diff variant_effect_predictor/Bio/EnsEMBL/IdMapping/TinyGene.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/IdMapping/TinyGene.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,303 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::IdMapping::TinyGene - lightweight gene object
+
+=head1 SYNOPSIS
+
+ # fetch a gene from the db and create a lightweight gene object from it
+  my $gene = $gene_adaptor->fetch_by_stable_id('ENSG000345437');
+  my $lightweight_gene = Bio::EnsEMBL::IdMapping::TinyGene->new_fast( [
+      $gene->dbID,                   $gene->stable_id,
+      $gene->version,                $gene->created_date,
+      $gene->modified_date,          $gene->start,
+      $gene->end,                    $gene->strand,
+      $gene->slice->seq_region_name, $gene->biotype,
+      $gene->status,                 $gene->analysis->logic_name,
+      ( $gene->is_known ? 1 : 0 ),
+  ] );
+
+=head1 DESCRIPTION
+
+This is a lightweight gene object for the stable Id mapping. See the
+documentation in TinyFeature for general considerations about its
+design.
+
+=head1 METHODS
+
+  start
+  end
+  strand
+  seq_region_name
+  biotype
+  status
+  logic_name
+  is_known
+  add_Transcript
+  get_all_Transcripts
+  length
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::TinyGene;
+
+# internal data structure (array indices):
+#
+#  0-4 see TinyFeature
+#  5  start
+#  6  end
+#  7  strand
+#  8  seq_region_name
+#  9  biotype
+# 10  status
+# 11  logic_name
+# 12  is_known
+# 13  [transcripts]
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IdMapping::TinyFeature;
+our @ISA = qw(Bio::EnsEMBL::IdMapping::TinyFeature);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+=head2 start
+
+  Arg[1]      : (optional) Int - the gene's start coordinate
+  Description : Getter/setter for the gene's start coordinate.
+  Return type : Int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub start {
+  my $self = shift;
+  $self->[5] = shift if (@_);
+  return $self->[5];
+}
+
+
+=head2 end
+
+  Arg[1]      : (optional) Int - the gene's end coordinate
+  Description : Getter/setter for the gene's end coordinate.
+  Return type : Int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub end {
+  my $self = shift;
+  $self->[6] = shift if (@_);
+  return $self->[6];
+}
+
+
+=head2 strand
+
+  Arg[1]      : (optional) Int - the gene's strand
+  Description : Getter/setter for the gene's strand.
+  Return type : Int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub strand {
+  my $self = shift;
+  $self->[7] = shift if (@_);
+  return $self->[7];
+}
+
+
+=head2 seq_region_name
+
+  Arg[1]      : (optional) String - seq_region name
+  Description : Getter/setter for the seq_region name of the slice the gene is
+                on.
+  Return type : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub seq_region_name {
+  my $self = shift;
+  $self->[8] = shift if (@_);
+  return $self->[8];
+}
+
+
+=head2 biotype
+
+  Arg[1]      : (optional) String - the gene's biotype
+  Description : Getter/setter for the gene's biotype.
+  Return type : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub biotype {
+  my $self = shift;
+  $self->[9] = shift if (@_);
+  return $self->[9];
+}
+
+
+=head2 strand
+
+  Arg[1]      : (optional) String - the gene's status
+  Description : Getter/setter for the gene's status.
+  Return type : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub status {
+  my $self = shift;
+  $self->[10] = shift if (@_);
+  return $self->[10];
+}
+
+
+=head2 logic_name
+
+  Arg[1]      : (optional) String - the gene's analysis' logic_name
+  Description : Getter/setter for the gene's analysis' logic_name.
+  Return type : String
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub logic_name {
+  my $self = shift;
+  $self->[11] = shift if (@_);
+  return $self->[11];
+}
+
+
+=head2 is_known
+
+  Arg[1]      : (optional) Boolean - the gene's "known" status
+  Description : Getter/setter for the gene's "known" status.
+  Return type : Boolean
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub is_known {
+  my $self = shift;
+  $self->[12] = shift if (@_);
+  return $self->[12];
+}
+
+
+=head2 add_Transcript
+
+  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyTranscript $tr - the transcript to
+                add
+  Example     : $tiny_gene->add_Transcript($tiny_transcript);
+  Description : Adds a transcript to a gene.
+  Return type : none
+  Exceptions  : thrown on wrong or missing argument
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub add_Transcript {
+  my $self = shift;
+  my $tr = shift;
+
+  unless ($tr && $tr->isa('Bio::EnsEMBL::IdMapping::TinyTranscript')) {
+    throw('Need a Bio::EnsEMBL::IdMapping::TinyTranscript.');
+  }
+
+  push @{ $self->[13] }, $tr;
+}
+
+
+=head2 get_all_Transcripts
+
+  Example     : foreach my $tr (@{ $tiny_gene->get_all_Transcripts }) {
+                  # do something with transcript
+                }
+  Description : Returns all transcripts attached to that gene.
+  Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyTranscript objects
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub get_all_Transcripts {
+  return $_[0]->[13] || [];
+}
+
+
+=head2 length
+
+  Description : Returns the gene length (distance between start and end).
+  Return type : Int
+  Exceptions  : none
+  Caller      : general
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub length {
+  my $self = shift;
+  return ($self->end - $self->start + 1);
+}
+
+
+1;
+