R/bt.sort.R

In PhanstielLab/bedtoolsr: Bedtools Wrapper

#' Sorts a feature file in various and useful ways.
#' 
#' @param i <bed/gff/vcf>
#' @param sizeA Sort by feature size in ascending order.
#' 
#' @param sizeD Sort by feature size in descending order.
#' 
#' @param chrThenSizeA Sort by chrom (asc), then feature size (asc).
#' 
#' @param chrThenSizeD Sort by chrom (asc), then feature size (desc).
#' 
#' @param chrThenScoreA Sort by chrom (asc), then score (asc).
#' 
#' @param chrThenScoreD Sort by chrom (asc), then score (desc).
#' 
#' @param g Sort according to the chromosomes declared in "genome.txt"
#' 
#' @param faidx Sort according to the chromosomes declared in "names.txt"
#' 
#' @param header Print the header from the A file prior to results.
#' 
#' @param output Output filepath instead of returning output in R.
#' 
bt.sort <- function(i, sizeA = NULL, sizeD = NULL, chrThenSizeA = NULL, chrThenSizeD = NULL, chrThenScoreA = NULL, chrThenScoreD = NULL, g = NULL, faidx = NULL, header = NULL, output = NULL)
{
	# Required Inputs
	i <- establishPaths(input=i, name="i", allowRobjects=TRUE)

	options <- ""

	# Options
	options <- createOptions(names=c("sizeA", "sizeD", "chrThenSizeA", "chrThenSizeD", "chrThenScoreA", "chrThenScoreD", "g", "faidx", "header"), values=list(sizeA, sizeD, chrThenSizeA, chrThenSizeD, chrThenScoreA, chrThenScoreD, g, faidx, header))

	# 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 sort ", options, " -i ", i[[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, i[[2]])
	deleteTempFiles(temp.files)

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