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' (NCBI taxonomy online), 'flatfile' (local NCBI taxonomy), 'greengenes' (local GreenGenes taxonomy), 'silva' (local Silva taxonomy), or 'list' (Do-It-Yourself taxonomy)
Title : get_num_taxa Usage : my $num = $db->get_num_taxa(); Function: Get the number of taxa stored in the database. Returns : A number Args : None
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 the 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. The nodes are also given an arbitrary branch length of 1. Returns : Bio::Tree::Tree Args : A list of species names (strings) to include in the tree.
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: Add an internal ID to a taxon object, ensuring that the taxon gets the same internal ID, regardless of which database it is retrieved from. Returns : The assigned internal ID Args : * A Bio::Taxon * An optional boolean to decide whether or not to try and do the job using scientific name & rank in addition to taxon ID. This is useful if your IDs are not comparable to that of other databases, e.g. if they are arbitrary, as in the case of Bio::DB::Taxonomy::list. CAVEAT: will handle ambiguous names within a database fine, but not across multiple databases.