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 $db = Bio::DB::Taxonomy->new( -source => 'list' );

my @ranks = ('superkingdom', 'class', 'genus', 'species');
my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
$db->add_lineage(-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:

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

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   : my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
          my @ranks = ('superkingdom', 'class', 'genus', 'species');
          $db->add_lineage( -names => \@names, -ranks => \@ranks );
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 : 1 for success
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_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    : A single value which is the ID of the taxon to retrieve
            OR named args, as follows:
          -taxonid => Taxonomy ID (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). A given taxon name
                      can match different taxonomy objects. When that is the
                      case, a warning is displayed and the first matching taxon
                      is reported. See get_taxonids() to get all matching taxon
                      IDs.
            OR
          -names   => Array ref of lineage names, like in add_lineage(). To
                      overcome the limitations of -name, you can use -names to
                      provide the full lineage of the taxon you want and get a
                      unique, unambiguous taxon object.

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)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq