New module to represent non-standard associations between genes and transcripts (antisense, etc).

modules/Bio/EnsEMBL/UnconventionalTranscriptAssociation.pm

+#
+# EnsEMBL module for Bio::EnsEMBL::UnconventionalTranscriptAssociation
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=pod 
+
+=head1 NAME
+
+       Bio::EnsEMBL::UnconventionalTranscriptAssociation -
+       A class representing an some sort of unconventional association
+       between a gene and a transcript.
+
+=head1 SYNOPSIS
+
+    $ex = new Bio::EnsEMBL::UnconventionalTranscriptAssociation(Gene g, Transcript t, String type);
+
+=cut
+
+
+package Bio::EnsEMBL::UnconventionalTranscriptAssociation;
+use vars qw(@ISA);
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+
+=head2 new
+
+  Args [1]   : Bio::EnsEMBL::Gene - the gene which is associated.
+  Args [2]   : Bio::EnsEMBL::Transcript - the transcript which is associated.
+  Args [3]   : String type - the type of assocation, e.g. "antisense",
+               "sense_intronic","sense_overlaping_exonic","chimeric_sense_exonic".
+  Example    : $uta = new Bio::EnsEMBL::UnconventionalTranscriptAssociation($gene, $transcript, "antisense")
+  Description: create an UnconventionalTranscriptAssociation object.
+  Returntype : Bio::EnsEMBL::UnconventionalTranscriptAssociation.
+  Exceptions : Wrong argument types
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub new {
+
+  my ($class, $transcript, $gene, $type) = @_;
+
+  $class = ref $class || $class;
+
+  my $self = {};
+
+  if( !ref $gene || ! $gene->isa("Bio::EnsEMBL::Gene") ) {
+    throw("$gene is not a Bio::EnsEMBL::Gene!");
+  }
+
+  if( !ref $transcript || ! $transcript->isa("Bio::EnsEMBL::Transcript") ) {
+    throw("$transcript is not a Bio::EnsEMBL::Transcript!");
+  }
+
+  $self->{'gene'} = $gene;
+  $self->{'transcript'} = $transcript;
+  $self->{'type'} = $type;
+
+  return bless $self, $class;
+}
+
+
+=head2 gene
+
+  Args       : none
+  Example    : $gene = $uta->gene()
+  Description: Getter/setter for the gene part of this association.
+  Returntype : Bio::EnsEMBL::Gene
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub gene {
+  my ($self) = shift;
+
+  $self->{'gene'} = shift if (@_);
+  return $self->{'gene'};
+
+}
+
+=head2 transcript
+
+  Args       : none
+  Example    : $transcript = $uta->transcript()
+  Description: Getter/setter for the transcript part of this association.
+  Returntype : Bio::EnsEMBL::Transcript
+  Exceptions : none
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub transcript {
+  my ($self) = shift;
+
+  $self->{'transcript'} = shift if (@_);
+  return $self->{'transcript'};
+
+}
+
+=head2 interaction_type
+
+  Args       : none
+  Example    : $type = $uta->interaction_type()
+  Description: Getter/setter for the interaction_type of this association.
+  Returntype : String
+  Exceptions : none
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub interaction_type {
+  my ($self) = shift;
+
+  $self->{'interaction_type'} = shift if (@_);
+  return $self->{'interaction_type'};
+
+}
+
+1;
+
+