--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combineAnnotations.R	Wed Nov 27 13:44:58 2019 -0500
@@ -0,0 +1,103 @@
+library(optparse)
+library(msPurity)
+print(sessionInfo())
+
+# 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("--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("--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))
+
+print(opt)
+
+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$ms1_lookup_checkAdducts)){
+  opt$ms1_lookup_checkAdducts <- FALSE
+}
+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
+               )
+print(weights)
+if (round(!sum(unlist(weights),0)==1)){
+
+  stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
+}
+
+if (opt$compoundDbType=='local_config'){
+  # load in compound config
+  # Soure local function taken from workflow4metabolomics
+  source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+  source_local("dbconfig.R")
+}else{
+  compoundDbPth = opt$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,
+
+                            compoundDbType = compoundDbType,
+                            compoundDbName = compoundDbName,
+                            compoundDbHost = compoundDbHost,
+                            compoundDbPort = compoundDbPort,
+                            compoundDbUser = compoundDbUser,
+                            compoundDbPass = compoundDbPass,
+                            weights = weights)
+
+write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
+
+
+closeAllConnections()
+