Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor:

Public Member Functions
public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor	new_public ()
public	helper ()
public	mapper ()
public Bio::EnsEMBL::TaxonomyNode	fetch_by_coredbadaptor ()
public Arrayref	fetch_by_coredbadaptors ()
public Bio::EnsEMBL::TaxonomyNode	fetch_by_taxon_id ()
public Bio::EnsEMBL::TaxonomyNode	fetch_by_taxon_name ()
public Arrayref	fetch_all_by_taxon_ids ()
public Arrayref	fetch_all_by_rank ()
public Arrayref	fetch_all_by_name ()
public Arrayref	fetch_all_by_name_and_class ()
public Arrayref	fetch_all_by_name_and_rank ()
public Bio::EnsEMBL::TaxonomyNode	fetch_parent ()
public Bio::EnsEMBL::TaxonomyNode	fetch_root ()
public Arrayref	fetch_children ()
public	fetch_all_common_ancestors ()
public	fetch_common_ancestor ()
public	fetch_ancestor_by_rank ()
protected	_get_node ()
protected	_get_node_id ()
public Arrayref	fetch_descendants ()
public Arrayref	fetch_descendant_ids ()
public Arrayref	fetch_leaf_nodes ()
public Arrayref	fetch_ancestors ()
public Boolean	node_has_ancestor ()
public Arrayref	fetch_descendants_offset ()
public void	add_descendants ()
public Bio::EnsEMBL::TaxonomyNode	associate_nodes ()
public void	set_num_descendants ()
protected Bio::EnsEMBL::TaxonomyNode	_get_parent_by_index ()
public void	build_pruned_tree ()
public void	collapse_tree ()
public Int	distance_between_nodes ()
protected Arrayref	_build_node_array ()
protected Arrayref	_restrict_set ()
protected Arrayref	_first_element ()

Detailed Description

Synopsis

#create an adaptor (Registry cannot be used currently)
my $tax_dba =  Bio::EnsEMBL::DBSQL::TaxonomyDBAdaptor->new(
                                      -user   => $tax_user,
                                      -pass   => $tax_pass,
                                      -dbname => $tax_db,
                                      -host   => $tax_host,
                                      -port   => $tax_port);                                      
my $node_adaptor = $tax_dba->get_TaxonomyNodeAdaptor();
# get a node for an ID
my $node = $node_adaptor->fetch_by_taxon_id(511145);
# print some info
printf "Node %d is %s %s\n",$node->taxon_id(),$node->rank(),$node->names()->{'scientific name'}->[0];
# Finding ancestors
my @lineage = @{$node_adaptor->fetch_ancestors($node)};
for my $node (@lineage) {
    printf "Node %d is %s %s\n",$node->taxon_id(),$node->rank(),$node->names()->{'scientific name'}->[0];
}

Description

A database adaptor allowing access to the nodes of the NCBI taxonomy. It is currently managed independently of the registry:
my $tax_dba =  Bio::EnsEMBL::DBSQL::TaxonomyDBAdaptor->new(
                                      -user   => $tax_user,
                                      -pass   => $tax_pass,
                                      -dbname => $tax_db,
                                      -host   => $tax_host,
                                      -port   => $tax_port);
                                                                          
my $node_adaptor = $tax_dba->get_TaxonomyNodeAdaptor();
# or alternatively
my $node_adaptor = Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor->new($tax_dba);

The TaxonomyNodeAdaptor handles TaxonomyNode objects, which represent nodes in the NCBI taxonomy

There are two main practical uses for the :
1. Accessing the taxonomy database to find species of interest and to then find those within the ENA databases e.g. to find all 
descendants of the node representing Escherichia coli:
    my $node = $node_adaptor->fetch_by_taxon_id(562);
    for my $child (\@{$node_adaptor->fetch_descendants($node)}) {
        my $dbas = $helper->get_all_by_taxon_id($node->taxon_id())
        if(defined $dbas) {
            for my $dba (\@{$dbas}) {
                # do something with the $dba
            }
        }
    }

2. Placing ENA species into a taxonomic hierarchy and manipulating that hierarchy (mainly for use in the web interface)
    # iterate over all dbas from a registry or ENARegistryHelper
    for my $dba (\@{$helper->get_all_DBAdaptors()}) {
        my $node = $node_adaptor->fetch_by_coredbadaptor($dba);
        # add the node to a hash set of leaf nodes if not already there
        if ( $leaf_nodes->{ $node->taxon_id() } ) {
            $node = $leaf_nodes->{ $node->taxon_id() };
        } else {
            $leaf_nodes->{ $node->taxon_id() } = $node;
        }
        # attach the DBA to the node
        push \@{$node->dba()}, $dba;
    }
    my \@leaf_nodes = values(%$leaf_nodes);
    # get the root of the tree
    my $root = $node_adaptor->fetch_by_taxon_id(1);
    # get rid of all branches of the taxonomy that don't involve a node from the dba
    $node_adaptor->build_pruned_tree( $root, \\@leaf_nodes );
    # collapse 
    $node_adaptor->collapse_tree($root);
    

Member Function Documentation

protected Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::_build_node_array

(

)

Description: Build a sparse array based on left/right indices of a set of nodes to allow speedy lookup
Argument: Arrayref of Bio::EnsEMBL::TaxonomyNode
Return type: Arrayref containing arrayref of 1/0 by left/right, min left index, max right index
 

Code:

protected Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::_first_element

(

)

  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
 

Code:

protected Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::_get_node

(

)

Undocumented method

Code:

protected Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::_get_node_id

(

)

Undocumented method

Code:

protected Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::_get_parent_by_index

(

)

Description: Find the parent of a node, initially based on left/right index to find direct parent, and then by recursion through parents to work back to the closest common ancestor.
Argument: Current node
Argument: Prospective parent
Return type: Bio::EnsEMBL::TaxonomyNode
 

Code:

protected Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::_restrict_set

(

)

Description: Restrict the input set to those needed to build a tree including all members of the leaf set
Argument: Arrayref of Bio::EnsEMBL::TaxonomyNode (leaf set)
Argument: Arrayref of Bio::EnsEMBL::TaxonomyNode (input set)
Return: Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public void Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::add_descendants

(

)

Description : Fetch descendants for the supplied node and assemble into a tree
Argument    : Bio::EnsEMBL::TaxonomyNode
Return type : None
 

Code:

public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::associate_nodes

(

)

Description : Associate the supplied nodes into a tree based on left/right indices and return the root node
Argument    : Arrayref of Bio::EnsEMBL::TaxonomyNode
Return type : Bio::EnsEMBL::TaxonomyNode
 

Code:

public void Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::build_pruned_tree

(

)

Description : Restrict supplied tree by list of key leaf nodes
Argument    : Bio::EnsEMBL::TaxonomyNode
Argument    : Array ref of Bio::EnsEMBL::TaxonomyNode
Return type : None
 

Code:

public void Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::collapse_tree

(

)

Description : Remove all nodes from tree that do not fit the required criteria. By default, these are not branch points, the root node, leaf nodes or nodes with database adaptors.
Argument    : Bio::EnsEMBL::TaxonomyNode
Argument    : Array ref of Bio::EnsEMBL::TaxonomyNode
Argument    : (Optional) Subroutine reference which is used to define whether to retain a node
Return type : None
 

Code:

public Int Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::distance_between_nodes

(

)

Description : Count the number of steps in the shortest route from one node to another (via the common ancestor)
Argument    : Bio::EnsEMBL::TaxonomyNode
Argument    : Bio::EnsEMBL::TaxonomyNode
Return type : Integer
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_all_by_name

(

)

Description : Fetch an array of nodes which have a name LIKE the supplied String
Argument    : Name as String (can contain SQL wildcards)
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_all_by_name_and_class

(

)

Description : Fetch an array of nodes which have a name and name class LIKE the supplied Strings
Argument    : Name as String (can contain SQL wildcards)
Argument    : Name class as String (can contain SQL wildcards)
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_all_by_name_and_rank

(

)

Description : Fetch an array of nodes which have the supplied rank and a name LIKE the supplied String
Argument    : Name as String (can contain SQL wildcards)
Argument    : Rank as String
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_all_by_rank

(

)

Description : Fetch an array of nodes which have the supplied rank
Argument    : String
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_all_by_taxon_ids

(

)

Description : Fetch an array of nodes corresponding to the supplied taxonomy IDs
Argument    : Arrayref of Int
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_all_common_ancestors

(

)

Undocumented method

Code:

public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_ancestor_by_rank

(

)

Undocumented method

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_ancestors

(

)

Description : Fetch an array of nodes which are above the supplied node on the tree (ordered ascending up the tree)
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_by_coredbadaptor

(

)

Description : Fetch a single node corresponding to the taxonomy ID found in the supplied Ensembl DBAdaptor. Warning: Passing 2 different DBAs with the same taxid will yield two distinct Node objects which will need merging! COnsider using fetch_by_coredbadaptors instead.
Argument    : Bio::EnsEMBL::DBSQL::DBAdaptor
Return type : Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_by_coredbadaptors

(

)

Description : Fetch an array of nodes corresponding to the taxonomy IDs found in the supplied Ensembl DBAdaptors.
Argument    : Bio::EnsEMBL::DBSQL::DBAdaptor
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_by_taxon_id

(

)

Description : Fetch a single node corresponding to the supplied taxon ID.
Argument    : Int
Return type : Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_by_taxon_name

(

)

Description : Fetch a single node where the name is as specified
Argument    : String
Return type : Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_children

(

)

Description : Fetch an array of nodes for which the parent is the supplied node
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_common_ancestor

(

)

Undocumented method

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_descendant_ids

(

)

Description : Fetch an array of taxon IDs below the supplied node on the tree
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Return type : Arrayref of integers
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_descendants

(

)

Description : Fetch an array of nodes below the supplied node on the tree
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_descendants_offset

(

)

Description : Fetch an array of nodes below the node the specified number of levels on the tree above the specified node
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Argument    : offset (number of rows to move up tree before getting descendants - default is 1)
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Arrayref Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_leaf_nodes

(

)

Description : Fetch an array of nodes which are the leaves below the supplied node on the tree
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_parent

(

)

 
Description : Fetch a single node corresponding to the parent of the node
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Return type : Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::fetch_root

(

)

Description : Fetch a single node corresponding to the root of the supplied node
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Return type : Bio::EnsEMBL::TaxonomyNode
 

Code:

public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::helper

(

)

Undocumented method

Code:

public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::mapper

(

)

Code:

public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::new_public

(

)

    Description : Build a new adaptor from the public database
    Returns     : Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor
 

Code:

public Boolean Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::node_has_ancestor

(

)

Description : Find if one node has another as an ancestor
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of desired node
Argument    : Bio::EnsEMBL::TaxonomyNode or ID of ancestor
Return type : 1 if ancestor 
 

Code:

public void Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor::set_num_descendants

(

)

Description : Traverse the supplied tree setting number of descendants based on current tree structure
Argument    : Bio::EnsEMBL::TaxonomyNode
Return type : None
 

Code:

---

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

• modules/Bio/EnsEMBL/DBSQL/TaxonomyNodeAdaptor.pm