Mercurial > repos > jeremie > breakdancer_bin
comparison breakdancer.py @ 19:b83483e9b1e8 draft
Uploaded
| author | jeremie |
|---|---|
| date | Mon, 07 Jul 2014 04:04:13 -0400 |
| parents | 0e73928aa0ca |
| children | 96e938d6904e |
comparison
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| 18:0e73928aa0ca | 19:b83483e9b1e8 |
|---|---|
| 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'] |
| 30 | 30 |
| 31 bam2cfgPath = binPath+"/bam2cfg.pl" | 31 # bam2cfgPath = binPath+"/bam2cfg.pl" |
| 32 breakdancer2vcfPath = binPath+"/breakdancer2vcf.py" | 32 # breakdancer2vcfPath = binPath+"/breakdancer2vcf.py" |
| 33 | 33 |
| 34 | 34 |
| 35 # def bam2cfg(args, tempDir): | 35 # def bam2cfg(args, tempDir): |
| 36 # config = tempDir+"/breakdancer_config" | 36 # config = tempDir+"/breakdancer_config" |
| 37 # cmd = 'perl %s %s' % (bam2cfgPath, args.inputBamFile) | 37 # cmd = 'perl %s %s' % (bam2cfgPath, args.inputBamFile) |
| 145 # breakdancer(args, config) | 145 # breakdancer(args, config) |
| 146 # breakdancer2vcf(args) | 146 # breakdancer2vcf(args) |
| 147 | 147 |
| 148 # bam2cfg | 148 # bam2cfg |
| 149 config = tempDir+"/breakdancer_config" | 149 config = tempDir+"/breakdancer_config" |
| 150 cmd = 'perl %s %s' % (bam2cfgPath, args.inputBamFile) | 150 cmd = 'bam2cfg.pl %s' % (args.inputBamFile) |
| 151 execute(cmd, output=config) | 151 execute(cmd, output=config) |
| 152 | 152 |
| 153 # breakdancer | 153 # breakdancer |
| 154 cmd = 'breakdancer-max %s' % (config) | 154 cmd = 'breakdancer-max %s' % (config) |
| 155 cmd += ' -s %d -c %d -m %d -q %d -r %d -x %d -b %d -y %d' % (args.minLength, args.cutoff, args.maxSvSize, args.minMapQuality, args.minReadDepth, args.maxHaploidCov, args.bufferSize, args.scoreFilter) | 155 cmd += ' -s %d -c %d -m %d -q %d -r %d -x %d -b %d -y %d' % (args.minLength, args.cutoff, args.maxSvSize, args.minMapQuality, args.minReadDepth, args.maxHaploidCov, args.bufferSize, args.scoreFilter) |
| 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 = "breakdancer2vcf.py -i %s -o %s" % (args.outputRawFile, args.outputVcfFile) |
| 175 execute(cmd) | 175 execute(cmd) |
| 176 | 176 |
| 177 # quelques tests | 177 # quelques tests |
| 178 # verifier que les fichiers de sorties ne sont pas vides | 178 # verifier que les fichiers de sorties ne sont pas vides |
| 179 check(args.outputRawFile) | 179 check(args.outputRawFile) |