R/check_annotation_file_completeness.R

In drostlab/homologr: Homology inference across multiple species

#' @title Check whether an annotation file contains outlier lines
#' @description Some annotation files include lines with character lengths greater than 65000. This causes problems when trying to import such annotation files into R using \code{\link[rtracklayer]{import}}.
#' To overcome this issue, this function screens for such lines
#' in a given annotation file and removes these lines so that
#' \code{\link[rtracklayer]{import}} can handle the file.
#' @param annotation_file a file path tp the annotation file.
#' @param remove_annotation_outliers shall outlier lines be removed from the input \code{annotation_file}?
#' If yes, then the initial \code{annotation_file} will be overwritten and the removed outlier lines will be stored at \code{\link{tempdir}}
#' for further exploration.
#' @author Hajk-Georg Drost
#' @examples \dontrun{
#' # download an example annotation file from NCBI RefSeq
#' Ath_path <- biomartr::getGFF(organism = "Arabidopsis thaliana")
#' # run annotation file check on the downloaded file
#' check_annotation_file_completeness(Ath_path)
#' # several outlier lines were detected, thus we re-run the
#' # function using 'remove_annotation_outliers = TRUE'
#' # to remove the outliers and overwrite the file
#' check_annotation_file_completeness(Ath_path, remove_annotation_outliers = TRUE)
#' }
#' @export

check_annotation_file_completeness <- function(annotation_file, remove_annotation_outliers = FALSE) {

  if (!file.exists(annotation_file))
    stop("The file '", annotation_file, "' does not seem to exist. Please provide a valid path to the annotation file.", call. = FALSE)

  if (suppressWarnings(require("benchmarkme"))) {
    ram <- check_ram()
    available_ram <- ram - ((ram / 100) * 20)
    annotation_file_size <-
      file.info(annotation_file)$size / 1000000000

    if (annotation_file_size > available_ram)
      stop(
        "The size of the annotation file '",
        annotation_file,
        " exceeds the available RAM (memory) of your computer. Please try running this function with more memory.",
        call. = FALSE
      )
  }

  message("Importing '", annotation_file, "' ...")

  import_annotation <- readr::read_lines(annotation_file)
  outlier_lines <- which(nchar(import_annotation) > 65000)

  if (length(outlier_lines) == 0)
    return(annotation_file)

  if (length(outlier_lines) > 0 & !remove_annotation_outliers) {
    warning("Your annotation file '", annotation_file, "' contains ", length(outlier_lines), " lines that have more than 65000 characters.",
            "This will cause the annotation import function to fail importing the annotation file into R.",
            " If you wish to remove the outlier lines and overwrite the existing annotation file then re-run this function and specify 'remove_annotation_outliers = TRUE'. A file with the removed lines will then be stored in the temp directory for you to explore.")
    return(annotation_file)
  }

  if (length(outlier_lines) > 0 & remove_annotation_outliers) {
    message("Reading annotation file '", annotation_file, "' and removing all outlier lines with number of characters greater 65000 ...")
    message("Overwriting '", annotation_file, "' with removed outlier lines ...")

    file_extension_check <- unlist(stringr::str_split(annotation_file, "[.]"))
    if (file_extension_check[length(file_extension_check)] == "gz"){
      message("Unzipping file ", annotation_file,"' ...")
      R.utils::gunzip(annotation_file, destname = paste0(file_extension_check[1],".", file_extension_check[2]))
    }

    readr::write_lines(import_annotation[-outlier_lines], paste0(file_extension_check[1],".", file_extension_check[2]))

    message("The new annotation file was created and has been stored at '", paste0(file_extension_check[1],".", file_extension_check[2]),"'.")

    outlier_output_file <- file.path(tempdir(), paste0(basename(annotation_file),"_outlier_lines.txt"))

    readr::write_lines(import_annotation[outlier_lines], outlier_output_file)
    message("The outlier lines were stored in a separate file to explore at '", outlier_output_file, "'.")
    return(paste0(file_extension_check[1],".", file_extension_check[2]))
  }

}