Raw content of Bio::DB::GFF::Aggregator::transcript =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