=head1 NAME
Bio::DB::GFF::Aggregator::wormbase_gene -- Wormbase gene aggregator
=head1 SYNOPSIS
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['wormbase_gene','clone'],
);
-------------------------------------------------------------------------------------
Aggregator method: transcript
Main method: Sequence
Sub methods: CDS UTR TSS PolyA
-------------------------------------------------------------------------------------
=head1 DESCRIPTION
This aggregator was written to be compatible with the C elegans GFF
files. It aggregates raw "CDS", "5'UTR", "3'UTR", "polyA" and "TSS"
features into "transcript" features. For compatibility with the
idiosyncrasies of the Sanger GFF format, it expects that the full
range of the transcript is contained in a main feature of type
"Sequence".
=cut
package Bio::DB::GFF::Aggregator::wormbase_gene;
use strict;
use Bio::DB::GFF::Aggregator;
use vars qw($VERSION @ISA);
@ISA = qw(Bio::DB::GFF::Aggregator);
$VERSION = '0.30';
=head2 method
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "transcript"
Args : none
Status : Public
=cut
sub method { 'transcript' }
# sub require_whole_object { 1; }
=head2 part_names
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list "CDS", "UTR", "TSS", "PolyA"
Args : none
Status : Public
=cut
sub part_names {
return qw(CDS UTR TSS PolyA);
}
=head2 main_name
Title : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "Sequence"
Args : none
Status : Public
=cut
sub main_name {
return 'Sequence';
}
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