Bio::DB::Taxonomy::silva - Use the Silva taxonomy
use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new( -source => 'silva', -taxofile => 'SSURef_108_tax_silva_trunc.fasta', );
This is an implementation of Bio::DB::Taxonomy which stores and accesses the Silva taxonomy. Internally, Bio::DB::Taxonomy::silva 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. sv72, are arbitrary, contrary to the pre-defined IDs that NCBI assigns to taxons. Note also that no rank names or common names are assigned to the taxa of Bio::DB::Taxonomy::silva.
The latest Silva taxonomy (2011) contains about 126,000 taxa and occupies about 124 MB of memory once parsed into a Bio::DB::Taxonomy::silva object. Obviously, it can take a little while to load.
The taxonomy file SSURef_108_tax_silva_trunc.fasta that this module uses is available from http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/.
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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::silva->new(); Function: Builds a new Bio::DB::Taxonomy::silva object Returns : an instance of Bio::DB::Taxonomy::silva Args : -taxofile => name of the FASTA file containing the taxonomic information, typically 'SSURef_108_tax_silva_trunc.fasta' (mandatory)