Bio::DB::Taxonomy::list(3) An implementation of Bio::DB::Taxonomy

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. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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 [email protected]

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)

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