NAME

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

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 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 "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.