Mercurial > repos > jjohnson > cummerbund
annotate cummerbund_wrapper.py @ 9:532a336a14c1 default tip
Need all_fasta.loc for cummerbund
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 13 Oct 2014 09:39:39 -0500 |
| parents | fdf01b3c1841 |
| children |
| rev | line source |
|---|---|
| 0 | 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 ) ): | |
|
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fdf01b3c1841
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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16 if fname.endswith(".txt"): |
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fdf01b3c1841
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
17 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) |
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fdf01b3c1841
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
18 else: |
|
fdf01b3c1841
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
19 html_out.write( '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) ) |
| 0 | 20 html_out.write( '</ul>\n</body>\n</html>\n' ) |
| 21 | |
| 22 def __main__(): | |
| 23 #Parse Command Line | |
| 24 parser = optparse.OptionParser() | |
| 25 | |
| 26 # wrapper options | |
| 27 parser.add_option('', '--r-script', dest='r_script', help='R script') | |
| 28 parser.add_option('', '--html-report-from-directory', dest='html_report_from_directory', type="string", nargs=2, help='"Target HTML File" "Directory"') | |
| 29 | |
| 30 (options, args) = parser.parse_args() | |
| 31 | |
| 32 (html_filename, html_dir) = options.html_report_from_directory | |
| 33 | |
| 34 # Make html report directory for output. | |
| 35 os.mkdir( html_dir ) | |
| 36 | |
| 37 # Make a tmp dir | |
| 38 tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' ) | |
| 39 | |
| 40 # Build command. | |
| 41 cmd = ( "Rscript --vanilla %s" % options.r_script ) | |
| 42 | |
| 43 # Debugging. | |
| 44 # print cmd | |
| 45 | |
| 46 #liubo added, for test, look at the generated R script | |
| 47 # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script') | |
| 48 | |
| 49 | |
| 50 # Run command. | |
| 51 try: | |
| 52 tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name | |
| 53 tmp_stderr = open( tmp_name, 'wb' ) | |
| 54 proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() ) | |
| 55 returncode = proc.wait() | |
| 56 tmp_stderr.close() | |
| 57 | |
| 58 # Get stderr, allowing for case where it's very large. | |
| 59 tmp_stderr = open( tmp_name, 'rb' ) | |
| 60 stderr = '' | |
| 61 buffsize = 1048576 | |
| 62 try: | |
| 63 while True: | |
| 64 stderr += tmp_stderr.read( buffsize ) | |
| 65 if not stderr or len( stderr ) % buffsize != 0: | |
| 66 break | |
| 67 except OverflowError: | |
| 68 pass | |
| 69 tmp_stderr.close() | |
| 70 | |
| 71 # Error checking. | |
| 72 if returncode != 0: | |
| 73 raise Exception, stderr | |
| 74 except Exception, e: | |
| 75 stop_err( 'Error running R script. ' + str( e ) ) | |
| 76 | |
| 77 # write the html report | |
| 78 html_report_from_directory( open( html_filename, 'wb' ), html_dir ) | |
| 79 | |
| 80 # Clean up temp dirs | |
| 81 if os.path.exists( tmp_dir ): | |
| 82 shutil.rmtree( tmp_dir ) | |
| 83 | |
| 84 if __name__=="__main__": __main__() |