diff variant_effect_predictor/Bio/EnsEMBL/Map/Qtl.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Map/Qtl.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,340 @@
+=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::Map::Qtl
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+Represents a Qtl in the EnsEMBL database. A quantitative trait locus is
+defined by three markers, two flanking and one peak (optional) marker.
+Its a region (or more often a group of regions) which is likely to
+affect the phenotype (trait) described in this Qtl.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::Map::Qtl;
+
+use strict;
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::Storable;
+use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+
+@ISA = qw(Bio::EnsEMBL::Storable);
+
+
+
+=head2 new
+
+  Arg [1]    : int $dbID
+  Arg [2]    : Bio::EnsEMBL::Map::DBSQL::QtlAdaptor $adaptor
+  Arg [3]    : Bio::EnsEMBL::Map::Marker $flank_marker_1
+  Arg [4]    : Bio::EnsEMBL::Map::Marker $peak_marker
+  Arg [5]    : Bio::EnsEMBL::Map::Marker $flank_marker_2
+  Arg [6]    : string $trait
+  Arg [7]    : float $lod_score
+  Arg [8]    : hashref $synonyms
+               A hashref with source keys and identifier values
+  Example    : none
+  Description: Creates a new Qtl object. Usually done by Adaptor
+  Returntype : Bio::EnsEMBL::Map::Qtl
+  Exceptions : none
+  Caller     : general, DBSQL::QtlAdaptor, DBSQL::QtlFeatureAdaptor
+  Status     : stable
+
+=cut
+
+sub new {
+  my ( $class, $dbID, $adaptor, $flank_marker_1, $peak_marker,
+       $flank_marker_2, $trait, $lod_score,
+       $synonyms ) = @_;
+
+  $class = ref( $class ) ||$class;
+  my $self = bless( {
+		     'dbID'           => $dbID,
+		     'flank_marker_1' => $flank_marker_1,
+		     'flank_marker_2' => $flank_marker_2,
+		     'peak_marker'    => $peak_marker,
+		     'trait'          => $trait,
+		     'lod_score'      => $lod_score,
+		     'synonyms'       => $synonyms
+		    }, $class );
+  $self->adaptor($adaptor);
+  return $self;
+}
+
+
+=head2 add_synonym
+
+  Arg [1]    : string $source
+               The source of the synonym
+  Arg [2]    : string $identifier
+               The identifier from this source
+  Example    : $qtl->add_synonym('rat genome database', '65516');
+  Description: Adds a synonym to this qtl
+  Returntype : none
+  Exceptions : thrown if arguments are not provided
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub add_synonym {
+  my $self = shift;
+  my $source = shift;
+  my $identifier = shift;
+
+  unless($source && $identifier) {
+    throw('Source and identifier arguments are required');
+  }
+
+  $self->{'synonyms'}->{$source} = $identifier;
+}
+
+
+=head2 get_synonyms
+
+  Arg [1]    : none
+  Example    :
+     foreach my $source ($keys %{$qtl->get_synonyms}) {
+       print $source . ':'. $qtl->get_synonyms->{$source};
+     }
+  Description: Returns a hashref of synonyms keyed on their source name 
+  Returntype : hashref of synonyms keyed on their source name
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub get_synonyms {
+  my $self = shift;
+
+  return $self->{'synonyms'} || {};
+}
+
+
+
+=head2 trait
+
+  Arg [1]    : string $trait
+               Phenotype of this Qtl
+  Example    : none
+  Description: Getter/Setter for the trait attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub trait {
+  my $self = shift;
+
+  if(@_) {
+    $self->{'trait'} = shift;
+  }
+
+  return $self->{'trait'};
+}
+
+
+=head2 lod_score
+
+  Arg [1]    : float $lod_score
+               A score for the Qtl
+  Example    : none
+  Description: Getter/Setter for attribute lod_score
+  Returntype : float
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub lod_score {
+  my $self = shift;
+
+  if(@_) {
+    $self->{'lod_score'} = shift;
+  }
+
+  return $self->{'lod_score'};
+}
+
+
+=head2 peak_marker
+
+  Arg [1]    : Bio::EnsEMBL::Map::Marker $peak_marker
+               an optional Marker which has the peak probablitity
+               for this traits occurence
+  Example    : none
+  Description: Getter/Setter for attribute peak_marker
+  Returntype : Bio::EnsEMBL::Map::Marker
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub peak_marker {
+  my $self = shift;
+
+  if(@_) {
+    $self->{'peak_marker'} = shift;
+  }
+
+  return $self->{'peak_marker'};
+}
+
+
+=head2 flank_marker_1
+
+  Arg [1]    : Bio::EnsEMBL::Map::Marker $flank_marker_1
+               One flanking marker of the interest region, the two flanking
+               markers define the region
+  Example    : none
+  Description: Getter/Setter attribute flanking_marker_1
+  Returntype : Bio::EnsEMBL::Map::Marker
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub flank_marker_1 {
+  my $self = shift;
+
+  if(@_) {
+    $self->{'flank_marker_1'} = shift;
+  }
+
+  return $self->{'flank_marker_1'};
+}
+
+
+
+=head2 flank_marker_2
+
+  Arg [1]    : Bio::EnsEMBL::Map::Marker $flank_marker_2
+               One flanking marker of the interest region, the two flanking
+               markers define the region
+  Example    : none
+  Description: Getter/Setter attribute flanking_marker_2
+  Returntype : Bio::EnsEMBL::Map::Marker
+  Exceptions : none
+  Caller     : general
+  Status     : stable
+
+=cut
+
+
+sub flank_marker_2 {
+  my $self = shift;
+
+  if(@_) {
+    $self->{'flank_marker_2'} = shift;
+  }
+
+  return $self->{'flank_marker_2'};
+}
+
+
+
+=head2 get_QtlFeatures
+
+  Args       : none
+  Example    : none
+  Description: return the qtl feature which is associated with this
+               Qtl. It comes in chromosomal slice coordinates. There can 
+               only be one.
+  Returntype : Bio::EnsEMBL::Map::QtlFeature
+  Exceptions : only works with adaptored Qtls
+  Caller     : general
+  Status     : stable
+
+=cut
+
+sub get_QtlFeature {
+  my $self = shift;
+
+  my $adaptor = $self->adaptor();
+  return undef unless $adaptor;
+  my $result = $adaptor->db()->get_QtlFeatureAdaptor()->
+    fetch_all_by_Qtl( $self );
+
+  if( @$result ) {
+    return $result->[0];
+  } else {
+    return;
+  }
+}
+
+
+
+
+
+=head2 source_database
+
+This method is deprecated.  Use get_synonyms or add_synonym instead.
+
+=cut
+
+sub source_database {
+  my $self = shift;
+
+  deprecate('Use get_synonyms or add_synonym instead');
+
+  my $syns = $self->get_synonyms;
+  my ($source) = keys %$syns;
+
+  return $source || '';
+}
+
+
+=head2 source_primary_id
+
+This method is deprecated. Use get_synonyms or add_synonym instead.
+
+=cut
+
+sub source_primary_id {
+  my $self = shift;
+
+  deprecate('Use get_synonyms or add_synonym instead');
+
+  my $syns = $self->get_synonyms;
+  my ($source) = keys %$syns;
+
+  if($source) {
+    return $syns->{$source};
+  }
+
+  return '';
+}
+
+
+1;