NAME

Bio::DB::Taxonomy - Access to a taxonomy database

SYNOPSIS

use Bio::DB::Taxonomy;
my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
# use NCBI Entrez over HTTP
my $taxonid = $db->get_taxonid('Homo sapiens');

# get a taxon
my $taxon = $db->get_taxon(-taxonid => $taxonid);

DESCRIPTION

This is a front end module for access to a taxonomy database.

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.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->new(-source => 'entrez');
Function: Builds a new Bio::DB::Taxonomy object.
Returns : an instance of Bio::DB::Taxonomy
Args    : -source => which database source 'entrez' or 'flatfile' or 'list'

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_tree

Title   : get_tree
Usage   : my $tree = $db->get_tree(@species_names)
Function: Generate a tree comprised of the full lineages of all the supplied
          species names. The nodes for the requested species are given
          name('supplied') values corresponding to the supplied name, such that
          they can be identified if the real species name in the database
          (stored under node_name()) is different.
Returns : Bio::Tree::Tree
Args    : a list of species names (strings)

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)

get_all_Descendents

Title   : get_all_Descendents
Usage   : my @taxa = $db->get_all_Descendents($taxon);
Function: Like each_Descendent(), but do a recursive fetchall
Returns : Array of Bio::Taxon objects
Args    : Bio::Taxon (that was retrieved from this database)

_load_tax_module

Title   : _load_tax_module
Usage   : *INTERNAL Bio::DB::Taxonomy stuff*
Function: Loads up (like use) a module at run time on demand

_handle_internal_id

Title   : _handle_internal_id
Usage   : *INTERNAL Bio::DB::Taxonomy stuff*
Function: Tries to ensure that when a taxon is requested from any database,
          the Taxon object returned will have the same internal id regardless
          of database.
Args    : Bio::Taxon, and optionally true value to try and do the job using
          scientific name & rank if your ids aren't comparable to other dbs.

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq