fix #457 remove attribute in gene_id and transcript_id to keep only t…

…he first … (#496)

* remove multi values in special attributes gene_id and transcript_id to keep only the first one. The others are saved in agat_other_gene_id or agat_other_ transcript_id

* when using merge_overlap_loci avoid to merge value for ID Parent and no gene_id too. Avoid to add ID created on the fly when creating merged_.

* add a deflate_attribute parameter. Make also a global variable for CONFIG to be available from everywhere (filled by get_agat_config)

* Update and add tests

bin/agat

@@ -193,6 +193,10 @@ force_gff_input_version, gtf_output_version, gff_output_version and output_forma
 							getopt      => 'gtf_output_version=s',
 							help        => 'Set the GTF output vesion. Choice 1, 2, 2.1, 2.2, 2.5, 3 or relax. [Default relax]',
 					 },
+					{
+							getopt      => 'deflate_attribute!',
+							help        => 'deflate multi-values attributes:  attribute_tag=att_value1,att_value2,att_value3 will will become attribute_tag=att_value1;attribute_tag2=att_value2;attribute_tag3=att_value3;',
+					 },
 					 {
 							getopt      => 'create_l3_for_l2_orphan!',
 							help        => 'To create l3 feature for l2 feature without any. [Default activated]',

lib/AGAT/AGAT.pm

@@ -17,8 +17,9 @@ use AGAT::PlotR;
 use Bio::Tools::GFF;
 
 our $VERSION     = "v1.4.1";
-our @ISA         = qw(Exporter);
-our @EXPORT      = qw(get_agat_header print_agat_version get_agat_config handle_levels);
+our $CONFIG; # This variable will be used to store the config and will be available from everywhere.
+our @ISA         = qw( Exporter );
+our @EXPORT      = qw( get_agat_header print_agat_version get_agat_config handle_levels );
 sub import {
     AGAT::AGAT->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
     AGAT::OmniscientI->export_to_level(1, @_);
@@ -159,6 +160,10 @@ sub get_agat_config{
 	# Load the config
 	my $config = load_config({ config_file => $config_file_checked});
 	check_config({ config => $config});
+
+	# Store the config in a Global variable accessible from everywhere.
+	$CONFIG = $config;
+
 	return $config;
 }
 
@@ -243,6 +248,7 @@ sub handle_config {
 		my $output_format = $general->{configs}[-1]{output_format};
 		my $gff_output_version = $general->{configs}[-1]{gff_output_version};
 		my $gtf_output_version = $general->{configs}[-1]{gtf_output_version};
+		my $deflate_attribute = $general->{configs}[-1]{deflate_attribute};
 		my $create_l3_for_l2_orphan = $general->{configs}[-1]{create_l3_for_l2_orphan};
 		my $clean_attributes_from_template = $general->{configs}[-1]{clean_attributes_from_template};
 		my $locus_tag = $general->{configs}[-1]{locus_tag};
@@ -325,6 +331,11 @@ sub handle_config {
 				$modified_on_the_fly = 1;
 			}
 			# bolean
+			if( defined($deflate_attribute) ){
+				$config->{ deflate_attribute } = _make_bolean($deflate_attribute);
+				$modified_on_the_fly = 1;
+			}
+			# bolean
 			if( defined($create_l3_for_l2_orphan) ){
 				$config->{ create_l3_for_l2_orphan } = _make_bolean($create_l3_for_l2_orphan);
 				$modified_on_the_fly = 1;

lib/AGAT/BioperlGFF.pm

@@ -149,6 +149,8 @@ package AGAT::BioperlGFF;
 use vars qw($HAS_HTML_ENTITIES);
 use strict;
 
+use AGAT::OmniscientTool;
+use AGAT::AGAT;
 use Bio::Seq::SeqFactory;
 use Bio::LocatableSeq;
 use Bio::SeqFeature::Generic;
@@ -699,6 +701,28 @@ sub write_feature {
         $self->_print($line);
     }
     $self->{'_first'} = 0;
+
+    # deflate multi-values attribute if asked by config
+    if ($AGAT::AGAT::CONFIG->{'deflate_attribute'}){
+        foreach my $feature ( @features ) {
+            my @list_tags= $feature->get_all_tags();
+			foreach my $tag (@list_tags){
+				my @tag_values = $feature->get_tag_values($tag);
+                if ($#tag_values >= 1){
+                    my $tag_counter=-1;
+					foreach my $tag_value (@tag_values){
+                        $tag_counter++;
+                        if ($tag_counter == 0){
+                            create_or_replace_tag($feature, $tag , $tag_value);
+                        } else {
+                            create_or_replace_tag($feature, $tag."_".$tag_counter , $tag_value);
+                        }	
+					}
+				}
+			}
+        }
+    }
+
     foreach my $feature ( @features ) {
         $self->_print($self->gxf_string($feature)."\n");
     }

lib/AGAT/Config.pm

@@ -175,7 +175,7 @@ sub check_config{
 		$error = 1;
 	}
 	if( !  exists_keys($config,("log") ) ){
-		print "progress_bar parameter missing in the configuration file.\n";
+		print "log parameter missing in the configuration file.\n";
 		$error = 1;
 	}
 	if( !  exists_keys($config, ("debug") ) ){
@@ -241,6 +241,10 @@ sub check_config{
 		print "gtf_output_version parameter missing in the configuration file.\n";
 		$error = 1;
 	}
+	if( ! exists_keys($config, ("deflate_attribute") ) ) {
+		print "deflate_attribute parameter missing in the configuration file.\n";
+		$error = 1;
+	}
 	if( ! exists_keys($config, ("create_l3_for_l2_orphan") ) ) {
 		print "create_level3_for_level2_orphan parameter missing in the configuration file.\n";
 		$error = 1;