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compmetagen / micca

micca - MICrobial Community Analysis
http://compmetagen.github.io/micca
GNU General Public License v3.0
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Micca assumes DataFrames are saved with the index on the first column #32

Closed glucksfall closed 2 years ago

glucksfall commented 3 years ago

Hello,

I found out that micca reads csv files from DataFrames with the index on the first column: table = pd.read_csv(input_fn, sep='\t', index_col=0) (line 12, micca/table.py file).

If the user isn't aware (as me), saving a csv without the index will result in the drop of the first sample when calculating table summaries and plotting the rarefaction curve.

Best regards.

davidealbanese commented 2 years ago

Dear @glucksfall, see https://micca.readthedocs.io/en/latest/formats.html#otu-sv-tables-and-taxonomy-tables.