Bio::DB::Taxonomy::flatfile - An implementation of Bio::DB::Taxonomy which uses local flat files use Bio::DB::Taxonomy; my $db = new Bio::DB::Taxonomy(-source => 'flatfile' -nodesfile => $nodesfile, -namesfile => $namefile); This is an implementation which uses local flat files and the DB_File module RECNO data structures to manage a local copy of the NCBI Taxonomy database. File can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

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/MailList.shtml - About the mailing lists

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: http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::DB::Taxonomy::flatfile(); 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 replace current indexes even if they exist

Bio::DB::Taxonomy Interface implementation

get_Taxonomy_Node
Title : get_Taxonomy_Node Usage : my $species = $db->get_Taxonomy_Node(-taxonid => $taxaid) Function: Get a Bio::Taxonomy::Taxon object for a taxonid Returns : Bio::Taxonomy::Taxon object Args : -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, species, genus, etc)

get_taxonid
Title : get_taxonid Usage : my $taxonid = $db->get_taxonid('Homo sapiens'); Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query string Returns : Integer ID Args : String representing species/node name

Helper methods

index_directory
Title : index_directory Usage : $obj->index_directory($newval) Function: Example : Returns : value of index_directory (a scalar) Args : on set, new value (a scalar or undef, optional)