INNER CODE UNIT · Python

read_bracken_report

StaPH-B/docker-builds · build-files/cbird-util/2.0/html_report.py:14

def read_bracken_report(taxon_report):
    # get bracken report
    df = pd.read_csv(taxon_report, sep = '\t')
    df = df.sort_values(by=['fraction_total_reads'], ascending=False)

    # find top tax id & write
    with open("taxid.txt", "w") as f:
        taxid = df["taxonomy_id"][0]
        f.write(str(taxid))

    # Species
    df2 = df.loc[:, ["name", "fraction_total_reads" ]].copy()
    df2['fraction_total_reads'] = df2['fraction_total_reads'].apply(lambda x: round(x*100, 2))
    df2 = df2.rename(columns={"name": "Microorganism", "fraction_total_reads": "Abundance(%)"})
    return df2

def read_mlst_report(mlst_report):
    df = pd.read_csv(mlst_report, sep="\t", skiprows=1, header=None)

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