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('-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') combinegenos('hapmap', snps, 'hapmapGenosArray25M', 1)