configuration scripts for the registry

modules/Bio/EnsEMBL/Utils/User_defined_load.pm

+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::DBSQL::DBConnection;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw(warning throw);
+
+
+=head2 Example off user defined loading
+
+Add new databases by creating the load method and use it by setting
+ENSEMBL_REGISTRY to your configuration file.
+
+
+sub load_dupgene{
+  my ($class, @args) = @_;
+
+  my ($species) = rearrange([qw(SPECIES)],@args);
+  my $group = 'dupgene';
+
+  push (@args, '-group');
+  push (@args, $group);
+
+  my ($spec,$gro) = Bio::EnsEMBL::Registry->check_if_already_there(@args);
+  if($spec){
+    print STDERR "already defined returning\n";
+    return;
+  }
+
+  my $dbc = new Bio::EnsEMBL::DBSQL::DBConnection(@args);
+
+  my $dba = new_fast  Bio::EnsEMBL::DBSQL::DBAdaptor('-con' => $dbc);
+
+  Bio::EnsEMBL::Registry->add_DBAdaptor($species, $group, $dba);
+
+  my %pairs =  ( 'Analysis'             => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor',
+		 'ArchiveStableId'      => 'Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor',
+		 'Attribute'            => 'Bio::EnsEMBL::DBSQL::AttributeAdaptor',
+		 'AssemblyExceptionFeature' => 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor',
+		 'AssemblyMapper'       => 'Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor',
+		 'Blast'                => 'Bio::EnsEMBL::External::BlastAdaptor',
+		 'MetaContainer'        => 'Bio::EnsEMBL::DBSQL::MetaContainer',
+		 'CoordSystem'   => 'Bio::EnsEMBL::DBSQL::CoordSystemAdaptor',
+		 'CompressedSequence' => 'Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor',
+		 'DBEntry'              => 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor',
+		 'DnaAlignFeature'      => 'Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor',
+		 'DensityFeature'       => 'Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor',
+		 'DensityType'          => 'Bio::EnsEMBL::DBSQL::DensityTypeAdaptor',
+		 'Exon'                 => 'Bio::EnsEMBL::DBSQL::ExonAdaptor',
+		 'Gene'                 => 'Bio::EnsEMBL::DBSQL::GeneAdaptor',
+		 'KaryotypeBand'        => 'Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor',
+		 'Marker'               => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor',
+		 'MarkerFeature'        =>
+		 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor',
+		 'MetaCoordContainer'   => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer',
+		 'MiscSet'              => 'Bio::EnsEMBL::DBSQL::MiscSetAdaptor',
+		 'MiscFeature'          => 'Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor',
+		 'PredictionTranscript' =>
+		 'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor',
+		 'PredictionExon'       => 'Bio::EnsEMBL::DBSQL::PredictionExonAdaptor',
+		 'ProteinFeature'       => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor',
+		 'ProteinAlignFeature'  =>
+		 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor',
+		 'ProxySNP'             => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor',
+		 'QtlFeature'           => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor',
+		 'Qtl'                  => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor',
+		 'RepeatConsensus'      => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor',
+		 'RepeatFeature'        => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor',
+		 'Sequence'             => 'Bio::EnsEMBL::DBSQL::SequenceAdaptor',
+		 'SimpleFeature'        => 'Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor',
+		 'Slice'                => 'Bio::EnsEMBL::DBSQL::SliceAdaptor',
+		 'SupportingFeature'    =>
+		 'Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor',
+		 'Transcript'           => 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor',
+		 'Translation'          => 'Bio::EnsEMBL::DBSQL::TranslationAdaptor' );
+
+  foreach my $key (keys %pairs){
+    Bio::EnsEMBL::Registry->add_adaptor($species, $group, $key, $pairs{$key});
+  }
+
+  #if dnadb has been set then for the follwing use it.
+  foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
+    Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($species,$type);
+  }
+}
+=cut