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Bio::DB::Taxonomy(3)  User Contributed Perl Documentation Bio::DB::Taxonomy(3)

NAME
       Bio::DB::Taxonomy - 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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

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

       bioperl-l@bioperl.org

       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:

	 http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason-at-bioperl.org

CONTRIBUTORS
       Sendu Bala: bix@sendu.me.uk

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' or 'flatfile' or 'list'

   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 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.
	Returns : Bio::Tree::Tree
	Args	: a list of species names (strings)

   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: Tries to ensure that when a taxon is requested from any database,
		  the Taxon object returned will have the same internal id regardless
		  of database.
	Args	: Bio::Taxon, and optionally true value to try and do the job using
		  scientific name & rank if your ids aren't comparable to other dbs.

perl v5.14.1			  2011-07-22		  Bio::DB::Taxonomy(3)
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