Added case of db adaptor for production database

modules/Bio/EnsEMBL/Registry.pm

@@ -150,6 +150,7 @@ my %group2adaptor = (
       'ontology'  => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor',
       'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
       'pipeline'      => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
+      'production' => 'Bio::EnsEMBL::Production::DBSQL::DBAdaptor',
       'snp'       => 'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
       'stable_ids' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
       'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
@@ -1587,6 +1588,9 @@ sub load_registry_from_db {
   my $ontology_db;
   my $ontology_version;
 
+  my $production_db;
+  my $production_version;
+
   my $stable_ids_db;
   my $stable_ids_version;
 
@@ -1652,6 +1656,19 @@ sub load_registry_from_db {
         $ontology_db      = $db;
         $ontology_version = $1;
       }
+    } elsif ( $db =~ /^ensembl(?:genomes)?_production(_\d+)?/x ) {
+      # production db can come with no version (i.e. that on ens-staging1),
+      # but it's backed up with a release number
+      my $version = $1;
+      if ($version) {
+	$version =~ s/_//;
+	if ($software_version and $version eq $software_version) {
+	  $production_db      = $db;
+	  $production_version = $version;
+	} 
+      } else { # this is the default choice
+	$production_db = $db if $db =~ /^ensembl(?:genomes)?_production$/;
+      }
     } elsif ( $db =~ /^ensembl(?:genomes)?_stable_ids_(?:\d+_)?(\d+)/x ) {
       if ( $1 eq $software_version ) {
         $stable_ids_db      = $db;
@@ -2127,6 +2144,30 @@ sub load_registry_from_db {
     print("No ontology database found\n");
   }
 
+  # Production
+
+  if ( defined($production_db) ) {
+    require Bio::EnsEMBL::Production::DBSQL::DBAdaptor;
+
+    my $dba =
+      Bio::EnsEMBL::Production::DBSQL::DBAdaptor->new(
+                                '-species' => 'multi' . $species_suffix,
+                                '-group'   => 'production',
+                                '-host'    => $host,
+                                '-port'    => $port,
+                                '-user'    => $user,
+                                '-pass'    => $pass,
+                                '-dbname'  => $production_db, );
+
+    if ($verbose) {
+      printf( "%s loaded\n", $production_db );
+    }
+  }
+  elsif ($verbose) {
+    print("No production database found\n");
+  }
+
+  # Stable IDs
 
   if ( defined($stable_ids_db) && $stable_ids_version != 0 ) {
 
@@ -2155,6 +2196,9 @@ sub load_registry_from_db {
     -species => 'multi'.$species_suffix,
     -alias   => ['ontology'.$species_suffix] );
 
+  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+    -species => 'multi'.$species_suffix,
+    -alias   => ['production'.$species_suffix] );
 
   Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
     -species => 'multi'.$species_suffix,

modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm

@@ -142,7 +142,9 @@ my %grouping_of_biotypes = (
     'short_noncoding'=> [qw( miRNA misc_RNA  Mt_tRNA 
                              rRNA snoRNA  snRNA 
                         )],
+
     # practical Ensembl core categories for fasta dumping
+    # protein coding/pseudogene
     'cdna'              => [qw( protein_coding polymorphic_pseudogene IG_V_gene TR_V_gene 
                                 IG_J_gene TR_J_gene IG_D_gene IG_C_gene TR_C_gene pseudogene
                                 retrotransposed IG_V_pseudogene TR_V_pseudogene 
@@ -150,10 +152,15 @@ my %grouping_of_biotypes = (
                                 antisense ambiguous_orf transcribed_processed_pseudogene
                                 disrupted_domain processed_pseudogene
                            )],
+
+    # protein coding transcript
+    # protein coding
     'peptide_producing' => [qw( protein_coding polymorphic_pseudogene IG_V_gene TR_V_gene 
                                 IG_J_gene TR_J_gene IG_D_gene IG_C_gene TR_C_gene IG_LV_gene
                                 nonsense_mediated_decay
                            )],
+
+    # short/long noncoding
     'ncrna'             => [qw( ncRNA miRNA miRNA_pseudogene misc_RNA misc_RNA_pseudogene Mt_tRNA 
                             Mt_tRNA_pseudogene Mt_rRNA rRNA rRNA_pseudogene scRNA_pseudogene 
                             snoRNA snoRNA_pseudogene snRNA snRNA_pseudogene tRNA_pseudogene

modules/Bio/EnsEMBL/Utils/SequenceOntologyMapper.pm

@@ -18,15 +18,15 @@ SequenceOntologyMapper - Translates EnsEMBL objects into Sequence Ontology terms
 
 use Bio::EnsEMBL::Utils::SequenceOntologyMapper
 
-# get an Ensembl feature somehow in $feature
+# get an Ensembl feature somehow in scalar $feature 
 ...
 ...
 
 my $ontology_adaptor = $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
 my $mapper = SequenceOntologyMapper->new($ontology_adaptor);
 
-print $mapper->to_SO_accession($feature), "\n";
-print $mapper->to_SO_name($feature), "\n";
+print $mapper->to_accession($feature), "\n";
+print $mapper->to_name($feature), "\n";
 
 =head1 DESCRIPTION
 
@@ -90,7 +90,6 @@ my %transcript_so_mapping =
    '3prime_overlapping_ncrna'			=> 'SO:0000483',
    'TR_V_gene'							=> 'SO:0000466',
    'TR_V_pseudogene'					=> 'SO:0000336',
-
    'TR_J_gene'							=> 'SO:0000470',
    'IG_C_gene'							=> 'SO:0000478',
    'IG_C_pseudogene'					=> 'SO:0000336',