Bio::DB::GFF::Aggregator::orf.3pm

Langue: en

Autres versions - même langue

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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 <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.