Bio::DB::Taxonomy::list man page on Pidora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Pidora logo
[printable version]

Bio::DB::Taxonomy::lisUser Contributed Perl DocumentBio::DB::Taxonomy::list(3)

NAME
       Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that
       accepts lists of words to build a database

SYNOPSIS
	 use Bio::DB::Taxonomy;

	 my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
	 my @ranks = qw(superkingdom class genus species);
	 my $db = Bio::DB::Taxonomy->new(-source => 'list', -names => \@names,
							   -ranks => \@ranks);

	 @names = ('Eukaryota', 'Mammalia', 'Mus', 'Mus musculus');
	 $db->add_lineage(-names => \@names, -ranks => \@ranks);

DESCRIPTION
       This is an implementation which uses supplied lists of words to create
       a database from which you can extract Bio::Taxon objects.

TODO
       It is possible this module could do something like store the data it
       builds up to disc. Would that be useful?	 At any rate, this is why the
       module is called 'list' and not 'in_memory' or similar.

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 - Sendu Bala
       Email 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::list->new();
	Function: Builds a new Bio::DB::Taxonomy::list object
	Returns : an instance of Bio::DB::Taxonomy::list
	Args	: optional, as per the add_lineage() method.

   add_lineage
	Title	: add_lineage
	Usage	: $db->add_lineage(-names => \@names)
	Function: Add a lineage to the database, where the lineage is described by
		  a list of scientific names in the order root->leaf. The rank of each
		  name can optionally be described by supplying an additional list
		  of rank names in the same order (eg. superkingdom->species).
	Returns : n/a
	Args	: -names => [] : array ref of scientific names, REQUIRED
		  -ranks => [] : array ref of rank names, same order as above, OPTIONAL

   Bio::DB::Taxonomy Interface implementation
   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; NB: these are not
			      NCBI taxonomy ids but 'list' pre-fixed ids unique to the
			      list database)
		   OR
		  -name	   => string (to query by a taxonomy name)

   get_taxonids
	Title	: get_taxonids
	Usage	: my @taxonids = $db->get_taxonids('Homo sapiens');
	Function: Searches for a taxonid (generated by the list module) 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

   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)

perl v5.14.1			  2011-07-22	    Bio::DB::Taxonomy::list(3)
[top]

List of man pages available for Pidora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net