Python dbLookupの例

コード例 #1

ファイル: mucor.py プロジェクト: blachlylab/mucor

def annotateDF(grp, databases):
    '''
    function to annotate variant dataframe with user-supplied vcf databases
    '''
    chrom = grp['chr'].unique()[0]
    pos = grp['pos'].unique()[0]
    ref = grp['ref'].unique()[0]
    alt = grp['alt'].unique()[0]
    var = Variant(source=None, sample=None, pos=HTSeq.GenomicPosition(chrom, pos), ref=ref, alt=alt, frac=None, dp=None, eff=None, fc=None)
    dbEntries = dbLookup(var, databases)
    return pd.Series(dbEntries)

コード例 #2

ファイル: mucor.py プロジェクト: xtmgah/mucor

def annotateDF(grp, databases):
    '''
    function to annotate variant dataframe with user-supplied vcf databases
    '''
    chrom = grp['chr'].unique()[0]
    pos = grp['pos'].unique()[0]
    ref = grp['ref'].unique()[0]
    alt = grp['alt'].unique()[0]
    var = Variant(source=None, pos=HTSeq.GenomicPosition(chrom, pos), ref=ref, alt=alt, frac=None, dp=None, eff=None, fc=None)
    dbEntries, dbVAFs = dbLookup(var, databases)
    for source, annot in dbEntries.items():
        grp.insert(len(grp.columns)-4, source, annot)
        grp.insert(len(grp.columns)-4, source + "_VAF", dbVAFs[source])
    return grp

コード例 #3

ファイル: mucor.py プロジェクト: xtmgah/mucor

def annotateDF(grp, databases):
    '''
    function to annotate variant dataframe with user-supplied vcf databases
    '''
    chrom = grp['chr'].unique()[0]
    pos = grp['pos'].unique()[0]
    ref = grp['ref'].unique()[0]
    alt = grp['alt'].unique()[0]
    var = Variant(source=None,
                  pos=HTSeq.GenomicPosition(chrom, pos),
                  ref=ref,
                  alt=alt,
                  frac=None,
                  dp=None,
                  eff=None,
                  fc=None)
    dbEntries, dbVAFs = dbLookup(var, databases)
    for source, annot in dbEntries.items():
        grp.insert(len(grp.columns) - 4, source, annot)
        grp.insert(len(grp.columns) - 4, source + "_VAF", dbVAFs[source])
    return grp