def main(argv):
opts, args = getopt.getopt(argv,"a:ghc:i",["report=", "genonames="])
for opt, arg in opts:
if opt == '-a':
report = arg
print "processing array, getting snps {0}".format(report)
getarraysnps(arg)
[f, e] = parsegenotypes.checkRef(report)
parsegenotypes.flipArray(report, f)
parsegenotypes.filterzeros(report)
parsegenotypes.printtabarray(report)
elif opt == '-g':
processgenotypes()
elif opt == '-h':
processhapmap()
elif opt == '-c':
snps = glob.json('Array251Msnps')
if arg == '':
genofiles = names1KG
else:
genofiles = arg
combinegenos(genofiles, snps)
elif opt == "-i":
genofiles = names.append('hapmap')
parser.add_argument('-inithapmap', action='store_true')
parser.add_argument('-int', action='store_true')
parser.add_argument('-pool', action='store_true')
parser.add_argument('-merge', action='store_true')
parser.add_argument('-i')
args = parser.parse_args()
print args
if args.a:
print "processing array, getting snps {0}".format(args.a)
report = args.a
getarraysnps(report)
[f, e] = parsegenotypes.checkRef(report)
parsegenotypes.flipArray(report, f, e)
parsegenotypes.filterzeros(report)
parsegenotypes.printtabarray(report)
if args.g:
processgenotypes()
if args.hapmap:
processhapmap()
if args.init1KG:
#snps = glob.json('25M1.1snps')
snps = glob.json('MKReportbySNP1.txtsnps')
#combinegenos(names1KG, snps, 'Genos1kgArray25M')
combinegenos(names1KG, snps, 'Genos1kgArrayOmni')
if args.inithapmap:
snps = glob.json('Array25M1snps')
combinegenos('hapmap', snps, 'hapmapGenosArray25M', 1)
if args.pool:
