Inheritance diagram for Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor:

Class Summary

Synopsis

# metadata_db is an instance of MetaDataDBAdaptor
my $adaptor = $metadata_db->get_GenomeInfoAdaptor();
my $md = $gdba->fetch_by_name("homo_sapiens");

Description

Adaptor for storing and retrieving GenomeInfo objects from MySQL ensembl_metadata database

To start working with an adaptor:

# getting an adaptor
## adaptor for latest public Ensembl release
my $gdba = Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor->build_ensembl_adaptor();
## adaptor for specified public Ensembl release
my $gdba = Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor->build_ensembl_adaptor(83);
## adaptor for latest public EG release
my $gdba = Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor->build_ensembl_genomes_adaptor();
## adaptor for specified public EG release
my $gdba = Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor->build_ensembl_genome_adaptor(30);
## manually specify a given database
my $gdba = Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor->new(-USER=>'anonymous',
-PORT=>4157,
-HOST=>'mysql-eg-publicsql.ebi.ac.uk',
-DBNAME=>'ensembl_metadata');

To find genomes, use the fetch methods. These will work with the release set on the adaptor
which is the latest Ensembl release by default.

# find a genome by name
my $genome = $gdba->fetch_by_name('homo_sapiens');

# find and iterate over all genomes
for my $genome (\@{$gdba->fetch_all()}) {
	print $genome->name()."\n";
}

# find and iterate over all genomes with variation
for my $genome (\@{$gdba->fetch_all_with_variation()}) {
	print $genome->name()."\n";
}

# to change the release
$gdba->set_ensembl_release(82);
$gdba->set_ensembl_genomes_release(82);

my $genome = $gdba->fetch_by_name('arabidopsis_thaliana');

# find and iterate over all genomes from plants
for my $genome (\@{$gdba->fetch_all_by_division('EnsemblPlants')}) {
	print $genome->name()."\n";
}

# find all comparas for the division of interest
my $comparas = $gdba->fetch_all_compara_by_division('EnsemblPlants');

# find the peptide compara
my ($compara) = grep {$_->is_peptide_compara()} \@$comparas;
print $compara->division()." ".$compara->method()."(".$compara->dbname().")\n";

# print out all the genomes in this compara
for my $genome (\@{$compara->genomes()}) {
	print $genome->name()."\n";
}

See-also

Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::GenomeComparaInfo Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::GenomeOrganismInfo

Definition at line 89 of file GenomeInfoAdaptor.pm.

Available Methods
protected	_args_to_sql ()
protected	_assembly_adaptor ()
protected void	_cache ()
protected void	_clear_cache ()
protected void	_fetch_annotations ()
protected	_fetch_assembly ()
protected void	_fetch_children ()
protected void	_fetch_comparas ()
protected void	_fetch_data_release ()
protected void	_fetch_databases ()
protected void	_fetch_features ()
protected Arrayref	_fetch_generic ()
protected Arrayref	_fetch_generic_with_args ()
protected void	_fetch_other_alignments ()
protected void	_fetch_variations ()
protected Arrayref	_first_element ()
protected	_get_base_sql ()
protected Object	_get_cached_obj ()
protected void	_get_division_id ()
protected	_get_id_field ()
protected	_get_obj_class ()
protected	_organism_adaptor ()
protected void	_store_alignments ()
protected void	_store_annotations ()
protected void	_store_cached_obj ()
protected void	_store_compara ()
protected void	_store_databases ()
protected void	_store_features ()
protected void	_store_variations ()
public	build_ensembl_adaptor ()
public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor	build_ensembl_genomes_adaptor ()
public void	data_release ()
public	fetch_all ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_all_by_assemblies ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_all_by_assembly_set_chain ()
public Arrayref	fetch_all_by_dbname ()
public Arrayref	fetch_all_by_division ()
public Arrayref	fetch_all_by_name_pattern ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_all_by_organisms ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_all_by_sequence_accession ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_all_by_sequence_accession_unversioned ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_all_by_sequence_accession_versioned ()
public Arrayref	fetch_all_by_taxonomy_branch ()
public	fetch_all_by_taxonomy_id ()
public	fetch_all_by_taxonomy_ids ()
public Arrayref	fetch_all_with_compara ()
public Arrayref	fetch_all_with_genome_alignments ()
public	fetch_all_with_other_alignments ()
public Arrayref	fetch_all_with_pan_compara ()
public Arrayref	fetch_all_with_peptide_compara ()
public Arrayref	fetch_all_with_variation ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_alias ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_any_name ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_assembly ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_assembly_accession ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbID ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_dbIDs ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_display_name ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_name ()
public Bio::EnsEMBL::MetaData::GenomeInfo	fetch_by_organism ()
public Arrayref	fetch_databases ()
public Arrayref	fetch_division_databases ()
public void	set_ensembl_genomes_release ()
public	set_ensembl_release ()
public void	store ()
public void	update ()
public void	update_booleans ()

Method Documentation

protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_args_to_sql ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_assembly_adaptor ( )

Undocumented method

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protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_cache ( ) [inherited]

  Arg	     : type of object for cache
  Description: Return internal cache for given type
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_clear_cache ( ) [inherited]

  Arg	     : (optional) type of object to clear
  Description: Clear internal cache (optionally just one type)
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_annotations ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo 
  Description: Add annotations to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_assembly ( )

Undocumented method

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_children ( )

  Arg	     : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Fetch all children of specified genome info object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_comparas ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo 
  Description: Add compara info to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_data_release ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo 
  Description: Add data release to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_databases ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo 
  Description: Add databases to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_features ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo 
  Description: Add features to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic ( ) [inherited]

  Arg	     : SQL to use to fetch object
  Arg	     : arrayref of bind parameters
  Arg        : (optional) if set to 1, all children will be fetched
  Description: Instantiate a GenomeInfo from the database using the specified SQL
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic_with_args ( ) [inherited]

  Arg	     : hashref of arguments by column
  Arg        : (optional) if set to 1, all children will be fetched
  Description: Instantiate a GenomeInfo from the database using a 
               generic method, with the supplied arguments
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_other_alignments ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo 
  Description: Add other_alignments to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_fetch_variations ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo 
  Description: Add variations to supplied object
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_first_element ( ) [inherited]

  Arg	     : arrayref
  Description: Utility method to return the first element in a list, undef if empty
  Returntype : arrayref element
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_get_base_sql ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected Object Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_cached_obj ( ) [inherited]

  Arg	     : type of object to retrieve
  Arg	     : ID of object to retrieve
  Description: Retrieve object from internal cache
  Returntype : object
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_division_id ( ) [inherited]

  Arg	     : division name
  Description: Return ID for division, storing if required
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_get_id_field ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_get_obj_class ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.

protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_organism_adaptor ( )

Undocumented method

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_store_alignments ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Stores the alignments for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_store_annotations ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Stores the annotations for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_store_cached_obj ( ) [inherited]

  Arg	     : type of object to store
  Arg	     : object to store
  Description: Store object in internal cache
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_store_compara ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Stores the compara analyses for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_store_databases ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Stores the databases for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_store_features ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Stores the features for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::_store_variations ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Stores the variations for the supplied object
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::build_ensembl_adaptor ( )

Undocumented method

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::build_ensembl_genomes_adaptor ( )

  Arg	     : (optional) EG release number  - default is latest
  Description: Build an adaptor for the public Ensembl Genomes metadata database
  Returntype : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor
  Exceptions : none
  Caller     : general
  Status     : Stable

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::data_release ( )

  Arg	     : Bio::EnsEMBL::MetaData::DataReleaseInfo
  Description: Default release to use when querying 
  Returntype : None
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_all ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_assemblies ( )

  Arg	     : array of Bio::EnsEMBL::MetaData::GenomeAssemblyInfo
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified assembly
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_assembly_set_chain ( )

  Arg	     : INSDC assembly set chain (unversioned accession)
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified assembly set chain
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_dbname ( )

  Arg	     : Name of database
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified database
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_division ( )

  Arg	     : Name of division
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome infos for specified division
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_name_pattern ( )

  Arg	     : Regular expression matching of genome
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified species
  Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_organisms ( )

  Arg	     : Array ref of Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified organisms
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_sequence_accession ( )

  Arg	     : INSDC sequence accession e.g. U00096.1 or U00096
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified sequence accession
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_sequence_accession_unversioned ( )

  Arg	     : INSDC sequence accession e.g. U00096
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified sequence accession
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_sequence_accession_versioned ( )

  Arg	     : INSDC sequence accession e.g. U00096.1
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified sequence accession
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_taxonomy_branch ( )

  Arg	     : Bio::EnsEMBL::TaxonomyNode
  Description: Fetch organism info for specified taxonomy node and its children
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_taxonomy_id ( )

Undocumented method

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_by_taxonomy_ids ( )

Undocumented method

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_compara ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have any compara or whole genome alignment data
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_genome_alignments ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have whole genome alignment data
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_other_alignments ( )

Undocumented method

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_pan_compara ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have pan comapra data
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_peptide_compara ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have peptide compara data
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_all_with_variation ( )

  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch all genome info that have variation data
  Returntype : arrayref of Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_alias ( )

  Arg	     : Alias of genome
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified species
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_any_name ( )

  Arg	     : Name of genome (display, species, alias etc)
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified species
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_assembly ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeAssemblyInfo
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified assembly
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_assembly_accession ( )

  Arg	     : INSDC assembly accession
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified assembly ID (versioned or unversioned)
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbID ( ) [inherited]

  Arg	     : ID of genome info
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified ID
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbIDs ( ) [inherited]

  Arg	     : IDs of genome info
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified ID
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_display_name ( )

  Arg	     : Production name of genome 
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified species
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_name ( )

  Arg	     : Display name of genome 
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified species
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_by_organism ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Arg        : (optional) if 1, expand children of genome info
  Description: Fetch genome info for specified organism
  Returntype : Bio::EnsEMBL::MetaData::GenomeInfo
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_databases ( )

  Arg        : release (optional)
  Description: Fetch all genome-associated databases for the specified release
  Returntype : Arrayref of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Arrayref Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::fetch_division_databases ( )

  Arg        : division
  Arg        : release (optional)
  Description: Fetch all genome-associated databases for the specified release
  Returntype : Arrayref of strings
  Exceptions : none
  Caller     : general
  Status     : Stable

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::set_ensembl_genomes_release ( )

  Arg	     : Ensembl Genomes release number
  Description: Set release to use when querying 
  Returntype : None
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::set_ensembl_release ( )

Undocumented method

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::store ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Stores the supplied object and all associated child objects (includes other genomes attached by compara if not already stored)
  Returntype : None
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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sub store {
  my ( $self, $genome ) = @_;
  if ( !defined $genome->data_release() ) {
    $genome->data_release( $self->data_release() );
  }
  if ( !defined $genome->data_release()->dbID() ) {
    $self->db()->get_DataReleaseInfoAdaptor()->store( $genome->data_release() );
  }
  if ( !defined $genome->assembly() ) {
    throw("Genome must be associated with an assembly");
  }
  if ( !defined $genome->assembly()->dbID() ) {
    $self->db()->get_GenomeAssemblyInfoAdaptor()->store( $genome->assembly() );
  }
  if ( !defined $genome->dbID() ) {
    # find out if genome exists first
    my ($dbID) =
      @{
      $self->dbc()->sql_helper()->execute_simple(
        -SQL =>
"select genome_id from genome where data_release_id=? and assembly_id=?",
        -PARAMS =>
          [ $genome->data_release()->dbID(), $genome->assembly()->dbID() ] ) };

    if ( defined $dbID ) {
      $genome->dbID($dbID);
      $genome->adaptor($self);
    }
  }

  if ( defined $genome->dbID() ) {
    return $self->update($genome);
  }
  $self->db()->get_GenomeAssemblyInfoAdaptor()->store( $genome->assembly() );
  $self->dbc()->sql_helper()->execute_update(
    -SQL => q/insert into genome(division_id,
genebuild,has_pan_compara,has_variations,has_peptide_compara,
has_genome_alignments,has_synteny,has_other_alignments,assembly_id,organism_id,data_release_id)
        values(?,?,?,?,?,?,?,?,?,?,?)/,
    -PARAMS => [ $self->_get_division_id( $genome->division() ),
                 $genome->genebuild(),
                 $genome->has_pan_compara(),
                 $genome->has_variations(),
                 $genome->has_peptide_compara(),
                 $genome->has_genome_alignments(),
                 $genome->has_synteny(),
                 $genome->has_other_alignments(),
                 $genome->assembly()->dbID(),
                 $genome->assembly()->organism()->dbID(),
                 $genome->data_release()->dbID() ],
    -CALLBACK => sub {
      my ( $sth, $dbh, $rv ) = @_;
      $genome->dbID( $dbh->{mysql_insertid} );
    } );
  $genome->adaptor($self);
  $self->_store_databases($genome);
  $self->_store_annotations($genome);
  $self->_store_features($genome);
  $self->_store_variations($genome);
  $self->_store_alignments($genome);
  $self->_store_compara($genome);
  $self->_store_cached_obj($genome);
  return;
} ## end sub store

public void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::update ( )

  Arg	     : Bio::EnsEMBL::MetaData::GenomeInfo
  Description: Updates the supplied object and all associated child objects (includes other genomes attached by compara if not already stored)
  Returntype : None
  Exceptions : none
  Caller     : general
  Status     : Stable

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public void Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor::update_booleans ( )

  Description: Updates boolean genome attributes for all genomes
  Returntype : None
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

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The documentation for this class was generated from the following file:

Bio/EnsEMBL/MetaData/DBSQL/GenomeInfoAdaptor.pm

Class Summary

Synopsis

Description

See-also

Available Methods

Method Documentation