R/run_tmhmm_to_file.R

In richelbilderbeek/tmhmm: Interface to TMHMM

#' Creates a FASTA-like file, that has the locations
#' of the amino acids.
#' @inheritParams default_params_doc
#' @examples
#' if (is_tmhmm_installed()) {
#'
#'   # Write results to a temporary file
#'   tmhmm_filename <- tempfile()
#'   run_tmhmm_to_file(
#'     fasta_filename = system.file(
#'       "extdata", "tmhmm.fasta", package = "tmhmm"
#'     ),
#'     tmhmm_filename = tmhmm_filename
#'   )
#'
#'   # Result is written to 'tmhmm_filename', cleaning up
#'   file.remove(tmhmm_filename)
#' }
#' @export
run_tmhmm_to_file <- function(
  fasta_filename,
  tmhmm_filename,
  one_protein_fasta_filename = tempfile(fileext = ".fasta"),
  folder_name = get_default_tmhmm_folder()

) {
  writeLines(
    text = tmhmm::run_tmhmm(
      fasta_filename = fasta_filename,
      one_protein_fasta_filename = one_protein_fasta_filename,
      folder_name  = folder_name
    ),
    con = tmhmm_filename
  )
}