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Hoohm / CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay
https://hoohm.github.io/CITE-seq-Count/
MIT License
79 stars 44 forks source link

Error when option are set to --bc_collapsing_dist 0 #157

Closed rule-110 closed 3 years ago

rule-110 commented 3 years ago

Hello,

I am using Cite-seq-count 1.4.4 and when I set the option --bc_collapsing_dist to 0 (but not when I set it to 1) I got this error


\ File "...conda/envs/py3/bin/CITE-seq-Count", line 11, in <module>
    load_entry_point('CITE-seq-Count==1.4.4', 'console_scripts', 'CITE-seq-Count')()
  File "...conda/envs/py3/lib/python3.6/site-packages/cite_seq_count/__main__.py", line 394, in main
    ab_map=ordered_tags_map)
  File "...conda/envs/py3/lib/python3.6/site-packages/cite_seq_count/processing.py", line 368, in correct_cells
    ab_map=ab_map,
  File "...conda/envs/py3/lib/python3.6/site-packages/cite_seq_count/processing.py", line 312, in collapse_cells
    for real_barcode in true_to_false:
TypeError: 'NoneType' object is not iterable

I saw that this error was raised by other users, but I thought it was fixed in version 1.4.4. Do I am doing anything wrong or is there anything I could do to fix this?

Thanks Nicolas

Hoohm commented 3 years ago

Hello @rule-110 I just pushed a hotfix, should deal with the issue and skip barcode correction when using a value that is less than 0.

Please let me know if it works for you.

rule-110 commented 3 years ago

Yes it works great with the hotfix. Thanks