INNER CODE UNIT · Python

main

StaPH-B/docker-builds · build-files/cbird-util/2.0/html_report.py:331

def main(args):
    samplename = args.samplename
    taxon_report = args.taxon_report
    mlst_report = args.mlst_report
    amr_report = args.amr_report
    plasmid_report = args.plasmid_report
    mash_report = args.mash_report
    version = args.cbird_version
    footer = args.footer_note
    blast_report = args.blast_report

    # read reports
    bracken = read_bracken_report(taxon_report)
    mlst = read_mlst_report(mlst_report)
    amr = read_amr_report(amr_report)[0]
    point = read_amr_report(amr_report)[1]
    stress = read_amr_report(amr_report)[2]
    virulence = read_amr_report(amr_report)[3]    

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