R/CN_Seg_GC_filter_correctionRG.R

In whtns/varbintools: Sequence Based Copy Number Detection Using Variable Bin Lengths

#Segmentation of Profiles
#Author: Anna Unruh
#Last Updated: August 13, 2014

#' Title
#'
#' @param myStr
#'
#' @return
#' @export
#'
#' @examples
CN_Seg_GC_filter_correctionRG <- function(myStr) {
  set.seed(1239)
  theArgs <- NULL
  for( myStr in commandArgs() )
  {
    message("processing command arg:", myStr)
    if (length(grep("^-sample=", myStr))>0)
    {
      dataName <- substring(myStr, nchar("-sample=")+1)
    }
    if (length(grep("^-undoprune=", myStr))>0)
    {
      undo.prune <- as.numeric(substring(myStr, nchar("-undoprune=")+1) )
    }
    if (length(grep("^-alpha=", myStr))>0)
    {
      alpha <- as.numeric(substring(myStr, nchar("-alpha=")+1))
    }
    if (length(grep("^-chrominfo=", myStr))>0)
    {
      chrominfo <- substring(myStr, nchar("-chrominfo=")+1)
    }
    if (length(grep("^-makeFig=", myStr))>0)
    {
      makeFig <- substring(myStr, nchar("-makeFig=")+1)
    }
    if (length(grep("^-source1=", myStr))>0)
    {
      source1 <- substring(myStr, nchar("-source1=")+1)
      source(source1)
    }
    if (length(grep("^-source2=", myStr))>0)
    {
      source2 <- substring(myStr, nchar("-source2=")+1)
      source(source2)
    }
    if (length(grep("^-cpu=", myStr))>0)
    {
    cpu <- as.numeric(substring(myStr, nchar("-cpu=")+1))
    }
    if(length(grep("^-outdir=",myStr))>0)
    {
    outArg <- substring(myStr, nchar("-outdir=")+1)
    }
  }

  print (source1)
  print (source2)

  dataDir <- paste(outArg, "blvb", sep="/")
  outputDir <- paste(outArg, "final_result", sep="/")

  print(dataName)
  print(undo.prune)
  print(alpha)
  print(makeFig)
  print(outputDir)
  print(dataDir)
  print(chrominfo)
  if (!file.exists(outputDir)) {
    dir.create(outputDir)
  }

  CNProcessingCentromeres(dataName= dataName, dataDir = dataDir, outputDir = outputDir, centName=chrominfo,
                          alpha = alpha,undo.prune = undo.prune,
                          makeFig = makeFig,cpu=cpu)
}