INNER CODE UNIT · Python

read_mlst_report

StaPH-B/docker-builds · build-files/cbird-util/2.0/html_report.py:30

def read_mlst_report(mlst_report):
    df = pd.read_csv(mlst_report, sep="\t", skiprows=1, header=None)
    df = df.drop(columns=0)
    columns = ['Scheme','Type (ST)','Alleles']
    if len(df.columns) < 3:
        df = pd.DataFrame(columns=columns)
    else:
        for i in range(3,len(df.columns)):
            columns.append('')
        df.columns = columns    
    return df

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(%)',

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