R/runCapR.R

In nearBynding: Discern RNA structure proximal to protein binding

#' @title runCapR
#'
#' @description Runs CapR
#'
#' @param in_file An .fa file like from ExtractTranscriptomeSequence that is a
#' list of fasta sequences to be folded. Required
#' @param out_file Name of the CapR output file of nucleotide folding
#' probabilities. Default is in_file prefix.out
#' @param max_dist Integer of maximum distance between folded nucleotides in
#' sequences. Recommeded between 50 and 100, with higher values yielding
#' potentially more accurate results but dramatically increasing run time.
#' Default 100.
#'
#' @return generates CapR outfile
#'
#' @examples
#'
#' ## make dummy file
#' write_fasta(paste0(sample(c("A", "T", "G", "C"), 50, replace = TRUE),
#'                   collapse = ""),
#'            "test",
#'            "test.fa")
#' ## run CapR
#' runCapR("test.fa")
#'
#' @export

runCapR <- function(in_file,
                    out_file = NA,
                    max_dist = 100) {
    if (is.na(out_file)) {
        out_file <- paste0(substr(in_file, 0, nchar(in_file) - 2), "out")
    }
    if(.is_CapR_installed()){
        .CapR_run(in_file, out_file, max_dist)
    }else{return("Please install CapR and place in working PATH")}
}