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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
 
 

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:

   http://bugzilla.open-bio.org/
 
 

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]