Bio::Das::ProServer::SourceAdaptor::Transport::ensembl
$LastChangedRevision: 688 $
A transport for using the Registry to retrieve Ensembl data.
This class is a Transport that provides an interface to the Ensembl API. It uses the Ensembl Resistry to determine the location of the appropriate databases, and can be used in a species specific or cross-species manner. The main advantage of using this Transport is that the registry automatically provides access to the latest data available to the installed API.
$oTransport->init(); Loads the registry from the Ensembl database, and applies a custom database override if specified.
$oAdaptor = $oTransport->adaptor(); $oAdaptor = $oTransport->adaptor('human', 'core'); Arguments: species (optional, default configured in INI or 'human') database group (optional, default configured in INI or 'core') Returns: L<Bio::EnsEMBL::DBSQL::DBAdaptor|Bio::EnsEMBL::DBSQL::DBAdaptor>
$oAdaptor = $oTransport->slice_adaptor(); $oAdaptor = $oTransport->slice_adaptor('human', 'core'); Arguments: species (optional, default configured in INI or 'human') database group (optional, default configured in INI or 'core') Returns: L<Bio::EnsEMBL::DBSQL::SliceAdaptor|Bio::EnsEMBL::DBSQL::SliceAdaptor>
$oAdaptor = $oTransport->gene_adaptor(); $oAdaptor = $oTransport->gene_adaptor('human', 'core'); Arguments: species (optional, default configured in INI or 'human') database group (optional, default configured in INI or 'core') Returns: L<Bio::EnsEMBL::DBSQL::GeneAdaptor|Bio::EnsEMBL::DBSQL::GeneAdaptor>
$oSlice = $oTransport->chromosome_by_region('X'); $oSlice = $oTransport->chromosome_by_region('X', 123453, 132424); $oSlice = $oTransport->chromosome_by_region('X', 123453, 132424, 'human', 'core'); Arguments: chromosome # (required) start (optional) end (optional) species (optional, default configured in INI or 'human') database group (optional, default configured in INI or 'core') Returns: L<Bio::EnsEMBL::Slice|Bio::EnsEMBL::Slice>
$aSlices = $oTransport->chromosomes(); $aSlices = $oTransport->chromosomes('human', 'core'); Arguments: species (optional, default configured in INI or 'human') database group (optional, default configured in INI or 'core') Returns: listref of L<Bio::EnsEMBL::Slice|Bio::EnsEMBL::Slice> objects
$oGene = $oTransport->gene_by_id('ENSG00000139618'); # BRCA2 $oGene = $oTransport->gene_by_id('ENSG00000139618', 'human', 'core'); Arguments: gene stable ID (required) species (optional, default configured in INI or 'human') database group (optional, default configured in INI or 'core') Returns: L<Bio::EnsEMBL::Gene|Bio::EnsEMBL::Gene>
$aGenes = $oTransport->genes(); $aGenes = $oTransport->genes('human', 'core'); Arguments: species (optional, default configured in INI or 'human') database group (optional, default configured in INI or 'core') Returns: listref of L<Bio::EnsEMBL::Gene|Bio::EnsEMBL::Gene> objects
$sVersion = $oTransport->version();
$oTransport->disconnect();
Configured as part of each source's ProServer 2 INI file.
The transport will automatically load database connection settings from the Ensembl Registry at ensembldb.ensembl.org. To skip this, set the 'skip_registry' INI property. A specific database may also be overridden using these INI properties: dbname host (defaults to localhost) port (defaults to 3306) username (defaults to ensro) password The 'default database' used in the transport's data access methods may be configured using these INI properties: species (defaults to human) group (defaults to core)
None reported
Andy Jenkinson <andy.jenkinson@ebi.ac.uk>
Copyright (c) 2007 EMBL-EBI
To install Bio::Das::ProServer, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Das::ProServer
CPAN shell
perl -MCPAN -e shell install Bio::Das::ProServer
For more information on module installation, please visit the detailed CPAN module installation guide.