my $adaptor = Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor->build_ensembl_genomesadaptor(); my $lookup = Bio::EnsEMBL::RemoteLookUp->new(-ADAPTOR=>$adaptor); my $dbas = $lookup->registry()->get_all(); $dbas = $lookup->get_all_by_taxon_id(388919); $dbas = $lookup->get_by_name_pattern("Escherichia.*");
This module is an implementation of Bio::EnsEMBL::LookUp that uses Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor to access a MySQL database containing information about Ensembl and Ensembl Genomes contents and then instantiate DBAdaptors. To instantiate using the public Ensembl/EG servers for creating DBAdaptors: my $lookup = Bio::EnsEMBL::LookUp::RemoteLookUp->new(-ADAPTOR=>$adaptor); To instantiate to use a specific server on which core databases are located: my $lookup = Bio::EnsEMBL::LookUp::RemoteLookUp->new(-USER=>$user, -HOST=>$host, -PORT=>$port, -ADAPTOR=>$adaptor); Once constructed, the LookUp instance can be used as documented in Bio::EnsEMBL::LookUp.
Definition at line 44 of file RemoteLookUp.pm.
Available Methods | |
protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor | _adaptor () |
protected | _cache () |
public Arrayref | compara_to_dba () |
public Bio::EnsEMBL::DBSQL::DBAdaptor | genome_to_dba () |
public Array | genomes_to_dbas () |
public Arrayref | get_all () |
public Arrayref | get_all_accessions () |
public Arrayref | get_all_assemblies () |
public Arrayref | get_all_by_accession () |
public Arrayref | get_all_by_dbname () |
public Arrayref | get_all_by_name_pattern () |
public Arrayref | get_all_by_taxon_branch () |
public Arrayref | get_all_by_taxon_id () |
public Arrayref | get_all_dbnames () |
public Arrayref | get_all_names () |
public Arrayref | get_all_taxon_ids () |
public Arrayref | get_all_versioned_accessions () |
public Arrayref | get_all_versioned_assemblies () |
public Bio::EnsEMBL::DBSQL::DatabaseAdaptor | get_by_assembly_accession () |
public Arrayref | get_by_name_exact () |
public | new () |
protected Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::LookUp::RemoteLookUp::_adaptor | ( | ) |
Description : Return GenomeInfoAdaptor Exceptions : None Return type : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor Caller : Internal Status : Stable
protected Bio::EnsEMBL::LookUp::RemoteLookUp::_cache | ( | ) |
Undocumented method
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::compara_to_dba | ( | ) |
Description : Build a Bio::EnsEMBL::Compara::DBSQL::DBAdaptor instance with the supplied info object Argument : Bio::EnsEMBL::MetaData::GenomeComparaInfo Exceptions : None Return type : Arrayref of strings
public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::LookUp::RemoteLookUp::genome_to_dba | ( | ) |
Description : Build a Bio::EnsEMBL::DBSQL::DBAdaptor instance with the supplied info object Argument : Bio::EnsEMBL::MetaData::GenomeInfo Argument : (optional) Group to use Exceptions : None Return type : Bio::EnsEMBL::DBSQL::DBAdaptor
public Array Bio::EnsEMBL::LookUp::RemoteLookUp::genomes_to_dbas | ( | ) |
Description : Build a set of Bio::EnsEMBL::DBSQL::DBAdaptor instances with the supplied info objects Argument : array ref of Bio::EnsEMBL::MetaData::GenomeInfo Exceptions : None Return type : array ref of Bio::EnsEMBL::DBSQL::DBAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all | ( | ) |
Description : Return all database adaptors that have been retrieved from registry Argument : None Exceptions : None Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_accessions | ( | ) |
Description : Return list of all INSDC sequence accessions (or other seq_region names) registered with the helper Exceptions : None Return type : Arrayref of strings
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_assemblies | ( | ) |
Description : Return list of all INSDC assembly accessions registered with the helper Exceptions : None Return type : Arrayref of strings
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_by_accession | ( | ) |
Description : Returns the database adaptor(s) that contains a seq_region with the supplied INSDC accession (or other seq_region name) Argument : Int Exceptions : None Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_by_dbname | ( | ) |
Description : Returns all database adaptors that have the supplied dbname Argument : String Exceptions : None Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_by_name_pattern | ( | ) |
Description : Return all database adaptors that have an alias/name that match the supplied regexp Argument : String Exceptions : None Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_by_taxon_branch | ( | ) |
Description : Returns all database adaptors that lie beneath the specified taxon node Argument : String Exceptions : None Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_by_taxon_id | ( | ) |
Description : Returns all database adaptors that have the supplied taxonomy ID Argument : String Exceptions : None Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_dbnames | ( | ) |
Description : Return all database names used by the DBAs retrieved from the registry Argument : None Exceptions : None Return type : Arrayref of strings
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_names | ( | ) |
Description : Return list of all species names registered with the helper Exceptions : None Return type : Arrayref of strings
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_taxon_ids | ( | ) |
Description : Return list of all taxon IDs registered with the helper Exceptions : None Return type : Arrayref of integers
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_versioned_accessions | ( | ) |
Description : Return list of all versioned INSDC sequence accessions (or other seq_region names) registered with the helper Exceptions : None Return type : Arrayref of strings
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_all_versioned_assemblies | ( | ) |
Description : Return list of all versioned INSDC assembly accessions registered with the helper Exceptions : None Return type : Arrayref of strings
public Bio::EnsEMBL::DBSQL::DatabaseAdaptor Bio::EnsEMBL::LookUp::RemoteLookUp::get_by_assembly_accession | ( | ) |
Description : Returns the database adaptor that contains the assembly with the supplied INSDC assembly accession Argument : Int Exceptions : None Return type : Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Arrayref Bio::EnsEMBL::LookUp::RemoteLookUp::get_by_name_exact | ( | ) |
Description : Return database adaptor that has the supplied string as an alias/name Argument : String Exceptions : None Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
public Bio::EnsEMBL::LookUp::RemoteLookUp::new | ( | ) |
Undocumented method