Bio::DB::GFF::Aggregator::gene.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::gene -- Sequence Ontology Geene

SYNOPSIS

   use Bio::DB::GFF;
 
   # Open the sequence database
   my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                    -dsn     => 'dbi:mysql:elegans42',
                                    -aggregator => ['gene'],
                                  );
 
  ------------------------------------------------------------------------
  Aggregator method: gene
  Main method:       mRNA
  Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site
  ------------------------------------------------------------------------
 
 

DESCRIPTION

Bio::DB::GFF::Aggregator::gene is identical to so_transcript, but is used in those cases where you would like the name of the aggregated feature to be ``gene'' rather than ``processed_transcript''. It aggregates raw ``exon,'' ``CDS'', ``five_prime_UTR'', ``three_prime_UTR'', ``transcription_start_site'' and ``polyA_site'' features into ``mRNA'' features. The UTRs may also be named ``untranslated_region,'' ``five_prime_untranslated_region,'' ``three_prime_untranslated_region,'', ``5'-UTR,'' and other synonyms.

method

  Title   : method
  Usage   : $aggregator->method
  Function: return the method for the composite object
  Returns : the string "gene"
  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 5'-UTR 3'-UTR transcription_start_site polyA_site
  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) 2008 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.