From 6b02a7e1f46c9010ff76cd2df254d5bb1dbf833c Mon Sep 17 00:00:00 2001
From: JoseCorCab <josecordoba@uma.es>
Date: Thu, 23 May 2024 11:31:50 +0200
Subject: [PATCH] Add_mirna_mature and add_annotation have been merged

---
 inst/scripts/add_annotation.R   | 29 ++++++++++++++++------
 inst/scripts/add_mirna_mature.R | 44 ---------------------------------
 2 files changed, 22 insertions(+), 51 deletions(-)
 delete mode 100755 inst/scripts/add_mirna_mature.R

diff --git a/inst/scripts/add_annotation.R b/inst/scripts/add_annotation.R
index aaf21ba..1fc190d 100755
--- a/inst/scripts/add_annotation.R
+++ b/inst/scripts/add_annotation.R
@@ -11,7 +11,7 @@ if( Sys.getenv('DEGHUNTER_MODE') == 'DEVELOPMENT' ){
   organisms_table_file <- file.path(root_path, "inst","external_data", 
         "organism_table.txt")
   # Load custom libraries
-   custom_libraries <- c('functional_analysis_library.R')
+   custom_libraries <- c('functional_analysis_library.R', 'miRNA_RNA_functions.R')
   for (lib in custom_libraries){
     source(file.path(root_path, 'R', lib))
   }
@@ -35,6 +35,8 @@ option_list <- list(
                         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("-m", "--mirna"), type= "logical", default = FALSE, action ="store_true",
+                        help= "Indicate if the ids to translate are miRNA (from miRBase to mature ID). If activated, -I and -K are ignored"),
 	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",
@@ -52,12 +54,25 @@ 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$output_keytype, org_db=org_db)
+if (opt$column == "rownames") {
+  ids_to_translate <- rownames(table_to_annot)
+} else {
+  ids_to_translate <- table_to_annot[,opt$column]
+}
+
+if (opt$mirna) {
+
+  table_to_annot$miRNA_name <- translate_miRNA_ids(ids_to_translate)
 
-translated_ids <- translated_keytypes[match(table_to_annot[,opt$column], 
-                                        translated_keytypes[,opt$input_keytype]) ,opt$output_keytype]
+} else {
 
-table_to_annot[,opt$output_keytype] <- translated_ids
+  translated_keytypes <- translate_ids_orgdb(ids = ids_to_translate, 
+                      input_id=opt$input_keytype, output_id = opt$output_keytype, org_db=org_db)
+
+  translated_ids <- translated_keytypes[match(ids_to_translate, 
+                                          translated_keytypes[,opt$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$output_file)
\ No newline at end of file
+write.table(table_to_annot, sep = "\t", quote = FALSE, row.names = (opt$column == "rownames"), file = opt$output_file)
\ No newline at end of file
diff --git a/inst/scripts/add_mirna_mature.R b/inst/scripts/add_mirna_mature.R
deleted file mode 100755
index 2c7dd6d..0000000
--- a/inst/scripts/add_mirna_mature.R
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env Rscript
-
-option_list <- list(
-	optparse::make_option(c("-i", "--input_file"), type="character", default=NULL,
-                        help="DEgenesHunter results table"),
-	optparse::make_option(c("-o", "--output_file"), type="character", default='./',
-                        help="Define the output path. Default = './'")
-)
-
-if( Sys.getenv('DEGHUNTER_MODE') == 'DEVELOPMENT' ){ 
-
-    full.fpath <- tryCatch(normalizePath(parent.frame(2)$ofile),  
-                   error=function(e) # works when using R CMD
-                  normalizePath(unlist(strsplit(commandArgs()[grep('^--file=', 
-                    commandArgs())], '='))[2]))
-    main_path_script <- dirname(full.fpath)
-    root_path <- file.path(main_path_script, '..', '..')
-    custom_libraries <- c("miRNA_RNA_functions.R")
-    for (lib in custom_libraries){
-        source(file.path(root_path, 'R', lib))
-      }
-    template_folder <- file.path(root_path, 'inst', 'templates')
-    organism_table_path <- file.path(root_path,"inst","external_data", 
-        "organism_table.txt")
-
-} else {
-    require('ExpHunterSuite')
-    root_path <- find.package('ExpHunterSuite')
-    template_folder <- file.path(root_path, 'templates')
-    organism_table_path <- file.path(root_path, "inst","external_data",
-        "organism_table.txt")
-}
-
-
-
-opt <- optparse::parse_args(optparse::OptionParser(option_list=option_list))
-
-original_table <- read.table(opt$input_file,header=TRUE, row.names=1, sep="\t")
-
-annotated_table <- original_table
-
-annotated_table$miRNA_name <- translate_miRNA_ids(rownames(annotated_table))
-
-write.table(annotated_table, file.path(opt$output_file, "hunter_results_table_translated.txt"), quote=FALSE, row.names=TRUE, sep="\t")