R/comp.R

In seqinr: Biological Sequences Retrieval and Analysis

##########################################
# complements a sequence
###########################################

comp <- function(seq, forceToLower = TRUE, ambiguous = FALSE){

  if(all(seq %in% LETTERS)){
  	  isUpper <- TRUE
  	} else {
  	  isUpper <- FALSE
  	}

  	seq <- tolower(seq)

  result <- as.vector(n2s((3-s2n(seq))))
  #
  # More work is required if ambiguous bases are taken into account
  #

  if(ambiguous){
    result[which(seq == "b")] <- "v"
    result[which(seq == "d")] <- "h"
    result[which(seq == "h")] <- "d"
    result[which(seq == "k")] <- "m"
    result[which(seq == "m")] <- "k"
    result[which(seq == "s")] <- "s"
    result[which(seq == "v")] <- "b"
    result[which(seq == "w")] <- "w"
    result[which(seq == "n")] <- "n"
    result[which(seq == "y")] <- "r"
    result[which(seq == "r")] <- "y"
  }

  # Checking for N in the sequence, thanks to Jeremy Shearman.
  # Now this is done only with ambigous option, thanks to Suzuki Haruo
  # result[which(seq == "n")] <- "n"


  if(isUpper && !forceToLower){
  	  result <- toupper(result)
  	}
  return(result)
}