library (SynthEx)
suppressPackageStartupMessages(library(optparse))
option_list <- list (
make_option (c("-t","--tumor"),
default="/input/tumor.bed",
help="The Tumor BED counts file [default %default]"),
make_option (c("-n","--normal"),
default="/input/normal.bed",
help="The normal BED counts file [default %default]"),
make_option (c("-s","--samplename"),
default="SAMPLE",
help="the sample name[default %default]"),
make_option (c("-G","--genotype"),
default= NULL,
help="The Tumor genotype file [default %default]"),
make_option (c("-o","--outdir"),
default=".",
help="the output directory [default %default]"),
make_option (c("-T","--tmpdir"),
default="/tmp",
help="the temporary directory [default %default]"),
make_option (c("-k","--numnormals"),
default="4",
help="the number of normals to use for normalization [default %default]"),
make_option (c("-b","--bin"),
default=50000,
help="The bin size for the genome windows[default %default]"),
# make_option (c("-","--")
# default="",
# help=""),
make_option (c("-d","--debug"),
action="store_true",
default=FALSE,
help="Enable Debugging options")
)
opt <- parse_args(OptionParser(#usage= "usage: %prog [options]",
option_list=option_list)
)
bin.size = opt$bin
intersectBed.dir <- system("which intersectBed", intern=TRUE)
data ("TargetAnnotations")
working.dir <- opt$tmpdir
result.dir <- opt$outdir
normal.file <- opt$normal
tumor.file <- opt$tumor
sample.name <- opt$samplename
genotype.file <- opt$genotype
numnormals <- opt$numnormals
debug <- opt$debug
if (debug) {
cat (paste("bin.size:", bin.size,"\n","tumor.file:",tumor.file,"\nnormal.file:",normal.file,"\ngenotype.file: ",genotype.file,"\n"))
}
if (debug) {cat ("Generating target Bins\n")}
targetAnnotateBins <- createTargetBins(TargetAnnotations$Target,bin.size=bin.size)
if (debug) {cat ("Generating centromere Bins\n")}
centromereBins <- createCentromereBins(bin.size=bin.size)
cat ("------Running SynthExPipeline------\n")
Segfrompipe <- SynthExPipeline (tumor.file,normal.file,
bin.size=bin.size,
intersectBed.dir,
genotype.file=genotype.file,
result.dir,working.dir,
prefix=sample.name,
verbose=debug,
K=numnormals)
cat ("------Finished running SynthExPipeline------\n")
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