Mercurial > repos > bobbledavidson > beagle4_0

comparison beagle4.py @ 1:c36b11eab590 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Beagle4 python wrapper Uploaded
author bobbledavidson
date Wed, 08 Jul 2015 10:18:45 -0400
parents
children b970ba62539e
comparison
equal deleted inserted replaced
0:430cda98caa4 1:c36b11eab590
1 import os
2 import optparse
3 import tempfile
4 import shutil
5 from subprocess import call
6
7 def main():
8
9 parser = optparse.OptionParser()
10 parser.add_option('--jar', dest='jarfile', default=None)
11 parser.add_option('--gtgl',dest='gtgl',default='gt')
12 parser.add_option('--gfile',dest='gfile',default=None)
13 parser.add_option('--ref', dest='ref',default=None )
14 parser.add_option('--impute-its',dest='impits', default="5")
15 parser.add_option('--phase-its',dest='phits',default="5")
16 parser.add_option('--out', dest='outfile', default='out.beagle4')
17
18 (options, args) = parser.parse_args()
19
20 if not options.jarfile:
21 parser.error('Jar option is not optional. Please provide full path to beagle4 jar file')
22
23 if not options.gfile:
24 parser.error('Genotype file not optional. Can be genotype or genotype likelihood. Please provide --gfile argument.')
25
26 print options.jarfile
27 cwd = os.getcwd()
28 outdir = tempfile.mkdtemp(dir=cwd)
29 outprefix = 'bglout'
30
31 if options.ref:
32 call(['java', '-Xmx2g', '-jar', options.jarfile, 'ref='+options.ref, options.gtgl+'='+options.gfile, 'phase-its='+options.phits,'impute-its='+options.impits , 'out='+outdir+'/'+outprefix ])
33 else:
34 call(['java', '-Xmx2g', '-jar', options.jarfile, options.gtgl+'='+options.gfile,'phase-its='+options.phits, 'impute-its='+options.impits , 'out='+outdir+'/'+outprefix ])
35
36
37 shutil.move(outdir+'/'+outprefix+'.vcf.gz',options.outfile)
38 shutil.rmtree(outdir)
39
40
41
42 if __name__=='__main__':
43 main()
44