Bio::DB::GFF::Aggregator::orf(3)           User Contributed Perl Documentation




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 <lsteinATcshl.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.



perl v5.12.2                                                 February 24, 2011