--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/purityX.R	Thu Mar 04 12:22:55 2021 +0000
@@ -0,0 +1,180 @@
+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"))