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:
https://redmine.open-bio.org/projects/bioperl/
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)