NAME

       Bio::DB::Taxonomy - Access to a taxonomy database

SYNOPSIS

         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);

DESCRIPTION

       This is a front end module for access to a taxonomy database.

FEEDBACK

   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.

         bioperl-l@bioperl.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:

       bioperl-l@bioperl.org

       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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

CONTRIBUTORS

       Sendu Bala: bix@sendu.me.uk

APPENDIX

       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' (NCBI taxonomy online),
                             'flatfile' (local NCBI taxonomy), 'greengenes' (local
                             GreenGenes taxonomy), 'silva' (local Silva taxonomy), or
                             'list' (Do-It-Yourself taxonomy)

   get_num_taxa
        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

   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 the 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. 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.

   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: 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.