Mercurial > repos > fubar > rg_gsea

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

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Uploaded
author fubar
date Sun, 09 Jun 2013 23:09:34 -0400
parents 71fa159646c9
children
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3:8e291f464aa0 4:89e89b70a867
159 os.makedirs(opts.output_dir) 159 os.makedirs(opts.output_dir)
160 except: 160 except:
161 print >> sys.stderr,'##Error: GSEA wrapper unable to create or find output directory %s. Stopping' % (opts.output_dir) 161 print >> sys.stderr,'##Error: GSEA wrapper unable to create or find output directory %s. Stopping' % (opts.output_dir)
162 sys.exit(1) 162 sys.exit(1)
163 fakeGMT = re.sub('[^a-zA-Z0-9_]+', '', opts.input_name) # gives a more useful title for the GSEA report 163 fakeGMT = re.sub('[^a-zA-Z0-9_]+', '', opts.input_name) # gives a more useful title for the GSEA report
164 fakeGMT = os.path.join(opts.output_dir,fakeGMT) 164 fakeGMT = os.path.join(opts.output_dir,fakeGMT)
165 fakeGMT = os.path.abspath(fakeGMT)
165 fakeRanks = '%s.rnk' % fakeGMT 166 fakeRanks = '%s.rnk' % fakeGMT
166 if not fakeGMT.endswith('.gmt'): 167 if not fakeGMT.endswith('.gmt'):
167 fakeGMT = '%s.gmt' % fakeGMT 168 fakeGMT = '%s.gmt' % fakeGMT
168 if opts.builtin_gmt and opts.history_gmt: 169 if opts.builtin_gmt and opts.history_gmt:
169 newfile = open(fakeGMT,'w') 170 newfile = open(fakeGMT,'w')
321 print >> sys.stdout, '## Fixed any lower case - now have',','.join([x[0] for x in ranks[:5]]) 322 print >> sys.stdout, '## Fixed any lower case - now have',','.join([x[0] for x in ranks[:5]])
322 ranks = ['\t'.join(x) for x in ranks] 323 ranks = ['\t'.join(x) for x in ranks]
323 if len(ranks) < 2: 324 if len(ranks) < 2:
324 print >> sys.stderr,'Input %s has 1 or less rows with two tab delimited fields - please check the tool documentation' % infname 325 print >> sys.stderr,'Input %s has 1 or less rows with two tab delimited fields - please check the tool documentation' % infname
325 sys.exit(1) 326 sys.exit(1)
327 print '### opening %s and writing %s' % (fakeRanks,str(ranks[:10]))
326 rclean = open(fakeRanks,'w') 328 rclean = open(fakeRanks,'w')
327 rclean.write('contig\tscore\n') 329 rclean.write('contig\tscore\n')
328 rclean.write('\n'.join(ranks)) 330 rclean.write('\n'.join(ranks))
329 rclean.write('\n') 331 rclean.write('\n')
330 rclean.close() 332 rclean.close()