Bio::Taxonomy(3pm)					User Contributed Perl Documentation					Bio::Taxonomy(3pm)

NAME

       Bio::Taxonomy - representing Taxonomy.

SYNOPSIS

	 # NB: This module is deprecated. Use Bio::Taxon in combination with
	 # Bio::Tree::Tree methods instead.

	 use Bio::Taxonomy;

	 # CREATION: You can either create an instance by assigning it,
	 # or fetch it through factory.

	 # Create the nodes first. See Bio::Taxonomy::Node for details.
	 my $node_species_sapiens = Bio::Taxonomy::Node->new(
	     -object_id => 9606, # or -ncbi_taxid. Requird tag
	     -names => {
		 'scientific' => ['sapiens'],
		 'common_name' => ['human']
	     },
	     -rank => 'species'  # Required tag
	 );
	 my $node_genus_Homo = Bio::Taxonomy::Node->new(
	     -object_id => 9605,
	     -names => { 'scientific' => ['Homo'] },
	     -rank => 'genus'
	 );
	 my $node_class_Mammalia = Bio::Taxonomy::Node->new(
	     -object_id => 40674,
	     -names => {
		 'scientific' => ['Mammalia'],
		 'common' => ['mammals']
	     },
	     -rank => 'class'
	 );
	 my $taxonomy = Bio::Taxonomy->new;
	 $taxonomy->add_node($node_class_Mammalia);
	 $taxonomy->add_node($node_species_sapiens);
	 $taxonomy->add_node($node_genus_Homo);

	 # OR you can fetch it through a factory implementing
	 # Bio::Taxonomy::FactoryI
	 my $factory;

	 my $taxonomy = $factory->fetch_by_ncbi_taxid(40674);

	 # USAGE

	 # In this case, binomial returns a defined value.
	 my $binomial = $taxonomy->binomial;

	 # 'common_names' refers to the lowest-rank node's common names, in
	 # array.
	 my @common_names = $taxonomy->common_names;

	 # 'get_node', will return undef if the rank is no defined in
	 # taxonomy object.  It will throw error if the rank string is not
	 # defined, say 'species lah'.
	 my $node = $taxonomy->get_node('class');
	 my @nodes = $taxonomy->get_all_nodes;

	 # Also, you can search for parent and children nodes, if taxonomy
	 # comes with factory.

	 my $parent_taxonomy = $taxonomy->get_parent

DESCRIPTION

       Bio::Taxonomy object represents any rank-level in taxonomy system, rather than Bio::Species which is able to represent only species-level.

       There are two ways to create Taxonomy object, e.g.  1) instantiate an object and assign all nodes on your own code; and 2) fetch an object
       by factory.

   Creation by instantiation
       The abstraction of Taxonomy is actually a hash in data structure term. The keys of the hash are the rank names, such as 'genus' and
       'species', and the values are the instances of Bio::Taxonomy::Node.

   Creation by Factory fetching
       NCBI Taxonomy system is well accepted as the standard. The Taxonomy Factories in bioperl access this system, through HTTP to NCBI Entrez,
       dump file, and advanced biosql database.

       Bio::Taxonomy::FactoryI defines all methods that all implementations must obey.

       $factory->fetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names.

       $factory->fetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument.

       $factory->fetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument.

   Usage of Taxonomy object
       ##

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://redmine.open-bio.org/projects/bioperl/

CONTACT

       Juguang Xiao, juguang@tll.org.sg

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->new();
	Function: Builds a new Bio::Taxonomy object
	Returns : Bio::Taxonomy
	Args	: -method  -> method used to decide classification
			      (none|trust|lookup)
		  -ranks   -> what ranks are there

   method
	Title	: method
	Usage	: $obj = taxonomy->method($method);
	Function: set or return the method used to decide classification
	Returns : $obj
	Args	: $obj

   classify
	Title	: classify
	Usage	: @obj[][0-1] = taxonomy->classify($species);
	Function: return a ranked classification
	Returns : @obj of taxa and ranks as word pairs separated by "@"
	Args	: Bio::Species object

   level_of_rank
	Title	: level_of_rank
	Usage	: $obj = taxonomy->level_of_rank($obj);
	Function: returns the level of a rank name
	Returns : $obj
	Args	: $obj

   rank_of_number
	Title	: rank_of_number
	Usage	: $obj = taxonomy->rank_of_number($obj);
	Function: returns the rank name of a rank level
	Returns : $obj
	Args	: $obj

   ranks
	Title	: ranks
	Usage	: @obj = taxonomy->ranks(@obj);
	Function: set or return all ranks
	Returns : @obj
	Args	: @obj

   add_node
	 Title:    add_node
	 Usage:    $obj->add_node($node[, $node2, ...]);
	 Function: add one or more Bio::Taxonomy::Node objects
	 Returns:  None
	 Args:	   any number of Bio::Taxonomy::Node(s)

   binomial
	 Title	 : binomial
	 Usage	 : my $val = $obj->binomial;
	 Function: returns the binomial name if this taxonomy reachs species level
	 Returns : the binomial name
		   OR undef if taxonmy does not reach species level
	 Args	 : [No arguments]

   get_node
	 Title	 : get_node
	 Usage	 : $node = $taxonomy->get_node('species');
	 Function: get a Bio::Taxonomy::Node object according to rank name
	 Returns : a Bio::Taxonomy::Node object or undef if null
	 Args	 : a vaild rank name

   classification
	 Title	 : classification
	 Usage	 : @names = $taxonomy->classification;
	 Function: get the classification names of one taxonomy
	 Returns : array of names
	 Args	 : [No arguments]

perl v5.14.2							    2012-03-02							Bio::Taxonomy(3pm)