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comparison fseq_wrapper.py @ 1:29760e9a840b draft

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author sjung
date Wed, 24 May 2017 00:35:08 -0400
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0:2d6315e241e4 1:29760e9a840b
1 #/usr/bin/python
2
3 import optparse, sys, subprocess, tempfile
4 import shutil, os
5
6 CHUNK_SIZE = 2**20 #1mbi
7
8 def cleanup_before_exit( tmp_dir ):
9 if tmp_dir and os.path.exists( tmp_dir ):
10 shutil.rmtree( tmp_dir )
11
12 def __main__():
13 parser = optparse.OptionParser()
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.' )
15 parser.add_option('', '--of', dest='output_format', action='store', type="string", help='output format')
16 parser.add_option('-i', '--input-files', dest='input_files', action='store', type="string", help='input files')
17 parser.add_option( '-o', '--output-file', dest='output_file', action='store', type="string", default=None, help='bed output' )
18
19 (options, args) = parser.parse_args()
20 pass_through = ""
21 if options.pass_through_options:
22 pass_through = ' '.join( options.pass_through_options )
23
24 cmd = "fseq %s -of %s %s" % (pass_through, options.output_format, options.input_files)
25 print cmd
26 tmp_dir = tempfile.mkdtemp( prefix='tmp-tool-' )
27
28 stdout = tempfile.NamedTemporaryFile( prefix="fseq-stdout-", dir=tmp_dir )
29 stderr = tempfile.NamedTemporaryFile( prefix="fseq-stderr-", dir=tmp_dir )
30 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
31 return_code = proc.wait()
32
33 if return_code:
34 stderr_target = sys.stderr
35 else:
36 stderr_target = sys.stdout
37 stderr.flush()
38 stderr.seek(0)
39
40 while True:
41 chunk = stderr.read( CHUNK_SIZE )
42 if chunk:
43 stderr_target.write( chunk )
44 else:
45 break
46 stderr.close()
47 stdout.close()
48 if options.output_format == 'bed':
49 os.system("cat %s/*.bed > %s/output.bed" % (tmp_dir, tmp_dir))
50 shutil.copy("%s/output.bed" % tmp_dir, options.output_file)
51 else:
52 os.system("cat %s/*.wig > %s/output.wig" % (tmp_dir, tmp_dir))
53 shutil.copy("%s/output.wig" % tmp_dir, options.output_file)
54
55 cleanup_before_exit( tmp_dir )
56
57 if __name__ == "__main__": __main__()