diff variant_effect_predictor/Bio/Tools/Prediction/Exon.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Prediction/Exon.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: Exon.pm,v 1.10 2002/10/22 07:38:48 lapp Exp $
+#
+# BioPerl module for Bio::Tools::Prediction::Exon
+#
+# Cared for by Hilmar Lapp <[e-mail]>
+#
+# Copyright Hilmar Lapp
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Prediction::Exon - A predicted exon feature
+
+=head1 SYNOPSIS
+
+See documentation of methods.
+
+=head1 DESCRIPTION
+
+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.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]          - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 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 email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Tools::Prediction::Exon;
+use vars qw(@ISA);
+use strict;
+
+use Bio::SeqFeature::Gene::Exon;
+
+@ISA = qw(Bio::SeqFeature::Gene::Exon);
+
+sub new {
+    my($class,@args) = @_;
+    
+    my $self = $class->SUPER::new(@args);
+
+    my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);
+
+    return $self;
+}
+
+
+=head2 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.
+
+=cut
+
+sub predicted_cds {
+    my ($self, $cds) = @_;
+
+    if(defined($cds)) {
+	$self->{'_predicted_cds'} = $cds;
+    }
+    return $self->{'_predicted_cds'};
+}
+
+=head2 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.
+
+=cut
+
+sub predicted_protein {
+    my ($self, $aa) = @_;
+
+    if(defined($aa)) {
+	$self->{'_predicted_aa'} = $aa;
+    }
+    return $self->{'_predicted_aa'};
+}
+
+=head2 significance
+
+ Title   : significance
+ Usage   : $evalue = $obj->significance();
+           $obj->significance($evalue);
+ Function: 
+ Returns : 
+ Args    : 
+
+
+=cut
+
+sub significance {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('signif', $value);
+}
+
+=head2 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    : 
+
+
+=cut
+
+sub start_signal_score {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('AccScore', $value);
+}
+
+=head2 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    : 
+
+
+=cut
+
+sub end_signal_score {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('DonScore', $value);
+}
+
+=head2 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    : 
+
+
+=cut
+
+sub coding_signal_score {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('CodScore', $value);
+}
+
+#
+# Everything else is just inherited from SeqFeature::Generic.
+#
+
+1;