Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::MAT
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::MAT
#
# Copyright (c) 2007 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::MAT
=head1 SYNOPSIS
my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::MAT->new
(
-db => $db,
-input_id => 'chromosome::20:1:100000:1',
-analysis => $analysis,
);
$runnable->fetch_input;
$runnable->run;
$runnable->write_output;
=head1 DESCRIPTION
This module provides an interface between the ensembl functional genomics
database and the Runnable MAT which wraps the program MAT (Model-based
Analysis of Tiling-array, see http://chip.dfci.harvard.edu/~wli/MAT).
=head1 AUTHOR
Stefan Graf, Ensembl Functional Genomics - /
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::MAT;
use strict;
use warnings;
use Data::Dumper;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::RunnableDB::Funcgen;
use Bio::EnsEMBL::Analysis::Runnable::Funcgen::MAT;
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::Analysis::Config::Funcgen::MAT;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Funcgen::Importer;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Funcgen);
=head2 new
Arg [1] :
Arg [2] :
Description : Instantiates new MAT runnabledb
Returntype : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::MAT object
Exceptions :
Example :
=cut
sub new {
print "Analysis::RunnableDB::Funcgen::MAT::new\n";
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->read_and_check_config($CONFIG);
return $self;
}
=head2 query
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB
Arg [2] : integer
Function : container for chip number
Returntype: integer
Exceptions: throws if passed the incorrect value
Example :
=cut
sub query {
my ($self, $chip) = @_;
if($chip){
throw("Must pass RunnableDB::Funcgen::MAT::query an integer ".
"specifying the chip to process not ".$chip)
unless($chip =~ m/^\d+$/);
$self->{'chip'} = $chip;
}
return $self->{'chip'};
}
=head2 check_Sets
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB
Function : fetch and set ResultSets of interest
Returntype: 1
Exceptions: none
Example :
=cut
sub check_Sets
{
warn("\nNEED TO IMPLEMENT SETTING OF RESULT/DATA/FEATURE SET!!!\n\n");
}
sub fetch_input {
my ($self) = @_;
print "Analysis::RunnableDB::Funcgen::MAT::fetch_input\n";
my $runnable = 'Bio::EnsEMBL::Analysis::Runnable::Funcgen::'
.$self->analysis->module;
warn("No input to fetch since we are going to work directly on the CEL files.");
$runnable = $runnable->new
(
-query => $self->query,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
);
$self->runnable($runnable);
return 1;
}
sub write_output{
print "RunnableDB::Funcgen::MAT::write_output\n";
my ($self) = @_;
my @result_files = map { $_->resultsfile } @{$self->runnable};
print Dumper @result_files;
my $Importer = Bio::EnsEMBL::Funcgen::Importer->new
(
-name => $ENV{EXPERIMENT},
-vendor => $ENV{VENDOR},
-format => $ENV{FORMAT},
-db => $self->db,
-host => $self->db->host,
-port => $self->db->port,
-user => $self->db->username,
-pass => $self->db->password,
-dbname => $self->db->dbname,
-species => $ENV{SPECIES},
-data_version => $ENV{DATA_VERSION},
-input_dir => $ENV{ANALYSIS_WORK_DIR},
-output_dir => $ENV{ANALYSIS_WORK_DIR},
-result_files => \@result_files,
-experimental_set_name => $ENV{EXP_SET},
-exp_date => $ENV{EXP_DATE},
-feature_analysis => $self->analysis->logic_name,
-feature_type_name => $ENV{FEATURE_TYPE},
-cell_type_name => $ENV{CELL_TYPE},
-location => $ENV{LOCATION},
-contact => $ENV{CONTACT},
-group => $ENV{EGROUP},
-recover => 1,
-verbose => 1,
# -ssh => $ssh,
# -array_set => $array_set,
# -array_name => $array_name,
# -result_set_name => $rset_name, #not implemented yet
# -write_mage => $write_mage,
# -update_xml => $update_xml,
# -no_mage => $no_mage,
# -data_root => $data_dir,
# -dump_fasta => $fasta,
# -norm_method => $nmethod,
# -farm => $farm,
# -input_dir => $input_dir,
# -exp_date => $exp_date,
# -result_files => \@result_files,
# -old_dvd_format => $old_dvd_format,
#Exp does not build input dir, but could
#This allows input dir to be somewhere
#other than efg dir structure
);
$Importer->register_experiment();
}
1;
]]>