Raw content of Bio::EnsEMBL::Funcgen::ExperimentalSet
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# 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: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=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;
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