R/run_cobalt.R

In richelbilderbeek/cobaltr: Interface Io COBALT

#' Run COBALT
#'
#' Will stop if COBALT has an error.
#' @inheritParams default_params_doc
#' @return text of a FASTA file
#' @export
run_cobalt <- function(
  fasta_filename,
  cobalt_options = create_cobalt_options(),
  cobalt_folder = get_default_cobalt_folder()
) {
  testthat::expect_true(file.exists(fasta_filename))
  testthat::expect_true(
    cobalt_options$score_matrix_name %in% get_matrix_names()
  )
  cobaltr::check_cobalt_installation(cobalt_folder = cobalt_folder)
  cobalt_bin_filename <- file.path(cobalt_folder, "cobalt.linux")
  testthat::expect_true(file.exists(cobalt_bin_filename))
  testthat::expect_equal(0, unname(file.access(cobalt_bin_filename, 1)))


  testthat::expect_true(file.exists(cobalt_options$conserved_block_filename))
  testthat::expect_true(file.exists(cobalt_options$search_pattern_filename))
  testthat::expect_true(
    file.exists(cobalt_options$residue_frequencies_filename)
  )
  cmds <- c(
    normalizePath(cobalt_bin_filename, mustWork = TRUE),
    cobaltr::create_cobalt_args(
      fasta_filename = fasta_filename,
      cobalt_options = cobalt_options
    )
  )
  if (cobalt_options$verbose) {
    message("Running cmds: ", paste0(cmds, collapse = " "))
  }
  tryCatch(
    suppressWarnings({
      out <- system2(
        command = cmds[1],
        args = cmds[-1],
        stdout = TRUE,
        stderr = TRUE
      )
    }
    ),
    error = function(e) {
      stop(
        "Running 'system2' failed for arguments\n",
        paste0(cmds, collapse = " "), "\n",
        "Error message: ", e$message
      )
    }
  )
  if (is.null(attributes(out))) return(out)
  stop(
    "Error in 'run_cobalt'.\n",
    "COBALT error message: ", paste0(out, collapse = "\n"), "\n",
    "cmds: '", paste0(cmds, collapse = " "), "'.\n"
  )
}