--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/purityX.R	Wed Nov 27 13:42:05 2019 -0500
@@ -0,0 +1,184 @@
+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")
+)
+
+
+opt<- parse_args(OptionParser(option_list=option_list))
+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)
+    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),]$medianPurity = 0
+}
+
+
+print(head(dfp))
+write.table(dfp, file.path(opt$out_dir, 'purityX_output.tsv'), row.names=FALSE, sep='\t')
+
+save.image(file.path(opt$out_dir, 'purityX_output.RData'))