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)
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
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
