Mercurial > repos > jeremie > breakdancer_bin
comparison breakdancer.py @ 14:2c3b8a1d8f4b draft
Uploaded
| author | jeremie |
|---|---|
| date | Wed, 02 Jul 2014 10:17:20 -0400 |
| parents | 62bf6aed1908 |
| children | 48d2f8be5c97 |
comparison
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| 13:62bf6aed1908 | 14:2c3b8a1d8f4b |
|---|---|
| 19 parser.add_argument('-t', dest='onlyTrans', action='store_true', help='only detect transchromosomal rearrangement', default=False) | 19 parser.add_argument('-t', dest='onlyTrans', action='store_true', help='only detect transchromosomal rearrangement', default=False) |
| 20 parser.add_argument('-d', dest='prefix', required=False, help='prefix of fastq files that SV supporting reads will be saved by library') | 20 parser.add_argument('-d', dest='prefix', required=False, help='prefix of fastq files that SV supporting reads will be saved by library') |
| 21 parser.add_argument('-g', dest='bedFormat', required=False, help='dump SVs and supporting reads in BED format for GBrowse') | 21 parser.add_argument('-g', dest='bedFormat', required=False, help='dump SVs and supporting reads in BED format for GBrowse') |
| 22 parser.add_argument('-l', dest='matePair', required=False, help='analyze Illumina long insert (mate-pair) library') | 22 parser.add_argument('-l', dest='matePair', required=False, help='analyze Illumina long insert (mate-pair) library') |
| 23 parser.add_argument('-a', dest='sortByLibrary', action='store_true', help='print out copy number and support reads per library rather than per bam', default=False) | 23 parser.add_argument('-a', dest='sortByLibrary', action='store_true', help='print out copy number and support reads per library rather than per bam', default=False) |
| 24 parser.add_argument('-h', dest='AFColumn', action='store_true', help='print out Allele Frequency column', default=False) | 24 # parser.add_argument('-h', dest='AFColumn', action='store_true', help='print out Allele Frequency column', default=False) |
| 25 parser.add_argument('-y', dest='scoreFilter', type=int, required=False, help='output score filter', default=30) | 25 parser.add_argument('-y', dest='scoreFilter', type=int, required=False, help='output score filter', default=30) |
| 26 | 26 |
| 27 | 27 |
| 28 | 28 |
| 29 binPath = os.environ['BREAKDANCER_BIN'] | 29 binPath = os.environ['BREAKDANCER_BIN'] |
| 163 cmd += ' -g %s ' % (args.bedFormat) | 163 cmd += ' -g %s ' % (args.bedFormat) |
| 164 if args.matePair: | 164 if args.matePair: |
| 165 cmd += ' -l ' | 165 cmd += ' -l ' |
| 166 if args.sortByLibrary: | 166 if args.sortByLibrary: |
| 167 cmd += ' -a ' | 167 cmd += ' -a ' |
| 168 if args.AFColumn: | 168 # if args.AFColumn: |
| 169 cmd += ' -h ' | 169 # cmd += ' -h ' |
| 170 execute(cmd, output=args.outputRawFile) | 170 execute(cmd, output=args.outputRawFile) |
| 171 | 171 |
| 172 # breakdancer2vcf | 172 # breakdancer2vcf |
| 173 if args.outputVcfFile: | 173 if args.outputVcfFile: |
| 174 cmd = "python %s -i %s -o %s" % (breakdancer2vcfPath, args.outputRawFile, args.outputVcfFile) | 174 cmd = "python %s -i %s -o %s" % (breakdancer2vcfPath, args.outputRawFile, args.outputVcfFile) |