--exclude-antibody-capture argument not working

[megan1111]

Hi authors,

I am trying to exclude the antibody captures in my multimodal CellRanger v3 analysis when running CellBender v0.2.0. However, when I input the argument in the command line

cellbender remove-background \ --input "${projDir[i]}/outs/raw_feature_bc_matrix" \ --output "$plotDir/cellbender_feature_bc_matrix.h5" \ --expected-cells ${expectedCellNum[i]} \ --total-droplets-included ${totalDroplet[i]}\ --exclude-antibody-capture\ --fpr 0.01

The output file shows an error stating the boolean object as no .sum() attribute:

Traceback (most recent call last):
File "/work/comp/TBX-SG/CBv2try/CBv2/bin/cellbender", line 33, in <module>
sys.exit(load_entry_point('cellbender', 'console_scripts', 'cellbender')())
File "/SFS/project/comp/TBX-SG/CBv2try/CBv2/CellBender/cellbender/base_cli.py", line 101, in main cli_dict[args.tool].run(args)
File "/SFS/project/comp/TBX-SG/CBv2try/CBv2/CellBender/cellbender/remove_background/cli.py", line 103, in run main(args)
File "/SFS/project/comp/TBX-SG/CBv2try/CBv2/CellBender/cellbender/remove_background/cli.py", line 196, in main run_remove_background(args)
File "/SFS/project/comp/TBX-SG/CBv2try/CBv2/CellBender/cellbender/remove_background/cli.py", line 153, in run_remove_background
fpr=args.fpr)
File "/SFS/project/comp/TBX-SG/CBv2try/CBv2/CellBender/cellbender/remove_background/data/dataset.py", line 100, in __init__
gene_blacklist=gene_blacklist)
File "/SFS/project/comp/TBX-SG/CBv2try/CBv2/CellBender/cellbender/remove_background/data/dataset.py", line 189, in _trim_dataset_for_analysis
logging.info(f"Excluding {antibody_logic.sum()} features that " AttributeError: 'bool' object has no attribute 'sum'

Would appreciate if you could advice what I am doing wrong?

Thank you!!

[sjfleming]

This very much looks like an error on my part. I will take a look! Sorry for the delayed response.

[sjfleming]

Thanks for reporting this, there are actually a few things I need to fix.

There is a difference in data types between the "feature_type"s that get read in from .h5 files versus the MTX directory files... I realize now that the code was not handling the MTX feature_type data correctly when excluding antibodies.

If you want to get the current code to work with your data, you can try the raw .h5 file as an input, instead of the MTX directory.

Alternatively, if you can try the code on the branch sf_antibody_capture, then this should be a fix for you. I'll get these fixes into the next official release.

[sjfleming]

Closed by #238