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Summary

Bio::EnsEMBL::Analysis::RunnableDB::FirstEF

Package variables

Included modules

Inherit

Bio::EnsEMBL::Analysis::RunnableDB

Synopsis

  my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::FirstEF->
  new(
      -input_id => 'contig::AL805961.22.1.166258:1:166258:1',
      -db => $db,
      -analysis => $analysis,
     );
  $runnabledb->fetch_input;
  $runnabledb->run;
  $runnabledb->write_output;

Description

This module provides an interface between the ensembl database and
the Runnable FirstEF which wraps the program FirstEF
This module can fetch appropriate input from the database
pass it to the runnable then write the results back to the database
in the simple_feature table

Methods

Methods description

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

  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::FirstEF
  Function  : get simple feature adaptor
  Returntype: Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
  Exceptions: none
  Example   :

Methods code

sub fetch_input {

  my ($self) = @_;
  my $slice = $self->fetch_sequence($self->input_id, $self->db, ['']); 
  #hard coded array is used here as it always wants all repeats in 
  #the table masked at somepoint the general variables will be replaced by
  #analysis specific variables and this will move back into confi
  $self->query($slice);

  if(!$self->analysis->program_file){
    $self->analysis->program_file('firstef');
  }


  my %parameters;
  if($self->parameters_hash){
    %parameters = %{$self->parameters_hash};
  }

  my $runnable = Bio::EnsEMBL::Analysis::Runnable::FirstEF->new
    (
     -query => $self->query,
     -program => $self->analysis->program_file,
     -analysis => $self->analysis,
     -param_dir => $PARAMETERS_DIR,
     -parse_script => $PARSE_SCRIPT,
     %parameters,
    );
  $self->runnable($runnable);
  return 1;

}

sub get_adaptor {

  my ($self) = @_;
  return $self->db->get_SimpleFeatureAdaptor;
}


1;

}

General documentation

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