Bio::Map::Prediction.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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