R/translatePattern.R

In LihuaJulieZhu/CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

#' translate pattern from IUPAC Extended Genetic Alphabet to regular expression
#' 
#' translate pattern containing the IUPAC nucleotide ambiguity codes to regular
#' expression. For example,Y->[C|T], R-> [A|G], S-> [G|C], W-> [A|T], K->
#' [T|U|G], M-> [A|C], B-> [C|G|T], D-> [A|G|T], H-> [A|C|T], V-> [A|C|G] and
#' N-> [A|C|T|G].
#' 
#' %% ~~ If necessary, more details than the description above ~~
#' 
#' @param pattern a character vector with the IUPAC nucleotide ambiguity codes
#' @return a character vector with the pattern represented as regular
#' expression
#' @note %% ~~further notes~~
#' @author Lihua Julie Zhu
#' @seealso %%
#' @references %% ~put references to the literature/web site here ~
#' @keywords misc
#' @examples
#' 
#' 	  pattern1 <- "AACCNWMK"
#' 	  translatePattern(pattern1)
#' @export
translatePattern <- function(pattern)
{
    pattern <- toupper(pattern)
    pattern <- gsub("Y", "[C|T]", pattern)
    pattern <- gsub("R", "[A|G]", pattern)
    pattern <- gsub("S", "[G|C]", pattern)
    pattern <- gsub("W", "[A|T]", pattern)
    pattern <- gsub("K", "[T|U|G]", pattern)
    pattern <- gsub("M", "[A|C]", pattern)
    pattern <- gsub("B", "[C|G|T]", pattern)
    pattern <- gsub("D", "[A|G|T]", pattern)
    pattern <- gsub("H", "[A|C|T]", pattern)
    pattern <- gsub("V", "[A|C|G]", pattern)
    pattern <- gsub("N", "[A|C|T|G]", pattern)	
    pattern
}