R/download_ic50s_lut.R

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

#' Download a lookup table for IC50 predictions of epitopes
#'
#' Download a lookup table for IC50 predictions of epitopes.
#' For the human reference proteome, each table is approx 300 megabytes.
#'
#' The scripts that created these look-up tables are at
#' by \url{https://github.com/richelbilderbeek/bbbq_article_issue_167}
#' @inheritParams default_params_doc
#' @return the local filename
#' @export
download_ic50s_lut <- function(
  target_name,
  haplotype,
  peptide_length,
  ic50_prediction_tool,
  verbose = TRUE
) {
  bbbq::check_target_name(target_name)
  bbbq::check_ic50_prediction_tool(ic50_prediction_tool)
  bbbq::check_haplotype(
    haplotype = haplotype,
    ic50_prediction_tool = ic50_prediction_tool
  )
  csv_filename <- paste0(
    target_name, "_",
    peptide_length, "_",
    stringr::str_replace_all(haplotype, "[:|/\\*]", "_"),
    "_ic50_", ic50_prediction_tool, ".csv"
  )
  local_filename <- file.path(
    rappdirs::user_data_dir(appname = "bbbq"),
    csv_filename
  )
  url <- paste0("http://richelbilderbeek.nl/", csv_filename)
  if (verbose) {
    message(
      "Starting big 300 Mb download (if target is human). \n",
      "If the URL cannot be found, it may be that the file is absent. \n",
      "See https://github.com/richelbilderbeek/bbbq_article_issue_167 \n",
      "to create and upload a LUT \n",
      "csv_filename: ", csv_filename, " \n",
      "local_filename: ", local_filename, " \n",
      "URL: ", url
    )
  }
  dir.create(
    path = dirname(local_filename),
    showWarnings = FALSE,
    recursive = TRUE
  )
  old_timeout <- getOption("timeout")
  options(timeout = 6000)
  utils::download.file(
    url = url,
    destfile = local_filename,
    quiet = TRUE
  )
  options(timeout = old_timeout)
  local_filename
}