R/kmr_response.R

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

#' kmr_response
#'
#' k should be an odd number.
#' In case of fastq files the file can also be in compressed format
#' (e.g. *.fastq.tar.gz).
#' This parameter will be inferred from the file name, if not set.
#'
#' @param fastx a fastq or fasta formatted file
#' @param k kmer size. One value or a sequence of values
#' @param fmt type of input file, fasta = f, fasta with multiple lines = m,
#'    fastq = q
#' @param ci cutoff value for min k
#' @importFrom utils setTxtProgressBar txtProgressBar
#' @return data.frame with results
#' @family kmer_help
#' @examples 
#' if (interactive()) {
#'   fa <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
#'     package = "kmerize"
#'   )
#'   k <- as.integer(seq(1, 3, 2))
#' 
#' 
#'   res <- kmr_response(fa, k, fmt = "q")
#' }
#' @export
kmr_response <- function(fastx,
                         k = c(5, 7, 9, 11),
                         fmt = NULL,
                         ci = 0) {
  if (!file.exists(fastx)) stop("Data file path does not exist!")

  msg <- "k must be a positive integer > 0 and < 256"
  if (any(is.null(k))) stop(msg)
  if (any(is.na(k))) stop(msg)
  if (any(is.character(k))) stop(msg)
  if (any(is.logical(k))) stop(msg)
  if (any(is.double(k))) stop(msg)
  if (any(k <= 0)) stop(msg)
  if (any(k > 255)) stop(msg)

  if (is.null(fmt)) {
    is_fastq <- detect_str(fastx, "f[ast]*[q\\.]{1}")
    fmt <- ifelse(is_fastq, "q", "m")
  }
  if (!fmt %in% c("a", "m", "q")) stop("fmt must be one of NULL, a, m, q!")

  res <- calc_kmer_summary(fastx, k = k[1], f = fmt, ci = ci)

  if (length(k) < 2) {
    return(res)
  }

  n <- length(k)

  
  pb <- txtProgressBar(min = 1, max = n, title = "Scanning Genomic Response:", 
                       width = n)
  for (i in 2:n) {
    try({
      res <- rbind(res, calc_kmer_summary(fastx, k = k[i], f = fmt, ci = ci))
      chk <- res$unique[i] / res$total[i]      
    })
    
    setTxtProgressBar(pb, i)
    if (chk > 0.9999) break
  }
  close(pb)
  return(res)
}