def nameVars(vars, snpeffFiles):
var2name = {}
for afile in snpeffFiles:
with open(snpeffFile) as f:
for line in f:
if line[0] != '#':
sp = line.split('\t')
if sp[0] in vars:
if sp[1] in vars[ sp[0] ]:
info = sp[-1]
gene = limitDbnsfpVcfSNVs.getGene(info)
if sp[0] == '1' and sp[1] == '865696':
print(info, gene)
print(gene)
if gene != '??':
var = sp[0] + ':' + sp[1]
var2name[var] = gene
return var2name
with open(vcfFile) as f:
with open(outFile, 'w') as fout:
print >> fout, header
for line in f:
l = line.strip()
if l[0] != '#':
(cgControlStatus, chrom, pos,
rs, ref, alts, qual, filterPass,
info) = l.split('\t')
if filterPass == 'PASS':
lof = parseLof(l.split('\t'))
euroAlleleCount = l.split('AC_NFE=')[1].split(';')[0]
euroTotalCount = l.split('AN_NFE=')[1].split(';')[0]
afrAlleleCount = l.split('AC_AFR=')[1].split(';')[0]
afrTotalCount = l.split('AN_AFR=')[1].split(';')[0]
gene = limitDbnsfpVcfSNVs.getGene(l)
# scoreClinvar.parseGene(l.split('\t'))
# found = False
# for alt in alts.split(','):
# if len(alt) == len(ref): #or not 'rs' in l: #len(alt) == len(ref):# or not 'rs' in l:
# found = True
# if found:
print >> fout, '\t'.join((gene, chrom, pos, ref, alts, '0',
str(euroAlleleCount), str(euroTotalCount),
str(afrAlleleCount), str(afrTotalCount),
cgControlStatus, lof))
