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)