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Summary

Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator

Package variables

Included modules

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 => ['coding'],
				 );

 ------------------------------------------------------------------------
 Aggregator method: coding
 Main method:       mRNA
 Sub methods:       CDS
 ------------------------------------------------------------------------

Description

Bio::DB::GFF::Aggregator::coding aggregates "CDS" features into a
feature called "coding" and was written to be compatible with the
Sequence Ontology canonical gene. The CDS features are expected to
belong to a parent of type "mRNA," but the aggregator will work even
if this isn't the case.

Methods

Methods description

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

 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 cds)
 Args    : none
 Status  : Public

Methods code

sub main_name {

  return 'mRNA';
}

1;
__END__

}

sub method {

 'coding'

}

sub part_names {

  return qw(CDS cds);

}

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.