Raw content of Bio::EnsEMBL::Funcgen::ExperimentalChip
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# Ensembl module for Bio::EnsEMBL::Funcgen::ExperimentalChip
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::ExperimentalChip - A module to represent a physical unique experimental chip.
=head1 SYNOPSIS
use Bio::EnsEMBL::Funcgen::ExperimentalChip;
my $ec = Bio::EnsEMBL::Funcgen::ExperimentalChip->new(
-dbID => $ec_id,
-unique_id => $c_uid,
-experiment_id => $exp_id,
-array_chip_id => $ac_id,
-feature_type => $ftpye,
-cell_type => $ctype,
-chip_set_id => 1,
);
=head1 DESCRIPTION
An ExperimentalChip object represent a physical array chip/slide used in an experiment. The data
(currently the unique_id, experiment_id, array_chip_id, and description) are stored
in the experimental_chip table.
=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::ExperimentalChip;
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 [-unique_id] : int - the unique id of this individual experimental chip
Arg [-experiment_id] : int - the experiment dbID
Arg [-array_chip_id] : int - the dbID or the array_chip
Arg [-feature_type ] : Bio::EnsEMBL::Funcgen::FeatureType
Arg [-cell_type ] : Bio::EnsEMBL::Funcgen::CellType
Arg [-biological_replicate ] : string - the name to define the biological replicate set
Arg [-technical_replicate ] : string - the name to define the technical replicate set
Example : my $array = Bio::EnsEMBL::Funcgen::ExperimentalChip->new(
-dbID => $ec_id,
-unique_id => $c_uid,
-experiment_id => $exp_id,
-array_chip_id => $ac_id,
-feature_type => $ftype,
-cell_type => $ftype,
-biological_replicate => 'BIOREP1',
-technical_replicate => 'techrep_1',
);
Description: Creates a new Bio::EnsEMBL::Funcgen::ExperimentalChip object.
Returntype : Bio::EnsEMBL::Funcgen::ExperimentalChip
Exceptions : None ? should throw if mandaotry params not set
Caller : General
Status : Medium Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
#can we lc these?
my ($c_uid, $exp_dbid, $ac_id, $ftype, $ctype, $brep, $trep)
= rearrange( ['UNIQUE_ID', 'EXPERIMENT_ID', 'ARRAY_CHIP_ID', 'FEATURE_TYPE', 'CELL_TYPE', 'BIOLOGICAL_REPLICATE', 'TECHNICAL_REPLICATE'], @_ );
$self->unique_id($c_uid) if defined $c_uid;
$self->experiment_id($exp_dbid) if defined $exp_dbid;
$self->array_chip_id($ac_id) if defined $ac_id;
$self->feature_type($ftype) if defined $ftype;
$self->cell_type($ctype) if defined $ctype;
$self->biological_replicate($brep) if defined $brep;
$self->technical_replicate($trep) if defined $trep;
return $self;
}
=head2 get_Experiment
Args : None
Example : my $exp = $exp_chip->get_Experiment();
Description: Returns the Experiment which this ExperimentalChip belongs to.
Returntype : Bio::EnsEMBL::Funcgen::Experiment
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_Experiment {
my $self = shift;
if (! $self->{'experiment'}){
if ($self->dbID() && $self->adaptor() ) {
$self->{'experiment'} = $self->adaptor->db->get_ExperimentAdaptor->fetch_by_dbID($self->experiment_id);
} else {
warning('Need database connection to retrieve Experiment');
}
}
return $self->{'experiment'};
}
=head2 get_Channels
Args : None
Example : my $channels = $exp_chip->get_Channels();
Description: Returns all channels on a ExperimentalChip. Needs a database connection.
Returntype : Listref of Bio::EnsEMBL::Funcgen::Channel objects
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_Channels {
my $self = shift;
if (! $self->{'channels'}){
if ($self->dbID() && $self->adaptor() ) {
foreach my $channel (@{$self->adaptor->db->get_ChannelAdaptor->fetch_all_by_ExperimentalChip($self)}){
$self->add_Channel($channel);
}
} else {
warning('Need database connection to retrieve Channels');
}
}
return [values %{$self->{'channels'}}];
}
=head2 add_Channel
Args : Bio::EnsEMBL::Funcgen::Channel
Example : $exp_chip->add_channel($chan);
Description: Sets ad channel object for the ExperimentalChip
Returntype : Listref of Bio::EnsEMBL::Funcgen::Channel objects
Exceptions : warns if Channel already set
Caller : General
Status : At Risk
=cut
sub add_Channel{
my ($self, $chan) = @_;
if(! ($chan && $chan->isa("Bio::EnsEMBL::Funcgen::Channel") && $chan->dbID())){
throw("Must provide a valid stored Bio::EnsEMBL::Funcgen::Channel object");
}
$self->{'channels'} ||= {};
if (exists $self->{'channels'}->{$chan->dbID()}){
#should this throw?
#This currently prevents haveing to check whether a channel has already been added
#If we were duplicating then we probably would have a different dbID
warn("You cannot add the same Channel to an ExperimentalChip more than once");
}else{
##change this to key on freq?
$self->{'channels'}{$chan->dbID()} = $chan;
}
return;
}
=head2 get_channel_ids
Args : None
Example : my @channel_ids = @{$array->get_channel_ids()};
Description: Returns all channel ids for an ExperimentalChip. Needs a database connection.
Returntype : List of ints
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub get_channel_ids{
my $self = shift;
$self->get_Channels();
return [keys %{$self->{'channels'}}];
}
=head2 get_Channel_by_dye
Args : string - dye used in channel
Example : my $chan = $echip->get_Channel_by_dye("CY5");
Description: Returnsthe channel corresponding to the frequency specified
Returntype : Bio::EnsEMBL::Funcgen::Channel
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_Channel_by_dye{
my ($self, $dye) = @_;
my @chans;
foreach my $chan(@{$self->get_Channels()}){
push @chans, $chan if uc($chan->dye()) eq uc($dye);
}
throw("Found more than one Channels with the same dye") if(scalar(@chans) > 1);
return (@chans) ? $chans[0] : undef;
}
=head2 contains_Channel
Args [1] : Bio::EnsEMBL::Funcgen::Channel
Example : if(! $echip->contains_Channel($chan){..add channel ..};
Description: Checks whether this Channel has already been added to the ExperimentalChip
Returntype : Boolean
Exceptions : Throws if arg not a valid stored Bio::EnseMBL::Funcgen::Channel
Caller : General
Status : At Risk
=cut
sub contains_Channel{
my ($self, $chan) = @_;
if(! ($chan && $chan->isa("Bio::EnsEMBL::Funcgen::Channel") && $chan->dbID())){
throw("Must provide a valid stored Bio::EnsEMBL::Funcgen::Channel object");
}
$self->get_Channels();
my $contains = 0;
$contains = 1 if(exists $self->{'channels'}->{$chan->dbID()});
return $contains;
}
=head2 unique_id
Arg [1] : (optional) int - the unique chip id for this ExperimentalChip
Example : my $c_uid = $array->unique_id();
Description: Getter, setter unique_id attribute.
Returntype : string
Exceptions : None
Caller : General
Status : at Risk
=cut
sub unique_id {
my $self = shift;
$self->{'unique_id'} = shift if @_;
return $self->{'unique_id'};
}
=head2 feature_type
Arg [1] : (optional) Bio::EnsEMBL::Funcgen::FeatureType
Example : $ec->feature_type($ftype);
Description: Getter/Setter thefeature_type attribute.
Returntype : Bio::EnsEMBL::Funcgen::FeatureType
Exceptions : Throws if arg is not a Bio::EnsEMBL::FeatureType
Caller : General
Status : At Risk
=cut
sub feature_type {
my $self = shift;
if(@_){
throw("Must pass a valid Bio::EnsEMBL::Funcgen::FeatureType object") if (! $_[0]->isa("Bio::EnsEMBL::Funcgen::FeatureType"));
$self->{'feature_type'} = shift;
}
return $self->{'feature_type'};
}
=head2 cell_type
Arg [1] : (optional) Bio::EnsEMBL::Funcgen::CellType
Example : $ec->cell_type($ctype);
Description: Getter/Setter the cell_type attribute.
Returntype : Bio::EnsEMBL::Funcgen::CellType
Exceptions : Throws if arg is not a Bio::EnsEMBL::CellType
Caller : General
Status : At Risk
=cut
sub cell_type {
my $self = shift;
if(@_){
throw("Must pass a valid Bio::EnsEMBL::Funcgen::CellType object") if (! $_[0]->isa("Bio::EnsEMBL::Funcgen::CellType"));
$self->{'cell_type'} = shift;
}
return $self->{'cell_type'};
}
=head2 biological_replicate
Arg [1] : (optional) string - the name or number of the chip biological replicate set
Example : $ec->biological_replicate('SAMPLENAME_BR1');
Description: Getter, setter for the biological_replicate attribute.
Returntype : string
Exceptions : None
Caller : General
Status : At Risk
=cut
sub biological_replicate {
my $self = shift;
$self->{'biological_replicate'} = shift if @_;
return $self->{'biological_replicate'};
}
=head2 technical_replicate
Arg [1] : (optional) string - the name or number of the chip technical replicate set
Example : $ec->technical_replicate('SAMPLENAME_BR1_TR1');
Description: Getter, setter for the technical_replicate attribute.
Returntype : string
Exceptions : None
Caller : General
Status : At Risk
=cut
sub technical_replicate {
my $self = shift;
$self->{'technical_replicate'} = shift if @_;
return $self->{'technical_replicate'};
}
=head2 experiment_id
Arg [1] : (optional) int - the experiment dbID
Example : my $exp_id = $array->experiment_id();
Description: Getter, setter experiment_id attribute
Returntype : int
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub experiment_id {
my $self = shift;
$self->{'experiment_id'} = shift if @_;
return $self->{'experiment_id'};
}
=head2 array_chip_id
Arg [1] : (optional) int - the array_chip dbID
Example : my $ac_id = $ec->array_chip_id();
Description: Getter, setter array_chip_id attribute
Returntype : int
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub array_chip_id {
my $self = shift;
$self->{'array_chip_id'} = shift if @_;
return $self->{'array_chip_id'};
}
=head2 get_ArrayChip
Example : my $array_chip = $exp_chip->get_ArrayChip();
Description: Getter for the array_chip attribute
Returntype : Bio::EnsEMBL::Funcgen::ArrayChip
Exceptions : None
Caller : General
Status : At Risk
=cut
sub get_ArrayChip {
my $self = shift;
if(! defined $self->{'array_chip'}){
$self->{'array_chip'} = $self->adaptor->db->get_ArrayChipAdaptor()->fetch_by_dbID($self->array_chip_id());
}
return $self->{'array_chip'};
}
1;
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