Mercurial > repos > jeremie > breakdancer_bin
changeset 13:62bf6aed1908 draft
Uploaded
| author | jeremie |
|---|---|
| date | Wed, 02 Jul 2014 10:15:33 -0400 |
| parents | c220f4acef3f |
| children | 2c3b8a1d8f4b |
| files | breakdancer.py |
| diffstat | 1 files changed, 17 insertions(+), 2 deletions(-) [+] |
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--- a/breakdancer.py Wed Jul 02 10:03:53 2014 -0400 +++ b/breakdancer.py Wed Jul 02 10:15:33 2014 -0400 @@ -20,8 +20,8 @@ parser.add_argument('-d', dest='prefix', required=False, help='prefix of fastq files that SV supporting reads will be saved by library') parser.add_argument('-g', dest='bedFormat', required=False, help='dump SVs and supporting reads in BED format for GBrowse') parser.add_argument('-l', dest='matePair', required=False, help='analyze Illumina long insert (mate-pair) library') -# 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) -# parser.add_argument('-h', dest='', action='store_true', help='print out Allele Frequency column', default=False) +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) +parser.add_argument('-h', dest='AFColumn', action='store_true', help='print out Allele Frequency column', default=False) parser.add_argument('-y', dest='scoreFilter', type=int, required=False, help='output score filter', default=30) @@ -152,6 +152,21 @@ # breakdancer cmd = 'breakdancer-max %s' % (config) + 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) + if args.chromosome: + cmd += ' -o %s ' % (args.chromosome) + if args.onlyTrans: + cmd += ' -t ' + if args.prefix: + cmd += ' -d %s ' % (args.prefix) + if args.bedFormat: + cmd += ' -g %s ' % (args.bedFormat) + if args.matePair: + cmd += ' -l ' + if args.sortByLibrary: + cmd += ' -a ' + if args.AFColumn: + cmd += ' -h ' execute(cmd, output=args.outputRawFile) # breakdancer2vcf