gerp

Bio::Map::Prediction(3pm)				User Contributed Perl Documentation				 Bio::Map::Prediction(3pm)

NAME

       Bio::Map::Prediction - An object representing the predictions of something that can have multiple locations in several maps.

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;

DESCRIPTION

       For example, used to model transcription factor binding site predictions, which can have multiple locations in several maps.

FEEDBACK

   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

   Support
       Please direct usage questions or support issues to the mailing list:

       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.

   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/

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   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

   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

perl v5.14.2							    2012-03-02						 Bio::Map::Prediction(3pm)