Bio::Phylo::Taxa::Taxon - Operational taxonomic unit
use Bio::Phylo::IO qw(parse); use Bio::Phylo::Factory; my $fac = Bio::Phylo::Factory->new; # 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 = $fac->create_taxa; # instantiate taxon objects, insert in taxa object foreach( @apes ) { my $taxon = $fac->create_taxon( -name => $_, ); $taxa->insert($taxon); } # crossreference tree and taxa $tree->cross_reference($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.
Associates argument data with invocant.
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
Associates argument node with invocant.
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
Removes association between argument data and invocant.
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
Removes association between argument node and invocant.
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
Retrieves associated datum objects.
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.
Retrieves associated node objects.
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.
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The taxon objects inherits from the Bio::Phylo::NeXML::Writable object. The methods defined there are also applicable to the taxon object.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
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.