--- a/frag4feature.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-library(optparse)
-library(msPurity)
-library(xcms)
-print(sessionInfo())
-
-xset_pa_filename_fix <- function(opt, pa, xset=NULL){
-
-
-  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
-    # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables 
-    # needs to be done due to Galaxy moving the files around and screwing up any links to files
-
-    filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
-    filepaths <- filepaths[filepaths != ""]
-    new_names <- basename(filepaths)
-
-    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
-    galaxy_names <- galaxy_names[galaxy_names != ""]
-
-    nsave <- names(pa@fileList)
-    old_filenames  <- basename(pa@fileList)
- 
-    pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
-    names(pa@fileList) <- nsave
-
-    pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
-    pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
-  }
-  print(pa@fileList)
-
-  if(!is.null(xset)){
-
-    print(xset@filepaths)
-
-    if(!all(basename(pa@fileList)==basename(xset@filepaths))){
-       if(!all(names(pa@fileList)==basename(xset@filepaths))){
-          print('FILELISTS DO NOT MATCH')
-          message('FILELISTS DO NOT MATCH')
-          quit(status = 1)
-       }else{
-          xset@filepaths <- unname(pa@fileList)
-       }
-   }
- }
-
-  return(list(pa, xset))
-}
-
-
-option_list <- list(
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option("--pa", type="character"),
-  make_option("--xset", type="character"),
-  make_option("--ppm", default=10),
-  make_option("--plim", default=0.0),
-  make_option("--convert2RawRT", action="store_true"),
-  make_option("--mostIntense", action="store_true"),
-  make_option("--createDB", action="store_true"),
-  make_option("--cores", default=4),
-  make_option("--mzML_files", type="character"),
-  make_option("--galaxy_names", type="character"),
-  make_option("--grp_peaklist", type="character"),
-  make_option("--use_group", action="store_true")
-)
-
-# store options
-opt<- parse_args(OptionParser(option_list=option_list))
-
-print(opt)
-
-loadRData <- function(rdata_path, name){
-#loads an RData file, and returns the named xset object if it is there
-    load(rdata_path)
-    return(get(ls()[ls() %in% name]))
-}
-
-# This function retrieve a xset like object
-#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
-getxcmsSetObject <- function(xobject) {
-    # XCMS 1.x
-    if (class(xobject) == "xcmsSet")
-        return (xobject)
-    # XCMS 3.x
-    if (class(xobject) == "XCMSnExp") {
-        # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
-        sampclass(xset) <- xset@phenoData$sample_group
-        return (xset)
-    }
-}
-
-# Requires
-pa <- loadRData(opt$pa, 'pa')
-xset <- loadRData(opt$xset, c('xset','xdata'))
-xset <- getxcmsSetObject(xset)
-
-pa@cores <- opt$cores
-
-print(pa@fileList)
-print(xset@filepaths)
-
-if(is.null(opt$mostIntense)){
-    mostIntense = FALSE
-}else{
-    mostIntense = TRUE
-}
-
-if(is.null(opt$convert2RawRT)){
-    convert2RawRT = FALSE
-}else{
-    convert2RawRT= TRUE
-}
-
-if(is.null(opt$createDB)){
-    createDB = FALSE
-}else{
-    createDB = TRUE
-}
-
-if(is.null(opt$use_group)){
-    fix <- xset_pa_filename_fix(opt, pa, xset)
-    pa <- fix[[1]]
-    xset <- fix[[2]]
-    use_group=FALSE
-}else{
-    # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
-    print('use_group')
-    fix <- xset_pa_filename_fix(opt, pa)
-    pa <- fix[[1]]
-    use_group=TRUE
-}
-
-
-if(is.null(opt$grp_peaklist)){
-    grp_peaklist = NA
-}else{
-    grp_peaklist = opt$grp_peaklist
-}
-
-print(pa@fileList)
-print(names(pa@fileList))
-print(xset@filepaths)
-saveRDS(pa, 'test_pa.rds')
-
-pa <- msPurity::frag4feature(pa=pa, xset=xset, ppm=opt$ppm, plim=opt$plim,
-                            intense=opt$mostIntense, convert2RawRT=convert2RawRT,
-                            db_name='alldata.sqlite', out_dir=opt$out_dir, grp_peaklist=grp_peaklist,
-                             create_db=createDB, use_group=use_group)
-
-save(pa, file=file.path(opt$out_dir, 'frag4feature.RData'))
-
-print(head(pa@grped_df))
-write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature.tsv'), row.names=FALSE, sep='\t')