def bySite(self):
for row in vcf_iter(self.FileObject):
yield row
key = args[0]
filename = args[1]
names1 = []
names2 = []
for k in open(filename, 'r'):
ksplit = k.rstrip().split(":")
if ksplit[0] == key:
if ksplit[1] == "case":
names1 += ksplit[2].split(",")
elif ksplit[1] == "control":
names2 += ksplit[2].split(",")
for row in vcf_iter(sys.stdin):
pop1 = list((row[ind1]['GT'] for ind1 in names1 if row[ind1]['GT'] != './.' and row[ind1]['DP'] > 7))
pop2 = list((row[ind2]['GT'] for ind2 in names2 if row[ind2]['GT'] != './.' and row[ind2]['DP'] > 7))
n1 = len(pop1)
n2 = len(pop2)
hom1 = pop1.count('0/0')
het1 = pop1.count('0/1')
alt1 = pop1.count('1/1')
hom2 = pop2.count('0/0')
het2 = pop2.count('0/1')
alt2 = pop2.count('1/1')
#startB = time.time()
#clB = TestB()
#for j in xrange(10000):
# clB.init_string = str(j)
#print time.time() - startB
######
# iter population sample
# need direct access to name of each sample from
######
vcfstream = vcf_iter(sys.stdin)
#vcfstream = vcf_iter4(sys.stdin)
#for line in sys.stdin:
# #if line.startswith('#') is False:
# if line[0] != '#':
# values = line.rstrip().split('\t')
# chrom = values[0]
# elif line[:2] == '##':
# pass
# else:
# pass
inc_chr = sys.argv[1].split(',')
for row in vcfstream:
#startB = time.time()
#clB = TestB()
#for j in xrange(10000):
# clB.init_string = str(j)
#print time.time() - startB
######
# iter population sample
# need direct access to name of each sample from
######
vcfstream = vcf_iter(sys.stdin)
#vcfstream = vcf_iter4(sys.stdin)
#for line in sys.stdin:
# #if line.startswith('#') is False:
# if line[0] != '#':
# values = line.rstrip().split('\t')
# chrom = values[0]
# elif line[:2] == '##':
# pass
# else:
# pass
inc_chr = sys.argv[1].split(',')
for row in vcfstream:
def bySite(self):
for row in vcf_iter(self.FileObject):
yield row
