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

Usage

  use Bio::DB::GFF;
  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
                                   -aggregator => ['so_transcript'],
                                 );
 ------------------------------------------------------------------------
 Aggregator method: processed_transcript
 Main method:       mRNA
 Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
 ------------------------------------------------------------------------

Overview

Bio::DB::GFF::Aggregator::so_transcript is identical to the processed_transcript aggregator, which was designed to be compatible with the Sequence Ontology canonical gene. 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.

The processed_transcript aggregator is loaded by default, so this is only needed for backward compatibility.

method

 Title   : method
 Usage   : $aggregator->method
 Function: return the method for the composite object
 Returns : the string "processed_transcript"
 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

Releases

9 releases since Debian 5.0 (Lenny); the text changed 6 times.

5.0
6.0
7
8
9
10
11–13