def filter(myPileupFile, outFile):
fout = open(outFile, 'w')
#pileupInfoStIdx = 11
header = 'gene\tchrom\tpos\tref\taltLs\tvariant'
with open(myPileupFile) as f:
print >> fout, header
for line in f:
if line[0] != '#':
sp = line.strip().split('\t')
chrom, pos, rs, ref, altLs = sp[0:5]
gene = scoreClinvar.parseGene(sp, 7)
callStatus = []
pileupData = []
idxLsLs = []
newAltLs = []
# GCGGCGGAGTGTTGTGCGAGTC
# changed to ACGGCGGAGTGTTGTGCGAGTC,G
# Need A list of list of idx
# and and a list of alternatives
# output will be idx1,idx2;idx1 w/ alt1,alt2
for alt in altLs.split(','):
newAltLs.append(alt)
for newAlt in newAltLs:
print >> fout, '\t'.join( (gene, chrom,
str(int(pos)),
ref, newAlt,
chrom + ':' + str(int(pos)) +
ref + '>' + altLs,
) )
fout.close()
def convert(myPileupFile, outFile):
fout = open(outFile, 'w')
#pileupInfoStIdx = 11
header = 'gene\tchrom\tpos\tref\taltLs\tvariant'
with open(myPileupFile) as f:
print >> fout, header
for line in f:
sp = line.strip().split('\t')
chrom, pos, rs, ref, altLs = sp[0:5]
gene = scoreClinvar.parseGene(sp, 7)
newAltLs = []
for alt in altLs.split(','):
newAltLs.append(alt)
for newAlt in newAltLs:
print >> fout, '\t'.join( (gene, chrom,
str(int(pos)),
ref, newAlt,
chrom + ':' + str(int(pos)) +
ref + '>' + altLs,
) )
fout.close()