Provided by: libbio-perl-perl_1.6.901-2_all
Bio::DB::Taxonomy - Access to a taxonomy database
use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new(-source => 'entrez'); # use NCBI Entrez over HTTP my $taxonid = $db->get_taxonid('Homo sapiens'); # get a taxon my $taxon = $db->get_taxon(-taxonid => $taxonid);
This is a front end module for access to a taxonomy database.
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. firstname.lastname@example.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: email@example.com 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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Sendu Bala: firstname.lastname@example.org
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::DB::Taxonomy->new(-source => 'entrez'); Function: Builds a new Bio::DB::Taxonomy object. Returns : an instance of Bio::DB::Taxonomy Args : -source => which database source 'entrez' or 'flatfile' or 'list' get_taxon Title : get_taxon Usage : my $taxon = $db->get_taxon(-taxonid => $taxonid) Function: Get a Bio::Taxon object from the database. Returns : Bio::Taxon object Args : just a single value which is the database id, OR named args: -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, scientific name, etc) get_taxonids Title : get_taxonids Usage : my @taxonids = $db->get_taxonids('Homo sapiens'); Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query string. Note that multiple taxonids can match to the same supplied name. Returns : array of integer ids in list context, one of these in scalar context Args : string representing taxon's name get_tree Title : get_tree Usage : my $tree = $db->get_tree(@species_names) Function: Generate a tree comprised of the full lineages of all the supplied species names. The nodes for the requested species are given name('supplied') values corresponding to the supplied name, such that they can be identified if the real species name in the database (stored under node_name()) is different. Returns : Bio::Tree::Tree Args : a list of species names (strings) ancestor Title : ancestor Usage : my $ancestor_taxon = $db->ancestor($taxon) Function: Retrieve the full ancestor taxon of a supplied Taxon from the database. Returns : Bio::Taxon Args : Bio::Taxon (that was retrieved from this database) each_Descendent Title : each_Descendent Usage : my @taxa = $db->each_Descendent($taxon); Function: Get all the descendents of the supplied Taxon (but not their descendents, ie. not a recursive fetchall). Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) get_all_Descendents Title : get_all_Descendents Usage : my @taxa = $db->get_all_Descendents($taxon); Function: Like each_Descendent(), but do a recursive fetchall Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database) _load_tax_module Title : _load_tax_module Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Loads up (like use) a module at run time on demand _handle_internal_id Title : _handle_internal_id Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Tries to ensure that when a taxon is requested from any database, the Taxon object returned will have the same internal id regardless of database. Args : Bio::Taxon, and optionally true value to try and do the job using scientific name & rank if your ids aren't comparable to other dbs.