INNER CODE UNIT · Python

read_blast_report

StaPH-B/docker-builds · build-files/cbird-util/2.0/html_report.py:99

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()
    m['Microorganism'] = m['Microorganism'].apply(lambda x: x.split()[0]+" "+x.split()[1])

    # report
    page_title = samplename
    title = "Whole Genome Sequencing Analysis Report"

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