INNER CODE UNIT · Python

main

torognes/swarm · scripts/amplicon_contingency_table.py:58

def main():
    """
    Read all fasta files and build a sorted amplicon contingency table
    """
    # Parse command line
    all_amplicons, amplicons2samples, samples = fasta_parse()

    # Sort amplicons by decreasing abundance (and by amplicon name)
    sorted_all_amplicons = sorted(iter(all_amplicons.items()),
                                  key=operator.itemgetter(1, 0))
    sorted_all_amplicons.reverse()

    # Print table header
    print("amplicon", "\t".join(samples), "total", sep="\t", file=sys.stdout)

    # Print table content
    for amplicon, abundance in sorted_all_amplicons:
        abundances = [amplicons2samples[amplicon].get(sample, 0)

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