R/script_helpers.R

In FrietzeLabUVM/peaksat: Peak saturation processing and analysis

get_str = function(psc){
  pow10 = max(3, -log10(psc@stat_value)+1)
  paste0(psc@stat, "_", formatC(psc@stat_value*10^pow10, width = pow10, format = "d", flag = "0"))
}

make_stat_arg = function(psc, out_dir = getOption("PS_OUTDIR", getwd())){
  str = get_str(psc)
  out = paste0(stat2flag[psc@stat], " ", psc@stat_value, " -o ", get_result_dir(psc), ifelse(psc@is_PE, " -pe", ""))
  names(out) = str
  out
}

get_submit_script = function(){
  system.file(package = "peaksat", "extdata/submit_subsample_peak.sh")
}

get_pool_script = function(){
  system.file(package = "peaksat", "extdata/run_pool_bams.sh")
}

get_run_script = function(){
  system.file(package = "peaksat", "extdata/run_subsample_peak.sh")
}

.check_path = function(cmd, opt){
  no_file = "____NO_FILE____"
  default_path = suppressWarnings(system(paste("which", cmd), intern = TRUE))
  if(length(default_path) == 0) default_path = no_file
  option_path = getOption(opt)
  if(is.null(option_path)) option_path = no_file

  if(option_path == no_file){
    sel_path = default_path
  }else{
    sel_path = option_path
  }
  if(!file.exists(sel_path)){
    stop("Could not locate macs2 via $PATH or R option ", opt, ".")
  }
  sel_path
}

get_macs2_path = function(){
  .check_path("macs2", "PS_MACS2_PATH")
}

get_samtools_path = function(){
  .check_path("samtools", "PS_SAMTOOLS_PATH")
}

#' get_result_dir
#'
#' @param psc
#'
#' @return
#' @export
#'
#' @examples
get_result_dir = function(psc){
  str = get_str(psc)
  file.path(psc@out_dir, paste0("results_", str))
}

get_pool_dir = function(psc){
  str = get_str(psc)
  file.path(psc@out_dir, paste0("pooled_bams"))
}

get_submit_command = function(job_scheduler = valid_job_schedulers[1]){
  if(job_scheduler == "SGE"){
    "qsub -cwd"
  }else if(job_scheduler == "SLURM"){
    "sbatch"
  }else if(job_scheduler == "bash"){
    "bash"
  }else{
    stop("job_scheduler must be one of SGE, SLURM, or bash was ", job_scheduler)
  }
}