Bio::Taxon(3)

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.