| Bio::DB::Taxonomy(3pm) | User Contributed Perl Documentation | Bio::DB::Taxonomy(3pm) |
Bio::DB::Taxonomy - Access to a taxonomy database
use Bio::DB::Taxonomy;
my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
# use NCBI Entrez over HTTP
my $taxonid = $db->get_taxonid('Homo sapiens');
# get a taxon
my $taxon = $db->get_taxon(-taxonid => $taxonid);
This is a front end module for access to a taxonomy database.
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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->new(-source => 'entrez');
Function: Builds a new Bio::DB::Taxonomy object.
Returns : an instance of Bio::DB::Taxonomy
Args : -source => which database source 'entrez' (NCBI taxonomy online),
'flatfile' (local NCBI taxonomy), 'greengenes' (local
GreenGenes taxonomy), 'silva' (local Silva taxonomy), or
'list' (Do-It-Yourself taxonomy)
Title : get_num_taxa Usage : my $num = $db->get_num_taxa(); Function: Get the number of taxa stored in the database. Returns : A number Args : None
Title : get_taxon
Usage : my $taxon = $db->get_taxon(-taxonid => $taxonid);
Function: Get a Bio::Taxon object from the database.
Returns : Bio::Taxon object
Args : just a single value which is the database id, OR named args:
-taxonid => taxonomy id (to query by taxonid)
OR
-name => string (to query by a taxonomy name: common name,
scientific name, etc)
Title : get_taxonids
Usage : my @taxonids = $db->get_taxonids('Homo sapiens');
Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query
string. Note that multiple taxonids can match to the same supplied
name.
Returns : array of integer ids in list context, one of these in scalar context
Args : string representing the taxon's name
Title : get_tree
Usage : my $tree = $db->get_tree(@species_names);
Function: Generate a tree comprised of the full lineages of all the supplied
species names. The nodes for the requested species are given
name('supplied') values corresponding to the supplied name, such that
they can be identified if the real species name in the database
(stored under node_name()) is different. The nodes are also given an
arbitrary branch length of 1.
Returns : Bio::Tree::Tree
Args : A list of species names (strings) to include in the tree.
Title : ancestor
Usage : my $ancestor_taxon = $db->ancestor($taxon);
Function: Retrieve the full ancestor taxon of a supplied Taxon from the
database.
Returns : Bio::Taxon
Args : Bio::Taxon (that was retrieved from this database)
Title : each_Descendent
Usage : my @taxa = $db->each_Descendent($taxon);
Function: Get all the descendents of the supplied Taxon (but not their
descendents, ie. not a recursive fetchall).
Returns : Array of Bio::Taxon objects
Args : Bio::Taxon (that was retrieved from this database)
Title : get_all_Descendents Usage : my @taxa = $db->get_all_Descendents($taxon); Function: Like each_Descendent(), but do a recursive fetchall Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database)
Title : _load_tax_module Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Loads up (like use) a module at run time on demand
Title : _handle_internal_id
Usage : *INTERNAL Bio::DB::Taxonomy stuff*
Function: Add an internal ID to a taxon object, ensuring that the taxon gets
the same internal ID, regardless of which database it is retrieved
from.
Returns : The assigned internal ID
Args : * A Bio::Taxon
* An optional boolean to decide whether or not to try and do the job
using scientific name & rank in addition to taxon ID. This is
useful if your IDs are not comparable to that of other databases,
e.g. if they are arbitrary, as in the case of Bio::DB::Taxonomy::list.
CAVEAT: will handle ambiguous names within a database fine, but not
across multiple databases.
| 2021-08-15 | perl v5.32.1 |