R/default_param_files.R

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

#' @importFrom jsonlite toJSON
#' @importFrom jsonlite fromJSON
#' @importFrom stringr str_replace_all str_c
NULL


move_file <- function(template, paramfile) {

  warning("recall: edit ", paramfile, " manually")
  params <- jsonlite::fromJSON(template)
  if (any(is.infinite(unlist(params)))) {
    inf_var <- which(is.infinite(unlist(params)))
    params[[names(inf_var)]] <- as.character(params[[names(inf_var)]])
  }
  readr::write_lines(jsonlite::toJSON(params), paramfile)

}

#' creates a default param file for the filter and trim process
#' @param paramfile name of the output json file with the
#'  filter and trim parameters
#' @export
dada2_param_filter_trim <- function(paramfile) {
  template <- system.file("template_params/filter_and_trim.json",
    package = "microbiome.onglab")
  move_file(template, paramfile)
}

#' creates a default param file for the learn error rates parameter
#' @param paramfile name of the output json file
#'  with the learn error rates parameters
#' @export
dada2_param_learn_error_rates <- function(paramfile) {
  template <- system.file("template_params/error_rates.json",
    package = "microbiome.onglab")
  move_file(template, paramfile)
}

#' creates a default param file for the merge pairs process
#' @param paramfile name of the output json file with the merge pairs parameters
#' @export
dada2_param_merge_pairs <- function(paramfile) {
  template <- system.file("template_params/merge_pairs.json",
    package = "microbiome.onglab")
  move_file(template, paramfile)
}

#' creates a default param file for the remove chimera process
#' @param paramfile name of the output json file with the
#'  remove chimera parameters
#' @export
dada2_param_remove_chimera <- function(paramfile) {
  template <- system.file("template_params/remove_chimera.json",
    package = "microbiome.onglab")
  move_file(template, paramfile)
}


#' copies all the parameter templates to a directory, and
#' uses a prefix to identify all
#' @param outdir directory where all the parameters are saved
#' @param prefix prefix for all the files
#' @export
dada2_param_copy_all <- function(outdir, prefix) {
  my_date <- stringr::str_replace_all(Sys.Date(), "-", "_")
  suffix <- stringr::str_c(my_date, ".json")

  dada2_param_filter_trim(
    file.path(outdir, stringr::str_c(prefix, "_filter_and_trim_", suffix)))
  dada2_param_learn_error_rates(
    file.path(outdir, stringr::str_c(prefix, "_learn_error_rates_", suffix)))
  dada2_param_merge_pairs(
    file.path(outdir, stringr::str_c(prefix, "_merge_pairs_", suffix)))
  dada2_param_remove_chimera(
    file.path(outdir, stringr::str_c(prefix, "_remove_chimera_", suffix)))
}

#' creates a default param file for the source tracker check
#' @param paramfile name of the output json file with the
#'  sourcetracker parameters
#' @export
sourcetracker_parameters <- function(paramfile) {
  template <- system.file("template_params/sourcetracker.json",
    package = "microbiome.onglab")
  move_file(template, paramfile)
}