INNER CODE UNIT · Python

read_mash_report

StaPH-B/docker-builds · build-files/cbird-util/2.0/html_report.py:94

def read_mash_report(mash_report):
    df = pd.read_csv(mash_report, sep = '\t', header=None)
    df.columns = ['Microorganism', 'Identity(%)']
    return df

def read_blast_report(blast_report):
    df = pd.read_csv(blast_report, sep = '\t')
    if not df.empty:
        df['Coverage(%)'] = df['length'] / df['qlen'] * 100
        df.drop(columns=['sseqid', 'mismatch','gapopen','qstart','qend','sstart','send','evalue','bitscore'], inplace=True)
        df.rename(columns={'qseqid':'Gene','pident':'Identity(%)','length':'Length'}, inplace=True)
        df=df[['Gene','Length','Coverage(%)','Identity(%)']].round(2)
    else:
        df=pd.DataFrame(columns=['Gene','Length','Coverage(%)','Identity(%)'])
    return df

def basic_report(samplename, mash, amr, point, version, footer):
    m = mash.copy()

View source record →