NAME

Bio::Das::ProServer::SourceAdaptor::Transport::ensembl_registry

VERSION

$Revision: 2.70 $

SYNOPSIS

A transport for using the Registry to retrieve Ensembl data.

DESCRIPTION

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.

AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

METHODS

init : Post-construction initialisation.

  $oTransport->init();
  
  Loads the registry from the Ensembl database, and applies a custom database
  override if specified.

adaptor : Gets an Ensembl adaptor.

  $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>

slice_adaptor : Gets an Ensembl slice adaptor.

  $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>

gene_adaptor : Gets an Ensembl gene adaptor.

  $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>

chromosome_by_region : Gets a chromosome slice.

  $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>

chromosomes : Gets all chromosomes.

  $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> objects

gene_by_id : Gets a gene.

  $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>

genes : Gets all genes.

  $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> objects

version : Gets the Ensembl API's release number.

  $sVersion = $oTransport->version();

last_modified : Gets a last modified date from the database.

  $sVersion = $oTransport->version();

disconnect : ProServer hook to disconnect all connected databases.

  $oTransport->disconnect();

CONFIGURATION AND ENVIRONMENT

Configured as part of each source's ProServer 2 INI file.

  The 'default database' is configured using these properties:
    species  (defaults to human)
    group    (defaults to core)

  A specific database may be overridden using these properties:
    dbname
    host     (defaults to localhost)
    port     (defaults to 3306)
    username (defaults to ensro)
    password

DEPENDENCIES

Carp
Bio::Das::ProServer::SourceAdaptor::Transport::generic
Bio::EnsEMBL::Registry
Bio::EnsEMBL::DBSQL::DBAdaptor

REFERENCES

http://www.ensembl.org/info/software/Pdoc/ensembl/ Ensembl API

INCOMPATIBILITIES

None reported

BUGS AND LIMITATIONS