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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/Gene/Exon.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,226 @@
+# $Id: Exon.pm,v 1.8 2002/10/22 07:38:41 lapp Exp $
+#
+# BioPerl module for Bio::SeqFeature::Gene::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::SeqFeature::Gene::Exon - a feature representing an exon
+
+=head1 SYNOPSIS
+
+    # obtain an exon instance $exon somehow
+    print "exon from ", $exon->start(), " to ", $exon->end(),
+          " on seq ", $exon->seq_id(), ", strand ", $exon->strand(),
+          ", encodes the peptide sequence ", 
+          $exon->cds()->translate()->seq(), "\n";
+
+=head1 DESCRIPTION
+
+This module implements a feature representing an exon by implementing the
+Bio::SeqFeature::Gene::ExonI interface. 
+
+Apart from that, this class also implements Bio::SeqFeatureI by inheriting
+off Bio::SeqFeature::Generic.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this
+and other Bioperl modules. Send your comments and suggestions preferably
+ to one of the Bioperl mailing lists.
+Your participation is much appreciated.
+
+  [e-mail]          - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+ the bugs and their resolution.
+ Bug reports can be submitted via email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::SeqFeature::Gene::Exon;
+use vars qw(@ISA);
+use strict;
+
+use Bio::SeqFeature::Generic;
+use Bio::SeqFeature::Gene::ExonI;
+
+@ISA = qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::ExonI);
+
+#
+# A list of allowed exon types. See primary_tag().
+#
+my @valid_exon_types = ('initial', 'internal', 'terminal');
+
+sub new {
+    my ($caller, @args) = @_;
+    my $self = $caller->SUPER::new(@args);
+    my ($primary) =
+	$self->_rearrange([qw(PRIMARY)],@args);
+
+    $primary = 'exon' unless $primary;
+    $self->primary_tag($primary); # this will also set is_coding()
+    $self->strand(0) if(! defined($self->strand()));
+    return $self;
+}
+
+
+=head2 is_coding
+
+ Title   : is_coding
+ Usage   : if($exon->is_coding()) {
+                   # do something
+           }
+           if($is_utr) {
+               $exon->is_coding(0);
+           }
+ Function: Get/set whether or not the exon codes for amino acid.
+ Returns : TRUE if the object represents a feature translated into protein,
+           and FALSE otherwise.
+ Args    : A boolean value on set.
+
+
+=cut
+
+sub is_coding {
+    my ($self,$val) = @_;
+
+    if(defined($val)) {
+	$self->{'_iscoding'} = $val;
+    }
+    return $self->{'_iscoding'};
+}
+
+=head2 primary_tag
+
+ Title   : primary_tag
+ Usage   : $tag = $feat->primary_tag()
+           $feat->primary_tag('exon')
+ Function: Get/set the primary tag for the exon feature.
+
+           This method is overridden here in order to allow only for
+           tag values following a certain convention. For consistency reasons,
+           the tag value must either contain the string 'exon' or the string
+           'utr' (both case-insensitive). In the case of 'exon', a string
+           describing the type of exon may be appended or prefixed. Presently,
+           the following types are allowed: initial, internal, and terminal
+           (all case-insensitive). 
+
+           If the supplied tag value matches 'utr' (case-insensitive),
+           is_coding() will automatically be set to FALSE, and to TRUE
+           otherwise.
+
+ Returns : A string.
+ Args    : A string on set.
+
+
+=cut
+
+# sub primary_tag {
+#    my ($self,$value) = @_;
+
+#    if(defined($value)) {
+#        if((lc($value) =~ /utr/i) || (lc($value) eq "exon") ||
+# 	  ((lc($value) =~ /exon/i) &&
+# 	   (grep { $value =~ /$_/i; } @valid_exon_types))) {
+# 	   $self->is_coding($value =~ /utr/i ? 0 : 1);
+#        } else {
+# 	   $self->throw("primary tag $value is invalid for object of class ".
+# 			ref($self));
+#        }
+#    }
+#    return $self->SUPER::primary_tag($value);
+# }
+
+=head2 location
+
+ Title   : location
+ Usage   : my $location = $exon->location()
+ Function: Returns a location object suitable for identifying the location 
+	   of the exon on the sequence or parent feature.
+
+           This method is overridden here to restrict allowed location types
+           to non-compound locations.
+
+ Returns : Bio::LocationI object
+ Args    : none
+
+
+=cut
+
+sub location {
+   my ($self,$value) = @_;  
+
+   if(defined($value) && $value->isa('Bio::Location::SplitLocationI')) {
+       $self->throw("split or compound location is not allowed ".
+		    "for an object of type " . ref($self));
+   }
+   return $self->SUPER::location($value);
+}
+
+=head2 cds
+
+ Title   : cds()
+ Usage   : $cds = $exon->cds();
+ Function: Get the coding sequence of the exon as a sequence object.
+
+           The sequence of the returned object is prefixed by Ns (lower case)
+           if the frame of the exon is defined and different from zero. The
+           result is that the first base starts a codon (frame 0).
+
+           This implementation returns undef if the particular exon is
+           not translated to protein, i.e., is_coding() returns FALSE. Undef
+           will also be returned if no sequence is attached to this exon
+           feature.
+
+ Returns : A Bio::PrimarySeqI implementing object.
+ Args    : 
+
+
+=cut
+
+sub cds {
+    my ($self) = @_;
+
+    # UTR is not translated
+    return undef if(! $self->is_coding());
+
+    my $seq = $self->seq();
+    if(defined($seq) && defined($self->frame()) && ($self->frame() != 0)) {
+	my $prefix = "n" x $self->frame();
+	$seq->seq($prefix . $seq->seq());
+    }
+    return $seq;
+}
+
+1;