Mercurial > repos > alenail > chipsequtil
comparison chipsequtil/map_to_known_genes.py @ 20:435adb6000f1 draft
Uploaded
| author | alenail |
|---|---|
| date | Mon, 04 Apr 2016 16:41:52 -0400 |
| parents | 4c645d02a428 |
| children |
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| 19:c5c452f9c237 | 20:435adb6000f1 |
|---|---|
| 198 #out_d = {'knownGeneID':gene['name']} | 198 #out_d = {'knownGeneID':gene['name']} |
| 199 out_d['knownGeneID'] = gene['name'] | 199 out_d['knownGeneID'] = gene['name'] |
| 200 if opts.symbol_xref : | 200 if opts.symbol_xref : |
| 201 out_d['geneSymbol'] = symbol_xref_map[gene['name']]['geneSymbol'] | 201 out_d['geneSymbol'] = symbol_xref_map[gene['name']]['geneSymbol'] |
| 202 peaks_writer.writerow(out_d) | 202 peaks_writer.writerow(out_d) |
| 203 print "wrote a row." | |
| 204 mapped = True | 203 mapped = True |
| 205 | 204 |
| 206 # reset map_type | 205 # reset map_type |
| 207 out_d['map type'] = '' | 206 out_d['map type'] = '' |
| 208 | 207 |
| 213 out_d['map type'] = 'intergenic' | 212 out_d['map type'] = 'intergenic' |
| 214 peaks_writer.writerow(out_d) | 213 peaks_writer.writerow(out_d) |
| 215 map_stats['intergenic'] += 1 | 214 map_stats['intergenic'] += 1 |
| 216 | 215 |
| 217 if peak_output != sys.stdout: | 216 if peak_output != sys.stdout: |
| 218 print "arrived here." | |
| 219 peak_output.close() | 217 peak_output.close() |
| 220 print "arrived here2." | |
| 221 | 218 |
| 222 #if opts.stats_output != sys.stderr : | 219 #if opts.stats_output != sys.stderr : |
| 223 # opts.stats_output = open(opts.stats_output,'w') | 220 # opts.stats_output = open(opts.stats_output,'w') |
| 224 | 221 |
| 225 #for k,v in map_stats.items() : | 222 #for k,v in map_stats.items() : |