#' run SICER on a set of file pairs
#'
#' @param projName name of the project
#' @param filePairs list of file pairs
#'
#' @export
runSICER <- function(projName,filePairs,bedDir,noControl=F,
pyMod="apps/python",
pyLib="libs/python2sitepkgs",
sicerPath="/scratch/pschofield/local/SICER",
outRoot="/scratch/pschofield/Projects",outPath="",
winsize=500,gapsize=4000,genome="GRCh37",esize="1E2",
insize=300,gencov=0.8){
outDir <- file.path(outRoot,projName,outPath)
lapply(names(filePairs),function(fpn){
if(noControl){
sicerCmd <- file.path(sicerPath,"SICER-rb.sh")
fileLine <- paste0(filePairs[[fpn]]["treat"], " ")
}else{
sicerCmd <- file.path(sicerPath,"SICER.sh")
fileLine <- paste0(filePairs[[fpn]]["treat"], " ", filePairs[[fpn]]["control"]," ")
}
script <- c(
paste0("module load ",pyMod),
paste0("module load ",pyLib),
paste0("mkdir -p ",file.path(outDir,fpn)),
paste0("cd ",file.path(outDir,fpn)),
paste0("sh ",sicerCmd," ", bedDir, " ", fileLine,
file.path(outDir,fpn)," ", genome," 1 ",winsize," ",insize," ",
gencov," ", gapsize," ",esize)
)
plib::runScript(jname=paste0("SICER_",fpn),jproj=projName,jscrp=script,nproc=2,mem="16Gb",
jdesc=paste0("Call peaks with SICER comparing ",
" treat = ",filePairs[[fpn]]["treat"],
" control = ",filePairs[[fpn]]["control"]))
})
}
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