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


  use Bio::DB::Taxonomy;

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


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


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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::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


 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)
           -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
 Returns : array of integer ids in list context, one of these in scalar context
 Args    : string representing taxon's name


 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())


 Title   : ancestor
 Usage   : my $ancestor_taxon = $db->ancestor($taxon)
 Function: Retrieve the full ancestor taxon of a supplied Taxon from the
 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)

Helper methods


 Title   : index_directory
 Function : 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)