NAME

       Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat files

SYNOPSIS

         use Bio::DB::Taxonomy;

         my $db = Bio::DB::Taxonomy->new(-source    => 'flatfile' ,
                                         -nodesfile => 'nodes.dmp',
                                         -namesfile => 'names.dmp');

DESCRIPTION

       This is an implementation of Bio::DB::Taxonomy which stores and accesses the NCBI taxonomy
       using flat files stored locally on disk and indexed using the DB_File module RECNO data
       structure for fast retrieval.

       The required database files, nodes.dmp and names.dmp can be obtained from
       ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-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::flatfile->new();
        Function: Builds a new Bio::DB::Taxonomy::flatfile object
        Returns : an instance of Bio::DB::Taxonomy::flatfile
        Args    : -directory => name of directory where index files should be created
                  -nodesfile => name of file containing nodes (nodes.dmp from NCBI)
                  -namesfile => name of the file containing names(names.dmp from NCBI)
                  -force     => 1 to replace current indexes even if they exist

   Bio::DB::Taxonomy interface implementation
   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 taxon's name

   get_Children_Taxids
        Title   : get_Children_Taxids
        Usage   : my @childrenids = $db->get_Children_Taxids
        Function: Get the ids of the children of a node in the taxonomy
        Returns : Array of Ids
        Args    : Bio::Taxon or a taxon_id
        Status  : deprecated (use each_Descendent())

   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)

   Helper methods
   index_directory
        Title   : index_directory
        Funtion : Get/set the location that index files are stored. (this module
                  will index the supplied database)
        Usage   : $obj->index_directory($newval)
        Returns : value of index_directory (a scalar)
        Args    : on set, new value (a scalar or undef, optional)