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comparison cummerbund_wrapper.py @ 0:8ba5f0460b1e

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author jjohnson
date Mon, 01 Oct 2012 14:08:13 -0400
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children 6a9bc26ab8d9
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-1:000000000000 0:8ba5f0460b1e
1 #!/usr/bin/env python
2
3 ### Runs "r_script" and generates a HTML report
4 ### Inspired on cuffdiff_wrapper.py and gatk_wrapper.py
5 ### Carlos Borroto <carlos.borroto@gmail.com>
6
7 import optparse, os, shutil, subprocess, sys, tempfile
8
9 def stop_err( msg ):
10 sys.stderr.write( "%s\n" % msg )
11 sys.exit()
12
13 def html_report_from_directory( html_out, dir ):
14 html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
15 for fname in sorted( os.listdir( dir ) ):
16 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
17 html_out.write( '</ul>\n</body>\n</html>\n' )
18
19 def __main__():
20 #Parse Command Line
21 parser = optparse.OptionParser()
22
23 # wrapper options
24 parser.add_option('', '--r-script', dest='r_script', help='R script')
25 parser.add_option('', '--html-report-from-directory', dest='html_report_from_directory', type="string", nargs=2, help='"Target HTML File" "Directory"')
26
27 (options, args) = parser.parse_args()
28
29 (html_filename, html_dir) = options.html_report_from_directory
30
31 # Make html report directory for output.
32 os.mkdir( html_dir )
33
34 # Make a tmp dir
35 tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' )
36
37 # Build command.
38 cmd = ( "Rscript --vanilla %s" % options.r_script )
39
40 # Debugging.
41 print cmd
42
43 #liubo added, for test, look at the generated R script
44 # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script')
45
46
47 # Run command.
48 try:
49 tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
50 tmp_stderr = open( tmp_name, 'wb' )
51 proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() )
52 returncode = proc.wait()
53 tmp_stderr.close()
54
55 # Get stderr, allowing for case where it's very large.
56 tmp_stderr = open( tmp_name, 'rb' )
57 stderr = ''
58 buffsize = 1048576
59 try:
60 while True:
61 stderr += tmp_stderr.read( buffsize )
62 if not stderr or len( stderr ) % buffsize != 0:
63 break
64 except OverflowError:
65 pass
66 tmp_stderr.close()
67
68 # Error checking.
69 if returncode != 0:
70 raise Exception, stderr
71 except Exception, e:
72 stop_err( 'Error running R script. ' + str( e ) )
73
74 # write the html report
75 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
76
77 # Clean up temp dirs
78 if os.path.exists( tmp_dir ):
79 shutil.rmtree( tmp_dir )
80
81 if __name__=="__main__": __main__()