R/aaa.R

In thomasp85/MSGFplus-release: An interface between R and MS-GF+

#' Create terminal compatible strings of input and output names
#' 
#' @param rawfile The location of the spectrum file
#' 
#' @param savename The location where the results should be saved
#' 
#' @return A character vector that is compatible with the OS that can be 
#' concatenated with the MS-GF+ call
#' 
#' @noRd
#' 
createFileCall <- function(rawfile, savename){
    if(Sys.info()["sysname"] == 'Windows'){
        rawfile <- paste0('\"', rawfile, '\"')
        savename <- paste0('\"', savename, '\"')
    } else {
        rawfile <- gsub(' ', '\\ ', rawfile, fixed=TRUE)
        savename <- gsub(' ', '\\ ', savename, fixed=TRUE)
    }
    paste0('-s ', rawfile, ' -o ', savename)
}

#' Download the MS-GF+ jar file
#' 
#' This function downloads and extracts MS-GF+ into the package directory
#' 
#' @noRd
#' 
getMSGFplus <- function() {
    zipFile <- tempfile()
    msgfLocation <- file.path(system.file(package='MSGFplus'), 'MSGFPlus')
    dir.create(msgfLocation)
    download.file('http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.20140630.zip', destfile = zipFile)
    unzip(zipfile = zipFile, exdir = msgfLocation)
}