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 

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)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq