R/write.fasta.R

In helixcn/seqRFLP: Simulation and visualization of restriction enzyme cutting pattern from DNA sequences.

write.fasta <-
function(sequences, file = NULL){
    if(is.null(file)){
        stop("You have to specify a file name.")
    }
    if(length(sequences) == 1) { 
        if(is.numeric(as.numeric(names(sequences)))){
            sequences = c(paste(">seq", names(sequences),sep = ""), sequences)
            class(sequences) <- "fasta"
	  	 }
    }
    if(length(sequences) >= 2) {
        if(!inherits(sequences, "fasta")){ 
	        stop("Make sure the data you want to save is a \"fasta\" object.") 
	  	  }
	    if(!any(grepl(">", sequences))){
	  	    index <- seq(1,length(sequences),by = 2)
            seqnames <- paste(">", sequences[index], sep = "")
	  	    sequences[index] <- seqnames
	  	  }
	 
	 }
    writeLines(sequences, file)
}