Support the attachement of DNADBs

misc-scripts/translation_attribs.pl

@@ -135,8 +135,8 @@ for my $db_args ( @{ $cli_helper->get_dba_args_for_opts($opts) } ) {
 		$other_dbname =~ s/$1/core/;
 
 		$opts->{dbname} = $other_dbname;
-		#for vega databases, add the core as the dna database
-		my $core_db = Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$db_args} );
+		#for vega and otherfeatures databases, add the core as the dna database
+		my $core_db = Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$db_args}, -DBNAME => $other_dbname, -GROUP => 'core' );
 		$dba->dnadb($core_db);
 	}
 

modules/Bio/EnsEMBL/Utils/CliHelper.pm

@@ -191,6 +191,9 @@ sub get_dba_args_for_opts {
 		}
 		for my $dbname (@dbnames) {
 
+      #Decipher group of DBAdaptor by capturing the name_name(_name?)_core_ code. Otherwise we don't know 
+      my ($group) = $dbname =~ /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_([a-z]+)(?:_\d+)?_\d+/;
+            
 			my $multi = 0;
 			my $species_ids = [ [ 1, undef ] ];
 			if ( !$single_species ) {
@@ -208,7 +211,7 @@ sub get_dba_args_for_opts {
 				}
 			}
 			for my $species_id ( @{$species_ids} ) {
-				push @db_args, {
+				my $args = {
 					-HOST            => $opts->{$host},
 					-USER            => $opts->{$user},
 					-PORT            => $opts->{$port},
@@ -218,6 +221,8 @@ sub get_dba_args_for_opts {
 					-SPECIES_ID      => $species_id->[0],
 					-SPECIES         => $species_id->[1],
 					-MULTISPECIES_DB => $multi };
+				$args->{-GROUP} = $group if $group;
+				push(@db_args, $args);
 			}
 		}
 	} ## end if ( defined $opts->{$host...})