NAME

       Bio::DB::GFF::Aggregator::transcript -- Transcript aggregator

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

BUGS

       None reported.

SEE ALSO

       Bio::DB::GFF, Bio::DB::GFF::Aggregator

AUTHOR

       Lincoln Stein <lstein@cshl.org>.

       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.