branch-1-6/Bio/DB/GFF/Aggregator/so_transcript.pm

   1 =head1 NAME
   2
   3 Bio::DB::GFF::Aggregator::so_transcript -- Sequence Ontology Transcript
   4
   5 =head1 SYNOPSIS
   6
   7   use Bio::DB::GFF;
   8
   9   # Open the sequence database
  10   my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
  11                                    -dsn     => 'dbi:mysql:elegans42',
  12                                    -aggregator => ['so_transcript'],
  13                                  );
  14
  15  ------------------------------------------------------------------------
  16  Aggregator method: processed_transcript
  17  Main method:       mRNA
  18  Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
  19  ------------------------------------------------------------------------
  20
  21 =head1 DESCRIPTION
  22
  23 Bio::DB::GFF::Aggregator::so_transcript is identical to the
  24 processed_transcript aggregator, which was designed to be compatible
  25 with the Sequence Ontology canonical gene.  It aggregates raw "exon,"
  26 "CDS", "five_prime_UTR", "three_prime_UTR", "transcription_start_site"
  27 and "polyA_site" features into "mRNA" features.  The UTRs may also be
  28 named "untranslated_region," "five_prime_untranslated_region,"
  29 "three_prime_untranslated_region,", "5'-UTR," and other synonyms.
  30
  31 The processed_transcript aggregator is loaded by default, so this is
  32 only needed for backward compatibility.
  33
  34 =cut
  35
  36 package Bio::DB::GFF::Aggregator::so_transcript;
  37
  38 use strict;
  39
  40 use base qw(Bio::DB::GFF::Aggregator);
  41
  42 =head2 method
  43
  44  Title   : method
  45  Usage   : $aggregator->method
  46  Function: return the method for the composite object
  47  Returns : the string "processed_transcript"
  48  Args    : none
  49  Status  : Public
  50
  51 =cut
  52
  53 sub method { 'so_transcript' }
  54
  55 =head2 part_names
  56
  57  Title   : part_names
  58  Usage   : $aggregator->part_names
  59  Function: return the methods for the sub-parts
  60  Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
  61  Args    : none
  62  Status  : Public
  63
  64 =cut
  65
  66 sub part_names {
  67   return qw(CDS 5'-UTR 3'-UTR transcription_start_site
  68             polyA_site UTR five_prime_untranslated_region
  69             three_prime_untranslated_region
  70            five_prime_UTR three_prime_UTR exon);
  71 }
  72
  73 =head2 main_name
  74
  75  Title   : main_name
  76  Usage   : $aggregator->main_name
  77  Function: return the method for the main component
  78  Returns : the string "mRNA"
  79  Args    : none
  80  Status  : Public
  81
  82 =cut
  83
  84 sub main_name {
  85   return 'mRNA';
  86 }
  87
  88 1;
  89 __END__
  90
  91 =head1 BUGS
  92
  93 None reported.
  94
  95
  96 =head1 SEE ALSO
  97
  98 L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
  99
 100 =head1 AUTHOR
 101
 102 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
 103
 104 Copyright (c) 2001 Cold Spring Harbor Laboratory.
 105
 106 This library is free software; you can redistribute it and/or modify
 107 it under the same terms as Perl itself.
 108
 109 =cut
 110