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

   1 =head1 NAME
   2
   3 Bio::DB::GFF::Aggregator::transcript -- Transcript aggregator
   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 => ['transcript','clone'],
  13                                  );
  14
  15  -------------------------------------------------
  16  Aggregator method: transcript
  17  Main method:       transcript
  18  Sub methods:       exon CDS 5'UTR 3'UTR TSS PolyA
  19  -------------------------------------------------
  20
  21 =head1 DESCRIPTION
  22
  23 Bio::DB::GFF::Aggregator::transcript is one of the default
  24 aggregators, and was written to be compatible with the C elegans GFF
  25 files.  It aggregates raw ""exon", "CDS", "5'UTR", "3'UTR", "polyA"
  26 and "TSS" features into "transcript" features.  For compatibility with
  27 the idiosyncrasies of the Sanger GFF format, it expects that the full
  28 range of the transcript is contained in a main feature of type
  29 "Transcript" (notice the capital "T").
  30
  31 Internally this module is very simple.  To override it with one that
  32 recognizes a main feature named "gene", simply follow this
  33 template:
  34
  35  my $db = Bio::DB::GFF->new(...etc...)
  36  my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript',
  37                                                 -main_method => 'gene',
  38                                                 -sub_parts => ['exon','CDS']);
  39  $db->add_aggregator($aggregator);
  40
  41 =cut
  42
  43 package Bio::DB::GFF::Aggregator::transcript;
  44
  45 use strict;
  46
  47 use base qw(Bio::DB::GFF::Aggregator);
  48
  49 =head2 method
  50
  51  Title   : method
  52  Usage   : $aggregator->method
  53  Function: return the method for the composite object
  54  Returns : the string "transcript"
  55  Args    : none
  56  Status  : Public
  57
  58 =cut
  59
  60 sub method { 'transcript' }
  61
  62 =head2 part_names
  63
  64  Title   : part_names
  65  Usage   : $aggregator->part_names
  66  Function: return the methods for the sub-parts
  67  Returns : the list "intron", "exon" and "CDS"
  68  Args    : none
  69  Status  : Public
  70
  71 =cut
  72
  73 sub part_names {
  74   return qw(exon CDS 5'UTR 3'UTR TSS PolyA);
  75 }
  76
  77 =head2 main_name
  78
  79  Title   : main_name
  80  Usage   : $aggregator->main_name
  81  Function: return the method for the main component
  82  Returns : the string "transcript"
  83  Args    : none
  84  Status  : Public
  85
  86 =cut
  87
  88 sub main_name {
  89   return 'transcript';
  90 }
  91
  92 1;
  93 __END__
  94
  95 =head1 BUGS
  96
  97 None reported.
  98
  99
 100 =head1 SEE ALSO
 101
 102 L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>
 103
 104 =head1 AUTHOR
 105
 106 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
 107
 108 Copyright (c) 2001 Cold Spring Harbor Laboratory.
 109
 110 This library is free software; you can redistribute it and/or modify
 111 it under the same terms as Perl itself.
 112
 113 =cut
 114