diff variant_effect_predictor/Bio/SeqFeature/Gene/UTR.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/Gene/UTR.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,106 @@
+# $Id: UTR.pm,v 1.6 2002/10/22 07:45:20 lapp Exp $
+#
+# BioPerl module for Bio::SeqFeature::Gene::UTR
+#
+# Cared for by David Block <[e-mail]>
+#
+# Copyright David Block
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region
+          that is part of a transcription unit
+
+=head1 SYNOPSIS
+
+See documentation of methods
+
+=head1 DESCRIPTION
+
+A UTR is a Bio::SeqFeature::Gene::ExonI compliant object that is
+non-coding, and can be either 5' or 3' in a transcript.
+
+=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
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - David Block
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+This is based on the Gene Structure scaffolding erected by Hilmar Lapp
+([e-mail]).
+
+=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::SeqFeature::Gene::UTR;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::SeqFeature::Gene::NC_Feature;
+
+@ISA = qw(Bio::SeqFeature::Gene::NC_Feature);
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+  return $self;
+}
+
+=head2 primary_tag
+
+ Title   : primary_tag
+ Usage   : $tag = $feat->primary_tag()
+ Function: Returns the primary tag for a feature,
+           eg 'utr5prime'.  This method insures that 5prime/3prime information
+           is uniformly stored
+ Returns : a string 
+ Args    : none
+
+=cut
+
+sub primary_tag{
+   my ($self,$val) = @_;
+   if( defined $val ) {
+       if ($val =~ /(3|5)/ ) { $val = "utr$1prime" }
+       else { $self->warn("tag should contain indication if this is 3 or 5 prime.  Preferred text is 'utr3prime' or 'utr5prime'.  Using user text of '$val'");}
+   }
+   $self->SUPER::primary_tag($val);
+
+}
+
+1;