Raw content of Bio::DB::GFF::Aggregator::processed_transcript
<![CDATA[=head1 NAME
Bio::DB::GFF::Aggregator::processed_transcript -- Sequence Ontology Transcript
=head1 SYNOPSIS
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['processed_transcript'],
);
------------------------------------------------------------------------
Aggregator method: processed_transcript
Main method: mRNA
Sub methods: CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
------------------------------------------------------------------------
=head1 DESCRIPTION
Bio::DB::GFF::Aggregator::processed_transcript is one of the default
aggregators, and was written to be compatible with the Sequence
Ontology canonical gene. It aggregates raw "CDS", "5'-UTR", "3'-UTR",
"transcription_start_site" and "polyA_site" features into "gene"
features. The UTRs may also be named "untranslated_region,"
"five_prime_untranslated_region," or
"three_prime_untranslated_region."
=cut
package Bio::DB::GFF::Aggregator::processed_transcript;
use strict;
use Bio::DB::GFF::Aggregator;
use vars qw(@ISA);
@ISA = qw(Bio::DB::GFF::Aggregator);
=head2 method
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "processed_transcript"
Args : none
Status : Public
=cut
sub method { 'processed_transcript' }
=head2 part_names
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
Args : none
Status : Public
=cut
sub part_names {
return qw(CDS 5'-UTR 3'-UTR transcription_start_site
polyA_site UTR five_prime_untranslated_region
three_prime_untranslated_region);
}
=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
]]>