Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME
=head1 SYNOPSIS
my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME->new
(
-db => $db,
-input_id => 'chromosome::20:1:100000:1',
-analysis => $analysis,
);
$runnable->fetch_input;
$runnable->run;
$runnable->write_output;
=head1 DESCRIPTION
This module provides an interface between the ensembl functional genomics
database and the Runnable ACME which wraps the R package ACME (for Algorithm
for Capturing Microarray Enrichment).
=head1 AUTHOR
Stefan Graf, Ensembl Functional Genomics - /
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME;
use strict;
use warnings;
use Data::Dumper;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::RunnableDB::Funcgen;
use Bio::EnsEMBL::Analysis::Runnable::Funcgen::ACME;
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::Analysis::Config::Funcgen::ACME;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Funcgen);
=head2 new
Arg [1] :
Arg [2] :
Description : Instantiates new ACME runnabledb
Returntype : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::ACME object
Exceptions :
Example :
=cut
sub new {
print "Analysis::RunnableDB::Funcgen::ACME::new\n";
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->read_and_check_config($CONFIG);
# make sure we have the correct analysis object
$self->check_Analysis();
# make sure we can store the correct feature_set, data_sets, and result_sets
$self->check_Sets();
return $self;
}
1;
]]>