R/seq_random.R

In Koohoko/SynMut: SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

#' Generate \code{n} random DNA sequnces of length \code{m}
#'
#' Generate \code{n} random DNA sequnces of length \code{m}, optional exclude
#' stop codons.
#'
#' @param n the number of the output sequence(s).
#' @param m the length of the ouput sequence(s). Eighter a fixed number or a
#'   vector of different numbers.
#' @param no.stop.codon Default FALSE. If TRUE, the stop codons in the frame 1
#'   would be substituted to another random codon.
#' @param ... ...
#'
#' @return a DNAStringSet object
#' @exportMethod seq_random
#'
#' @examples
#' seq_random(n = 1, m = 99)
#' seq_random(n = 10, m = 30)
#' seq_random(n = 10, m = 1:10)
#' seq.nsc <- seq_random(n = 10, m = 100, no.stop.codon = TRUE)
#' get_cu(seq.nsc)
#' @name seq_random
#' @import Biostrings
#' @rdname seq_random-methods
setGeneric(
    name = "seq_random",
    def = function(n = 1, m, no.stop.codon = FALSE,
                   ...) standardGeneric("seq_random")
)

#' @rdname seq_random-methods
setMethod(
    f = "seq_random",
    signature = signature(n = "numeric", m = "numeric"),
    definition = function(n, m, no.stop.codon) {
        check.m.length <- length(m) == 1
        if (check.m.length) {
            tmp <- vapply(seq_len(n), function(x) {
                paste0(sample(
                    x = c("a", "t", "g", "c"),
                    size = m,
                    replace = TRUE
                ), collapse = "")
            }, character(1))
        } else {
            tmp <- mapply(function(x, y) {
                paste0(sample(
                    x = c("a", "t", "g", "c"),
                    size = y,
                    replace = TRUE
                ), collapse = "")
            }, seq_len(n), m)
        }
        if (no.stop.codon) {
            stop.codons <- c("taa", "tga", "tag")
            ok.codons <- setdiff(mkAllStrings(c("a", "t", "c", "g"), 3),
                                 stop.codons)
            tmp <- vapply(tmp, function(x) {
                sst <- strsplit(x, "")[[1]]
                if (length(sst) %% 3 != 0) {
                    mut.length <- floor(length(sst) / 3) * 3
                    sst.mut <- sst[seq_len(mut.length)]
                    sst.tail <- sst[(mut.length + 1):length(sst)]
                } else{
                    sst.mut <- sst
                    sst.tail <- ""
                }
                codons <- paste0(sst.mut[c(TRUE, FALSE, FALSE)],
                    sst.mut[c(FALSE, TRUE, FALSE)],
                    sst.mut[c(FALSE, FALSE, TRUE)])
                stop.id <- which(codons %in% stop.codons)
                if (length(stop.id) > 0) {
                    codons[stop.id] <- vapply(seq_along(stop.id), function(x) {
                        sample(ok.codons, size = 1)
                    }, character(1))
                    return(paste0(
                        paste0(codons, collapse = ""),
                        sst.tail,
                        collapse = ""
                    ))
                } else {
                    return(x)
                }
            }, character(1), USE.NAMES = FALSE)
        }
        DNAStringSet(tmp)
    }
)