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.
[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: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 [email protected]CONTRIBUTORS
Jason Stajich, jason-at-bioperl-dot-org (original Bio::Taxonomy::Node) Juguang Xiao, [email protected] Gabriel Valiente, [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::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::IdentifiableIversion
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.