Manual Reference Pages - BIO::DB::TAXONOMY::SILVA (3)
Bio::DB::Taxonomy::silva - Use the Silva 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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AUTHOR - Florent Angly
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)
|perl v5.20.3 ||BIO::DB::TAXONOMY::SILVA (3) ||2016-04-05 |
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