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Package variables

Included modules

Inherit

Bio::EnsEMBL::Analysis::RunnableDB::Genscan

Synopsis

  my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::Finished::Augustus->
  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
augustus runnable, this inherits from the Genscan runnableDB an as such doesnt
implement much itself

Methods

Methods description

  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::Finished::Augustus
  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,
                               );

Methods code

sub runnable_path {

  my ($self);
  return "Bio::EnsEMBL::Analysis::Runnable::Finished::Augustus";

}

sub write_output {

  my ($self) = @_;
  my $adaptor = $self->db->get_PredictionTranscriptAdaptor;
  my $dbh = $self->db->dbc->db_handle;
  my @output = @{$self->output};
  my $ff = $self->feature_factory;

  $dbh->begin_work;

  eval {
	  foreach my $pt(@output){
	    $pt->analysis($self->analysis);
	    $pt->slice($self->query) if(!$pt->slice);
	    print STDERR "Validate transcript ".$pt->seqname."\n";
	    # dismiss transcript with invalid translation
	    eval {
	    	$ff->validate_prediction_transcript($pt, 1);
	    };
	    if($@){ warning($@); next; }
	    $adaptor->store($pt);
	  }
	  $dbh->commit;
  };
  if ($@) {
      $dbh->rollback;
	  throw("UNABLE TO WRITE PREDICTION TRANSCRIPTS IN DATABASE\n[$@]\n");
  }
}



1;

}

General documentation

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