Roger Pettett
and 1 contributors

NAME

Bio::Das::ProServer::SourceAdaptor::Transport::ensembl

VERSION

$LastChangedRevision: 688 $

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.

SUBROUTINES/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|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|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|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|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|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|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|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 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)

DIAGNOSTICS

CONFIGURATION AND ENVIRONMENT

DEPENDENCIES

Carp
English
Bio::Das::ProServer::SourceAdaptor::Transport::generic
Ensembl core API
Additional Ensembl APIs if used

INCOMPATIBILITIES

None reported

BUGS AND LIMITATIONS

None reported

REFERENCES

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

AUTHOR

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

LICENSE AND COPYRIGHT

Copyright (c) 2007 EMBL-EBI