Mercurial > repos > jjohnson > cummerbund
comparison cummerbund_wrapper.py @ 15:2d7eee38ab5b
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 08 Nov 2013 13:28:44 -0600 |
| parents | b0d11fcbc3ac |
| children |
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| 14:d10befb0867a | 15:2d7eee38ab5b |
|---|---|
| 11 sys.exit(1) | 11 sys.exit(1) |
| 12 | 12 |
| 13 def html_report_from_directory( html_out, dir ): | 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' ) | 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 ) ): | 15 for fname in sorted( os.listdir( dir ) ): |
| 16 # html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) | 16 if fname.endswith(".txt"): |
| 17 html_out.write( '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) ) | 17 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) |
| 18 else: | |
| 19 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' ) | 20 html_out.write( '</ul>\n</body>\n</html>\n' ) |
| 19 | 21 |
| 20 def __main__(): | 22 def __main__(): |
| 21 #Parse Command Line | 23 #Parse Command Line |
| 22 parser = optparse.OptionParser() | 24 parser = optparse.OptionParser() |