Bio::DB::GFF::Aggregator
coding
Summary
Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['coding'],
);
------------------------------------------------------------------------
Aggregator method: coding
Main method: mRNA
Sub methods: CDS
------------------------------------------------------------------------
Description
Bio::DB::GFF::Aggregator::coding aggregates "CDS" features into a
feature called "coding" and was written to be compatible with the
Sequence Ontology canonical gene. The CDS features are expected to
belong to a parent of type "mRNA," but the aggregator will work even
if this isn't the case.
Methods
Methods description
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "processed_transcript"
Args : none
Status : Public |
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list (CDS cds)
Args : none
Status : Public |
Title : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "mRNA"
Args : none
Status : Public |
Methods code
sub part_names
{ return qw(CDS cds); } | sub main_name
{ return 'mRNA'; } | General documentation
None reported.
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.