Bio::DB::Taxonomy::flatfile(3)

NAME
Bio::DB::Taxonomy::flatfile - An implementation of Bio::DB::Taxonomy which uses local flat files

SYNOPSIS
  use Bio::DB::Taxonomy;

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

DESCRIPTION
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

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/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/

AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org

Describe contact details here

CONTRIBUTORS
Additional contributors names and emails here

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 = 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

  get_Children_Taxids
 Title   : get_Children_Taxids
 Usage   : my @childrenids = $db->get_Children_Taxids
 Function: Get the children of a node in the taxonomy
 Returns : Array of Ids
 Args    : L<Bio::Taxonomy::Node> or a taxon_id

  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)