Bio::Map::Prediction(3User Contributed Perl DocumentatiBio::Map::Prediction(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Map::Prediction(3)
