Bio::Phylo::Taxa::Taxon - The operational taxonomic unit.
use Bio::Phylo::IO qw(parse); use Bio::Phylo::Taxa; use Bio::Phylo::Taxa::Taxon; # array of names my @apes = qw( Homo_sapiens Pan_paniscus Pan_troglodytes Gorilla_gorilla ); # newick string my $str = '(((Pan_paniscus,Pan_troglodytes),'; $str .= 'Homo_sapiens),Gorilla_gorilla);'; # create tree object my $tree = parse( -format => 'newick', -string => $str )->first; # instantiate taxa object my $taxa = Bio::Phylo::Taxa->new; # instantiate taxon objects, insert in taxa object foreach( @apes ) { my $taxon = Bio::Phylo::Taxa::Taxon->new( -name => $_, ); $taxa->insert($taxon); } # crossreference tree and taxa $tree->crossreference($taxa); # iterate over nodes while ( my $node = $tree->next ) { # check references if ( $node->get_taxon ) { # prints crossreferenced tips print "match: ", $node->get_name, "\n"; } }
The taxon object models a single operational taxonomic unit. It is useful for cross-referencing datum objects and tree nodes.
Type : Constructor Title : new Usage : my $taxon = Bio::Phylo::Taxa::Taxon->new; Function: Instantiates a Bio::Phylo::Taxa::Taxon object. Returns : A Bio::Phylo::Taxa::Taxon object. Args : none.
Type : Mutator Title : set_data Usage : $taxon->set_data( $datum ); Function: Associates data with the current taxon. Returns : Modified object. Args : Must be an object of type Bio::Phylo::Matrices::Datum
Type : Mutator Title : set_nodes Usage : $taxon->set_nodes($node); Function: Associates tree nodes with the current taxon. Returns : Modified object. Args : A Bio::Phylo::Forest::Node object
Type : Mutator Title : unset_datum Usage : $taxon->unset_datum($node); Function: Disassociates datum from the invocant taxon (i.e. removes reference). Returns : Modified object. Args : A Bio::Phylo::Matrix::Datum object
Type : Mutator Title : unset_node Usage : $taxon->unset_node($node); Function: Disassociates tree node from the invocant taxon (i.e. removes reference). Returns : Modified object. Args : A Bio::Phylo::Forest::Node object
Type : Accessor Title : get_data Usage : @data = @{ $taxon->get_data }; Function: Retrieves data associated with the current taxon. Returns : An ARRAY reference of Bio::Phylo::Matrices::Datum objects. Args : None.
Type : Accessor Title : get_nodes Usage : @nodes = @{ $taxon->get_nodes }; Function: Retrieves tree nodes associated with the current taxon. Returns : An ARRAY reference of Bio::Phylo::Trees::Node objects Args : None.
Type : Destructor Title : DESTROY Usage : $phylo->DESTROY Function: Destroys Phylo object Alias : Returns : TRUE Args : none Comments: You don't really need this, it is called automatically when the object goes out of scope.
The taxon objects inherits from the Bio::Phylo object. The methods defined there are also applicable to the taxon object.
Also see the manual: Bio::Phylo::Manual.
CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo
Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:
bug-bio-phylo@rt.cpan.org
$Id: Taxon.pm 1343 2006-06-13 19:41:41Z rvosa $
Rutger A. Vos,
rvosa@sfu.ca
The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.
Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.