Bio::EnsEMBL::LookUp Class Reference

Public Member Functions
public	new ()
public	register_all_dbs ()
public	AUTOLOAD ()
public	DESTROY ()
public	uniq ()

Detailed Description

Synopsis

# default creation using latest public release of Ensembl Genomes
my $lookup = Bio::EnsEMBL::LookUp->new();

Description

This module is a helper that provides additional methods to aid navigating a registry of >6000 species across >25 databases. 
It does not replace the Registry but provides some additional methods for finding species e.g. by searching for species that 
have an alias that match a regular expression, or species which are derived from a specific ENA/INSDC accession, or species
that belong to a particular part of the taxonomy. 

There are a number of ways of creating a lookup but the simplest is to use the default setting of the latest publicly 
available Ensembl Genomes databases: 

    my $lookup = Bio::EnsEMBL::LookUp->new();

Once a lookup has been created, there are various methods to retreive DBAdaptors for species of interest:

1. To find species by name - all DBAdaptors for species with a name or alias matching the supplied string:

    $dbas = $lookup->get_by_name_exact('Escherichia coli str. K-12 substr. MG1655');

2. To find species by name pattern - all DBAdaptors for species with a name or alias matching the supplied regexp:

    $dbas = $lookup->get_by_name_exact('Escherichia coli .*);

3. To find species with the supplied taxonomy ID:

    $dbas = $lookup->get_all_by_taxon_id(388919);
    
4. In coordination with a taxonomy node adaptor to get DBAs for all descendants of a node:

    my $node = $node_adaptor->fetch_by_taxon_id(511145);
    for my $child (\@{$node_adaptor->fetch_descendants($node)}) {
        my $dbas = $lookup->get_all_by_taxon_id($node->taxon_id())
        if(defined $dbas) {
            for my $dba (\@{$dbas}) {
                # do something with the $dba
            }
        }
    }

The retrieved DBAdaptors can then be used as normal e.g.

    for my $gene (\@{$dba->get_GeneAdaptor()->fetch_all_by_biotype('protein_coding')}) {
        print $gene->external_name."\n";
    }

Once retrieved, the arguments needed for constructing a DBAdaptor directly can be dumped for later use e.g.

    my $args = $lookup->dba_to_args($dba);
    ... store and retrieve $args for use in another script ... 
    my $resurrected_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(\@$args);

Local implementation

The default implementation of LookUp is a remoting implementation that uses a MySQL database backend
to look up genome information. The previous implementation loaded an internal hash from either a JSON file
(remote or local) or by processing the contents of the Registry. 

This implementation is still available, but has been renamed Bio::EnsEMBL::LookUp::LocalLookUp and should
be constructed directly.
  

Member Function Documentation

public Bio::EnsEMBL::LookUp::AUTOLOAD

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Undocumented method

Code:

public Bio::EnsEMBL::LookUp::DESTROY

(

)

Undocumented method

Code:

public Bio::EnsEMBL::LookUp::new

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Undocumented method

Code:

public Bio::EnsEMBL::LookUp::register_all_dbs

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Undocumented method

Code:

public Bio::EnsEMBL::LookUp::uniq

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Undocumented method

Code:

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

• modules/Bio/EnsEMBL/LookUp.pm