#
# BioPerl module for Bio::Taxon
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala, based heavily on a module by Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Taxon - A node in a represented taxonomy
=head1 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);
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 CONTRIBUTORS
Jason Stajich, jason-at-bioperl-dot-org (original Bio::Taxonomy::Node)
Juguang Xiao, juguang@tll.org.sg
Gabriel Valiente, valiente@lsi.upc.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Taxon;
use strict;
use Scalar::Util qw(blessed);
use Bio::DB::Taxonomy;
use base qw(Bio::Tree::Node Bio::IdentifiableI);
=head2 new
Title : new
Usage : my $obj = Bio::Taxonomy::Node->new();
Function: Builds a new Bio::Taxonomy::Node object
Returns : an instance of Bio::Taxonomy::Node
Args : -dbh => a reference to a Bio::DB::Taxonomy object
[no default]
-name => a string representing the taxon name
(scientific name)
-id => human readable id - typically NCBI taxid
-ncbi_taxid => same as -id, but explicitly say that it is an
NCBI taxid
-rank => node rank (one of 'species', 'genus', etc)
-common_names => array ref of all common names
-division => 'Primates', 'Rodents', etc
-genetic_code => genetic code table number
-mito_genetic_code => mitochondrial genetic code table number
-create_date => date created in database
-update_date => date last updated in database
-pub_date => date published in database
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($name, $id, $objid, $rank, $div, $dbh, $ncbitaxid, $commonname,
$commonnames, $gcode, $mitocode, $createdate, $updatedate, $pubdate,
$parent_id) = $self->_rearrange([qw(NAME ID OBJECT_ID RANK DIVISION DBH
NCBI_TAXID COMMON_NAME COMMON_NAMES
GENETIC_CODE MITO_GENETIC_CODE
CREATE_DATE UPDATE_DATE PUB_DATE
PARENT_ID)], @args);
if (defined $id && (defined $ncbitaxid && $ncbitaxid ne $id || defined $objid && $objid ne $id)) {
$self->warn("Only provide one of -id, -object_id or -ncbi_taxid, using $id\n");
}
elsif(!defined $id) {
$id = $objid || $ncbitaxid;
}
defined $id && $self->id($id);
$self->{_ncbi_tax_id_provided} = 1 if $ncbitaxid;
defined $rank && $self->rank($rank);
defined $name && $self->node_name($name);
my @common_names;
if ($commonnames) {
$self->throw("-common_names takes only an array reference") unless $commonnames
&& ref($commonnames) eq 'ARRAY';
@common_names = @{$commonnames};
}
if ($commonname) {
my %c_names = map { $_ => 1 } @common_names;
unless (exists $c_names{$commonname}) {
unshift(@common_names, $commonname);
}
}
@common_names > 0 && $self->common_names(@common_names);
defined $gcode && $self->genetic_code($gcode);
defined $mitocode && $self->mitochondrial_genetic_code($mitocode);
defined $createdate && $self->create_date($createdate);
defined $updatedate && $self->update_date($updatedate);
defined $pubdate && $self->pub_date($pubdate);
defined $div && $self->division($div);
defined $dbh && $self->db_handle($dbh);
# deprecated and will issue a warning when method called,
# eventually to be removed completely as option
defined $parent_id && $self->parent_id($parent_id);
# some things want to freeze/thaw Bio::Species objects, but
# _root_cleanup_methods contains a CODE ref, delete it.
delete $self->{_root_cleanup_methods};
return $self;
}
=head1 Bio::IdentifiableI interface
Also see L<Bio::IdentifiableI>
=head2 version
Title : version
Usage : $taxon->version($newval)
Returns : value of version (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub version {
my $self = shift;
return $self->{'version'} = shift if @_;
return $self->{'version'};
}
=head2 authority
Title : authority
Usage : $taxon->authority($newval)
Returns : value of authority (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub authority {
my $self = shift;
return $self->{'authority'} = shift if @_;
return $self->{'authority'};
}
=head2 namespace
Title : namespace
Usage : $taxon->namespace($newval)
Returns : value of namespace (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub namespace {
my $self = shift;
return $self->{'namespace'} = shift if @_;
return $self->{'namespace'};
}
=head1 Bio::Taxonomy::Node implementation
=head2 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 L<Bio::DB::Taxonomy>
=cut
sub db_handle {
my $self = shift;
if (@_) {
my $db = shift;
if (! ref($db) || ! $db->isa('Bio::DB::Taxonomy')) {
$self->throw("Must provide a valid Bio::DB::Taxonomy object to db_handle()");
}
if (!$self->{'db_handle'} || ($self->{'db_handle'} && $self->{'db_handle'} ne $db)) {
my $new_self = $self->_get_similar_taxon_from_db($self, $db);
$self->_merge_taxa($new_self) if $new_self;
}
# NB: The Bio::DB::Taxonomy modules access this data member directly
# to avoid calling this method and going infinite
$self->{'db_handle'} = $db;
}
return $self->{'db_handle'};
}
=head2 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)
=cut
sub rank {
my $self = shift;
return $self->{'rank'} = shift if @_;
return $self->{'rank'};
}
=head2 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
=cut
sub id {
my $self = shift;
return $self->SUPER::id(@_);
}
*object_id = \&id;
=head2 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
=cut
sub ncbi_taxid {
my ($self, $id) = @_;
if ($id) {
$self->{_ncbi_tax_id_provided} = 1;
return $self->SUPER::id($id);
}
if ($self->{_ncbi_tax_id_provided}) {
return $self->SUPER::id;
}
return;
}
=head2 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
=cut
sub parent_id {
my $self = shift;
if (@_) {
$self->warn("You can no longer set the parent_id - use ancestor() instead");
}
my $ancestor = $self->ancestor() || return;
return $ancestor->id;
}
*parent_taxon_id = \&parent_id;
=head2 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)
=cut
sub genetic_code {
my $self = shift;
return $self->{'genetic_code'} = shift if @_;
return $self->{'genetic_code'};
}
=head2 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)
=cut
sub mitochondrial_genetic_code {
my $self = shift;
return $self->{'mitochondrial_genetic_code'} = shift if @_;
return $self->{'mitochondrial_genetic_code'};
}
=head2 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)
=cut
sub create_date {
my $self = shift;
return $self->{'create_date'} = shift if @_;
return $self->{'create_date'};
}
=head2 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)
=cut
sub update_date {
my $self = shift;
return $self->{'update_date'} = shift if @_;
return $self->{'update_date'};
}
=head2 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)
=cut
sub pub_date {
my $self = shift;
return $self->{'pub_date'} = shift if @_;
return $self->{'pub_date'};
}
=head2 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
=cut
sub ancestor {
my $self = shift;
my $ancestor = $self->SUPER::ancestor(@_);
if ($ancestor) {
return $ancestor;
}
my $dbh = $self->db_handle;
#*** could avoid the db lookup if we knew our current id was definitely
# information from the db...
my $definitely_from_dbh = $self->_get_similar_taxon_from_db($self);
return $dbh->ancestor($definitely_from_dbh);
}
=head2 get_Parent_Node
Title : get_Parent_Node
Function: Synonym of ancestor()
Status : deprecated
=cut
sub get_Parent_Node {
my $self = shift;
$self->warn("get_Parent_Node is deprecated, use ancestor() instead");
return $self->ancestor(@_);
}
=head2 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.
=cut
# implemented by Bio::Tree::Node
=head2 get_Children_Nodes
Title : get_Children_Nodes
Function: Synonym of each_Descendent()
Status : deprecated
=cut
sub get_Children_Nodes {
my $self = shift;
$self->warn("get_Children_Nodes is deprecated, use each_Descendent() instead");
return $self->each_Descendent(@_);
}
=head2 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
=cut
sub name {
my ($self, $name_class, @names) = @_;
$self->throw('No name class specified') unless defined $name_class;
if (@names) {
if ($name_class =~ /scientific|division/i) {
delete $self->{'_names_hash'}->{$name_class};
@names = (shift(@names));
}
push @{$self->{'_names_hash'}->{$name_class}}, @names;
}
return $self->{'_names_hash'}->{$name_class} || return;
}
=head2 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)
=cut
sub node_name {
my $self = shift;
my @v = @{$self->name('scientific', @_) || []};
return pop @v;
}
*scientific_name = \&node_name;
=head2 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)
=cut
sub common_names {
my $self = shift;
my @v = @{$self->name('common', @_) || []};
return ( wantarray ) ? @v : pop @v;
}
*common_name = \&common_names;
=head2 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)
=cut
sub division {
my $self = shift;
my @v = @{$self->name('division',@_) || []};
return pop @v;
}
# get a node from the database that is like the supplied node
sub _get_similar_taxon_from_db {
#*** not really happy with this having to be called so much; there must be
# a better way...
my ($self, $taxon, $db) = @_;
$self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa("Bio::Taxon");
($self->id || $self->node_name) || return;
$db ||= $self->db_handle || return;
if (!blessed($db) || !$db->isa('Bio::DB::Taxonomy')) {
$self->throw("DB handle is not a Bio::DB::Taxonomy: got $db in node ".$self->node_name)
}
my $db_taxon = $db->get_taxon(-taxonid => $taxon->id) if $taxon->id;
unless ($db_taxon) {
my @try_ids = $db->get_taxonids($taxon->node_name) if $taxon->node_name;
my $own_rank = $taxon->rank || 'no rank';
foreach my $try_id (@try_ids) {
my $try = $db->get_taxon(-taxonid => $try_id);
my $try_rank = $try->rank || 'no rank';
if ($own_rank eq 'no rank' || $try_rank eq 'no rank' || $own_rank eq $try_rank) {
$db_taxon = $try;
last;
}
}
}
return $db_taxon;
}
# merge data from supplied Taxon into self
sub _merge_taxa {
my ($self, $taxon) = @_;
$self->throw("Must supply a Bio::Taxon object") unless ref($taxon) && $taxon->isa('Bio::Taxon');
return if ($taxon eq $self);
foreach my $attrib (qw(scientific_name version authority namespace genetic_code mitochondrial_genetic_code create_date update_date pub_date division id)) {
my $own = $self->$attrib();
my $his = $taxon->$attrib();
if (!$own && $his) {
$self->$attrib($his);
}
}
my $own = $self->rank || 'no rank';
my $his = $taxon->rank || 'no rank';
if ($own eq 'no rank' && $his ne 'no rank') {
$self->rank($his);
}
my %own_cnames = map { $_ => 1 } $self->common_names;
my %his_cnames = map { $_ => 1 } $taxon->common_names;
foreach (keys %his_cnames) {
unless (exists $own_cnames{$_}) {
$self->common_names($_);
}
}
#*** haven't merged the other things in names() hash, could do above much easier with direct access to object data
}
=head2 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.
=cut
sub remove_Descendent {
# need to override this method from Bio::Tree::Node since it casually
# throws away nodes if they don't branch
my ($self,@nodes) = @_;
my $c= 0;
foreach my $n ( @nodes ) {
if ($self->{'_desc'}->{$n->internal_id}) {
$self->{_removing_descendent} = 1;
$n->ancestor(undef);
$self->{_removing_descendent} = 0;
$self->{'_desc'}->{$n->internal_id}->ancestor(undef);
delete $self->{'_desc'}->{$n->internal_id};
$c++;
}
}
return $c;
}
1;