diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/ProbeSet.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/ProbeSet.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,300 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::ProbeSet
+#
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2011 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]>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Funcgen::ProbeSet - A module to represent a probeset.
+
+=head1 SYNOPSIS
+
+ use Bio::EnsEMBL::Registry;
+ use Bio::EnsEMBL::Funcgen::ProbeSet;
+
+
+ my $reg = Bio::EnsEMBL::Registry->load_adaptors_from_db(-host    => 'ensembldb.ensembl.org',
+                                                         -user    => 'anonymous');
+
+ my $pset_adaptor = $reg->get_adaptor($species, 'funcgen', 'ProbeSet');
+
+ ### Creating/storing a ProbeSet ###
+
+ my $probe_set = Bio::EnsEMBL::Funcgen::ProbeSet->new(-NAME          => 'ProbeSet-1',
+                                                      -SIZE          => 1,
+                                                      -FAMILY        => "ENCODE REGIONS",#optional
+                                                     );
+
+ $pset_adaptor->store($probe_set);
+
+
+ ### Fetching associated transcripts ###
+ # Generated by the Ensembl array mapping pipeline
+
+ my @dbentries     = @{$probe_set->fetch_all_Transcript_DBEntries};
+ my $trans_adaptor = $reg->get_adpator($species, 'core', 'Transcript');
+
+ foreach my $dbe(@dbentries){
+
+    my $tx = $trans_adaptor->fetch_by_stable_id($dbe->primary_id);
+   
+    #Print the transcript info and the linkage annotation
+    print $tx->stable_id."\t".$probe_set->name.' '.$dbe->linkage_annotation."\n";
+ }
+
+ #Alternatively these annotations are also available in a transcript centric manner
+ #using the ProbeSetAdaptor
+
+
+=head1 DESCRIPTION
+
+A ProbeSet object represents a set of probes on a microarray. The
+data (currently the name, size, and family) are stored in the probe_set 
+table. ProbeSets are only really relevant for Affy probes, or when 
+avaliable these will be analagous to Nimblegen feature sets.
+
+For Affy arrays, a probeset can be part of more than one array, containing unique
+probes. 
+
+#Need to rewrite this bit
+#Something about array_chip_id i.e. experimental validation etc
+On each Affy array the probe has a slightly different name. For
+example, two different complete names for the same probe might be
+DrosGenome1:AFFX-LysX-5_at:535:35; and Drosophila_2:AFFX-LysX-5_at:460:51;. In
+the database, these two probes will have the same probe_id. Thus the same
+Affy probe can have a number of different names and complete names depending on
+which array it is on.
+
+
+=head1 SEE ALSO
+
+  Bio::EnsEMBL::Funcgen::ProbeSetAdaptor
+  ensembl-functgenomics/scripts/examples/microarray_annotation_example.pl
+
+  Or for details on how to run the array mapping pipeline see:
+  ensembl-functgenomics/docs/array_mapping.txt
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::ProbeSet;
+
+use Bio::EnsEMBL::Utils::Argument qw( rearrange ) ;
+use Bio::EnsEMBL::Utils::Exception qw( throw warning );
+use Bio::EnsEMBL::Funcgen::Storable;
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
+
+
+=head2 new
+
+  Arg [-NAME]           : string - probeset name
+  Arg [-SIZE]           : int - probe set size
+        Will be the same for all probes sets if same probe set
+		is on multiple arrays.
+  Arg [-FAMILY]         : string - probe set family, generic descriptor for probe set e.g. ENCODE REGIONS, RANDOM
+        Will be the same for all probes sets if same probe set is on multiple arrays.
+  Example    : my $probeset = Bio::EnsEMBL::Funcgen::ProbeSet->new(
+                   -NAME          => 'ProbeSet-1',
+				   -SIZE          => 1,
+                   -FAMILY        => "ENCODE_REGIONS",
+               );
+  Description: Creates a new Bio::EnsEMBL::Funcgen::ProbeSet object.
+  Returntype : Bio::EnsEMBL::Funcgen::ProbeSet
+  Exceptions : Throws if not supplied with probeset name and array chip id(s)
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub new {
+	my $caller = shift;
+	
+	my $class = ref($caller) || $caller;
+	
+	my $self = $class->SUPER::new(@_);
+
+	#warn("The only way to get array names/ids, is to retrieve all the probes!!!");
+
+	
+	my (
+		$name,          $size,
+		$family
+	) = rearrange([
+		'NAME',          'SIZE',
+		'FAMILY',
+	], @_);
+	
+		
+	$self->name($name)     if defined $name;
+	$self->family($family) if defined $family;
+	$self->size($size)     if defined $size;
+	
+	return $self;
+}
+
+
+
+#=head2 get_all_ProbeFeatures
+
+#  Args       : None
+#  Example    : my $features = $probeset->get_all_ProbeFeatures();
+#  Description: Get all features produced by this probeset. The probeset needs to be
+#               database persistent.
+#  Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeFeature objects
+#  Exceptions : None
+#  Caller     : General
+#  Status     : Medium Risk
+
+#=cut
+
+sub get_all_ProbeFeatures {
+	my $self = shift;
+
+	throw("Not implemented yet, do we want to do this for ProbeSet or just probe?");
+
+	if ( $self->adaptor() && $self->dbID() ) {
+		return $self->adaptor()->db()->get_ProbeFeatureAdaptor()->fetch_all_by_ProbeSet($self);
+	} else {
+		warning('Need database connection to retrieve Features');
+		return [];
+	}    
+}
+
+=head2 get_all_Arrays
+
+  Args       : None
+  Example    : my $arrays = $probeset->get_all_Arrays();
+  Description: Returns all arrays that this probeset is part of. Only works if the
+               probedet was retrieved from the database or created using
+			   add_Array_probename.
+  Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub get_all_Arrays {
+  my $self = shift;
+
+  if (defined $self->{'arrays'}) {
+	return $self->{'arrays'};
+  } 
+  else{
+	$self->{arrays} = $self->adaptor->db->get_ArrayAdaptor->fetch_all_by_ProbeSet($self);
+  }
+  
+  $self->{arrays}
+}
+
+
+=head2 get_all_Probes
+
+  Args       : None
+  Example    : my @probes = @{$probeset->get_all_Probes();
+  Description: Returns all probes belonging to this ProbeSet
+  Returntype : Listref of Bio::EnsEMBL::Funcgen::Probe objects
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_all_Probes {
+  my $self = shift;
+
+  if (defined $self->{'probes'}) {
+	return $self->{'probes'};
+  } 
+  else{
+	$self->{probes} = $self->adaptor->db->get_ProbeAdaptor->fetch_all_by_ProbeSet($self);
+  }
+  
+  $self->{probes}
+}
+
+
+
+#sub get_all_array_chips_ids?
+#sub get_all_Results? from_Experiment?
+
+=head2 name
+
+  Arg [1]    : string - aprobeset name
+  Example    : my $probesetname = $probeset->name('probeset-1');
+  Description: Getter/Setter for the name attribute of ProbeSet objects.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub name {
+    my $self = shift;
+	$self->{'name'} = shift if @_;
+    return $self->{'name'};
+}
+
+
+=head2 family
+
+  Arg [1]    : (optional) string - family
+  Example    : my $family = $probe->family();
+  Description: Getter and setter of family attribute for ProbeSet
+               objects. e.g. EXPERIMENTAL or CONTROL
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub family {
+    my $self = shift;
+    $self->{'family'} = shift if @_;
+    return $self->{'family'};
+}
+
+=head2 size
+
+  Arg [1]    : (optional) int - probeset size
+  Example    : my $probeset_size = $probeset->size();
+  Description: Getter and setter of probeset size attribute for ProbeSet
+               objects.
+  Returntype : int
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub size {
+    my $self = shift;
+    $self->{'size'} = shift if @_;
+    return $self->{'size'};
+}
+
+1;
+