INNER CODE UNIT · Python

main

franciscozorrilla/metaGEM · workflow/scripts/kallisto2concoct.py:16

def main(args):
    sample_dfs = []

    samplenames = samplenames_from_file(args.samplenames)
    for i, sample in enumerate(args.quantfiles):
        if samplenames:
            samplename = samplenames[i]
        else:
            samplename = os.path.basename(sample)        
        sample_df = pd.read_table(sample, index_col=0)
        
        sample_dfs.append((samplename, sample_df))
    kallisto_df = pd.DataFrame(index=sample_df.index)

    for sample, sample_df in sample_dfs:
        kallisto_df['kallisto_coverage_{0}'.format(sample)] = 200*sample_df['est_counts'].divide(sample_df['length'])
    kallisto_df.to_csv(sys.stdout, sep="\t", float_format="%.6f")

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