Bio::EnsEMBL::Analysis::RunnableDB::Funcgen Nessie
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Summary
Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Config::Funcgen::Nessie
Bio::EnsEMBL::Analysis::Config::General
Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie
Bio::EnsEMBL::Analysis::RunnableDB
Bio::EnsEMBL::Analysis::RunnableDB::Funcgen
Bio::EnsEMBL::Utils::Exception qw ( throw warning stack_trace_dump )
Data::Dumper
Inherit
Bio::EnsEMBL::Analysis::RunnableDB::Funcgen
Synopsis
  my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie->new
(
-db => $db,
-input_id => 'chromosome::20:1:100000:1',
-analysis => $analysis,
);
$runnable->fetch_input;
$runnable->run;
$runnable->write_output;
Description
This module provides an interface between the ensembl database and
the Runnable Nessie which wraps the program Nessie
Methods
PEAK_PARAMETERS
No description
Code
TRAIN_PARAMETERS
No description
Code
newDescriptionCode
Methods description
newcode    nextTop
  Arg [1]     : 
Arg [2] :
Description : Instantiates new Nessie runnabledb
Returntype : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie object
Exceptions :
Example :
Methods code
PEAK_PARAMETERSdescriptionprevnextTop
sub PEAK_PARAMETERS {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{'_CONFIG_PEAK_PARAMETERS'} = $value;
    }

    if ( exists( $self->{'_CONFIG_PEAK_PARAMETERS'} ) ) {
        return $self->{'_CONFIG_PEAK_PARAMETERS'};
    } else {
        return undef;
    }
}




1;
}
TRAIN_PARAMETERSdescriptionprevnextTop
sub TRAIN_PARAMETERS {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{'_CONFIG_TRAIN_PARAMETERS'} = $value;
    }

    if ( exists( $self->{'_CONFIG_TRAIN_PARAMETERS'} ) ) {
        return $self->{'_CONFIG_TRAIN_PARAMETERS'};
    } else {
        return undef;
    }
}
newdescriptionprevnextTop
sub new {
    print "Analysis::RunnableDB::Funcgen::Nessie::new\n";
    my ($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    $self->read_and_check_config($CONFIG);

    # add some runnable/program special params to analysis
$self->PARAMETERS(join('; ', $self->PARAMETERS.$self->TRAIN_PARAMETERS, $self->PEAK_PARAMETERS)); #print Dumper $self->PARAMETERS;
# 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;
}
General documentation
AUTHORTop
Stefan Graf, Ensembl Functional Genomics - /
CONTACTTop
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk