R/tally_tmhs.R

In richelbilderbeek/tmhmm: Interface to TMHMM

#' Count the number of transmembrane helices in a topology
#' @inheritParams default_params_doc
#' @return a \link[tibble]{tibble} with the number of
#' TMHs per protein
#' @examples
#' if (is_tmhmm_installed()) {
#'   tally_tmhs(
#'     fasta_text_to_tibble(
#'       c(
#'         ">my_protein",
#'         "FASTASTIC"
#'       )
#'     )
#'   )
#' }
#' @export
tally_tmhs <- function(
  topology
) {
  tmhmm::check_topology(topology)
  tally <- tibble::tibble(
    name = topology$name,
    n_tmhs = NA
  )
  n_rows <- nrow(tally)
  for (i in seq_len(n_rows)) {
    t <- topology$topology[i]
    n_tmhs <- stringr::str_count(t, "(i|I|o|O)(m|M)")
    if (substring(t, 1, 1) == "m" || substring(t, 1, 1) == "M") {
      n_tmhs <- n_tmhs + 1
    }
    tally$n_tmhs[i] <- n_tmhs
  }
  tally
}