Mercurial > repos > sjung > bdds
comparison fseq_wrapper.py @ 1:29760e9a840b draft
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author | sjung |
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date | Wed, 24 May 2017 00:35:08 -0400 |
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0:2d6315e241e4 | 1:29760e9a840b |
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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__() |