INNER CODE UNIT · Python

read_amr_report

StaPH-B/docker-builds · build-files/cbird-util/2.0/html_report.py:42

def read_amr_report(amr_report):

    df =  pd.read_csv(amr_report, sep = '\t')    
    df2 = df.loc[:, ['Element symbol','Element name','Scope','Subclass','% Coverage of reference','% Identity to reference', 'Type', 'Subtype','Method']].copy()
    df2 = df2.rename(columns={'Element symbol':'Gene','Element name':'Description',
                                    'Subclass':'Resistance / Mechanism','% Coverage of reference':'Coverage(%)',
                                    '% Identity to reference':'Identity(%)'})

    conditions = [
        (df2['Method'].str.contains('ALLELE')),
        (df2['Method'].str.contains('BLAST')),
        (df2['Method'].str.contains('EXACT')),
        (df2['Method'].str.contains('HMM')),
        (df2['Method'].str.contains('INTERNAL_STOP')),
        (df2['Method'].str.contains('PARTIALX')),
        (df2['Method'].str.contains('PARTIALP')),
        (df2['Method'].str.contains('POINT')),
        (df2['Method'].str.contains('PARTIAL_CONTIG_END')),

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