--- a/anticipated_purity_lcms.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,188 +0,0 @@
-library(msPurity)
-library(optparse)
-print(sessionInfo())
-
-option_list <- list(
-  make_option(c("--xset_path"), type="character"),
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option(c("--mzML_path"), type="character"),
-  make_option("--minOffset", default=0.5),
-  make_option("--maxOffset", default=0.5),
-  make_option("--ilim", default=0.05),
-  make_option("--iwNorm", default="none", type="character"),
-  make_option("--exclude_isotopes", action="store_true"),
-  make_option("--isotope_matrix", type="character"),
-  make_option("--purityType", default="purityFWHMmedian"),
-  make_option("--singleFile", default=0),
-  make_option("--cores", default=4),
-  make_option("--xgroups", type="character"),
-  make_option("--rdata_name", default='xset'),
-  make_option("--camera_xcms", default='xset'),
-  make_option("--files", type="character"),
-  make_option("--galaxy_files", type="character"),
-  make_option("--choose_class", type="character"),
-  make_option("--ignore_files", type="character"),
-  make_option("--rtraw_columns",  action="store_true")
-)
-
-# store options
-opt<- parse_args(OptionParser(option_list=option_list))
-
-print(sessionInfo())
-print(opt)
-
-if (!is.null(opt$xgroups)){
-    xgroups = as.numeric(strsplit(opt$xgroups, ',')[[1]])
-}else{
-    xgroups = NULL
-}
-
-
-
-print(xgroups)
-
-if (!is.null(opt$remove_nas)){
-  df <- df[!is.na(df$mz),]
-}
-
-if (is.null(opt$isotope_matrix)){
-    im <- NULL
-}else{
-    im <- read.table(opt$isotope_matrix,
-                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
-}
-
-if (is.null(opt$exclude_isotopes)){
-    isotopes <- FALSE
-}else{
-    isotopes <- TRUE
-}
-
-if (is.null(opt$rtraw_columns)){
-    rtraw_columns <- FALSE
-}else{
-    rtraw_columns <- TRUE
-}
-
-loadRData <- function(rdata_path, xset_name){
-#loads an RData file, and returns the named xset object if it is there
-    load(rdata_path)
-    print(ls())
-    return(get(ls()[ls() == xset_name]))
-}
-
-target_obj <- loadRData(opt$xset_path, opt$rdata_name)
-
-if (opt$camera_xcms=='camera'){
-    xset <- target_obj@xcmsSet
-}else{
-    xset <- target_obj
-}
-
-print(xset)
-
-minOffset = as.numeric(opt$minOffset)
-maxOffset = as.numeric(opt$maxOffset)
-
-
-if (opt$iwNorm=='none'){
-    iwNorm = FALSE
-    iwNormFun = NULL
-}else if (opt$iwNorm=='gauss'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='rcosine'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
-}else if (opt$iwNorm=='QE5'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormQE.5()
-}
-
-print(xset@filepaths)
-
-
-
-if (!is.null(opt$files)){
-  updated_filepaths <- trimws(strsplit(opt$files, ',')[[1]])
-  updated_filepaths <- updated_filepaths[updated_filepaths != ""]
-  print(updated_filepaths)
-  updated_filenames = basename(updated_filepaths)
-  original_filenames = basename(xset@filepaths)
-  update_idx = match(updated_filenames, original_filenames)
-
-    if (!is.null(opt$galaxy_files)){
-        galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]])
-        galaxy_files <- galaxy_files[galaxy_files != ""]
-        xset@filepaths <- galaxy_files[update_idx]
-    }else{
-        xset@filepaths <- updated_filepaths[update_idx]
-    }
-}
-
-if (!is.null(opt$choose_class)){
-  classes <- trimws(strsplit(opt$choose_class, ',')[[1]])
-
-
-  ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
-
-  print('choose class')
-  print(ignore_files_class)
-}else{
-  ignore_files_class <- NA
-}
-
-if (!is.null(opt$ignore_files)){
-  ignore_files_string <- trimws(strsplit(opt$ignore_files, ',')[[1]])
-  filenames <- rownames(xset@phenoData)
-  ignore_files <- which(filenames %in% ignore_files_string)
-
-  ignore_files <- unique(c(ignore_files, ignore_files_class))
-  ignore_files <- ignore_files[ignore_files != ""]
-}else{
-  if (anyNA(ignore_files_class)){
-    ignore_files <- NULL
-  }else{
-    ignore_files <- ignore_files_class
-  }
-
-}
-
-print('ignore_files')
-print(ignore_files)
-
-
-ppLCMS <- msPurity::purityX(xset=xset,
-                                offsets=c(minOffset, maxOffset),
-                                cores=opt$cores,
-                                xgroups=xgroups,
-                                purityType=opt$purityType,
-                                ilim = opt$ilim,
-                                isotopes = isotopes,
-                                im = im,
-                                iwNorm = iwNorm,
-                                iwNormFun = iwNormFun,
-                                singleFile = opt$singleFile,
-                                fileignore = ignore_files,
-                                rtrawColumns=rtraw_columns)
-
-
-dfp <- ppLCMS@predictions
-
-# to make compatable with deconrank
-colnames(dfp)[colnames(dfp)=='grpid'] = 'peakID'
-colnames(dfp)[colnames(dfp)=='median'] = 'medianPurity'
-colnames(dfp)[colnames(dfp)=='mean'] = 'meanPurity'
-colnames(dfp)[colnames(dfp)=='sd'] = 'sdPurity'
-colnames(dfp)[colnames(dfp)=='stde'] = 'sdePurity'
-colnames(dfp)[colnames(dfp)=='RSD'] = 'cvPurity'
-colnames(dfp)[colnames(dfp)=='pknm'] = 'pknmPurity'
-if(sum(is.na(dfp$medianPurity))>0){
-    dfp[is.na(dfp$medianPurity),]$medianPurity = 0
-}
-
-print('saving tsv')
-print(head(dfp))
-write.table(dfp, file.path(opt$out_dir, 'anticipated_purity_lcms.tsv'), row.names=FALSE, sep='\t')
-print('saving RData')
-save.image(file.path(opt$out_dir, 'anticipated_purity_lcms.RData'))