Bio::EnsEMBL::Analysis::RunnableDB Genefinder
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Summary
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Config::General
Bio::EnsEMBL::Analysis::Runnable::Genefinder
Bio::EnsEMBL::Analysis::RunnableDB::Genscan
Inherit
Bio::EnsEMBL::Analysis::RunnableDB::Genscan
Synopsis
  my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::Genefinder->
  new(
      -input_id => 'contig::AL805961.22.1.166258:1:166258:1',
      -db => $db,
      -analysis => $analysis,
     );
  $runnabledb->fetch_input;
  $runnabledb->run;
  $runnabledb->write_output;
Description
fetches sequence data from database an instantiates and runs the
genefinder runnable
Methods
runnable_pathDescriptionCode
standard_argsDescriptionCode
Methods description
runnable_pathcode    nextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::Genefinder
  Function  : return the runnable path
  Returntype: string
  Exceptions: 
  Example   : my $runnable = $self->runnable_path->new
                               (
                                -query    => $self->query,
                                -program  => $self->analysis->program_file,
                                -analysis => $self->analysis,
                                %parameters,
                               );
standard_argscodeprevnextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::Genefinder
  Function  : to return a hash which contains the 
  standard constructor args for the genscan runnable
  Returntype: hashref
  Exceptions: none
  Example   :
Methods code
runnable_pathdescriptionprevnextTop
sub runnable_path {
  my ($self) = @_;
  return "Bio::EnsEMBL::Analysis::Runnable::Genefinder";
}
standard_argsdescriptionprevnextTop
sub standard_args {
  my ($self) = @_;
  my %parameters;
  if($self->parameters_hash){
    %parameters = %{$self->parameters_hash};
  }
  return {
          -query => $self->query,
          -program => $self->analysis->program_file,
          -analysis => $self->analysis,
          %parameters,
         };
}

1;
}
General documentation
CONTACTTop
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