def filter_known(dbsnpH, inFileN):
inFile = open(inFileN, 'r')
outFile = open('%s.dbsnp_flt' % inFileN, 'w')
for line in inFile:
colL = line.rstrip().split('\t')
chrom = colL[0]
pos = int(colL[1])
idx = mybasic.index(dbsnpH[chrom], pos)
if idx < 0:## not found in dbsnp
outFile.write(line)
outFile.flush()
outFile.close()
def get_alt_frac_mutscan(sampN, snpH, fileL):
outH = {}
for chrom in snpH:
for pos in snpH[chrom]:
outH[(chrom, pos)] = {}
for alt in snpH[chrom][pos]:
outH[(chrom, pos)][alt] = 'NA'
chromL = snpH.keys()
chromL.sort()
for file in fileL:
inFile = open(file, 'r')
prevChr = ''
posL = []
for line in inFile:
colL = line.rstrip().split('\t')
chrom = colL[0]
pos = int(colL[1])
alt = colL[3]
r1 = int(colL[4])
r2 = int(colL[5])
frac = float(colL[6])
if chrom == 'chrM' or (r1 + r2) < 15:
continue
if prevChr != chrom:
prevChr = chrom
posL = snpH[chrom].keys()
posL.sort()
idx = mybasic.index(posL, pos)
if idx >= 0 and alt in snpH[chrom][pos]: ## mutation is in dbsnp
outH[(chrom, pos)][alt] = frac
##for line
##for file
for chrom in chromL:
posL = snpH[chrom].keys()
posL.sort()
for pos in posL:
altL = list(snpH[chrom][pos])
for alt in altL:
sys.stdout.write(
'%s\t%s:%s:%s\t%s\n' %
(sampN, chrom, pos, alt, outH[(chrom, pos)][alt]))
def get_alt_frac_mutscan(sampN, snpH, fileL):
outH = {}
for chrom in snpH:
for pos in snpH[chrom]:
outH[(chrom, pos)] = {}
for alt in snpH[chrom][pos]:
outH[(chrom,pos)][alt] = 'NA'
chromL = snpH.keys()
chromL.sort()
for file in fileL:
inFile = open(file, 'r')
prevChr = ''
posL = []
for line in inFile:
colL = line.rstrip().split('\t')
chrom = colL[0]
pos = int(colL[1])
alt = colL[3]
r1 = int(colL[4])
r2 = int(colL[5])
frac = float(colL[6])
if chrom == 'chrM' or (r1 + r2) < 15:
continue
if prevChr != chrom:
prevChr = chrom
posL = snpH[chrom].keys()
posL.sort()
idx = mybasic.index(posL, pos)
if idx >= 0 and alt in snpH[chrom][pos]: ## mutation is in dbsnp
outH[(chrom,pos)][alt] = frac
##for line
##for file
for chrom in chromL:
posL = snpH[chrom].keys()
posL.sort()
for pos in posL:
altL = list(snpH[chrom][pos])
for alt in altL:
sys.stdout.write('%s\t%s:%s:%s\t%s\n' % (sampN, chrom,pos,alt, outH[(chrom,pos)][alt]))
