Mercurial > repos > alenail > chipsequtil
comparison chipsequtil/map_to_known_genes.py @ 12:182e829571f7 draft
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| author | alenail |
|---|---|
| date | Mon, 04 Apr 2016 15:41:41 -0400 |
| parents | 0eaa8225a09a |
| children | 425c48c48dde |
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| 11:45d2e58bcaf8 | 12:182e829571f7 |
|---|---|
| 197 #out_d = {'knownGeneID':gene['name']} | 197 #out_d = {'knownGeneID':gene['name']} |
| 198 out_d['knownGeneID'] = gene['name'] | 198 out_d['knownGeneID'] = gene['name'] |
| 199 if opts.symbol_xref : | 199 if opts.symbol_xref : |
| 200 out_d['geneSymbol'] = symbol_xref_map[gene['name']]['geneSymbol'] | 200 out_d['geneSymbol'] = symbol_xref_map[gene['name']]['geneSymbol'] |
| 201 peaks_writer.writerow(out_d) | 201 peaks_writer.writerow(out_d) |
| 202 | 202 print "wrote a row." |
| 203 mapped = True | 203 mapped = True |
| 204 | 204 |
| 205 # reset map_type | 205 # reset map_type |
| 206 out_d['map type'] = '' | 206 out_d['map type'] = '' |
| 207 | 207 |
| 211 out_d['geneSymbol'] = 'None' | 211 out_d['geneSymbol'] = 'None' |
| 212 out_d['map type'] = 'intergenic' | 212 out_d['map type'] = 'intergenic' |
| 213 peaks_writer.writerow(out_d) | 213 peaks_writer.writerow(out_d) |
| 214 map_stats['intergenic'] += 1 | 214 map_stats['intergenic'] += 1 |
| 215 | 215 |
| 216 if peak_output != sys.stdout : | 216 if peak_output != sys.stdout: |
| 217 print "arrived here." | |
| 217 peak_output.close() | 218 peak_output.close() |
| 218 | 219 |
| 219 #if opts.stats_output != sys.stderr : | 220 #if opts.stats_output != sys.stderr : |
| 220 # opts.stats_output = open(opts.stats_output,'w') | 221 # opts.stats_output = open(opts.stats_output,'w') |
| 221 | 222 |