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

Uploaded

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+++ b/variant_effect_predictor/Bio/Tools/Prediction/Gene.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: Gene.pm,v 1.8 2002/10/22 07:38:48 lapp Exp $
+#
+# BioPerl module for Bio::Tools::Prediction::Gene
+#
+# 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::Gene - a predicted gene structure feature
+
+=head1 SYNOPSIS
+
+See documentation of methods.
+
+=head1 DESCRIPTION
+
+A feature representing a predicted gene structure. This class actually
+inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that
+functionality, plus a few methods supporting predicted sequence features,
+like a predicted CDS and a predicted translation.
+
+Exons held by an instance of this class will usually be instances of
+Bio::Tools::Prediction::Exon, although they do not have to be. Refer to the
+documentation of the class that produced the instance.
+
+Normally, you will not want to create an instance of this class yourself.
+Instead, classes representing the results of gene structure prediction
+programs will do that.
+
+=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] or [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::Gene;
+use vars qw(@ISA);
+use strict;
+
+use Bio::SeqFeature::Gene::Transcript;
+
+
+@ISA = qw(Bio::SeqFeature::Gene::Transcript);
+
+sub new {
+    my($class,@args) = @_;
+    
+    my $self = $class->SUPER::new(@args);
+
+    my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);
+
+    $primary = 'predicted_gene' unless $primary;
+    $self->primary_tag($primary);
+    return $self; 
+}
+
+
+=head2 predicted_cds
+
+ Title   : predicted_cds
+ Usage   : $predicted_cds_dna = $gene->predicted_cds();
+           $gene->predicted_cds($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 = $gene->predicted_protein();
+           $gene->predicted_protein($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'};
+}
+
+#
+# Everything else is just inherited from SeqFeature::GeneStructure.
+#
+
+1;