annotate fseq_wrapper.py @ 8:777faad85c7c draft default tip

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author sjung
date Wed, 24 May 2017 01:03:50 -0400
parents 29760e9a840b
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1 #/usr/bin/python
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2
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3 import optparse, sys, subprocess, tempfile
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4 import shutil, os
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5
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6 CHUNK_SIZE = 2**20 #1mbi
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7
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8 def cleanup_before_exit( tmp_dir ):
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9 if tmp_dir and os.path.exists( tmp_dir ):
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10 shutil.rmtree( tmp_dir )
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12 def __main__():
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13 parser = optparse.OptionParser()
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14 parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to GATK, without any modification.' )
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15 parser.add_option('', '--of', dest='output_format', action='store', type="string", help='output format')
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16 parser.add_option('-i', '--input-files', dest='input_files', action='store', type="string", help='input files')
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17 parser.add_option( '-o', '--output-file', dest='output_file', action='store', type="string", default=None, help='bed output' )
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18
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19 (options, args) = parser.parse_args()
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20 pass_through = ""
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21 if options.pass_through_options:
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22 pass_through = ' '.join( options.pass_through_options )
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23
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24 cmd = "fseq %s -of %s %s" % (pass_through, options.output_format, options.input_files)
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25 print cmd
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26 tmp_dir = tempfile.mkdtemp( prefix='tmp-tool-' )
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27
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28 stdout = tempfile.NamedTemporaryFile( prefix="fseq-stdout-", dir=tmp_dir )
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29 stderr = tempfile.NamedTemporaryFile( prefix="fseq-stderr-", dir=tmp_dir )
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30 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
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31 return_code = proc.wait()
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32
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33 if return_code:
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34 stderr_target = sys.stderr
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35 else:
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36 stderr_target = sys.stdout
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37 stderr.flush()
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38 stderr.seek(0)
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39
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40 while True:
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41 chunk = stderr.read( CHUNK_SIZE )
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42 if chunk:
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43 stderr_target.write( chunk )
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44 else:
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45 break
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46 stderr.close()
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47 stdout.close()
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48 if options.output_format == 'bed':
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49 os.system("cat %s/*.bed > %s/output.bed" % (tmp_dir, tmp_dir))
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50 shutil.copy("%s/output.bed" % tmp_dir, options.output_file)
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51 else:
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52 os.system("cat %s/*.wig > %s/output.wig" % (tmp_dir, tmp_dir))
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53 shutil.copy("%s/output.wig" % tmp_dir, options.output_file)
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54
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55 cleanup_before_exit( tmp_dir )
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56
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57 if __name__ == "__main__": __main__()