INNER CODE UNIT · Python

write_output

nf-core/eager · bin/kraken_parse.py:79

def write_output(resdict, infile, outfile):
    with open(outfile, 'w') as f:
        basename = _get_basename(infile)
        f.write(f"TAXID,{basename}\n")
        for akey in resdict.keys():
            f.write(f"{akey},{resdict[akey]}\n")


if __name__ == '__main__':
    INFILE, COUNTLIM, readout, kmerout = _get_args()

    if not readout:
        read_outfile = _get_basename(INFILE)+".read_kraken_parsed.csv"
    else:
        read_outfile = readout
    if not kmerout:    
        kmer_outfile = _get_basename(INFILE)+".kmer_kraken_parsed.csv"
    else:

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