Bio::DB::Taxonomy::list.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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)