R/bt.nuc.R

In PhanstielLab/bedtoolsr: Bedtools Wrapper

#' Profiles the nucleotide content of intervals in a fasta file.
#' 
#' @param fi <fasta>
#' @param bed <bed/gff/vcf>
#' @param s Profile the sequence according to strand.
#' 
#' @param seq Print the extracted sequence
#' 
#' @param pattern Report the number of times a user-defined sequence
#'     is observed (case-sensitive).
#' 
#' @param C Ignore case when matching -pattern. By defaulty, case matters.
#' 
#' @param fullHeader Use full fasta header.
#'   - By default, only the word before the first space or tab is used.
#' 
#' @param output Output filepath instead of returning output in R.
#' 
bt.nuc <- function(fi, bed, s = NULL, seq = NULL, pattern = NULL, C = NULL, fullHeader = NULL, output = NULL)
{
	# Required Inputs
	fi <- establishPaths(input=fi, name="fi", allowRobjects=TRUE)
	bed <- establishPaths(input=bed, name="bed", allowRobjects=TRUE)

	options <- ""

	# Options
	options <- createOptions(names=c("s", "seq", "pattern", "C", "fullHeader"), values=list(s, seq, pattern, C, fullHeader))

	# establish output file 
	tempfile <- tempfile("bedtoolsr", fileext=".txt")
	tempfile <- gsub("\\", "/", tempfile, fixed=TRUE)
	bedtools.path <- getOption("bedtools.path")
	if(!is.null(bedtools.path)) bedtools.path <- paste0(bedtools.path, "/")
	cmd <- paste0(bedtools.path, "bedtools nuc ", options, " -fi ", fi[[1]], " -bed ", bed[[1]], " > ", tempfile)
	if(.Platform$OS.type == "windows") shell(cmd) else system(cmd)
	if(!is.null(output)) {
		if(file.info(tempfile)$size > 0)
			file.copy(tempfile, output)
	} else {
		if(file.info(tempfile)$size > 0)
			results <- utils::read.table(tempfile, header=FALSE, sep="\t", quote='')
		else
			results <- data.frame()
	}

	# Delete temp files
	temp.files <- c(tempfile, fi[[2]], bed[[2]])
	deleteTempFiles(temp.files)

	if(is.null(output))
		return(results)
}