#!/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,
)
