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