#!/usr/bin/env python ''' ============================================================ Re-generate all test sets (chr22 data). Created on August 16, 2012 @author: Oren Livne <*****@*****.**> ============================================================ ''' from impute.phasing import examples from impute.preprocess import convert from impute.phasing.examples import CHR22 from impute import impute_test_util as itu # Need to be done once given the original PLINK TPED Hutterites data set convert.main(pedigree=itu.HUTT_PED, prefix=CHR22 + '/hutt', npz=CHR22 + '/hutt.npz', target='npz', debug=True) for stage in xrange(1, 5): examples.phase_chr22('hutt.%snpz' % ('stage%d.' % (stage - 1, ) if stage > 1 else ''), 'hutt.stage%d.npz' % (stage, ), stage=stage) examples.generate_test_sets()
(options, args) = parser.parse_args(sys.argv[1:]) if len(args) != 4: print usage sys.exit(1) # in_dir = 'phasing.20121130/split_chr' # out_dir = 'phasing.20121130/individual' # chrom = 5 # part = 0 in_dir, out_dir, chrom, part = args[0], args[1], int(args[2]), int(args[3]) print 'Running phasing in stages' print 'in_dir = %s' % (in_dir,) print 'out_dir = %s' % (out_dir,) print 'chrom = %d' % (chrom,) print 'part = %d' % (part,) out_dir = '%s/chr%d' % (out_dir, chrom) util.mkdir_if_not_exists(out_dir) npz_file = '%s/hutt.stage0.npz' % (out_dir,) if not os.path.exists(npz_file) and options.stage == 0: convert.main(pedigree=itu.HUTT_PED, prefix='%s/chr%d/hutt_chr%d_part%d' % (in_dir, chrom, chrom, part), npz=npz_file, target='npz', debug=True) for stage in (range(1, 5) if options.stage == 0 else [options.stage]): phase.main(pedigree=itu.HUTT_PED, input='%s/hutt.stage%d.npz' % (out_dir, stage - 1), output='%s/hutt.stage%d.npz' % (out_dir, stage), stage=stage, debug=options.debug)
#!/usr/bin/env python ''' ============================================================ Re-generate all test sets (chr22 data). Created on August 16, 2012 @author: Oren Livne <*****@*****.**> ============================================================ ''' from impute.phasing import examples from impute.preprocess import convert from impute.phasing.examples import CHR22 from impute import impute_test_util as itu # Need to be done once given the original PLINK TPED Hutterites data set convert.main(pedigree=itu.HUTT_PED, prefix=CHR22 + '/hutt', npz=CHR22 + '/hutt.npz', target='npz', debug=True) for stage in xrange(1, 5): examples.phase_chr22('hutt.%snpz' % ('stage%d.' % (stage - 1,) if stage > 1 else ''), 'hutt.stage%d.npz' % (stage,), stage=stage) examples.generate_test_sets()
# chrom = 5 # part = 0 in_dir, out_dir, chrom, part = args[0], args[1], int(args[2]), int(args[3]) print "Running phasing in stages" print "in_dir = %s" % (in_dir,) print "out_dir = %s" % (out_dir,) print "chrom = %d" % (chrom,) print "part = %d" % (part,) out_dir = "%s/chr%d" % (out_dir, chrom) util.mkdir_if_not_exists(out_dir) npz_file = "%s/hutt.stage0.npz" % (out_dir,) if not os.path.exists(npz_file) and options.stage == 0: convert.main( pedigree=itu.HUTT_PED, prefix="%s/chr%d/hutt_chr%d_part%d" % (in_dir, chrom, chrom, part), npz=npz_file, target="npz", debug=True, ) for stage in range(1, 5) if options.stage == 0 else [options.stage]: phase.main( pedigree=itu.HUTT_PED, input="%s/hutt.stage%d.npz" % (out_dir, stage - 1), output="%s/hutt.stage%d.npz" % (out_dir, stage), stage=stage, debug=options.debug, )