NAME

       Bio::DB::GFF::Aggregator::so_transcript -- Sequence Ontology Transcript

SYNOPSIS

         use Bio::DB::GFF;

         # Open the sequence database
         my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                          -dsn     => 'dbi:mysql:elegans42',
                                          -aggregator => ['so_transcript'],
                                        );

        ------------------------------------------------------------------------
        Aggregator method: processed_transcript
        Main method:       mRNA
        Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
        ------------------------------------------------------------------------

DESCRIPTION

       Bio::DB::GFF::Aggregator::so_transcript is identical to the processed_transcript
       aggregator, which was designed to be compatible with the Sequence Ontology canonical gene.
       It aggregates raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR",
       "transcription_start_site" and "polyA_site" features into "mRNA" features.  The UTRs may
       also be named "untranslated_region," "five_prime_untranslated_region,"
       "three_prime_untranslated_region,", "5'-UTR," and other synonyms.

       The processed_transcript aggregator is loaded by default, so this is only needed for
       backward compatibility.

   method
        Title   : method
        Usage   : $aggregator->method
        Function: return the method for the composite object
        Returns : the string "processed_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 CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
        Args    : none
        Status  : Public

   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

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.

perl v5.18.2                                2014-01-1Bio::DB::GFF::Aggregator::so_transcript(3pm)