R/utils.R

In toddknutson/toddr: A collection of functions for RNAseq, scRNAseq, variant calling, and other bioinformatics methods.

#' Write out current R session information
#'
#' The function writes our R session info, with a time and date stamped into the filename. The function will overwrite previous files with updated timestamp.
#'
#' @param out_file_prefix File path, including a filename prefix if desired.
#'
#' @return None
#'
#' @examples
#' \dontrun{
#' out_file_prefix <- "code_out/dir/050_"
#' write_session_info(out_file_prefix)
#' }
#'
#' @export
write_session_info <- function(out_file_prefix) {
	out_dir <- dirname(as.character(out_file_prefix))

	# If previous session info is present, delete.
	if (length(grep("session_info", list.files(out_dir))) > 0) { 
	invisible(file.remove(grep("session_info", list.files(out_dir, full.names = TRUE), value = TRUE)))
	}
	# Write out session info
	writeLines(capture.output(devtools::session_info()), paste0(out_file_prefix, "session_info_", gsub(" |:", "_", Sys.time()), ".txt"))
	print(Sys.time())
}






#' Release memory
#'
#' Run after deleting large objects to initiate garbage collection multiple times.
#' [Reference](https://stackoverflow.com/a/1467334/2367748)

#' @param n Integer, Number of times to run garbage collection. Default is 10.
#'
#' @return None
#'
#' @examples
#' \dontrun{
#' clean_mem()
#' }
#'
#' @export
clean_mem <- function(n = 10) {
    for (i in 1:n) gc()
}









#' Make an output directory using scratch location 
#'
#' @param out_dir String, path to output directory
#' @param use_scratch Logical. Should the output dir be created on scratch, with a symlink to the scratch location placed at out_dir?
#'
#' @return None
#'
#' @examples
#' \dontrun{
#' mkoutdir()
#' }
#'
#' @export
mkoutdir <- function(out_dir, use_scratch = FALSE) {
    if (use_scratch == "TRUE") {
        out_dir_scratch <- glue("/scratch.global/knut0297_scratch{out_dir}")

        if (!dir.exists(glue("{out_dir_scratch}"))) {dir.create(glue("{out_dir_scratch}"), recursive = TRUE)}

        # If an old symlink or exists, remove it
        system(glue("if [ -L {out_dir} ]; then rm -rf {out_dir}; fi"))
        system(glue("if [ -d {out_dir} ]; then rm -rf {out_dir}; fi"))
        file.symlink(glue("{out_dir_scratch}"), dirname(glue("{out_dir}")))
        setwd(glue("{out_dir}"))
    } else {
        # If an old symlink or dir exists, remove it
        system(glue("if [ -L {out_dir} ]; then rm -rf {out_dir}; fi"))
        system(glue("if [ -d {out_dir} ]; then rm -rf {out_dir}; fi"))
        if (!dir.exists(glue("{out_dir}"))) {dir.create(glue("{out_dir}"), recursive = TRUE)}
        setwd(glue("{out_dir}"))
    }
}