--- a/combineAnnotations.R	Fri Nov 13 10:16:03 2020 +0000
+++ b/combineAnnotations.R	Thu Mar 04 12:28:18 2021 +0000
@@ -4,115 +4,120 @@
 
 # Get the parameter
 option_list <- list(
-  make_option(c("-s","--sm_resultPth"),type="character"),
-  make_option(c("-m","--metfrag_resultPth"),type="character"),
-  make_option(c("-c","--sirius_csi_resultPth"),type="character"),
-  make_option(c("-p","--probmetab_resultPth"),type="character"),
-  make_option(c("-l","--ms1_lookup_resultPth"),type="character"),
+  make_option(c("-s", "--sm_resultPth"), type = "character"),
+  make_option(c("-m", "--metfrag_resultPth"), type = "character"),
+  make_option(c("-c", "--sirius_csi_resultPth"), type = "character"),
+  make_option(c("-p", "--probmetab_resultPth"), type = "character"),
+  make_option(c("-l", "--ms1_lookup_resultPth"), type = "character"),
 
-  make_option("--ms1_lookup_checkAdducts", action="store_true"),
-  make_option("--ms1_lookup_keepAdducts", type="character", default=NA),
-  make_option("--ms1_lookup_dbSource", type="character", default="hmdb"),
+  make_option("--ms1_lookup_checkAdducts", action = "store_true"),
+  make_option("--ms1_lookup_keepAdducts", type = "character", default = NA),
+  make_option("--ms1_lookup_dbSource", type = "character", default = "hmdb"),
 
-  make_option("--sm_weight", type="numeric"),
-  make_option("--metfrag_weight", type="numeric"),
-  make_option("--sirius_csi_weight", type="numeric"),
-  make_option("--probmetab_weight", type="numeric"),
-  make_option("--ms1_lookup_weight", type="numeric"),
-  make_option("--biosim_weight", type="numeric"),
-  
-  make_option("--summaryOutput", action="store_true"),
-  
-  make_option("--create_new_database", action="store_true"),
-  make_option("--outdir", type="character", default="."),
+  make_option("--sm_weight", type = "numeric"),
+  make_option("--metfrag_weight", type = "numeric"),
+  make_option("--sirius_csi_weight", type = "numeric"),
+  make_option("--probmetab_weight", type = "numeric"),
+  make_option("--ms1_lookup_weight", type = "numeric"),
+  make_option("--biosim_weight", type = "numeric"),
+
+  make_option("--summaryOutput", action = "store_true"),
 
-  make_option("--compoundDbType", type="character", default="sqlite"),
-  make_option("--compoundDbPth", type="character", default=NA),
-  make_option("--compoundDbHost", type="character", default=NA)
+  make_option("--create_new_database", action = "store_true"),
+  make_option("--outdir", type = "character", default = "."),
+
+  make_option("--compoundDbType", type = "character", default = "sqlite"),
+  make_option("--compoundDbPth", type = "character", default = NA),
+  make_option("--compoundDbHost", type = "character", default = NA)
 )
-opt <- parse_args(OptionParser(option_list=option_list))
+opt <- parse_args(OptionParser(option_list = option_list))
 
 print(opt)
 
-if (!is.null(opt$create_new_database)){
-  sm_resultPth <-  file.path(opt$outdir, 'combined_annotations.sqlite')
+if (!is.null(opt$create_new_database)) {
+  sm_resultPth <- file.path(opt$outdir, "combined_annotations.sqlite")
   file.copy(opt$sm_resultPth, sm_resultPth)
 }else{
   sm_resultPth <- opt$sm_resultPth
 }
 
-if (is.null(opt$ms1_lookup_checkAdducts)){
+if (is.null(opt$ms1_lookup_checkAdducts)) {
   opt$ms1_lookup_checkAdducts <- FALSE
 }
-if (!is.null(opt$ms1_lookup_keepAdducts)){
+if (!is.null(opt$ms1_lookup_keepAdducts)) {
     opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
     opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
     ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
 }
 
-weights <-list('sm'=opt$sm_weight,
-               'metfrag'=opt$metfrag_weight,
-               'sirius_csifingerid'= opt$sirius_csi_weight,
-               'probmetab'=opt$probmetab_weight,
-               'ms1_lookup'=opt$ms1_lookup_weight,
-               'biosim'=opt$biosim_weight
+weights <- list("sm" = opt$sm_weight,
+               "metfrag" = opt$metfrag_weight,
+               "sirius_csifingerid" = opt$sirius_csi_weight,
+               "probmetab" = opt$probmetab_weight,
+               "ms1_lookup" = opt$ms1_lookup_weight,
+               "biosim" = opt$biosim_weight
                )
 print(weights)
 
-if (is.null(opt$probmetab_resultPth)){
-  opt$probmetab_resultPth = NA
+if (is.null(opt$probmetab_resultPth)) {
+  opt$probmetab_resultPth <- NA
 }
 
-if (round(!sum(unlist(weights),0)==1)){
-  stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
+if (round(!sum(unlist(weights), 0) == 1)) {
+  stop(paste0("The weights should sum to 1 not ", sum(unlist(weights))))
 }
 
-if (is.null(opt$summaryOutput)){
-  summaryOutput = FALSE
+if (is.null(opt$summaryOutput)) {
+  summaryOutput <- FALSE
 }else{
- summaryOutput = TRUE
+ summaryOutput <- TRUE
 }
 
-if (opt$compoundDbType=='local_config'){
+if (opt$compoundDbType == "local_config") {
   # load in compound config
   # Soure local function taken from workflow4metabolomics
-  source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+  source_local <- function(fname) {
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep = "/"))
+  }
   source_local("dbconfig.R")
 }else{
-  compoundDbPth = opt$compoundDbPth
-  compoundDbType = opt$compoundDbType
-  compoundDbName = NA
-  compoundDbHost = NA
-  compoundDbPort = NA
-  compoundDbUser = NA
-  compoundDbPass = NA
+  compoundDbPth <- opt$compoundDbPth
+  compoundDbType <- opt$compoundDbType
+  compoundDbName <- NA
+  compoundDbHost <- NA
+  compoundDbPort <- NA
+  compoundDbUser <- NA
+  compoundDbPass <- NA
 }
 
 summary_output <- msPurity::combineAnnotations(
-                            sm_resultPth = sm_resultPth,
-                            compoundDbPth = compoundDbPth,
-                            metfrag_resultPth = opt$metfrag_resultPth,
-                            sirius_csi_resultPth = opt$sirius_csi_resultPth,
-                            probmetab_resultPth = opt$probmetab_resultPth,
-                            ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
-                            ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
-                            ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
+                          sm_resultPth = sm_resultPth,
+                          compoundDbPth = compoundDbPth,
+                          metfrag_resultPth = opt$metfrag_resultPth,
+                          sirius_csi_resultPth = opt$sirius_csi_resultPth,
+                          probmetab_resultPth = opt$probmetab_resultPth,
+                          ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
+                          ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
+                          ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
 
-                            compoundDbType = compoundDbType,
-                            compoundDbName = compoundDbName,
-                            compoundDbHost = compoundDbHost,
-                            compoundDbPort = compoundDbPort,
-                            compoundDbUser = compoundDbUser,
-                            compoundDbPass = compoundDbPass,
-                            weights = weights,
-                            summaryOutput = summaryOutput)
-if (summaryOutput){
-  write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
+                         compoundDbType = compoundDbType,
+                         compoundDbName = compoundDbName,
+                         compoundDbHost = compoundDbHost,
+                         compoundDbPort = compoundDbPort,
+                         compoundDbUser = compoundDbUser,
+                         compoundDbPass = compoundDbPass,
+                         weights = weights,
+                         summaryOutput = summaryOutput)
+if (summaryOutput) {
+  write.table(summary_output,
+              file.path(opt$outdir, "combined_annotations.tsv"),
+              sep = "\t", row.names = FALSE)
 }
 
-
-write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
-
+write.table(summary_output,
+            file.path(opt$outdir, "combined_annotations.tsv"),
+            sep = "\t", row.names = FALSE)
 
 closeAllConnections()
-