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import argparse, csv, os, sys
parser=argparse.ArgumentParser(description="Determines the index of individuals\
of a given ethnicity within a 1000 Genomes VCF")
parser.add_argument("VCF", type=str, help="VCF of 1000 Genomes individuals")
parser.add_argument("Population", type=str, help="1KG identifier for population\
to be found in the index, enter \"ALL|\" to print index for all populations in \
the VCF")
arg=parser.parse_args()
a=os.path.abspath(sys.argv[0]).split("/")[:-1]
b="/".join(a)
try:
open(b+"/1KG_IDs.txt")
except IOError:
print "Missing file \"1KG_IDs.txt\" containing the IDs for 1000 Genomes"
popdict={}
with open(b+"/1KG_IDs.txt") as t:
for line in csv.reader(t,delimiter='\t'):
popdict[line[1]]=line[0]
with open(arg.VCF) as t:
for line in csv.reader(t,delimiter='\t'):
if line[0]=='#CHROM':
for j in range(len(line)):
if 'NA' in line[j] or 'HG' in line[j]:
vcfind=line[j:]
break
indict={}
for i in range(len(vcfind)):
try:
eth=popdict[vcfind[i]]
except:
print"Non 1000 Genomes individuals found in VCF"
if eth in indict.keys():
indict[eth].append(i)
else:
indict[eth]=[i]
if arg.Population=="All":
for j in indict.keys():
l=[str(i) for i in indict[j]]
print j,"=",",".join(l)
else:
try:
indict[arg.Population]
except IOError:
print "Population not in VCF or invalid population ID"
l=[str(i) for i in indict[arg.Population]]
print ",".join(l)
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