Bio::EnsEMBL::Analysis::RunnableDB RepeatMasker
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Summary
Bio::EnsEMBL::Analysis::RunnableDB::RepeatMasker
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Runnable::RepeatMasker
Bio::EnsEMBL::Analysis::RunnableDB
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;
$repeat_masker->write_output;
Description
This module provides an interface between the ensembl database and
the Runnable RepeatMasker which wraps the program RepeatMasker
This module can fetch appropriate input from the database
pass it to the runnable then write the results back to the database
in the repeat_feature and repeat_consensus tables
Methods
fetch_inputDescriptionCode
get_adaptorDescriptionCode
Methods description
fetch_inputcode    nextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::RepeatMasker
Function : fetch data out of database and create runnable
Returntype: 1
Exceptions: none
Example :
get_adaptorcodeprevnextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::RepeatMasker
Function : get repeatfeature adaptor
Returntype: Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor
Exceptions: none
Example :
Methods code
fetch_inputdescriptionprevnextTop
sub fetch_input {
  my ($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;
}
get_adaptordescriptionprevnextTop
sub get_adaptor {
  my ($self) = @_;
  return $self->db->get_RepeatFeatureAdaptor;
}


1;
}
General documentation
CONTACTTop
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk