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Bio::Taxon.3pm

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 $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:

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

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 explicitely 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
  Status  : deprecated
 
 

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.