Raw content of Bio::DB::GFF::Aggregator::transcript
<![CDATA[=head1 NAME
Bio::DB::GFF::Aggregator::transcript -- Transcript 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 => ['transcript','clone'],
);
-------------------------------------------------
Aggregator method: transcript
Main method: transcript
Sub methods: exon CDS 5'UTR 3'UTR TSS PolyA
-------------------------------------------------
=head1 DESCRIPTION
Bio::DB::GFF::Aggregator::transcript is one of the default
aggregators, and was written to be compatible with the C elegans GFF
files. It aggregates raw ""exon", "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
"Transcript" (notice the capital "T").
Internally this module is very simple. To override it with one that
recognizes a main feature named "gene", simply follow this
template:
my $db = Bio::DB::GFF->new(...etc...)
my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript',
-main_method => 'gene',
-sub_parts => ['exon','CDS']);
$db->add_aggregator($aggregator);
=cut
package Bio::DB::GFF::Aggregator::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 "transcript"
Args : none
Status : Public
=cut
sub method { 'transcript' }
=head2 part_names
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list "intron", "exon" and "CDS"
Args : none
Status : Public
=cut
sub part_names {
return qw(exon CDS 5'UTR 3'UTR TSS PolyA);
}
=head2 main_name
Title : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "transcript"
Args : none
Status : Public
=cut
sub main_name {
return 'transcript';
}
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
]]>