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Inherit

Bio::EnsEMBL::Analysis::RunnableDB

Synopsis

  my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::Genscan->
  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
genscan runnable

Methods

Methods description

  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::Genscan
  Function  : fetch data out of database and create runnable
  Returntype: 1
  Exceptions: none
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::Genscan
  Function  : to return a hash which contains the 
  standard constructor args for the genscan runnable
  Returntype: hashref
  Exceptions: none
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::Genscan
  Function  : writes the prediction transcripts back to the database
  after validation
  Returntype: none
  Exceptions: 
  Example   :

Methods code

sub fetch_input {

  my ($self) = @_;
  my $slice = $self->fetch_sequence($self->input_id, $self->db, 
                                    $ANALYSIS_REPEAT_MASKING);
  $self->query($slice);
  my %args = %{$self->standard_args};
  my $runnable = $self->runnable_path->new
    (
     %args,
    );
  
  my $seq = $self->query->seq; 
  if ($seq =~ /[CATG]{3}/) {
     $self->input_is_void(0);
  } else {
     $self->input_is_void(1);
     warning("Need at least 3 nucleotides - maybe your sequence was fully repeatmasked ...");
  }
  
  $self->runnable($runnable);
  return 1;

}

sub runnable_path {

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

}

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,
          -matrix => $self->analysis->db_file,
         };
}
1;

}

sub write_output {

  my ($self) = @_;
  my $adaptor = $self->db->get_PredictionTranscriptAdaptor;
  my @output = @{$self->output};
  my $ff = $self->feature_factory;
  foreach my $pt(@output){
    $pt->analysis($self->analysis);
    $pt->slice($self->query) if(!$pt->slice);
    $ff->validate_prediction_transcript($pt, 1);
    $adaptor->store($pt);
  }

}

General documentation

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