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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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'
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)
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
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)
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)
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)
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)
Title : _load_tax_module Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Loads up (like use) a module at run time on demand
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.