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Summary

Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie

Package variables

Included modules

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

Methods description

  Arg [1]     : 
  Arg [2]     : 
  Description : Instantiates new Nessie runnabledb
  Returntype  : Bio::EnsEMBL::Analysis::RunnableDB::Funcgen::Nessie object
  Exceptions  : 
  Example     :

Methods code

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;

}

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;
    }

}

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

Stefan Graf, Ensembl Functional Genomics - /

Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk