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
-------------------------------------------------

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);

method

 Title   : method
 Usage   : $aggregator->method
 Function: return the method for the composite object
 Returns : the string "transcript"
 Args    : none
 Status  : Public

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

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

AUTHOR

Lincoln Stein <[email protected]>.

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.