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BioPerl-1.7.8
River stage two • 60 direct dependents • 64 total dependents
/ Bio::Taxon

NAME

Bio::Taxon - A node in a represented taxonomy

SYNOPSIS


            

              
              
use Bio::Taxon;
# Typically you will get a Taxon from a Bio::DB::Taxonomy object
# but here is how you initialize one
my $taxon = Bio::Taxon->new(-name      => $name,
                            -id        => $id,
                            -rank      => $rank,
                            -division  => $div);
# Get one from a database
my $dbh = Bio::DB::Taxonomy->new(-source   => 'flatfile',
                                 -directory=> '/tmp',
                                 -nodesfile=> '/path/to/nodes.dmp',
                                 -namesfile=> '/path/to/names.dmp');
my $human = $dbh->get_taxon(-name => 'Homo sapiens');
$human = $dbh->get_taxon(-taxonid => '9606');
print "id is ", $human->id, "\n"; # 9606
print "rank is ", $human->rank, "\n"; # species
print "scientific name is ", $human->scientific_name, "\n"; # Homo sapiens
print "division is ", $human->division, "\n"; # Primates
my $mouse = $dbh->get_taxon(-name => 'Mus musculus');
# You can quickly make your own lineages with the list database
my @ranks = qw(superkingdom class genus species);
my @h_lineage = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
my $list_dbh = Bio::DB::Taxonomy->new(-source => 'list', -names => \@h_lineage,
                                                         -ranks => \@ranks);
$human = $list_dbh->get_taxon(-name => 'Homo sapiens');
my @names = $human->common_names; # @names is empty
$human->common_names('woman');
@names = $human->common_names; # @names contains woman
# You can switch to another database when you need more information
my $entrez_dbh = Bio::DB::Taxonomy->new(-source => 'entrez');
$human->db_handle($entrez_dbh);
@names = $human->common_names; # @names contains woman, human, man
# Since Bio::Taxon implements Bio::Tree::NodeI, we have access to those
# methods (and can manually create our own taxa and taxonomy without the use
# of any database)
my $homo = $human->ancestor;
# Though be careful with each_Descendent - unless you add_Descendent()
# yourself, you won't get an answer because unlike for ancestor(), Bio::Taxon
# does not ask the database for the answer. You can ask the database yourself
# using the same method:
($human) = $homo->db_handle->each_Descendent($homo);
# We can also take advantage of Bio::Tree::Tree* methods:
# a) some methods are available with just an empty tree object
use Bio::Tree::Tree;
my $tree_functions = Bio::Tree::Tree->new();
my @lineage = $tree_functions->get_lineage_nodes($human);
my $lineage = $tree_functions->get_lineage_string($human);
my $lca = $tree_functions->get_lca($human, $mouse);
# b) for other methods, create a tree using your Taxon object
my $tree = Bio::Tree::Tree->new(-node => $human);
my @taxa = $tree->get_nodes;
$homo = $tree->find_node(-rank => 'genus');
# Normally you can't get the lca of a list-database derived Taxon and an
# entrez or flatfile-derived one because the two different databases might
# have different roots and different numbers of ranks between the root and the
# taxa of interest. To solve this, make a tree of the Taxon with the more
# detailed lineage and splice out all the taxa that won't be in the lineage of
# your other Taxon:
my $entrez_mouse = $entrez_dbh->get_taxon(-name => 'Mus musculus');
my $list_human = $list_dbh->get_taxon(-name => 'Homo sapiens');
my $mouse_tree = Bio::Tree::Tree->new(-node => $entrez_mouse);
$mouse_tree->splice(-keep_rank => \@ranks);
$lca = $mouse_tree->get_lca($entrez_mouse, $list_human);

DESCRIPTION

This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the species nodes and can relate their connections.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.


            

              
              
bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:


            

              
              
https://github.com/bioperl/bioperl-live/issues

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

CONTRIBUTORS

Jason Stajich, jason-at-bioperl-dot-org (original Bio::Taxonomy::Node) Juguang Xiao, juguang@tll.org.sg Gabriel Valiente, valiente@lsi.upc.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new


            

              
              
Title   : new
Usage   : my $obj = Bio::Taxonomy::Node->new();
Function: Builds a new Bio::Taxonomy::Node object 
Returns : an instance of Bio::Taxonomy::Node
Args    : -dbh               => a reference to a Bio::DB::Taxonomy object
                                [no default]
          -name              => a string representing the taxon name
                                (scientific name)
          -id                => human readable id - typically NCBI taxid
          -ncbi_taxid        => same as -id, but explicitly say that it is an
                                NCBI taxid
          -rank              => node rank (one of 'species', 'genus', etc)
          -common_names      => array ref of all common names
          -division          => 'Primates', 'Rodents', etc
          -genetic_code      => genetic code table number
          -mito_genetic_code => mitochondrial genetic code table number
          -create_date       => date created in database
          -update_date       => date last updated in database
          -pub_date          => date published in database

Bio::IdentifiableI interface

Also see Bio::IdentifiableI

version


            

              
              
Title   : version
Usage   : $taxon->version($newval)
Returns : value of version (a scalar)
Args    : on set, new value (a scalar or undef, optional)

authority


            

              
              
Title   : authority
Usage   : $taxon->authority($newval)
Returns : value of authority (a scalar)
Args    : on set, new value (a scalar or undef, optional)

namespace


            

              
              
Title   : namespace
Usage   : $taxon->namespace($newval)
Returns : value of namespace (a scalar)
Args    : on set, new value (a scalar or undef, optional)

Bio::Taxonomy::Node implementation

db_handle


            

              
              
Title   : db_handle
Usage   : $taxon->db_handle($newval)
Function: Get/Set Bio::DB::Taxonomy Handle
Returns : value of db_handle (a scalar) (Bio::DB::Taxonomy object)
Args    : on set, new value (a scalar, optional) Bio::DB::Taxonomy object

Also see Bio::DB::Taxonomy

rank


            

              
              
Title   : rank
Usage   : $taxon->rank($newval)
Function: Get/set rank of this Taxon, 'species', 'genus', 'order', etc...
Returns : value of rank (a scalar)
Args    : on set, new value (a scalar or undef, optional)

id


            

              
              
Title   : id
Usage   : $taxon->id($newval)
Function: Get/Set id (NCBI Taxonomy ID in most cases); object_id() and
          ncbi_taxid() are synonyms of this method.
Returns : id (a scalar)
Args    : none to get, OR scalar to set

ncbi_taxid


            

              
              
Title   : ncbi_taxid
Usage   : $taxon->ncbi_taxid($newval)
Function: Get/Set the NCBI Taxonomy ID; This actually sets the id() but only
          returns an id when ncbi_taxid has been explictely set with this
          method.
Returns : id (a scalar)
Args    : none to get, OR scalar to set

parent_id


            

              
              
Title   : parent_id
Usage   : $taxon->parent_id()
Function: Get parent ID, (NCBI Taxonomy ID in most cases);
          parent_taxon_id() is a synonym of this method.
Returns : value of parent_id (a scalar)
Args    : none

trusted_parent_id


            

              
              
Title   : trusted_parent_id
Usage   : $taxon->trusted_parent_id()
Function: If the parent_id is explicitly set, trust it
Returns : simple boolean value (whether or not it has been set)
Args    : none
Notes   : Previously, the parent_id method was to be deprecated in favor of
          using ancestor(). However this removes one key optimization point,
          namely when an implementation has direct access to the taxon's
          parent ID when retrieving the information for the taxon ID.  This
          method is in place so implementations can choose to (1) check whether
          the parent_id is set and (2) trust that the implementation (whether
          it is self or another implementation) set the parent_id correctly.

genetic_code


            

              
              
Title   : genetic_code
Usage   : $taxon->genetic_code($newval)
Function: Get/set genetic code table
Returns : value of genetic_code (a scalar)
Args    : on set, new value (a scalar or undef, optional)

mitochondrial_genetic_code


            

              
              
Title   : mitochondrial_genetic_code
Usage   : $taxon->mitochondrial_genetic_code($newval)
Function: Get/set mitochondrial genetic code table
Returns : value of mitochondrial_genetic_code (a scalar)
Args    : on set, new value (a scalar or undef, optional)

create_date


            

              
              
Title   : create_date
Usage   : $taxon->create_date($newval)
Function: Get/Set Date this node was created (in the database)
Returns : value of create_date (a scalar)
Args    : on set, new value (a scalar or undef, optional)

update_date


            

              
              
Title   : update_date
Usage   : $taxon->update_date($newval)
Function: Get/Set Date this node was updated (in the database)
Returns : value of update_date (a scalar)
Args    : on set, new value (a scalar or undef, optional)

pub_date


            

              
              
Title   : pub_date
Usage   : $taxon->pub_date($newval)
Function: Get/Set Date this node was published (in the database)
Returns : value of pub_date (a scalar)
Args    : on set, new value (a scalar or undef, optional)

ancestor


            

              
              
Title   : ancestor
Usage   : my $ancestor_taxon = $taxon->ancestor()
Function: Retrieve the ancestor taxon. Normally the database is asked what the
          ancestor is.
          If you manually set the ancestor (or you make a Bio::Tree::Tree with
          this object as an argument to new()), the database (if any) will not
          be used for the purposes of this method.
          To restore normal database behaviour, call ancestor(undef) (which
          would remove this object from the tree), or request this taxon again
          as a new Taxon object from the database.
Returns : Bio::Taxon
Args    : none

get_Parent_Node


            

              
              
Title   : get_Parent_Node
Function: Synonym of ancestor()
Status  : deprecated

each_Descendent


            

              
              
Title   : each_Descendent
Usage   : my @taxa = $taxon->each_Descendent();
Function: Get all the descendents for this Taxon (but not their descendents,
          ie. not a recursive fetchall). get_Children_Nodes() is a synonym of
          this method.
          Note that this method never asks the database for the descendents;
          it will only return objects you have manually set with
          add_Descendent(), or where this was done for you by making a
          Bio::Tree::Tree with this object as an argument to new().
          To get the database descendents use
          $taxon->db_handle->each_Descendent($taxon).
Returns : Array of Bio::Taxon objects
Args    : optionally, when you have set your own descendents, the string
          "height", "creation", "alpha", "revalpha", or coderef to be used to
          sort the order of children nodes.

get_Children_Nodes


            

              
              
Title   : get_Children_Nodes
Function: Synonym of each_Descendent()
Status  : deprecated

name


            

              
              
Title:    name
Usage:    $taxon->name('scientific', 'Homo sapiens');
          $taxon->name('common', 'human', 'man');
          my @names = @{$taxon->name('common')};
Function: Get/set the names. node_name(), scientific_name() and common_names()
          are shorthands to name('scientific'), name('scientific') and
          name('common') respectively.
Returns:  names (a array reference)
Args:     Arg1 => the name_class. You can assign any text, but the words
              'scientific' and 'common' have the special meaning, as
              scientific name and common name, respectively. 'scientific' and
              'division' are treated specially, allowing only the first value
              in the Arg2 list to be set.
          Arg2 ... => list of names

node_name


            

              
              
Title   : node_name
Usage   : $taxon->node_name($newval)
Function: Get/set the name of this taxon (node), typically the scientific name
          of the taxon, eg. 'Primate' or 'Homo'; scientific_name() is a synonym
          of this method.
Returns : value of node_name (a scalar)
Args    : on set, new value (a scalar or undef, optional)

common_names


            

              
              
Title   : common_names
Usage   : $taxon->common_names($newval)
Function: Get/add the other names of this taxon, typically the genbank common
          name and others, eg. 'Human' and 'man'. common_name() is a synonym
          of this method.
Returns : array of names in list context, one of those names in scalar context
Args    : on add, new list of names (scalars, optional)

division


            

              
              
Title   : division
Usage   : $taxon->division($newval)
Function: Get/set the division this taxon belongs to, eg. 'Primates' or
          'Bacteria'.
Returns : value of division (a scalar)
Args    : on set, new value (a scalar or undef, optional)

remove_Descendent


            

              
              
Title   : remove_Descendent
Usage   : $node->remove_Descedent($node_foo);
Function: Removes a specific node from being a Descendent of this node
Returns : nothing
Args    : An array of Bio::Node::NodeI objects which have been previously
          passed to the add_Descendent call of this object.