R/bt.annotate.R

In PhanstielLab/bedtoolsr: Bedtools Wrapper

#' Annotates the depth & breadth of coverage of features from mult. files
#' on the intervals in -i.
#' 
#' @param i <bed/gff/vcf>
#' @param files FILE1 FILE2..FILEn
#' @param names A list of names (one / file) to describe each file in -i.
#'   These names will be printed as a header line.
#' 
#' @param counts Report the count of features in each file that overlap -i.
#'   - Default is to report the fraction of -i covered by each file.
#' 
#' @param both Report the counts followed by the  percent coverage.
#'   - Default is to report the fraction of -i covered by each file.
#' 
#' @param s Require same strandedness.  That is, only counts overlaps
#'   on the _same_ strand.
#'   - By default, overlaps are counted without respect to strand.
#' 
#' @param S Require different strandedness.  That is, only count overlaps
#'   on the _opposite_ strand.
#'   - By default, overlaps are counted without respect to strand.
#' 
#' @param output Output filepath instead of returning output in R.
#' 
bt.annotate <- function(i, files, names = NULL, counts = NULL, both = NULL, s = NULL, S = NULL, output = NULL)
{
	# Required Inputs
	i <- establishPaths(input=i, name="i", allowRobjects=TRUE)
	files <- establishPaths(input=files, name="files", allowRobjects=TRUE)

	options <- ""

	# Options
	options <- createOptions(names=c("names", "counts", "both", "s", "S"), values=list(names, counts, both, s, S))

	# 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 annotate ", options, " -i ", i[[1]], " -files ", files[[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]], files[[2]])
	deleteTempFiles(temp.files)

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