/usr/share/perl5/Bio/Map/Prediction.pm is in libbio-perl-perl 1.6.923-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 | # $Id: Prediction.pm,v 1.10 2006/09/28 14:09:40 sendu Exp $
#
# BioPerl module for Bio::Map::Prediction
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::Prediction - An object representing the predictions of something
that can have multiple locations in several maps.
=head1 SYNOPSIS
use Bio::Map::Prediction;
use Bio::Map::Position;
# normally you would get predictions from a run wrapper like
# Bio::Tools::Run::Meme, but here we create some manually:
my $pred1 = Bio::Map::Prediction->new(-source => 'meme');
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene1',
-species => 'species1'),
-start => 950,
-end => 960);
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene1',
-species => 'species2'),
-start => 1950,
-end => 1960);
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene2',
-species => 'species1'),
-start => 955,
-end => 965);
Bio::Map::Position->new(-element => $prediction1,
-map => Bio::Map::GeneMap->get(-gene => 'gene2',
-species => 'species2'),
-start => 1955,
-end => 1965);
my $pred2 = Bio::Map::Prediction->new(-source => 'gerp');
Bio::Map::Position->new(-element => $prediction2,
-map => Bio::Map::GeneMap->get(-gene => 'gene1',
-species => 'species1'),
-start => 950,
-end => 960);
# etc.
# find the places where predictions agree
use Bio::Map::GeneRelative;
my $rel = Bio::Map::GeneRelative->new(-gene => 0);
my $di = Bio::Map::Mappable->disconnected_intersections([$pred1, $pred2],
-min_mappables_percent => 100,
-min_map_percent => 100,
-relative => $rel);
my @positions = $di->get_positions;
=head1 DESCRIPTION
For example, used to model transcription factor binding site predictions, which
can have multiple locations in several maps.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::Prediction;
use strict;
use base qw(Bio::Map::Mappable);
=head2 new
Title : new
Usage : my $prediction = Bio::Map::Prediction->new();
Function: Builds a new Bio::Map::Prediction object
Returns : Bio::Map::Prediction
Args : -name => string : name of the mappable element
-id => string : id of the mappable element
-source => string : name of the prediction program
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($source) = $self->_rearrange([qw(SOURCE)], @args);
$self->source($source) if $source;
return $self;
}
=head2 source
Title : name
Usage : $mappable->name($new_name);
my $name = $mappable->name();
Function: Get/Set the name for this Mappable
Returns : A scalar representing the current name of this Mappable
Args : none to get
string to set
=cut
sub source {
my $self = shift;
if (@_) { $self->{_source} = shift }
return $self->{_source} || '';
}
1;
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