--- a/dimsPredictPuritySingle.R	Fri Nov 13 10:16:03 2020 +0000
+++ b/dimsPredictPuritySingle.R	Thu Mar 04 12:28:18 2021 +0000
@@ -3,27 +3,27 @@
 print(sessionInfo())
 
 option_list <- list(
-  make_option(c("--mzML_file"), type="character"),
-  make_option(c("--mzML_files"), type="character"),
-  make_option(c("--mzML_filename"), type="character", default=''),
-  make_option(c("--mzML_galaxy_names"), type="character", default=''),
-  make_option(c("--peaks_file"), type="character"),
-  make_option(c("-o", "--out_dir"), type="character"),
-  make_option("--minoffset", default=0.5),
-  make_option("--maxoffset", default=0.5),
-  make_option("--ilim", default=0.05),
-  make_option("--ppm", default=4),
-  make_option("--dimspy", action="store_true"),
-  make_option("--sim", action="store_true"),
-  make_option("--remove_nas", action="store_true"),
-  make_option("--iwNorm", default="none", type="character"),
-  make_option("--file_num_dimspy", default=1),
-  make_option("--exclude_isotopes", action="store_true"),
-  make_option("--isotope_matrix", type="character")
+  make_option(c("--mzML_file"), type = "character"),
+  make_option(c("--mzML_files"), type = "character"),
+  make_option(c("--mzML_filename"), type = "character", default = ""),
+  make_option(c("--mzML_galaxy_names"), type = "character", default = ""),
+  make_option(c("--peaks_file"), type = "character"),
+  make_option(c("-o", "--out_dir"), type = "character"),
+  make_option("--minoffset", default = 0.5),
+  make_option("--maxoffset", default = 0.5),
+  make_option("--ilim", default = 0.05),
+  make_option("--ppm", default = 4),
+  make_option("--dimspy", action = "store_true"),
+  make_option("--sim", action = "store_true"),
+  make_option("--remove_nas", action = "store_true"),
+  make_option("--iwNorm", default = "none", type = "character"),
+  make_option("--file_num_dimspy", default = 1),
+  make_option("--exclude_isotopes", action = "store_true"),
+  make_option("--isotope_matrix", type = "character")
 )
 
 # store options
-opt<- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 print(sessionInfo())
 print(opt)
@@ -31,119 +31,118 @@
 print(opt$mzML_files)
 print(opt$mzML_galaxy_names)
 
-str_to_vec <- function(x){
+str_to_vec <- function(x) {
     print(x)
-    x <- trimws(strsplit(x, ',')[[1]])
+    x <- trimws(strsplit(x, ",")[[1]])
     return(x[x != ""])
 }
 
-find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename){
+find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename) {
     mzML_filename <- trimws(mzML_filename)
     mzML_files <- str_to_vec(mzML_files)
     galaxy_names <- str_to_vec(galaxy_names)
-    if (mzML_filename %in% galaxy_names){
-        return(mzML_files[galaxy_names==mzML_filename])
+    if (mzML_filename %in% galaxy_names) {
+        return(mzML_files[galaxy_names == mzML_filename])
     }else{
         stop(paste("mzML file not found - ", mzML_filename))
     }
 }
 
 
-if (is.null(opt$dimspy)){
-    df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
-    if (file.exists(opt$mzML_file)){
+if (is.null(opt$dimspy)) {
+    df <- read.table(opt$peaks_file, header = TRUE, sep = "\t")
+    if (file.exists(opt$mzML_file)) {
         mzML_file <- opt$mzML_file
-    }else if (!is.null(opt$mzML_files)){
-        mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, 
+    }else if (!is.null(opt$mzML_files)) {
+        mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names,
                                     opt$mzML_filename)
     }else{
-        mzML_file <- file.path(opt$mzML_file, filename)    
-    }	
+        mzML_file <- file.path(opt$mzML_file, filename)
+    }
 }else{
     indf <- read.table(opt$peaks_file,
-                       header = TRUE, sep='\t', stringsAsFactors = FALSE)
-    
+                       header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+
     filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
     print(filename)
     # check if the data file is mzML or RAW (can only use mzML currently) so
     # we expect an mzML file of the same name in the same folder
-    indf$i <- indf[,colnames(indf)==filename]
-    indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
-    
-    filename = sub("raw", "mzML", filename, ignore.case = TRUE)
+    indf$i <- indf[, colnames(indf) == filename]
+    indf[, colnames(indf) == filename] <- as.numeric(indf[, colnames(indf) == filename])
+
+    filename <- sub("raw", "mzML", filename, ignore.case = TRUE)
     print(filename)
-    
-    
-    if (file.exists(opt$mzML_file)){
+
+    if (file.exists(opt$mzML_file)) {
         mzML_file <- opt$mzML_file
-    }else if (!is.null(opt$mzML_files)){
+    }else if (!is.null(opt$mzML_files)) {
         mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename)
     }else{
-        mzML_file <- file.path(opt$mzML_file, filename)    
-    }	
-    
-    # Update the dimspy output with the correct information 
-    df <- indf[4:nrow(indf),]
-    if ('blank_flag' %in% colnames(df)){
-        df <- df[df$blank_flag==1,]
+        mzML_file <- file.path(opt$mzML_file, filename)
     }
-    colnames(df)[colnames(df)=='m.z'] <- 'mz'
-    
-    if ('nan' %in% df$mz){
-        df[df$mz=='nan',]$mz <- NA
+
+    # Update the dimspy output with the correct information
+    df <- indf[4:nrow(indf), ]
+    if ("blank_flag" %in% colnames(df)) {
+        df <- df[df$blank_flag == 1, ]
+    }
+    colnames(df)[colnames(df) == "m.z"] <- "mz"
+
+    if ("nan" %in% df$mz) {
+        df[df$mz == "nan", ]$mz <- NA
     }
     df$mz <- as.numeric(df$mz)
 }
 
-if (!is.null(opt$remove_nas)){
-  df <- df[!is.na(df$mz),]
+if (!is.null(opt$remove_nas)) {
+  df <- df[!is.na(df$mz), ]
 }
 
-if (is.null(opt$isotope_matrix)){
+if (is.null(opt$isotope_matrix)) {
     im <- NULL
 }else{
     im <- read.table(opt$isotope_matrix,
-                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
+                     header = TRUE, sep = "\t", stringsAsFactors = FALSE)
 }
 
-if (is.null(opt$exclude_isotopes)){
+if (is.null(opt$exclude_isotopes)) {
     isotopes <- FALSE
 }else{
     isotopes <- TRUE
 }
 
-if (is.null(opt$sim)){
-    sim=FALSE
+if (is.null(opt$sim)) {
+    sim <- FALSE
 }else{
-    sim=TRUE
+    sim <- TRUE
 }
 
-minOffset = as.numeric(opt$minoffset)
-maxOffset = as.numeric(opt$maxoffset)
+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()
+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('FIRST ROWS OF PEAK FILE')
+print("FIRST ROWS OF PEAK FILE")
 print(head(df))
 print(mzML_file)
 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
-                                     filepth=mzML_file,
-                                     minOffset=minOffset,
-                                     maxOffset=maxOffset,
-                                     ppm=opt$ppm,
-                                     mzML=TRUE,
+                                     filepth = mzML_file,
+                                     minOffset = minOffset,
+                                     maxOffset = maxOffset,
+                                     ppm = opt$ppm,
+                                     mzML = TRUE,
                                      sim = sim,
                                      ilim = opt$ilim,
                                      isotopes = isotopes,
@@ -154,10 +153,8 @@
 predicted <- cbind(df, predicted)
 
 print(head(predicted))
-print(file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'))
+print(file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"))
 
-write.table(predicted, 
-            file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'),
-            row.names=FALSE, sep='\t')
-
-
+write.table(predicted,
+            file.path(opt$out_dir, "dimsPredictPuritySingle_output.tsv"),
+            row.names = FALSE, sep = "\t")