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#' Start MiTCR directly from the package.
#'
#' @description
#' Start the MiTCR tools directly from the package with given settings.
#'
#' @param .input,.output Input and output files.
#' @param .file.path Path prepending to \code{.input} and \code{.output}.
#' If input and output is empty, but .file.path is specified,
#' than process all files from the folder \code{.file.path}
#' @param ... Specify input and output files and arguments
#' of the MITCR without first '-' to run it.
#' @param .mitcr.path Path to MiTCR .jar file.
#' @param .mem Volume of memory available to MiTCR.
#'
#' @details
#' Don't use spaces in paths!
#' You should have insalled JDK 1.7 to make it works.
#'
#' @examples
#' \dontrun{
#' # Equal to
#' # java -Xmx8g -jar ~/programs/mitcr.jar -pset flex
#' # -level 2 ~/data/raw/TwA1_B.fastq.gz ~/data/mitcr/TwA1_B.txt
#' startmitcr('raw/TwA1_B.fastq.gz', 'mitcr/TwA1_B.txt', .file.path = '~/data/',
#' pset = 'flex', level = 1, 'debug', .mitcr.path = '~/programs/', .mem = '8g')
#' }
startmitcr <- function (.input = '', .output = '', ..., .file.path = '', .mitcr.path = '~/programs/', .mem = '4g') {
if (.input == '') {
startmitcr(list.files(.file.path), paste0('/mitcr/', list.files(.file.path), '.txt'), ..., .file.path = .file.path, .mitcr.path = .mitcr.path, .mem = .mem)
}
else if (length(.input) > 1) {
for (i in 1:length(.input)) {
startmitcr(.input[i], .output[i], ..., .file.path = .file.path, .mitcr.path = .mitcr.path, .mem = .mem)
}
} else {
if (.file.path[length(.file.path)] != '/' && .file.path != '') {
.file.path <- paste(.file.path, '/', sep = '')
}
.input <- paste(.file.path, .input, sep = '')
.output <- paste(.file.path, .output, sep = '')
args <- list(...)
args.names <- names(args)
if (is.null(names(args))) {
args.names <- rep('', length(args))
}
args.str <- ''
for (i in 1:length(args)) {
if (args.names[i] == '') {
args.str <- paste(args.str, paste('-', args[[i]], sep = ''))
} else {
args.str <- paste(args.str, paste('-', args.names[i], sep = ''), args[[i]])
}
}
args.str <- paste(args.str, .input, .output)
system(paste('java',
paste('-Xmx', .mem, sep = ''),
'-jar',
paste(.mitcr.path, 'mitcr.jar', sep = ''),
args.str))
}
}
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