From 939a7fe87c465bf44d5984ea63a88a0f4180bcad Mon Sep 17 00:00:00 2001
From: JoseCorCab <josecordoba@uma.es>
Date: Thu, 25 Apr 2024 13:31:05 +0200
Subject: [PATCH] Script for table annotation added

---
 inst/scripts/add_annotation.R | 63 +++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100755 inst/scripts/add_annotation.R

diff --git a/inst/scripts/add_annotation.R b/inst/scripts/add_annotation.R
new file mode 100755
index 0000000..aaf21ba
--- /dev/null
+++ b/inst/scripts/add_annotation.R
@@ -0,0 +1,63 @@
+#!/usr/bin/env Rscript
+
+options(warn=1)
+if( Sys.getenv('DEGHUNTER_MODE') == 'DEVELOPMENT' ){
+  # Obtain this script directory
+  full.fpath <- normalizePath(unlist(strsplit(commandArgs()[grep('^--file=', 
+                  commandArgs())], '='))[2])
+
+  main_path_script <- dirname(full.fpath)
+  root_path <- file.path(main_path_script, '..', '..')
+  organisms_table_file <- file.path(root_path, "inst","external_data", 
+        "organism_table.txt")
+  # Load custom libraries
+   custom_libraries <- c('functional_analysis_library.R')
+  for (lib in custom_libraries){
+    source(file.path(root_path, 'R', lib))
+  }
+
+  source_folder <- file.path(root_path, 'inst')
+}else{
+  require('ExpHunterSuite')
+  root_path <- find.package('ExpHunterSuite')
+  source_folder <- file.path(root_path)
+  organisms_table_file <- file.path(root_path, "external_data", 
+        "organism_table.txt")
+
+}
+
+
+
+option_list <- list(
+	optparse::make_option(c("-i", "--input_file"), type="character", default=NULL,
+                        help="Table to annotate"),
+	optparse::make_option(c("-o", "--output_file"), type="character", default='Annotated_table.txt',
+                        help="Define the output path. Default = %default"),
+	optparse::make_option(c("-c", "--column"), type="character", default=1,
+                        help="Column name or index with ensembl_IDs. Default = %default"),
+	optparse::make_option(c("-I", "--input_keytype"), type="character", default=NULL,
+                        help="Set the input keytype. Default=%default : All possible keytypes will be printed"),
+	optparse::make_option(c("-K", "--output_keytype"), type="character", default="SYMBOL",
+                        help="Set the output keytype. Default=%default"),
+	optparse::make_option(c("-O", "--organism"), type="character", default="Human",
+                        help="Set the model organism. Default = %default")
+)
+opt <- optparse::parse_args(optparse::OptionParser(option_list=option_list))
+
+organisms_table <- get_organism_table(organisms_table_file)
+current_organism_info <- organisms_table[rownames(organisms_table) %in% opt$organism,]
+org_db <- get_org_db(current_organism_info)
+
+if (grepl("[0-9]+", opt$column)) opt$column <- as.numeric(opt$column)
+
+table_to_annot <- read.table(opt$input_file, sep = "\t", header = TRUE)
+
+translated_keytypes <- translate_ids_orgdb(ids = table_to_annot[,opt$column], 
+                    input_id=opt$input_keytype, output_id = opt$output_keytype, org_db=org_db)
+
+translated_ids <- translated_keytypes[match(table_to_annot[,opt$column], 
+                                        translated_keytypes[,opt$input_keytype]) ,opt$output_keytype]
+
+table_to_annot[,opt$output_keytype] <- translated_ids
+
+write.table(table_to_annot, sep = "\t", quote = FALSE, row.names = FALSE, file = opt$output_file)
\ No newline at end of file