Bio::DB::Taxonomy(3) User Contributed Perl Documentation Bio::DB::Taxonomy(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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.
perl v5.14.1 2011-07-22 Bio::DB::Taxonomy(3)
