++ed by:
DEMIAN ILUX FIBO CJFIELDS GENEHACK

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

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

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)