R/systemdf.R

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

# == title
# Wrapper of system calls in which input and output are all table-like files
# 
# == param
# -cmd     shell command
# -envir   environment where to look for variables encoded in ``cmd``
# -verbose whether print messages
#
# == details
# This function (system + data frame) provides a convinient way to invoke
# system calls in R. Since most of system calls expect tables as inputs and outputs, 
# `systemdf` does following things step by step:
#
# - use backtick to mark variables which are data frames or other variables which can be converted
#    to data frames by `base::as.data.frame`
# - extract data frames
# - write data frames into temporary files 
# - replace variables names with paths that correspond to temporary files
# - make the system call 
# - finally send back the output by piping back to R
#
# A simple example is as follows:
#
#     bed1 = circlize::generateRandomBed(nr = 1000)
#     bed2 = circlize::generateRandomBed(nr = 1000)
#     df = systemdf("bedtools closest -a `bed1` -b `bed2` | awk '$1==\"chr1\"'")
#
# == value
# A data frame. Sometimes column names may be lost.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# if(Sys.info()["sysname"] \%in\% c("Linux", "Darwin")) {
#     df = data.frame(x = sample(1:10, 10), y = sample(11:20, 10))
#     systemdf("sort -k1,1n `df`")
# }
systemdf = function(cmd, envir = parent.frame(), verbose = FALSE) {
	
	op = qq.options(READ.ONLY = FALSE)
	qq.options(code.pattern = "@\\{CODE\\}")
	
	tmpdir = tempdir()
	if(length(grep("^.*`.+?`.*$", cmd))) {
		re = gregexpr("`.+?`", cmd)[[1]]
		gr = character(length(re))
		file = character(length(re))
		cmd2 = cmd
		matched_name = NULL
		for(i in seq_along(re)) {
			gr[i] = substr(cmd, as.numeric(re)[i]+1, as.numeric(re)[i] + attr(re, "match.length")[i] - 2)
			if(gr[i] %in% matched_name) {
				next
			}
			matched_name = c(matched_name, gr[i])
			grv = eval(parse(text = gr[i]), envir = envir)
			file[i] = paste(tempfile(fileext = ".bed", tmpdir = tmpdir), sep = "/")
			# just in case `grv` is a GRanges object
			write.table(as.data.frame(grv), file = file[i], sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
			if(verbose) message(qq("writing @{gr[i]} into temporary file: @{file[i]}\n"))
			cmd2 = gsub(qq("`@{gr[i]}`"), file[i], cmd2, fixed = TRUE)
		}
		if(verbose) message(qq("Command: @{cmd2}\n"))
		eo = try(tb <- read.table(pipe(cmd2), sep = "\t", stringsAsFactors = FALSE, flush = TRUE, comment.char = ""))
		file = file[!is.null(file)]
		file = file[file != ""]
		file.remove(file)

		if(class(eo) == "try-error") {
			stop(eo)
		}
	} else {
		tb <- read.table(pipe(cmd), sep = "\t", stringsAsFactors = FALSE, flush = TRUE, comment.char = "")
	}

	# if(class(eo) == "try-error") {
	# 	# empty pipe, it is not an error
	# 	# if(grepl("no lines available in input", eo)) {
	# 	# 	tb = data.frame(character(0), numeric(0), numeric(0))
	# 	# } else {
	# 		stop(msg)
	# 	# }
	# }
	
	qq.options(op)
	return(tb)
}