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1 import os
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2 import optparse
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3 import tempfile
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4 import shutil
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5 from subprocess import call
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6
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7 def main():
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8
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9 parser = optparse.OptionParser()
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10 parser.add_option('--jar', dest='jarfile', default=None)
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11 parser.add_option('--gtgl',dest='gtgl',default='gt')
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12 parser.add_option('--gfile',dest='gfile',default=None)
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13 parser.add_option('--ref', dest='ref',default=None )
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14 parser.add_option('--impute-its',dest='impits', default="5")
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15 parser.add_option('--phase-its',dest='phits',default="5")
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16 parser.add_option('--out', dest='outfile', default='out.beagle4')
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17
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18 (options, args) = parser.parse_args()
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19
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20 if not options.jarfile:
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21 parser.error('Jar option is not optional. Please provide full path to beagle4 jar file')
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22
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23 if not options.gfile:
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24 parser.error('Genotype file not optional. Can be genotype or genotype likelihood. Please provide --gfile argument.')
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25
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26 print options.jarfile
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27 cwd = os.getcwd()
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28 outdir = tempfile.mkdtemp(dir=cwd)
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29 outprefix = 'bglout'
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30
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31 if options.ref:
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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 ])
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33 else:
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34 call(['java', '-Xmx2g', '-jar', options.jarfile, options.gtgl+'='+options.gfile,'phase-its='+options.phits, 'impute-its='+options.impits , 'out='+outdir+'/'+outprefix ])
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35
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36
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37 shutil.move(outdir+'/'+outprefix+'.vcf.gz',options.outfile)
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38 shutil.rmtree(outdir)
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39
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40
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41
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42 if __name__=='__main__':
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43 main()
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44
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