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comparison cummerbund_wrapper.py @ 0:da7241f92ecf

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author jjohnson
date Mon, 04 Feb 2013 19:50:25 -0500
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children fdf01b3c1841
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-1:000000000000 0:da7241f92ecf
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(1)
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( '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) )
18 html_out.write( '</ul>\n</body>\n</html>\n' )
19
20 def __main__():
21 #Parse Command Line
22 parser = optparse.OptionParser()
23
24 # wrapper options
25 parser.add_option('', '--r-script', dest='r_script', help='R script')
26 parser.add_option('', '--html-report-from-directory', dest='html_report_from_directory', type="string", nargs=2, help='"Target HTML File" "Directory"')
27
28 (options, args) = parser.parse_args()
29
30 (html_filename, html_dir) = options.html_report_from_directory
31
32 # Make html report directory for output.
33 os.mkdir( html_dir )
34
35 # Make a tmp dir
36 tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' )
37
38 # Build command.
39 cmd = ( "Rscript --vanilla %s" % options.r_script )
40
41 # Debugging.
42 # print cmd
43
44 #liubo added, for test, look at the generated R script
45 # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script')
46
47
48 # Run command.
49 try:
50 tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
51 tmp_stderr = open( tmp_name, 'wb' )
52 proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() )
53 returncode = proc.wait()
54 tmp_stderr.close()
55
56 # Get stderr, allowing for case where it's very large.
57 tmp_stderr = open( tmp_name, 'rb' )
58 stderr = ''
59 buffsize = 1048576
60 try:
61 while True:
62 stderr += tmp_stderr.read( buffsize )
63 if not stderr or len( stderr ) % buffsize != 0:
64 break
65 except OverflowError:
66 pass
67 tmp_stderr.close()
68
69 # Error checking.
70 if returncode != 0:
71 raise Exception, stderr
72 except Exception, e:
73 stop_err( 'Error running R script. ' + str( e ) )
74
75 # write the html report
76 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
77
78 # Clean up temp dirs
79 if os.path.exists( tmp_dir ):
80 shutil.rmtree( tmp_dir )
81
82 if __name__=="__main__": __main__()