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')
def processhapmap():
print "parsing hapmap genotypes chrom files"
parsegenotypes.parsehapmap()
print "now filtering SNPs"
b = parsegenotypes.filterSNPs('../genotypes/hapmap')
print "{0} SNPs filtered out".format(len(b))
[flips, errors] = parsegenotypes.checkRef('../genotypes/hapmap')
print "{0} flips and {1} errors".format(len(flips),len(errors))
#flips = glob.json('../genotypes/hapmapflips')
#errors = glob.json('../genotypes/hapmaperrors')
parsegenotypes.flipGeno('hapmapGeno', flips, errors)
def processgenotypes():
"""parse genotype files and flip them around according to hg19
"""
for i, n in enumerate(homedirnames):
parsegenotypes.parse1KGvcf(vcffiles[i], names1KG[i])
b = parsegenotypes.filterSNPs(names1KG[i])
print "{0} SNPs filtered out".format(len(b))
c = parsegenotypes.checkRef(n)
print "{0} errors and {1} flipped".format(len(c[1]),len(c[0]))
#parsegenotypes.corrRef(c[0], n)
parsegenotypes.flipGeno(n+'Geno', c[0], c[1])
import parsegenotypes d = parsegenotypes.checkRef(parsegenotypes.names[3])
parser.add_argument('-g', action='store_true')
parser.add_argument('-hapmap', action='store_true')
parser.add_argument('-init1KG', action='store_true')
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')
