Reference

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

NAME

Bio::DB::GFF::Aggregator::orf -- An aggregator for orf regions

SYNOPSIS

  use Bio::DB::GFF;
  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
                                   -aggregator => ['orf','clone'],
                                 );
 ---------------------------
 Aggregator method: orf
 Main method:       -none-
 Sub methods:       ORF
 ---------------------------

DESCRIPTION

Bio::DB::GFF::Aggregator::orf was written to work with the "cds" glyph. GFF files. It aggregates raw "ORF" features into "coding" features. This is basically identical to the "coding" aggregator, except that it looks for features of type "ORF" rather than "cds".

method

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

BUGS

None reported.

SEE ALSO

Bio::DB::GFF, Bio::DB::GFF::coding, Bio::DB::GFF::Aggregator, Bio::Graphics::Glyph::cds

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