R/helper_functions.R

In kstagaman/sharpton-lab-metaGTx.processing: Sharpton Lab Metagenomic & Metatranscriptomic Processing

#' @name helper.functions
#' @title Helper functions
#' @description Functions for printing help, tarring, zipping, and moving files.
#' @aliases print.tool.help
#' @aliases tgz.directories
#' @aliases remove.directories
#' @aliases gzip.files
#' @aliases gunzip.files
#' @aliases move.files
#' @param tool character; name of the appropriate tool, e.g. "kneaddata" or "humann".
#' @param match.pattern character; pattern to match desired files and directories. Default NULL
#' @param location character; path to directory with files/directories you want to manipulate.
#' @param move.from character; path to directory you want to move files/directories from.
#' @param move.to character; path to directory you want to move files/directories to.
#' @param n.cores integer; if 1, will run serially, otherwise will extract in parallel utilzing up to the number of cores specified. Default is 1.
#' @seealso \code{\link{system}}, \code{\link{generate.full.commands}}, \code{\link{generate.tool.commands}}

#' @rdname helper.functions
#' @export

show.tool.help <- function(tool) {
  system(paste(tool, "--help"))
}

#' @rdname helper.functions
#' @export

tgz.directories <- function(location, match.pattern = NULL, n.cores = 1) {
  require(magrittr)
  require(stringr)
  if (is.null(match.pattern)) {
    target.dirs <- location
  } else {
    target.dirs <- list.dirs(path = location, full.names = TRUE) %>%
      str_subset(match.pattern)
  }
  if (length(target.dirs) > 1) {
    if (n.cores == 1) {
      for (target.dir in target.dirs) {
        tar(tarfile = paste0(target.dir, ".tgz"), files = target.dir, compression = "gzip")
      }
    } else {
      require(doParallel)
      require(foreach)
      cl <- parallel::makeCluster(n.cores, type = "FORK")
      doParallel::registerDoParallel(cl, n.cores)
      par.loop <- foreach::foreach(target.dir = target.dirs) %dopar% {
        tar(tarfile = paste0(target.dir, ".tgz"), files = target.dir, compression = "gzip")
      } %>% try(silent = T)
      parallel::stopCluster(cl)
      if ("try-error" %in% class(par.loop)) {
        cat(par.loop, sep = "\n")
      }
    }
  } else if (length(target.dirs) == 0) {
    rlang::inform("No directories detected, nothing done.")
  } else {
    tar(tarfile = paste0(target.dirs, ".tgz"), files = target.dirs, compression = "gzip")
  }
}

#' @rdname helper.functions
#' @export

remove.directories <- function(location, match.pattern = NULL, n.cores = 1) {
  require(magrittr)
  require(stringr)
  if (is.null(match.pattern)) {
    target.dirs <- location
  } else {
    target.dirs <- list.dirs(path = location, full.names = TRUE) %>%
      str_subset(match.pattern)
  }
  if (length(target.dirs) == 0) {
    rlang::inform("No directories detected, nothing done.")
  } else {
    if (n.cores == 1) {
      for (target.dir in target.dirs) {
        file.remove(list.files(path = target.dir, full.names = T, recursive = T))
        file.remove(target.dir)
      }
    } else {
      require(doParallel)
      require(foreach)
      cl <- parallel::makeCluster(n.cores, type = "FORK")
      doParallel::registerDoParallel(cl, n.cores)
      par.loop <- foreach::foreach(target.dir = target.dirs) %dopar% {
        file.remove(list.files(path = target.dir, full.names = T, recursive = T))
        file.remove(target.dir)
      } %>% try(silent = T)
      parallel::stopCluster(cl)
      if ("try-error" %in% class(par.loop)) {
        cat(par.loop, sep = "\n")
      }
    }
  }
}

#' @rdname helper.functions
#' @export

gzip.files <- function(location, match.pattern = NULL, n.cores = 1) {
  files <- list.files(path = location, pattern = match.pattern, full.names = T)
  if (n.cores == 1) {
    for (file in files) {
      cmd <- paste("gzip -v", file)
      system(cmd)
    }
  } else {
    require(doParallel)
    require(foreach)
    cl <- parallel::makeCluster(n.cores, type = "FORK")
    doParallel::registerDoParallel(cl, n.cores)
    par.loop <- foreach::foreach(file = files) %dopar% {
      cmd <- paste("gzip -v", file)
      system(cmd)
    } %>% try(silent = T)
    parallel::stopCluster(cl)
    if ("try-error" %in% class(par.loop)) {
      cat(par.loop, sep = "\n")
    }
  }
}

#' @rdname helper.functions
#' @export

gunzip.files <- function(location, match.pattern = NULL, n.cores = 1) {
  files <- list.files(path = location, pattern = match.pattern, full.names = T)
  if (n.cores == 1) {
    for (file in files) {
      cmd <- paste("gunzip -v", file)
      system(cmd)
    }
  } else {
    require(doParallel)
    require(foreach)
    cl <- parallel::makeCluster(n.cores, type = "FORK")
    doParallel::registerDoParallel(cl, n.cores)
    par.loop <- foreach::foreach(file = files) %dopar% {
      cmd <- paste("gunzip -v", file)
      system(cmd)
    } %>% try(silent = T)
    parallel::stopCluster(cl)
    if ("try-error" %in% class(par.loop)) {
      cat(par.loop, sep = "\n")
    }
  }
}

#' @rdname helper.functions
#' @export

move.files <- function(move.from, move.to, match.pattern = NULL, n.cores = 1) {
  require(magrittr)
  if (is.null(match.pattern)) {
    copy.res <- file.copy(from = move.from, to = move.to) %>% try()
    if (!{"try-error" %in% class(copy.res)}) { file.remove(move.from) }
  } else {
    files <- list.files(path = move.from, pattern = match.pattern, full.names = T)
    if (n.cores == 1) {
      for (file in files) {
        copy.res <- file.copy(from = file, to = move.to) %>% try()
        if (!{"try-error" %in% class(copy.res)}) { file.remove(file) }
      }
    } else {
      require(doParallel)
      require(foreach)
      cl <- parallel::makeCluster(n.cores, type = "FORK")
      doParallel::registerDoParallel(cl, n.cores)
      par.loop <- foreach::foreach(file = files) %dopar% {
        copy.res <- file.copy(from = file, to = move.to) %>% try()
        if (!{"try-error" %in% class(copy.res)}) { file.remove(file) }
      } %>% try(silent = T)
      parallel::stopCluster(cl)
      if ("try-error" %in% class(par.loop)) {
        cat(par.loop, sep = "\n")
      }
    }
  }
}