Bio/DB/GFF/Aggregator/gene.pm

   1 =head1 NAME
   2
   3 Bio::DB::GFF::Aggregator::gene -- Sequence Ontology Geene
   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 => ['gene'],
  13                                  );
  14
  15  ------------------------------------------------------------------------
  16  Aggregator method: gene
  17  Main method:       mRNA
  18  Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site
  19  ------------------------------------------------------------------------
  20
  21 =head1 DESCRIPTION
  22
  23 Bio::DB::GFF::Aggregator::gene is identical to so_transcript, but is
  24 used in those cases where you would like the name of the aggregated
  25 feature to be "gene" rather than "processed_transcript". It aggregates
  26 raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR",
  27 "transcription_start_site" and "polyA_site" features into "mRNA"
  28 features.  The UTRs may also be named "untranslated_region,"
  29 "five_prime_untranslated_region," "three_prime_untranslated_region,",
  30 "5'-UTR," and other synonyms.
  31
  32 =cut
  33
  34 package Bio::DB::GFF::Aggregator::gene;
  35
  36 use strict;
  37
  38 use base qw(Bio::DB::GFF::Aggregator);
  39
  40 =head2 method
  41
  42  Title   : method
  43  Usage   : $aggregator->method
  44  Function: return the method for the composite object
  45  Returns : the string "gene"
  46  Args    : none
  47  Status  : Public
  48
  49 =cut
  50
  51 sub method { 'gene' }
  52
  53 =head2 part_names
  54
  55  Title   : part_names
  56  Usage   : $aggregator->part_names
  57  Function: return the methods for the sub-parts
  58  Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
  59  Args    : none
  60  Status  : Public
  61
  62 =cut
  63
  64 sub part_names {
  65   return qw(CDS transcription_start_site
  66             polyA_site UTR five_prime_untranslated_region
  67             three_prime_untranslated_region
  68            five_prime_UTR three_prime_UTR exon);
  69 }
  70
  71 =head2 main_name
  72
  73  Title   : main_name
  74  Usage   : $aggregator->main_name
  75  Function: return the method for the main component
  76  Returns : the string "mRNA"
  77  Args    : none
  78  Status  : Public
  79
  80 =cut
  81
  82 sub main_name {
  83   return 'mRNA';
  84 }
  85
  86 1;
  87 __END__
  88
  89 =head1 BUGS
  90
  91 None reported.
  92
  93
  94 =head1 SEE ALSO
  95
  96 L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
  97
  98 =head1 AUTHOR
  99
 100 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
 101
 102 Copyright (c) 2008 Cold Spring Harbor Laboratory.
 103
 104 This library is free software; you can redistribute it and/or modify
 105 it under the same terms as Perl itself.
 106
 107 =cut
 108