Bio::DB::Taxonomy(3) Access to a taxonomy database

SYNOPSIS


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);

DESCRIPTION

This is a front end module for access to a taxonomy database.

FEEDBACK

Mailing Lists

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. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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.

Reporting Bugs

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: 

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Sendu Bala: [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 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)

get_num_taxa

 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

get_taxon

 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)

get_taxonids

 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

get_tree

 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.

ancestor

 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)

each_Descendent

 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)

get_all_Descendents

 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)

_load_tax_module

 Title   : _load_tax_module
 Usage   : *INTERNAL Bio::DB::Taxonomy stuff*
 Function: Loads up (like use) a module at run time on demand

_handle_internal_id

 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.

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