Mercurial > repos > jjohnson > cummerbund
comparison cummerbund_wrapper.py @ 0:8ba5f0460b1e
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| author | jjohnson |
|---|---|
| date | Mon, 01 Oct 2012 14:08:13 -0400 |
| parents | |
| children | 6a9bc26ab8d9 |
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| -1:000000000000 | 0:8ba5f0460b1e |
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| 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__() |