readfile2=opts.readFile2, indexfile=opts.indexFile, indexes=opts.index) else: demultiplex(readfile=opts.readFile1, readfile2=opts.readFile2, indexfile=opts.indexFile, indexfile2=opts.indexFile2, indexes=opts.index) else: demultiplex(readfile=opts.readFile1, indexfile=opts.indexFile, indexes=opts.index) utils_parser = subparsers.add_parser('utils') utils_subparsers = utils_parser.add_subparsers(help="General utilities") demultiplex_parser = utils_subparsers.add_parser( 'demultiplex', help="Demultiplex a set of fastq files") demultiplex_parser.add_argument('-1', '--readFile1', help="read1 filename") demultiplex_parser.add_argument('-2', '--readFile2', help="read2 filename") demultiplex_parser.add_argument('-i', '--indexFile', help="index Filename") demultiplex_parser.add_argument('-j', '--indexFile2', help="index Filename") demultiplex_parser.add_argument( '-x', '--index', type=str, action='append', help= "The indexes, one per index or comma-separated pairs for dual-barcode indexing" )
def RNAcounts(opts): if(opts.vcf): f = open(opts.vcf,mode='r',errors='ignore') v = vcf.Reader(f) else: v = vcf.Reader(sys.stdin) if(opts.outfile): outfile = open(opts.outfile,'w') else: outfile = sys.stdout bamfile = pysam.Samfile(opts.bamfile) seqtools.seqvcf.countBases(v,outfile,bamfile) outfile.close() varscan_parser = subparsers.add_parser('vcf') varscan_subparsers = varscan_parser.add_subparsers(help="vcf subcommands") meltVcf_parser = varscan_subparsers.add_parser('melt', help="Melt a VCF file into a tab-delimited text file with special treatment of snpEff annotation") meltVcf_parser.add_argument('-f','--vcf', help='Filename of VCF file [default=stdin]') meltVcf_parser.add_argument('-o','--outfile', help='Filename of VCF file [default=stdout]') meltVcf_parser.add_argument('-s','--samplename',default=None, help='Sample name to include in first column of output [default=None]') meltVcf_parser.add_argument('-i','--includeHeader',action='store_true', help='Include VCF header in the output; useful for including definitions of columns') meltVcf_parser.add_argument('-g','--includeGenotypes',action='store_true', help='Include genotypes for each sample (XXX.GT in column header) if available') meltVcf_parser.set_defaults(func=meltVcf)
def RNAcounts(opts): if (opts.vcf): f = open(opts.vcf, mode='r', errors='ignore') v = vcf.Reader(f) else: v = vcf.Reader(sys.stdin) if (opts.outfile): outfile = open(opts.outfile, 'w') else: outfile = sys.stdout bamfile = pysam.Samfile(opts.bamfile) seqtools.seqvcf.countBases(v, outfile, bamfile) outfile.close() varscan_parser = subparsers.add_parser('vcf') varscan_subparsers = varscan_parser.add_subparsers(help="vcf subcommands") meltVcf_parser = varscan_subparsers.add_parser( 'melt', help= "Melt a VCF file into a tab-delimited text file with special treatment of snpEff annotation" ) meltVcf_parser.add_argument('-f', '--vcf', help='Filename of VCF file [default=stdin]') meltVcf_parser.add_argument('-o', '--outfile', help='Filename of VCF file [default=stdout]') meltVcf_parser.add_argument( '-s', '--samplename',
import sys import argparse from seqtools.main import subparsers from seqtools.varscan import fixVarscanVcfFile def fixVcf(opts): if (not opts.varscan): varscan = fixVarscanVcfFile(sys.stdin) else: varscan = fixVarscanVcfFile(opts.varscan) for line in varscan: print(line) varscan_parser = subparsers.add_parser('varscan') varscan_subparsers = varscan_parser.add_subparsers(help="VarScan subcommands") fixVcf_parser = varscan_subparsers.add_parser( 'fixVcf', help="Fix the FREQ field and the ALT field in varscan VCF output") fixVcf_parser.add_argument('-f', '--varscan', default=sys.stdin, type=argparse.FileType('r'), help='Filename of varscan VCF file [default=stdin]') fixVcf_parser.set_defaults(func=fixVcf)
import sys import argparse from seqtools.main import subparsers from seqtools.varscan import fixVarscanVcfFile def fixVcf(opts): if(not opts.varscan): varscan = fixVarscanVcfFile(sys.stdin) else: varscan = fixVarscanVcfFile(opts.varscan) for line in varscan: print(line) varscan_parser = subparsers.add_parser('varscan') varscan_subparsers = varscan_parser.add_subparsers(help="VarScan subcommands") fixVcf_parser = varscan_subparsers.add_parser('fixVcf', help="Fix the FREQ field and the ALT field in varscan VCF output") fixVcf_parser.add_argument('-f','--varscan',default=sys.stdin, type=argparse.FileType('r'), help='Filename of varscan VCF file [default=stdin]') fixVcf_parser.set_defaults(func=fixVcf)
from seqtools.main import subparsers import seqtools.strucvar import seqtools.strucvar.crest def crestToBed(opts): with open(opts.predSVfile,'r') as f: for line in f: if(opts.samplename is not None): print(seqtools.strucvar.crest.crestLineToBedLines(line,opts.samplename)) else: print(seqtools.strucvar.crest.crestLineToBedLines(line)) strucvar_parser = subparsers.add_parser('strucvar') strucvar_subparsers = strucvar_parser.add_subparsers(help="Structural variation subcommands") crestToBed_parser = strucvar_subparsers.add_parser('crestToBed', help="convert CREST output to two BED records per line") crestToBed_parser.add_argument('-s','--samplename',default=None,type=str, help="sample information to add to the BED 'name' column") crestToBed_parser.add_argument('predSVfile',help="The name of the CREST predSV.txt file") crestToBed_parser.set_defaults(func=crestToBed)
demultiplex(readfile = opts.readFile1, readfile2 = opts.readFile2, indexfile = opts.indexFile, indexes = opts.index) else: demultiplex(readfile = opts.readFile1, readfile2 = opts.readFile2, indexfile = opts.indexFile, indexfile2 = opts.indexFile2, indexes = opts.index) else: demultiplex(readfile = opts.readFile1, indexfile = opts.indexFile, indexes = opts.index) utils_parser = subparsers.add_parser('utils') utils_subparsers = utils_parser.add_subparsers(help="General utilities") demultiplex_parser = utils_subparsers.add_parser('demultiplex', help="Demultiplex a set of fastq files") demultiplex_parser.add_argument('-1','--readFile1', help="read1 filename") demultiplex_parser.add_argument('-2','--readFile2', help="read2 filename") demultiplex_parser.add_argument('-i','--indexFile', help="index Filename") demultiplex_parser.add_argument('-j','--indexFile2', help="index Filename") demultiplex_parser.add_argument('-x','--index',type=str,action='append', help="The indexes, one per index or comma-separated pairs for dual-barcode indexing") demultiplex_parser.set_defaults(func=demultiplex_setup)