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#' Find fasta files present in a folder
#'
#' @param dir Path to the directory which should be examined. If not provided,
#' the current working directory (as returned by \code{\link{getwd}}) is
#' used.
#' @param pattern Regular expression used by \code{\link{list.files}} to detect
#' the fasta files. The default is to list all files ending in ".fa",
#' ".fas", and ".fasta".
#' @param exclude Optional regular expression used to exclude some filenames
#' from the list of detected files.
#'
#' @return A vector with the full paths to the found files.
#'
#' @examples
#' # Get the directory containing the package example files
#' dir <- system.file("extdata", package = "concatipede")
#' # List the fasta files containing in that directory
#' find_fasta(dir)
#' # Exclude some files
#' find_fasta(dir, exclude = "COI")
#'
#' @export
find_fasta <- function(dir, pattern = "\\.fa$|\\.fas$|\\.fasta$", exclude) {
# Parse the dir argument
if (missing(dir)) {
dir <- getwd()
}
if (length(dir) != 1) {
stop("The `dir` argument must contain exactly one path.")
}
# Read files in the `dir` folder and create a list
files <- list.files(path = dir, pattern = pattern)
# Exclude the files matching the `exclude` pattern in their filename
if (!missing(exclude)){
to_keep <- !grepl(pattern = exclude, x = files)
files <- files[to_keep]
}
# Build the full paths to the found files
out <- file.path(dir, files)
# Return
out
}
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