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|
=head1 NAME
Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator
=head1 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
------------------------------------------------------------------------
=head1 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.
=cut
package Bio::DB::GFF::Aggregator::coding;
$Bio::DB::GFF::Aggregator::coding::VERSION = '1.7.4';
use strict;
use base qw(Bio::DB::GFF::Aggregator);
=head2 method
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "coding"
Args : none
Status : Public
=cut
sub method { 'coding' }
=head2 part_names
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list (CDS cds)
Args : none
Status : Public
=cut
sub part_names {
return qw(CDS cds);
}
=head2 main_name
Title : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "mRNA"
Args : none
Status : Public
=cut
sub main_name {
return 'mRNA';
}
1;
__END__
=head1 BUGS
None reported.
=head1 SEE ALSO
L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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.
=cut
|
