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Bio::Map::Prediction(3User Contributed Perl DocumentatiBio::Map::Prediction(3)

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08	       Bio::Map::Prediction(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sendu Bala | APPENDIX

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