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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/ExperimentalSet.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,281 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::ExperimentalSubset
+#
+# You may distribute this module under the same terms as Perl itself
+
+=head1 NAME
+
+Bio::EnsEMBL::ExperimentalSet - A module to represent ExperimentalSet object.
+ 
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::ExpeimentalSet;
+
+my $data_set = Bio::EnsEMBL::Funcgen::ExperimentalSet->new(
+	                                                      -DBID            => $dbID,
+							 					          -ADAPTOR         => $self,
+                                                          -EXPERIMENT   => $exp,
+                                                          -FEATURE_TYPE => $ftype,
+                                                          -CELL_TYPE    => $ctype,
+                                                          -FORMAT       => 'READ_FORMAT',
+                                                          -VENDOR       => 'SOLEXA',
+                                                          -NAME         => 'ExpSet1',
+                                                          );
+
+
+
+=head1 DESCRIPTION
+
+An ExperimentalSet object provides a generic container for any non-array based feature import, 
+allowing tracking of file import via the status table and integration into Data and FeatureSets to
+provide traceability to the source experiment from a given FeatureSet.
+
+=head1 AUTHOR
+
+This module was created by Nathan Johnson.
+
+This module is part of the Ensembl project: http://www.ensembl.org/
+
+=head1 CONTACT
+
+Post comments or questions to the Ensembl development list: [e-mail]
+
+=head1 METHODS
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::ExperimentalSet;
+
+use Bio::EnsEMBL::Funcgen::ExperimentalSubset;
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate);
+use Bio::EnsEMBL::Funcgen::Set;
+
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Set);#change to Set once we have implemented analysis properly
+
+
+=head2 new
+
+
+
+  Example    : my $eset = Bio::EnsEMBL::Funcgen::ExperimentalSet->new(
+                                                                     -EXPERIMENT   => $exp,
+                                                                     -FEATURE_TYPE => $ftype,
+                                                                     -CELL_TYPE    => $ctype,
+                                                                     -FORMAT       => 'READ_FORMAT',
+                                                                     -VENDOR       => 'SOLEXA',
+                                                                     -NAME         => 'ExpSet1',
+                                                                     -ANALYSIS     => $anal,
+                                                                     );
+
+  Do we want to define subsets likes this or are we more likely to add them one by one?
+
+  Description: Constructor for ExperimentalSet objects.
+  Returntype : Bio::EnsEMBL::Funcgen::ExperimentalSet
+  Exceptions : Throws if no Experiment defined
+               Throws if CellType or FeatureType are not valid or stored
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+	
+  my $class = ref($caller) || $caller;
+	
+  my $self = $class->SUPER::new(@_);
+	
+  #do we need to add $fg_ids to this?  Currently maintaining one feature_group focus.(combi exps?)
+  my ($exp, $format, $vendor)
+    = rearrange(['EXPERIMENT', 'FORMAT', 'VENDOR'], @_);
+    
+  if (! (ref $exp && $exp->isa('Bio::EnsEMBL::Funcgen::Experiment') && $exp->dbID())){
+	throw('Must specify a valid stored Bio::EnsEMBL::Funcgen::Experiment');
+  }
+
+  
+  #These are set in Set, just validate here
+  throw ('Must provide a FeatureType') if(! defined $self->feature_type);
+  throw ('Must provide a CellType') if(! defined $self->cell_type);
+
+
+
+  if(! defined $self->analysis){
+	#default analysis hack for v47
+	#Set directly to avoid dbID boolean check
+	$self->{'analysis'} = Bio::EnsEMBL::Analysis->new(-logic_name => 'external',
+													  -id       => 0,#??someone needs to rewrite analysis
+													 );
+  }
+
+  $self->format($format) if defined $format;
+  $self->vendor($vendor) if defined $vendor;
+  $self->{'experiment'} = $exp;
+  $self->{'subsets'} = {};
+  
+  return $self;
+}
+
+
+=head2 add_new_subset
+
+  Arg [1]    : string - sub set name e.g. the file name (not path as we're restricted to 30 chars)
+  Example    : $expset->add_new_subset($ss_name, $exp_subset);
+  Description: Adds experimental_subset
+  Returntype : none
+  Exceptions : Throws if set is already present
+               Throws if ExperimentalSubset is not valid or stored
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub add_new_subset {
+  my ($self, $ss_name, $exp_sset) = @_;
+	
+  if($self->get_subset_by_name($ss_name)){
+	throw("Subset $ss_name is already present in this ExperimentalSet, maybe you need to alter the filename?");
+  }
+
+  if(defined $exp_sset){
+
+	if(!(ref($exp_sset) && $exp_sset->isa('Bio::EnsEMBL::Funcgen::ExperimentalSubset') && $exp_sset->dbID())){
+	  throw('ExperimentalSubsets must be valid and stored');
+	}
+  }
+  else{
+	
+	$exp_sset = Bio::EnsEMBL::Funcgen::ExperimentalSubset->new(
+															   -name => $ss_name,
+															   -experimental_set => $self,
+															  );
+  }
+
+  $self->{'subsets'}{$ss_name} = $exp_sset;
+
+  return $self->{'subsets'}{$ss_name};
+}
+
+
+=head2 get_Experiment
+
+  Example    : my $exp = $exp_set->get_Experiment();
+  Description: Getter for the Experiment of this DataSet.
+  Returntype : Bio::EnsEMBL::Fuuncgen::Experiment
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_Experiment{
+  my $self = shift;
+
+  return $self->{'experiment'};  
+}
+
+
+=head2 get_subsets
+
+  Example    : my @subsets = @{$exp_set->get_subsets()};
+  Description: Getter for the subsets for this ExperimentalSet.
+  Returntype : Arrayref
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_subsets{
+  my ($self)  = shift;
+
+  return [ values %{$self->{'subsets'}} ];
+}
+
+=head2 get_subset_by_name
+
+  Example    : my $subsets = $exp_set->get_subset_by_name('subset1');
+  Description: Getter for the subset of a given name for this ExperimentalSet.
+  Returntype : Bio::EnsEMBL::Funcgen::ExpeirmentalSubset
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_subset_by_name{
+  my ($self, $name) = @_;
+
+  return (exists $self->{'subsets'}{$name}) ? $self->{'subsets'}{$name} : undef;
+}
+
+=head2 get_subset_names
+
+  Example    : my @subset_names = @{$exp_set->get_subset_names()};
+  Description: Getter for the subset names for this ExperimentalSet.
+  Returntype : Arrayref
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_subset_names{
+  my ($self) = shift;
+
+  return [ keys %{$self->{'subsets'}} ];
+}
+
+
+
+
+=head2 vendor
+
+  Arg[1]     : string - vendor 
+  Example    : my $eset->vendor('SOLEXA');
+  Description: Getter/Setter for the vendor attribute of this DataSet.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub vendor {
+  my $self = shift;
+     	
+  $self->{'vendor'} = shift if @_;
+
+  return $self->{'vendor'};
+}
+
+
+=head2 format
+
+  Arg[1]     : string - format i.e. product type/format
+  Example    : my $eset->format('DATASET1');
+  Description: Getter/Setter for the format attribute of this ExperimentalSet.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub format {
+  my $self = shift;
+     	
+  $self->{'format'} = shift if @_;
+  
+  return $self->{'format'};
+}
+
+1;
+