Bio::Map Prediction
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Summary
Bio::Map::Prediction - An object representing the predictions of something
that can have multiple locations in several maps.
Package variables
No package variables defined.
Inherit
Bio::Map::Mappable
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.
Methods
newDescriptionCode
sourceDescriptionCode
Methods description
newcode    nextTop
 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
sourcecodeprevnextTop
 Title   : name
Usage : $mappable->name($new_name);
my $name = $mappable->name();
Function: Get/Set the name for this Mappable
Returns : A scalar representing the current name of this Mappable
Args : none to get
string to set
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    my ($source) = $self->_rearrange([qw(SOURCE)], @args);
    $self->source($source) if $source;
    
    return $self;
}
sourcedescriptionprevnextTop
sub source {
    my $self = shift;
    if (@_) { $self->{_source} = shift }
    return $self->{_source} || '';
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _