Bio::DB::Taxonomy::greengenes - Use the Greengenes 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
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
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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)