Mercurial > repos > bobbledavidson > beagle4_0
annotate beagle4.py @ 4:b970ba62539e draft default tip
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
| author | bobbledavidson |
|---|---|
| date | Wed, 16 Sep 2015 05:58:13 -0400 |
| parents | c36b11eab590 |
| children |
| rev | line source |
|---|---|
| 1 | 1 import os |
| 2 import optparse | |
| 3 import tempfile | |
| 4 import shutil | |
| 5 from subprocess import call | |
|
4
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
6 import gzip |
| 1 | 7 |
| 8 def main(): | |
| 9 | |
| 10 parser = optparse.OptionParser() | |
| 11 parser.add_option('--jar', dest='jarfile', default=None) | |
| 12 parser.add_option('--gtgl',dest='gtgl',default='gt') | |
| 13 parser.add_option('--gfile',dest='gfile',default=None) | |
| 14 parser.add_option('--ref', dest='ref',default=None ) | |
| 15 parser.add_option('--impute-its',dest='impits', default="5") | |
| 16 parser.add_option('--phase-its',dest='phits',default="5") | |
| 17 parser.add_option('--out', dest='outfile', default='out.beagle4') | |
| 18 | |
| 19 (options, args) = parser.parse_args() | |
| 20 | |
| 21 if not options.jarfile: | |
| 22 parser.error('Jar option is not optional. Please provide full path to beagle4 jar file') | |
| 23 | |
| 24 if not options.gfile: | |
| 25 parser.error('Genotype file not optional. Can be genotype or genotype likelihood. Please provide --gfile argument.') | |
| 26 | |
| 27 print options.jarfile | |
| 28 cwd = os.getcwd() | |
| 29 outdir = tempfile.mkdtemp(dir=cwd) | |
| 30 outprefix = 'bglout' | |
| 31 | |
| 32 if options.ref: | |
| 33 call(['java', '-Xmx2g', '-jar', options.jarfile, 'ref='+options.ref, options.gtgl+'='+options.gfile, 'phase-its='+options.phits,'impute-its='+options.impits , 'out='+outdir+'/'+outprefix ]) | |
| 34 else: | |
| 35 call(['java', '-Xmx2g', '-jar', options.jarfile, options.gtgl+'='+options.gfile,'phase-its='+options.phits, 'impute-its='+options.impits , 'out='+outdir+'/'+outprefix ]) | |
| 36 | |
| 37 | |
|
4
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
38 #shutil.move(outdir+'/'+outprefix+'.vcf.gz',options.outfile) |
|
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
39 #shutil.rmtree(outdir) |
|
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
40 with gzip.open(outdir+os.sep+outprefix+'.vcf.gz','rb') as gzinfile: |
|
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
41 with open(options.outfile,'w') as vcfoutfile: |
|
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
42 for line in gzinfile: |
|
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
43 vcfoutfile.write(line) |
|
b970ba62539e
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ
bobbledavidson
parents:
1
diff
changeset
|
44 |
| 1 | 45 shutil.rmtree(outdir) |
| 46 | |
| 47 | |
| 48 if __name__=='__main__': | |
| 49 main() | |
| 50 |