R/isPatternUnique.R

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

isPatternUnique <- function(seq, patterns)
{
   if (missing(seq) || missing(patterns) || length(seq) == 0 || length(patterns) ==0)
		IsUnique = "NA"
   else
   {
	   IsUnique <- character(length(patterns))
	   seq <- as.character(seq)
	   for (j in 1:length(patterns))
	   {
		   pattern <- patterns[[j]]
		   revpattern <- reverseComplement(pattern)
		   pattern = as.character(pattern)[[1]]
		   if (nchar(pattern) == 0)
		   {
				IsUnique[j] = "NA"
				next
		   }
		   pattern = translatePattern(pattern)
		   revpattern = as.character(revpattern)[[1]]
		   revpattern = translatePattern(revpattern)
		   res.plus <- as.numeric(gregexpr(pattern, seq,
			  perl = TRUE,fixed = FALSE,ignore.case = TRUE)[[1]])
		   n.plus <- length(res.plus[res.plus >0])
		   if (revpattern != pattern)
		   {
		      res.minus <- as.numeric(gregexpr(revpattern, seq,
			     perl = TRUE,fixed = FALSE,ignore.case = TRUE)[[1]])
			  n.minus <- length(res.minus[res.minus >0])
		   }
		   else
			  n.minus <- 0
		   if (n.plus + n.minus > 1)
			   IsUnique[j] <- "No"
		   else if (n.plus + n.minus == 1)
			   IsUnique[j] <- "Yes"
		   else
		       IsUnique[j] <- "NotFound"
	   }
   }
   IsUnique
}