Summary

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

Package variables

Inherit

Bio::DB::GFF::Aggregator

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.

Methods

Methods description

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

 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

 Title   : main_name
 Usage   : $aggregator->main_name
 Function: return the method for the main component
 Returns : the string "mRNA"
 Args    : none
 Status  : Public

Methods code

sub method {

 'so_transcript'

}

sub part_names {

  return qw(CDS 5'-UTR 3'-UTR transcription_start_site
	    polyA_site UTR five_prime_untranslated_region
	    three_prime_untranslated_region
	   five_prime_UTR three_prime_UTR exon);

}

sub main_name {

  return 'mRNA';

}

General documentation

None reported.

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

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.