### narrowPeak2bed.r
### Ivory Blakley
### 5 November 2014

### usage: Rscript narrowPeak2bed.r prefix outDir
### prefix (required) sample name of narrowPeak file
### outDir (optional) a directory where the bed files should be saved

###################################################
### code chunk number 0: options and variables
###################################################
options(echo=TRUE)
date()
args=commandArgs(trailingOnly=T)
prefix=args[1]
prefix=gsub(".narrowPeak", "", prefix) #the prefix should not include the file extension
outDir=NULL
if (length(args)>1) {
  outDir = paste0(args[2], "/")
  outDir = gsub("//", "/", outDir)
}
print(prefix)

###################################################
### code chunk number 1: read in narrowPeak file
###################################################
fname.in=paste(prefix, "narrowPeak", sep=".")
peaks = read.table(fname.in)
fname.out=paste0(outDir, prefix, ".bed")

###################################################
### code chunk number 2: convert from narrowPeak format to bed format
###################################################
peaks$V4 = paste("spp", prefix, 1:nrow(peaks), sep="_")
peaks$V5 = peaks$V9
peaks$V7 = peaks$V10 + peaks$V2
peaks$V8 = peaks$V7 + 1
peaks = peaks[,1:8]
peaks$V9 = NA
peaks$V10 = 1
peaks$V11 = peaks$V3 - peaks$V2
peaks$V12 = 0

###################################################
### code chunk number 3: write out bed file
###################################################
write.table(peaks, file=fname.out, sep="\t", row.names=F, col.names=F, quote=F)

###################################################
###code chunk number 4: session Info
###################################################
sessionInfo()