R/complement.R

In insect: Informatic Sequence Classification Trees

#' Reverse complement DNA in character string format.
#'
#' This function reverse complements a DNA sequence or vector of DNA
#'   sequences that are stored as character strings.
#'
#' @param z a vector of DNA sequences in upper case character string format.
#' @return a vector of DNA sequences as upper case character strings.
#' @details This function accepts only DNA sequences in concatenated character
#'   string format, see \code{\link[ape]{complement}} in the \code{\link[ape]{ape}}
#'   package for "DNAbin" input objects, and \code{\link[seqinr]{comp}} in the
#'   \code{\link[seqinr]{seqinr}} package for when the input object is a character
#'   vector.
#' @author Shaun Wilkinson
#' @examples rc("TATTG")
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rc <- function(z){
  rc1 <- function(zz){
    s <- strsplit(zz, split = "")[[1]]
    s <- rev(s)
    dchars <- strsplit("ACGTMRWSYKVHDBNI", split = "")[[1]]
    comps <- strsplit("TGCAKYWSRMBDHVNI", split = "")[[1]]
    s <- s[s %in% dchars] # remove spaces etc
    s <- dchars[match(s, comps)]
    s <- paste0(s, collapse = "")
    return(s)
  }
  z <- toupper(z)
  tmpnames <- names(z)
  res <- unname(sapply(z, rc1))
  if(!is.null(attr(z, "quality"))){
    strev <- function(x) sapply(lapply(lapply(unname(x), charToRaw), rev), rawToChar)
    attr(res, "quality") <- unname(sapply(attr(z, "quality"), strev))
  }
  names(res) <- tmpnames
  return(res)
}
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