Bio::DB::Taxonomy::greengenes - Use the Greengenes taxonomy
use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new( -source => 'greengenes', -taxofile => 'taxonomy_16S_candiv_gg_2011_1.txt' );
This module is in beta. Its interface or its results may change in a future update.
Bio::DB::Taxonomy::greengenes is an implementation of Bio::DB::Taxonomy which stores and accesses the Greengenes taxonomy of Bacteria and Archaea. Internally, it keeps the taxonomy into memory by using Bio::DB::Taxonomy::list. As a consequence, note that the IDs assigned to the taxonomy nodes, e.g. gg123, are arbitrary, contrary to the pre-defined IDs that NCBI assigns to taxons.
The latest release of the Greengene taxonomy (2011) contains about 4,600 taxa and occupies about 4MB of memory once parsed into a Bio::DB::Taxonomy::greengenes object. The taxonomy files taxonomy_16S_all_gg_2011_1.txt and taxonomy_16S_candiv_gg_2011_1.txt that this module can use are available from http://www.secondgenome.com/go/2011-greengenes-taxonomy/.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::DB::Taxonomy::greengenes->new(); Function: Builds a new Bio::DB::Taxonomy::greengenes object Returns : an instance of Bio::DB::Taxonomy::greengenes Args : -taxofile => name of the file containing the taxonomic information, typically 'taxonomy_16S_candiv_gg_2011_1.txt' (mandatory)