typo in delimiter for read_csv

borenstein-lab / fishtaco

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of microbiome functional shifts

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typo in delimiter for read_csv #10

Open mmp3 opened 3 years ago

mmp3 commented 3 years ago

compute_contribution_to_DA.py::355 reads:

pd.read_csv(function_mapping_file, dtype={0: str}, sep="]t")

which causes the file to be read incorrectly and therefore FishTaco fails to aggregate KOs to pathways or modules.

The sep argument should be \t.

engal commented 3 years ago

Thank you for letting us know, I've fixed the issue in this repository and am propagating it to the PIP version.