Bio/Map/Prediction.pm

   1 # $Id: Prediction.pm,v 1.10 2006/09/28 14:09:40 sendu Exp $
   2 #
   3 # BioPerl module for Bio::Map::Prediction
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Sendu Bala <bix@sendu.me.uk>
   8 #
   9 # Copyright Sendu Bala
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Map::Prediction - An object representing the predictions of something
  18 that can have multiple locations in several maps.
  19
  20 =head1 SYNOPSIS
  21
  22   use Bio::Map::Prediction;
  23   use Bio::Map::Position;
  24
  25   # normally you would get predictions from a run wrapper like
  26   # Bio::Tools::Run::Meme, but here we create some manually:
  27   my $pred1 = Bio::Map::Prediction->new(-source => 'meme');
  28   Bio::Map::Position->new(-element => $prediction1,
  29                                                   -map => Bio::Map::GeneMap->get(-gene => 'gene1',
  30                                                                                  -species => 'species1'),
  31                                                   -start => 950,
  32                                                   -end => 960);
  33   Bio::Map::Position->new(-element => $prediction1,
  34                           -map => Bio::Map::GeneMap->get(-gene => 'gene1',
  35                                                                                  -species => 'species2'),
  36                           -start => 1950,
  37                           -end => 1960);
  38   Bio::Map::Position->new(-element => $prediction1,
  39                           -map => Bio::Map::GeneMap->get(-gene => 'gene2',
  40                                                                                  -species => 'species1'),
  41                           -start => 955,
  42                           -end => 965);
  43   Bio::Map::Position->new(-element => $prediction1,
  44                           -map => Bio::Map::GeneMap->get(-gene => 'gene2',
  45                                                                          -species => 'species2'),
  46                           -start => 1955,
  47                           -end => 1965);
  48
  49   my $pred2 = Bio::Map::Prediction->new(-source => 'gerp');
  50   Bio::Map::Position->new(-element => $prediction2,
  51                           -map => Bio::Map::GeneMap->get(-gene => 'gene1',
  52                                                                                  -species => 'species1'),
  53                           -start => 950,
  54                           -end => 960);
  55   # etc.
  56
  57   # find the places where predictions agree
  58   use Bio::Map::GeneRelative;
  59   my $rel = Bio::Map::GeneRelative->new(-gene => 0);
  60   my $di = Bio::Map::Mappable->disconnected_intersections([$pred1, $pred2],
  61                                                 -min_mappables_percent => 100,
  62                                                 -min_map_percent => 100,
  63                                                 -relative => $rel);
  64   my @positions = $di->get_positions;
  65
  66 =head1 DESCRIPTION
  67
  68 For example, used to model transcription factor binding site predictions, which
  69 can have multiple locations in several maps.
  70
  71 =head1 FEEDBACK
  72
  73 =head2 Mailing Lists
  74
  75 User feedback is an integral part of the evolution of this and other
  76 Bioperl modules. Send your comments and suggestions preferably to the
  77 Bioperl mailing list.  Your participation is much appreciated.
  78
  79   bioperl-l@bioperl.org                  - General discussion
  80   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  81
  82 =head2 Support
  83
  84 Please direct usage questions or support issues to the mailing list:
  85
  86 I<bioperl-l@bioperl.org>
  87
  88 rather than to the module maintainer directly. Many experienced and
  89 reponsive experts will be able look at the problem and quickly
  90 address it. Please include a thorough description of the problem
  91 with code and data examples if at all possible.
  92
  93 =head2 Reporting Bugs
  94
  95 Report bugs to the Bioperl bug tracking system to help us keep track
  96 of the bugs and their resolution. Bug reports can be submitted via the
  97 web:
  98
  99   https://github.com/bioperl/bioperl-live/issues
 100
 101 =head1 AUTHOR - Sendu Bala
 102
 103 Email bix@sendu.me.uk
 104
 105 =head1 APPENDIX
 106
 107 The rest of the documentation details each of the object methods.
 108 Internal methods are usually preceded with a _
 109
 110 =cut
 111
 112 # Let the code begin...
 113
 114 package Bio::Map::Prediction;
 115 use strict;
 116
 117 use base qw(Bio::Map::Mappable);
 118
 119 =head2 new
 120
 121  Title   : new
 122  Usage   : my $prediction = Bio::Map::Prediction->new();
 123  Function: Builds a new Bio::Map::Prediction object
 124  Returns : Bio::Map::Prediction
 125  Args    : -name   => string : name of the mappable element
 126            -id     => string : id of the mappable element
 127            -source => string : name of the prediction program
 128
 129 =cut
 130
 131 sub new {
 132     my ($class, @args) = @_;
 133     my $self = $class->SUPER::new(@args);
 134
 135     my ($source) = $self->_rearrange([qw(SOURCE)], @args);
 136     $self->source($source) if $source;
 137
 138     return $self;
 139 }
 140
 141 =head2 source
 142
 143  Title   : name
 144  Usage   : $mappable->name($new_name);
 145                my $name = $mappable->name();
 146  Function: Get/Set the name for this Mappable
 147  Returns : A scalar representing the current name of this Mappable
 148  Args    : none to get
 149            string to set
 150
 151 =cut
 152
 153 sub source {
 154     my $self = shift;
 155     if (@_) { $self->{_source} = shift }
 156     return $self->{_source} || '';
 157 }
 158
 159 1;