Reference

Bio::DB::GFF::Aggregator::coding(3pm)

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 "coding"
 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 <[email protected]>.

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.

History