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Summary

Bio::EnsEMBL::Analysis::RunnableDB::RepeatMasker

Package variables

Included modules

Inherit

Bio::EnsEMBL::Analysis::RunnableDB

Synopsis

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

Description

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

Methods

Methods description

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

  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::RepeatMasker
  Function  : get repeatfeature adaptor
  Returntype: Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor
  Exceptions: none
  Example   :

Methods code

sub fetch_input {

  my ($self) = @_;
  my $slice = $self->fetch_sequence;
  $self->query($slice);
  my %parameters;
  if($self->parameters_hash){
    %parameters = %{$self->parameters_hash};
  }
  my $runnable = Bio::EnsEMBL::Analysis::Runnable::RepeatMasker->new
    (
     -query => $self->query,
     -program => $self->analysis->program_file,
     -analysis => $self->analysis,
     %parameters,
    );
  $self->runnable($runnable);
  return 1;

}

sub get_adaptor {

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


1;

}

General documentation

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