R/learn_error_rates_functions.R

In welch16/microbiome.onglab: Wrapper functions to run dada2 with htCondor

#' function to add default parameters for learn error rates script
#'
#' @param param_name name of the parameter to look for
#' @param param_frame data.frame with the chosen parameters
#' @return the option in param_frame of the default value for
#'     \code{param_name}
#' @export
get_param_error_rates <- function(param_name, param_frame) {

  out <- param_frame[[param_name]]

  if (is.null(out)) {
    if (param_name %in% c("nbases")) out <- 1e8
  }else{
    if (class(out) == "list") {
      out <- out[[1]]
    }else{
      if (out == "Inf") out <- Inf
    }
  }
  out
}


#' generate the input to learn the error rates with condor
#'
#' @param error_queue_files vector with names of the file with the c(R1,R2)
#'  fastq files
#' @param error_prefixes vector with the names of the output error rates
#'  prefix for the c(R1,R2) files
#' @param error_param_file name of the file with the
#'  learned error rates parameters
#' @param error_outdir directory where the output is going to be saved
#' @param condor_file name of the file with condor instructions
#' @param batch_name string with the name of the batch
#' @param request_cores number of cpus per machine
#' @param request_mem number of GB required as memory
#' @export
condor_error_rates <- function(
  error_queue_files = c("", ""),
  error_prefixes = c("R1", "R2"),
  error_param_file = "",
  error_outdir = ".",
  condor_file = "./condor_error_rates",
  batch_name = "dada2_error_rates",
  request_cores = 4,
  request_mem = "4 GB") {

  warning_file(error_queue_files[1],
    "Need to define error rates R1 queue file")
  warning_file(error_queue_files[2],
    "Need to define error rates R2 queue file")
  warning_file(error_param_file, "Need to define error rates parameters file")

  rscript <- system("which Rscript", intern = TRUE)
  file_connection <- file(condor_file)

  writeLines(
    c(
      "universe         = vanilla",
      stringr::str_c("batch_name       = ", batch_name),
      stringr::str_c("executable       = ", rscript),
      stringr::str_c("args             = $(script_r) --rate_files $(rate_file)",
        "--R1_end $(end) --param_file $(param_file) --outprefix $(outprefix)",
        "--outdir $(outdir) --cores", request_cores, sep = " "),
      stringr::str_c("request_cpus     = ", request_cores),
      stringr::str_c("request_memory   = ", request_mem),
      "on_exit_hold     = (ExitBySignal == True) || (ExitCode != 0)",
      stringr::str_c("periodic_release = (NumJobStarts < 5) &&",
        "((CurrentTime - EnteredCurrentStatus) > 180)", sep = " "),
      stringr::str_c("script_r         = ",
        system.file("scripts/learn_error_rates.R",
        package = "microbiome.onglab")),
      stringr::str_c("param_file       = ", error_param_file),
      stringr::str_c("outdir           = ", error_outdir),
      stringr::str_c("output           = $(outdir)/out/",
        "dada2_error_rates_$(cluster).$(process)_$(outprefix).out"),
      stringr::str_c("error            = $(outdir)/err/",
        "dada2_error_rates_$(cluster).$(process)_$(outprefix).err"),
      stringr::str_c("log              = $(outdir)/log/",
        "dada2_error_rates_$(cluster).$(process)_$(outprefix).log"),
      stringr::str_c("rate_file        = ", error_queue_files[1]),
      stringr::str_c("outprefix        = ", error_prefixes[1]),
      stringr::str_c("end              = ", "TRUE"),
      "queue 1",
      stringr::str_c("rate_file        = ", error_queue_files[2]),
      stringr::str_c("outprefix        = ", error_prefixes[2]),
      stringr::str_c("end              = ", "FALSE"),
      "queue 1"), file_connection)

  close(file_connection)

}