Mercurial > repos > rlegendre > ribo_tools
comparison kmer_analysis.py @ 18:a121cce43f90 draft
Uploaded
| author | rlegendre |
|---|---|
| date | Tue, 09 Jun 2015 09:06:17 -0400 |
| parents | 7c944fd9907e |
| children | 385fc64fa988 |
comparison
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| 17:c87c40e642af | 18:a121cce43f90 |
|---|---|
| 365 (options, args) = parser.parse_args() | 365 (options, args) = parser.parse_args() |
| 366 sys.stdout.write("Begin kmer and phasing analysis at %s\n" % time.asctime( time.localtime( time.time() ) ) ) | 366 sys.stdout.write("Begin kmer and phasing analysis at %s\n" % time.asctime( time.localtime( time.time() ) ) ) |
| 367 | 367 |
| 368 try: | 368 try: |
| 369 | 369 |
| 370 if os.path.exists(options.dirout): | 370 if not os.path.exists(options.dirout): |
| 371 raise | 371 try: |
| 372 try: | 372 os.mkdir(options.dirout) |
| 373 os.mkdir(options.dirout) | 373 except Exception, e : |
| 374 except: | 374 stop_err('Error running make directory : ' + str(e)) |
| 375 raise | |
| 376 | 375 |
| 377 ##testing indexed bam file | 376 ##testing indexed bam file |
| 378 if os.path.isfile(options.bamfile+".bai") : | 377 if os.path.isfile(options.bamfile+".bai") : |
| 379 pass | 378 pass |
| 380 else : | 379 else : |
| 402 #GFF = store_gff(options.gff) | 401 #GFF = store_gff(options.gff) |
| 403 #GFF = ribo_functions.store_gtf(options.gff) | 402 #GFF = ribo_functions.store_gtf(options.gff) |
| 404 ## check gff reading | 403 ## check gff reading |
| 405 if not GFF['order'] : | 404 if not GFF['order'] : |
| 406 stop_err( 'Incorrect GFF file' ) | 405 stop_err( 'Incorrect GFF file' ) |
| 407 | 406 for gene in GFF['order']: |
| 407 if not GFF[gene]['exon'] : | |
| 408 del GFF[gene] | |
| 409 GFF['order'].remove(gene) | |
| 408 ## split bam | 410 ## split bam |
| 409 split_bam(options.bamfile,tmpdir) | 411 split_bam(options.bamfile,tmpdir) |
| 410 ################################### | 412 ################################### |
| 411 ## First analysis with 28mer : | 413 ## First analysis with 28mer : |
| 412 ################################### | 414 ################################### |