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comparison cummerbund_wrapper.py @ 2:fdf01b3c1841

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Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
author Jim Johnson <jj@umn.edu>
date Fri, 08 Nov 2013 14:54:01 -0600
parents da7241f92ecf
children
comparison
equal deleted inserted replaced
1:ebb9a992508d 2:fdf01b3c1841
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()