diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/Array.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Array.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,588 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::Array
+#
+# You may distribute this module under the same terms as Perl itself
+
+
+=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::Array - A module to represent a nucleotide microarray.
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::Array;
+
+my $array = Bio::EnsEMBL::Funcgen::Array->new(
+	    -NAME        => 'Array-1',
+        -FORMAT      => 'Tiled',
+        -SIZE        => '1',
+     	-VENDOR      => 'Nimblegen',
+        -DESCRIPTION => $desc,
+        -TYPE        => 'OLIGO',
+        -CLASS       => 'VENDOR_FORMAT'
+);
+
+my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
+my $array_adaptor = $db_adaptor->get_ArrayAdaptor();
+my $array = $array_adaptor->fetch_by_name($array_name)
+
+=head1 DESCRIPTION
+
+An Array object represents a nucleotide (OLIGO, PCR etc.) microarray. The data
+(currently the name, format, size, species, vendor and description) are stored
+in the array table.
+
+=cut
+
+
+use strict;
+use warnings;
+
+
+package Bio::EnsEMBL::Funcgen::Array;
+
+
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw warning );
+use Bio::EnsEMBL::Funcgen::Storable;
+
+use vars qw(@ISA);# %VALID_TYPE);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
+
+
+# Possible types for OligoArray objects
+#This should match the vendor enum values?
+#%VALID_TYPE = (
+#	'AFFY'  => 1,
+#	'OLIGO' => 1,
+#);
+
+
+=head2 new
+
+  Arg [-NAME]        : string - the name of this array
+  Arg [-VENDOR]      : string - the vendor of this array (AFFY, NIMBLEGEN etc)
+  Arg [-TYPE]        : string - type of array e.g. OLIGO, PCR
+  Arg [-FORMAT]      : string - the format of this array (TILED, TARGETTED, GENE etc)
+  Arg [-DESCRIPTION] : strin - description of the array 
+
+#array_chips is array of hashes or design_id and name, dbID will be populated on store, this should be a simple object!
+
+  Example    : my $array = Bio::EnsEMBL::Funcgen::Array->new(
+								  -NAME        => 'Array-1',
+								  -FORMAT      => 'Tiled',
+								  -SIZE        => '1',
+								  -VENDOR      => 'Nimblegen',
+                                  -TYPE        => 'OLIGO',
+								  -DESCRIPTION => $desc,
+                                  -CLASS       => 'VENDOR_FORMAT',#e.g. AFFY_UTR, ILLUMINA_WG
+								 );
+  Description: Creates a new Bio::EnsEMBL::Funcgen::Array object.
+  Returntype : Bio::EnsEMBL::Funcgen::Array
+  Exceptions : None ? should throw if mandatort params not set/valid
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+
+  my $class = ref($caller) || $caller;
+  my $self = $class->SUPER::new(@_);
+  
+  my ($name, $format, $size,  $vendor, $type, $desc, $aclass)
+    = rearrange( ['NAME', 'FORMAT', 'SIZE',  'VENDOR', 'TYPE', 'DESCRIPTION', 'CLASS'], @_ );
+  
+  #mandatory params?
+  #name, format, vendor
+  #enum on format?
+
+  my @stack = caller();
+
+  if($self->dbID() && $stack[0] ne "Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor"){
+    throw("You must use the ArrayAdaptor($stack[0]) to generate Arrays with a dbID i.e. from the DB, as this module accomodates updating which may cause incorrect data if the object is not generated form the DB");
+  } 
+
+
+  throw("Must provide a vendor parameter") if ! $vendor;
+  throw("Must provide a name parameter") if ! $name;
+  #any others?
+
+  
+  $self->name($name);
+  $self->format($format)    if defined $format;
+
+  if(defined $format && $format eq 'EXPRESSION' && ! defined $class){
+	throw('You must defined a class if you are importing and array with an EXPRESSION format');
+  }
+
+  $self->class(uc($aclass))     if defined $aclass;
+  $self->size($size)        if defined $size;
+  $self->vendor($vendor);
+  $self->description($desc) if defined $desc;
+  $self->type($type)        if defined $type;
+  
+  return $self;
+}
+
+=head2 get_all_Probes
+
+  Args       : None
+  Example    : my $probes = $array->get_all_Probes();
+  Description: Returns all probes on an array. Needs a database connection.
+  Returntype : Listref of Bio::EnsEMBL::Funcgen::Probe objects
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_all_Probes {
+	my $self = shift;
+
+	if ( $self->dbID() && $self->adaptor() ) {
+		my $opa = $self->adaptor()->db()->get_ProbeAdaptor();
+		my $probes = $opa->fetch_all_by_Array($self);
+		return $probes;
+	} else {
+		warning('Need database connection to retrieve Probes');
+		return [];
+	}
+}
+
+=head2 get_all_Probe_dbIDs
+
+  Args       : None
+  Example    : my @dbids = @{$array->get_all_Probe_dbIDs};
+  Description: Returns an array ref of all the Probe database IDs for this array
+  Returntype : arrayref of ints
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_all_Probe_dbIDs {
+  my $self = shift;
+
+  if(!  $self->{probe_dbids}){
+	#check for adaptor here?
+	
+	if(! $self->adaptor){
+	  throw('Must have set an adaptor to get_all_Probe_dbIDs');
+	}
+	
+	$self->{probe_dbids} = $self->adaptor->fetch_Probe_dbIDs_by_Array($self);
+  }
+
+  return  $self->{probe_dbids};
+}
+
+
+
+
+#Nath new get methods
+
+=head2 get_all_ProbeSets
+
+  Args       : None
+  Example    : my $probesets = $array->get_all_ProbeSets();
+  Description: Returns all probesets on an array. Needs a database connection.
+  Returntype : Listref of Bio::EnsEMBL::Funcgen::ProbeSets objects
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub get_all_ProbeSets {
+	my $self = shift;
+
+	if ( $self->dbID() && $self->adaptor() ) {
+		my $opsa = $self->adaptor()->db()->get_ProbeSetAdaptor();
+		my $probesets = $opsa->fetch_all_by_Array($self);
+		return $probesets;
+	} else {
+		warning('Need database connection to retrieve ProbeSets');
+		return [];
+	}
+}
+
+
+#All the array_chip methods will be migrated to ArrayChip.pm
+
+=head2 get_array_chip_ids
+
+  Example    : my @ac_ids = @{$array->get_array_chip_ids()};
+  Description: Returns all array_chip_ids for this array.
+  Returntype : Listref of array_chip ids
+  Exceptions : Throws if none retrieved
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_array_chip_ids {
+  my $self = shift;
+
+  my @ac_ids;
+
+
+  $self->get_ArrayChips();
+
+  #should we get_ArrayChips is we have none cached?
+  #this may cause problem
+
+
+  foreach my $achip(values %{$self->{'array_chips'}}){
+    push @ac_ids, $achip->dbID();
+  }
+
+  if(! @ac_ids){
+    throw("No array_chip_ids available"); # should this be warn?
+  }
+  
+  return \@ac_ids;
+}
+
+=head2 get_design_ids
+
+  Example    : my @design_ids = @{$array->get_design_ids()};
+  Description: Returns a the design_ids for each array_chip contained within this array
+  Returntype : list
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+
+
+sub get_design_ids{
+  my $self = shift;
+  return [keys %{$self->{'array_chips'}}];
+}
+    
+
+
+=head2 name
+
+  Arg [1]    : (optional) string - the name of this array
+  Example    : my $name = $array->name();
+  Description: Getter, setter of the name attribute for Array
+               objects.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub name{
+  my $self = shift;
+  
+  $self->{'name'} = shift if @_;
+  
+  #do we need this?
+  #if ( !exists $self->{'name'} && $self->dbID() && $self->adaptor() ) {
+  #  $self->adaptor->fetch_attributes($self);
+  #}
+  
+  return $self->{'name'};
+}
+
+
+=head2 type
+
+  Arg [1]    : (optional) string - the type of this array
+  Example    : $array->type('OLIGO');
+  Description: Getter, setter of the type attribute for Array
+               objects.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub type{
+  my $self = shift;
+  
+  $self->{'type'} = shift if @_;
+    
+  return $self->{'type'};
+}
+
+
+=head2 format
+
+  Arg [1]    : (optional) string - the format of the array
+  Example    : my $format = $array->format();
+  Description: Getter, setter of format attribute for
+               Array objects e.g. Tiled, Targetted etc...
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub format {
+  my $self = shift;
+  
+  $self->{'format'} = shift if @_;
+  
+  #do we need this?
+  #if ( !exists $self->{'format'} && $self->dbID() && $self->adaptor() ) {
+  #  $self->adaptor->fetch_attributes($self);
+  #}
+  
+  return $self->{'format'};
+}
+
+=head2 class
+
+  Arg [1]    : (optional) string - the class of the array
+  Example    : my $class = $array->class('AFFY_UTR');
+  Description: Getter, setter of class attribute for
+               Array objects e.g. AFFY_UTR, AFFY_ST
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub class {
+  my $self = shift;
+  
+  $self->{'class'} = shift if @_;
+  
+  return $self->{'class'};
+}
+
+
+=head2 size
+
+  Arg [1]    : (optional) int - the number of ? in the array
+  Example    : my $size = $array->size();
+  Description: Getter of size attribute for Array objects. This
+               simply counts the constituent ArrayChips
+  Returntype : int
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub size {
+  my $self = shift;
+
+  return scalar(keys %{$self->{'array_chips'}});
+}
+
+
+=head2 vendor
+
+  Arg [1]    : (optional) string - the name of the array vendor
+  Example    : my $vendor = $array->vendor();
+  Description: Getter, setter of vendor attribute for
+               Array objects.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub vendor {
+  my $self = shift;
+  $self->{'vendor'} = shift if @_;
+  
+  #do we need this?
+  #if ( !exists $self->{'vendor'} && $self->dbID() && $self->adaptor() ) {
+  #  $self->adaptor->fetch_attributes($self);
+  #}
+
+  return $self->{'vendor'};
+}
+
+=head2 description
+
+  Arg [1]    : (optional) string - the description of the array
+  Example    : my $size = $array->description();
+  Description: Getter, setter of description attribute for
+               Array objects. 
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub description {
+  my $self = shift;
+  $self->{'description'} = shift if @_;
+  
+  #do we need this?
+  #if ( !exists $self->{'description'} && $self->dbID() && $self->adaptor() ) {
+  #  $self->adaptor->fetch_attributes($self);
+  #}
+
+  return $self->{'description'};
+}
+
+=head2 probe_count
+
+  Example    : my $num_probes = $array->probe_count();
+  Description: Return number of probes on array
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub probe_count {
+  my ($self)  = @_;
+  #Do we want a distinct flag here?
+
+  if(! defined $self->{'probe_count'}){
+	$self->{'probe_count'} = $self->adaptor->fetch_probe_count_by_Array($self);
+  }
+  
+  return $self->{'probe_count'};
+}
+
+
+
+=head2 get_ArrayChips
+
+  Example    : my @achips = @{$array->get_ArrayChips()};
+  Description: Getter, setter and lazy loader of array_chip hashes
+  Returntype : Arrays of ArrayChip objects
+  Exceptions : Throws exception if none found for array_id
+  Caller     : General
+  Status     : High Risk - migrate to ArrayChip.pm
+
+=cut
+
+sub get_ArrayChips {
+  my $self = shift;
+ 
+  #lazy loaded as we won't want this for light DB
+  #should do meta check and want here
+
+  if ( ! exists $self->{'array_chips'}){
+
+    if( $self->dbID() && $self->adaptor() ) {
+      #$self->adaptor->fetch_attributes($self);
+      #need to do this differently as we're accessing a different table
+      $self->{'array_chips'} = {};
+
+      foreach my $achip(@{$self->adaptor->db->get_ArrayChipAdaptor->fetch_all_by_array_id($self->dbID())}){
+	$self->{'array_chips'}{$achip->design_id} = $achip;
+	#%{$self->{'array_chips'}} = %{$self->adaptor->db->get_ArrayAdaptor->_fetch_array_chips_by_array_dbID($self->dbID())};
+      }
+    }
+    else{
+      throw("Need array dbID and DB connection to retrieve array_chips");
+    }
+  }
+
+  return [ values %{$self->{'array_chips'}} ];
+}
+
+=head2 get_ArrayChip_by_design_id
+
+  Arg [1]    : (mandatory) int - design_id
+  Example    : my %ac = %{$array->get_ArrayChip_by_design_id('1234')};
+  Description: Getter for array_chip hashes
+  Returntype : Hashref
+  Exceptions : Throws exception if no design_id defined, warns if not part of array
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub get_ArrayChip_by_design_id{
+  my ($self, $design_id) = @_;
+
+
+  #warn "This needs to get the array chip if not defined?? but we're using it to test whether is has been stored same problem as probe_design?";
+
+  my ($achip);
+  throw("Must supply a valid array chip design_id") if (! defined $design_id);
+
+  if(defined $self->{'array_chips'}{$design_id}){
+    $achip = $self->{'array_chips'}{$design_id};
+  }else{
+    #No we use this to check whether it has been stored with the array
+    #warn("should this throw? Array does not contain ArrayChip:$design_id\n"); 
+  }
+
+  return $achip;
+}
+
+=head2 add_ArrayChip
+
+  Arg [1]    : mandatory - Bio::EnsEMBL::Funcgen::ArrayChip
+  Example    : $array->add_ArrayChip($array_chip);
+  Description: Setter for array chips
+  Returntype : None
+  Exceptions : Throws if arg not a Bio::EnsEMBL::Funcgen::ArrayChip, or Array not stored
+  Caller     : General
+  Status     : Ar risk
+
+=cut
+
+#This uses previosuly stored array_chips withotu warning
+#Need to implement fetch_store method?
+
+sub add_ArrayChip{
+  my ($self, $array_chip) = @_;
+
+  throw("You must supply a stored Bio::EnsEMBL::Funcgen::ArrayChip") if(! ($array_chip && 
+									   $array_chip->isa("Bio::EnsEMBL::Funcgen::ArrayChip") && 
+									   $array_chip->dbID()));
+  
+  if ($self->dbID() && $self->adaptor()){
+    $self->get_ArrayChips() if (! $self->{'array_chips'});
+
+    if(exists $self->{'array_chips'}{$array_chip->design_id}){
+      $array_chip = $self->{'array_chips'}{$array_chip->design_id};
+      #warn("Array chip for ".$array_chip->design_id()." already exists, using previous stored array chip\n");
+    }else{
+      $self->{'array_chips'}{$array_chip->design_id} = $array_chip;
+    }
+
+  }else{
+    throw("Array must be stored before adding an array_chip");
+  }
+
+  return;
+}
+
+
+1;
+