Bio::EnsEMBL::Analysis::RunnableDB tRNAscan_SE
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Summary
Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE
Bio::EnsEMBL::Analysis::RunnableDB
Inherit
Bio::EnsEMBL::Analysis::RunnableDB
Synopsis
  my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE->
new(
-input_id => 'contig::AL805961.22.1.166258:1:166258:1',
-db => $db,
-analysis => $analysis,
);
$runnable->fetch_input;
$runnable->run;
$runnable->write_output;
Description
This module provides an interface between the ensembl database and
the Runnable tRNAscan_SE which wraps the program tRNAscan_SE
This module can fetch appropriate input from the database
pass it to the runnable then write the results back to the database
in the simple_feature table
Methods
fetch_inputDescriptionCode
get_adaptorDescriptionCode
Methods description
fetch_inputcode    nextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
Function : fetch data out of database and create runnable
Returntype: 1
Exceptions: none
Example :
get_adaptorcodeprevnextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
Function : get simple_feature adaptor
Returntype: Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
Exceptions: none
Example :
Methods code
fetch_inputdescriptionprevnextTop
sub fetch_input {
  my ($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::tRNAscan_SE->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_SimpleFeatureAdaptor;
}

1;
}
General documentation
CONTACTTop
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