--- a/anticipated_purity_dims.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-library(msPurity)
-library(optparse)
-print(sessionInfo())
-
-option_list <- list(
-  make_option(c("--mzML_file"), type="character"),
-  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))
-
-print(sessionInfo())
-print(opt)
-
-if (is.null(opt$dimspy)){
-
-  df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
-  filename = NA
-  mzml_file <- opt$mzML_file
-}else{
-  indf <- read.table(opt$peaks_file,
-                     header = TRUE, sep='\t', stringsAsFactors = FALSE)
-  
-
-  if (file.exists(opt$mzML_file)){
-     mzml_file <- opt$mzML_file
-  }else{
-     
-     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)
-     print(filename)
-
-     mzml_file <- file.path(opt$mzML_file, filename)
-
-  }	
-  
-  df <- indf[4:nrow(indf),]
-  if ('blank_flag' %in% colnames(df)){
-      df <- df[df$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$mz),]
-}
-
-if (is.null(opt$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$sim)){
-    sim=FALSE
-}else{
-    sim=TRUE
-}
-
-minOffset = as.numeric(opt$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$iwNorm=='QE5'){
-    iwNorm = TRUE
-    iwNormFun = msPurity::iwNormQE.5()
-}
-
-print('FIRST ROWS OF PEAK FILE')
-print(head(df))
-print(mzml_file)
-predicted <- msPurity::dimsPredictPuritySingle(df$mz,
-                                     filepth=mzml_file,
-                                     minOffset=minOffset,
-                                     maxOffset=maxOffset,
-                                     ppm=opt$ppm,
-                                     mzML=TRUE,
-                                     sim = sim,
-                                     ilim = opt$ilim,
-                                     isotopes = isotopes,
-                                     im = im,
-                                     iwNorm = iwNorm,
-                                     iwNormFun = iwNormFun
-                                     )
-predicted <- cbind(df, predicted)
-
-print(head(predicted))
-print(file.path(opt$out_dir, 'anticipated_purity_dims.tsv'))
-write.table(predicted, file.path(opt$out_dir, 'anticipated_purity_dims.tsv'), row.names=FALSE, sep='\t')