 2
    189     center_extended_peaks_with_2_counts = center_extended_peaks_merged[
--> 190         center_extended_peaks_merged.Count == 2
    191     ]
    192     if len(center_extended_peaks_with_2_counts) > 0:

/opt/venv/lib/python3.8/site-packages/pyranges/pyranges.py in __getattr__(self, name)
    268         from pyranges.methods.attr import _getattr
    269 
--> 270         return _getattr(self, name)
    271 
    272     def __setattr__(self, column_name, column):

/opt/venv/lib/python3.8/site-packages/pyranges/methods/attr.py in _getattr(self, name)
     65         return pd.concat([df[name] for df in self.values()])
     66     else:
---> 67         raise AttributeError("PyRanges object has no attribute", name)

AttributeError: ('PyRanges object has no attribute', 'Count')

To Reproduce

from pycisTopic.iterative_peak_calling import *
# Other param
peak_half_width=250
path_to_blacklist='/staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/pycisTopic/blacklist/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)

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cbravo93 commented 3 years ago

Hi Irina!

The bug is solved in the last push. This happened if none of your summits overlap from the beginning, usually happens if you have a very small number of peaks per pseudobulk (if they come from small clusters).

Thanks for reporting!

C