R/convert_seq_into_org.R

In avidaR: A Computational Biologist’s Toolkit To Get Data From 'avidaDB'

#' Converts a genome instruction sequence into a digital organism file
#'
#' @description Converts a genome instruction sequence into a digital organism
#' file.
#'
#' @param genome_seq String of letters.
#' @param inst_set Name of the instruction set. It must be one of the
#' following: `heads` (default), `heads-sex`, or `transsmt`. The names
#' correspond to the instruction set configuration files (e.g.,
#' `instset-heads.cfg` for `heads`).
#' @param save Logical value (TRUE/FALSE) indicating whether the output should
#' or should not be saved to a file ("FALSE" by default).
#' @param file_name String of characters representing the name of the file
#' without any extension ("organism.org" by default).
#' @param save_path String of characters representing the name of the folder
#' where the digital organism file will be saved.
#' @param format String of characters representing the format of the file
#' ("org" by default).
#' @param silent Logical value (TRUE/FALSE) to show/hide messages
#' ("FALSE" by default).
#'
#' @return Data frame. Column names: "instruction".
#'
#' @examples
#'
#' # Create triplestore object
#' avidaDB <- triplestore_access$new()
#'
#' # Set access options
#' avidaDB$set_access_options(
#'   url = "https://graphdb.fortunalab.org",
#'   user = "public_avida",
#'   password = "public_avida",
#'   repository = "avidaDB_test"
#' )
#'
#' sequence <- get_genome_seq_from_genome_id(
#'   genome_id = 1,
#'   triplestore = avidaDB
#' )$genome_seq[[1]]
#'
#' convert_seq_into_org(genome_seq = sequence)
#'
#' @export
convert_seq_into_org <- function(genome_seq, inst_set = "heads", save = FALSE, file_name = NULL, save_path = getwd(), format = "org", silent = FALSE) {
  # verify output path
  if (isTRUE(save)) {
    if (!dir.exists(save_path)) {
      dir.create(save_path)
    }
  }

  # split genome_seq
  if (is.null(genome_seq))
    return(invisible(NULL))
  
  seq <- as.data.frame(strsplit(genome_seq, "")[[1]])

  # rename column
  colnames(seq)[[1]] <- "letter"

  # join
  org <- dplyr::inner_join(seq, instruction_set(inst_set = inst_set), by = "letter") %>% dplyr::select("instruction")

  # save to file
  if (isTRUE(save)) {
    if (is.null(file_name)) {
      file_name <- "genome"
    }

    output_file <- paste0(save_path, "/", file_name, paste0(".", format))

    readr::write_csv(org, file = output_file, col_names = FALSE)

    if (isFALSE(silent)) {
      message(paste0("output saved to ", output_file))
    }
  }

  # return org
  return(org)
}