diff variant_effect_predictor/Bio/EnsEMBL/Utils/ensembl_init.example @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Utils/ensembl_init.example	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,83 @@
+#
+# Example of configuration file used by Bio::EnsEMBL::Registry::load_all
+# method to store/register all kind of Adaptors.
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Utils::ConfigRegistry;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
+
+my @aliases;
+
+new Bio::EnsEMBL::DBSQL::DBAdaptor(
+                                 '-host'    => 'ensembldb.ensembl.org',
+                                 '-user'    => 'anonymous',
+                                 '-port'    => '3306',
+                                 '-species' => 'Homo sapiens',
+                                 '-group'   => 'core',
+                                 '-dbname' => 'homo_sapiens_core_23_34e'
+);
+
+@aliases = ( 'H_Sapiens',    'homo sapiens',
+             'Homo_Sapiens', 'Homo_sapiens',
+             'Homo',         'homo',
+             'human' );
+
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+                                           '-species' => 'Homo sapiens',
+                                           '-alias'   => [@aliases] );
+
+new Bio::EnsEMBL::DBSQL::DBAdaptor(
+                                 '-host'    => 'ensembldb.ensembl.org',
+                                 '-user'    => 'anonymous',
+                                 '-port'    => '3306',
+                                 '-species' => 'Mus musculus',
+                                 '-group'   => 'core',
+                                 '-dbname' => 'mus_musculus_core_23_32c'
+);
+
+@aliases = ( 'M_Musculus',   'mus musculus',
+             'Mus_Musculus', 'Mus_musculus',
+             'Mus',          'mus',
+             'mouse' );
+
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+                                           '-species' => 'Mus musculus',
+                                           '-alias'   => [@aliases] );
+
+new Bio::EnsEMBL::DBSQL::DBAdaptor(
+                             '-host'    => 'ensembldb.ensembl.org',
+                             '-user'    => 'anonymous',
+                             '-port'    => '3306',
+                             '-species' => 'Rattus norvegicus',
+                             '-group'   => 'core',
+                             '-dbname' => 'rattus_norvegicus_core_23_3c'
+);
+
+@aliases = ( 'R_Norvegicus',      'rattus norvegicus',
+             'Rattus_Norvegicus', 'Rattus_norvegicus',
+             'Rattus',            'rattus',
+             'rat' );
+
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+                                      '-species' => 'Rattus norvegicus',
+                                      '-alias'   => [@aliases] );
+
+new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
+                                     '-host' => 'ensembldb.ensembl.org',
+                                     '-user' => 'anonymous',
+                                     '-port' => '3306',
+                                     '-species' => 'Compara23',
+                                     '-dbname' => 'ensembl_compara_23_1'
+);
+
+@aliases = ( 'ensembl_compara_23_1', 'compara23' );
+
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+                                              '-species' => 'Compara23',
+                                              '-alias'   => [@aliases]
+);
+
+1;