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/.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
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)