Mercurial > repos > jeremie > breakdancer_bin

comparison breakdancer.py @ 13:62bf6aed1908 draft

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Uploaded
author jeremie
date Wed, 02 Jul 2014 10:15:33 -0400
parents c971e3f6de9f
children 2c3b8a1d8f4b
comparison
equal deleted inserted replaced
12:c220f4acef3f 13:62bf6aed1908
18 parser.add_argument('-b', dest='bufferSize', type=int, required=False, help='buffer size for building connection', default=100) 18 parser.add_argument('-b', dest='bufferSize', type=int, required=False, help='buffer size for building connection', default=100)
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='', 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']
150 cmd = 'perl %s %s' % (bam2cfgPath, args.inputBamFile) 150 cmd = 'perl %s %s' % (bam2cfgPath, 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)
156 if args.chromosome:
157 cmd += ' -o %s ' % (args.chromosome)
158 if args.onlyTrans:
159 cmd += ' -t '
160 if args.prefix:
161 cmd += ' -d %s ' % (args.prefix)
162 if args.bedFormat:
163 cmd += ' -g %s ' % (args.bedFormat)
164 if args.matePair:
165 cmd += ' -l '
166 if args.sortByLibrary:
167 cmd += ' -a '
168 if args.AFColumn:
169 cmd += ' -h '
155 execute(cmd, output=args.outputRawFile) 170 execute(cmd, output=args.outputRawFile)
156 171
157 # breakdancer2vcf 172 # breakdancer2vcf
158 if args.outputVcfFile: 173 if args.outputVcfFile:
159 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)