comparison rgGSEA/rgGSEA.py @ 4:89e89b70a867 draft default tip

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3:8e291f464aa0

                os.makedirs(opts.output_dir)
            except:
                print >> sys.stderr,'##Error: GSEA wrapper unable to create or find output directory %s. Stopping' % (opts.output_dir)
                sys.exit(1)
        fakeGMT = re.sub('[^a-zA-Z0-9_]+', '', opts.input_name) # gives a more useful title for the GSEA report
        fakeGMT = os.path.join(opts.output_dir,fakeGMT) 
        fakeRanks = '%s.rnk' % fakeGMT
        if not fakeGMT.endswith('.gmt'):
            fakeGMT = '%s.gmt' % fakeGMT
        if opts.builtin_gmt and opts.history_gmt:
            newfile = open(fakeGMT,'w')

             print >> sys.stdout, '## Fixed any lower case - now have',','.join([x[0] for x in ranks[:5]])
        ranks = ['\t'.join(x) for x in ranks]
        if len(ranks) < 2:
             print >> sys.stderr,'Input %s has 1 or less rows with two tab delimited fields - please check the tool documentation' % infname
             sys.exit(1)
        rclean = open(fakeRanks,'w')
        rclean.write('contig\tscore\n')
        rclean.write('\n'.join(ranks)) 
        rclean.write('\n')
        rclean.close()

4:89e89b70a867

                os.makedirs(opts.output_dir)
            except:
                print >> sys.stderr,'##Error: GSEA wrapper unable to create or find output directory %s. Stopping' % (opts.output_dir)
                sys.exit(1)
        fakeGMT = re.sub('[^a-zA-Z0-9_]+', '', opts.input_name) # gives a more useful title for the GSEA report
        fakeGMT = os.path.join(opts.output_dir,fakeGMT)
        fakeGMT = os.path.abspath(fakeGMT)
        fakeRanks = '%s.rnk' % fakeGMT
        if not fakeGMT.endswith('.gmt'):
            fakeGMT = '%s.gmt' % fakeGMT
        if opts.builtin_gmt and opts.history_gmt:
            newfile = open(fakeGMT,'w')

             print >> sys.stdout, '## Fixed any lower case - now have',','.join([x[0] for x in ranks[:5]])
        ranks = ['\t'.join(x) for x in ranks]
        if len(ranks) < 2:
             print >> sys.stderr,'Input %s has 1 or less rows with two tab delimited fields - please check the tool documentation' % infname
             sys.exit(1)
        print '### opening %s and writing %s' % (fakeRanks,str(ranks[:10]))
        rclean = open(fakeRanks,'w')
        rclean.write('contig\tscore\n')
        rclean.write('\n'.join(ranks)) 
        rclean.write('\n')
        rclean.close()