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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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

CONTACT

Juguang Xiao, [email protected]

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 reaches 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 valid rank name

classification

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