R/kmr_count.R

In c5sire/kmerize: K-Mer Tools for Building Databases

#' kmr_count
#'
#' Count kmers.
#'
#' A few parameters of the kmc3 counting program are not supported:
#'   p signature length; default is 9.
#'  sf Number of threads for FASTQ reading. Default is 4.
#'  sp Number of threads for splitting. Default is 4.
#'  sr Number of threads for second stage. Default is 4
#'
#' @note Counts kmers up to a maximum of size of k = 255. Uses kmc3 in the
#'   backend on Windows, Linux, and
#'  Mac. The parameter lists corresponds to the list of options of kmc3.
#'
#' @param in_files a name of a single file, a vector of file names, or a
#'   directory containing files.
#' @param out_file name of the output file
#' @param k kmer size; default is 11.
#' @param m RAM memory size; default is 12.
#' @param sm strict memory mode; default is FALSE.
#' @param f format of input files; options: a fasta, m multiple fasta, q fastq.
#'    Default is a.
#' @param ci minimum occurrence of kmers; default is 2.
#' @param cx maximum occurrence of kmers: default is 1e9.
#' @param cs maximum size of counter; default is 255.
#' @param b do not use canonical transformation of kmers. Default is FALSE.
#' @param r turn on RAM only. Default is FALSE.
#' @param n Number of bins. Default is 255.
#' @param t Number of threads. Default is all available number of CPUs.
#' @param v Use verbose mode. Default is FALSE.
#'
#' @return out_file
#' @author Reinhard Simon
#' @references Kokot M, Dlugosz M, Deorowicz S. KMC 3: counting and manipulating
#'    k-mer statistics. Bioinformatics. 2017 Sep 1;33(17):2759-61.
#'
#' @export
#' @family kmer_core
#' @examples
#' if (interactive()) {
#'   fa <- system.file("testdata/phix174_m-pe_w_err_5k_30q.fastq.gz",
#'     package = "kmerize"
#'   )
#'   k <- 13
#'   out_file <- file.path(tempdir(), "phwei11")
#'   kmerize:::kmr_count(fa, out_file, k = k, f = "q")
#' }
kmr_count <- function(in_files,
                      out_file,
                      k = 11,
                      m = 12, # RAM
                      sm = FALSE, # strict memory mode
                      f = "a", # format: fa, fm , fq
                      ci = 2, # minim k occurrence
                      cx = 1e9, # max k occ
                      cs = 255, # max counter
                      b = FALSE, # turn canonical transformation off
                      r = FALSE, # turn on RAM only
                      n = 255, # number of bins
                      t = parallel::detectCores(), # number of cores
                      v = FALSE # verbose mode; use to turn off
) {
  # first check if in_files are in a directory
  if (is_dir(in_files)) {
    in_files <- list.files(in_files, full.names = TRUE)
  }

  # check if files exists

  in_files <- sapply(in_files, get_safe_path)
  out_file <- get_safe_path(out_file)
  out_dir <- dirname(out_file)
  if (!dir.exists(out_dir)) dir.create(out_dir, recursive = TRUE)
  tmd <- tempdir()

  if (!all(file.exists(in_files))) {
    message(paste0(in_files[!file.exists(in_files)], "\n"))
    stop("The listed file paths do not exist.")
  }

  if (length(in_files) > 1) {
    tmp_in_files <- file.path(tmd, "_tmp_kmc3_infiles.txt")
    if (file.exists(tmp_in_files)) unlink(tmp_in_files)
    writeLines(in_files, tmp_in_files)
    in_files <- paste0("@", tmp_in_files)
  }

  # TODO check parameter values

  # if more than input file use a temp archive to store the list and change
  # in_files to pointer
  tmp <- file.path(tmd, "_kmer") %>% get_safe_path()

  if (!dir.exists(tmp)) dir.create(tmp, recursive = TRUE)

  params <- " -k%i -m%i -f%s -ci%i -cx%i -cs%i -n%i -t%i"
  params <- sprintf(params, k, m, f, ci, cx, cs, n, t)

  if (sm) params <- paste0(params, " -sm", sm)

  if (sm) params <- paste(params, "-sm")
  if (b) params <- paste(params, "-b")
  if (r && !sm) params <- paste(params, "-r")
  if (v) params <- paste(params, "-v")

  cmd <- paste0(kmc(), params)
  cmd <- paste0(cmd, " ", in_files[1], " ", out_file, " ", tmp)

  system(cmd, wait = TRUE, show.output.on.console = FALSE)

  return(path.expand(out_file))
}