Bio::Tools::Prediction::Exon - A predicted exon feature

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Tools::Prediction::Exon - A predicted exon feature

SYNOPSIS

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  # See documentation of methods.

DESCRIPTION

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A feature representing a predicted exon. This class actually inherits off Bio::SeqFeature::Gene::Exon and therefore has all that functionality (also implements Bio::SeqFeatureI), plus a few methods supporting predicted features, like various scores and a significance. Even though these were inspired by GenScan results, at least a subset should be generally useable for exon prediction results.

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp

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Email hlapp-at-gmx.net

APPENDIX

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

predicted_cds

 Title   : predicted_cds
 Usage   : $predicted_cds_dna = $exon->predicted_cds();
           $exon->predicted_cds($predicted_cds_dna);
 Function: Get/Set the CDS (coding sequence) as predicted by a program.

           This method is independent of an attached_seq. There is no
           guarantee whatsoever that the returned CDS has anything to do
           (e.g., matches) with the sequence covered by the exons as annotated
           through this object.

 Example :
 Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
           defined as coding by a prediction of a program.
 Args    : On set, a Bio::PrimarySeqI implementing object holding the DNA 
           sequence defined as coding by a prediction of a program.

predicted_protein

 Title   : predicted_protein
 Usage   : $predicted_protein_seq = $exon->predicted_protein();
           $exon->predicted_protein($predicted_protein_seq);
 Function: Get/Set the protein translation as predicted by a program.

           This method is independent of an attached_seq. There is no
           guarantee whatsoever that the returned translation has anything to
           do with the sequence covered by the exons as annotated
           through this object, or the sequence returned by predicted_cds(),
           although it should usually be just the standard translation.

 Example :
 Returns : A Bio::PrimarySeqI implementing object holding the protein 
           translation as predicted by a program.
 Args    : On set, a Bio::PrimarySeqI implementing object holding the protein 
           translation as predicted by a program.

significance

 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: 
 Returns : 
 Args    :

start_signal_score

 Title   : start_signal_score
 Usage   : $sc = $obj->start_signal_score();
           $obj->start_signal_score($evalue);
 Function: Get/Set a score for the exon start signal (acceptor splice site
           or initiation signal).
 Returns : 
 Args    :

end_signal_score

 Title   : end_signal_score
 Usage   : $sc = $obj->end_signal_score();
           $obj->end_signal_score($evalue);
 Function: Get/Set a score for the exon end signal (donor splice site
           or termination signal).
 Returns : 
 Args    :

coding_signal_score

 Title   : coding_signal_score
 Usage   : $sc = $obj->coding_signal_score();
           $obj->coding_signal_score($evalue);
 Function: Get/Set a score for the exon coding signal (e.g., coding potential).
 Returns : 
 Args    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tools::Prediction::Exon
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Tools::Prediction::Exon;
use strict;


use base qw(Bio::SeqFeature::Gene::Exon);

sub new {
    my($class,@args) = @_;
    
    my $self = $class->SUPER::new(@args);

    return $self;
}



sub predicted_cds {
    my ($self, $cds) = @_;

    if(defined($cds)) {
	$self->{'_predicted_cds'} = $cds;
    }
    return $self->{'_predicted_cds'};
}


sub predicted_protein {
    my ($self, $aa) = @_;

    if(defined($aa)) {
	$self->{'_predicted_aa'} = $aa;
    }
    return $self->{'_predicted_aa'};
}


sub significance {
    return shift->_tag_value('signif', @_);
}


sub start_signal_score {
    return shift->_tag_value('AccScore', @_);
}


sub end_signal_score {
    return shift->_tag_value('DonScore', @_);
}


sub coding_signal_score {
    return shift->_tag_value('CodScore', @_);
}

#
# Everything else is just inherited from SeqFeature::Generic.
#

1;