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Summary

Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE

Package variables

Included modules

Inherit

Bio::EnsEMBL::Analysis::Runnable

Synopsis

  my $runnable = Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE->new
  (
   -query => $slice,
   -program => 'trnascan-SE',
  );
  $runnable->run;
  my @simple_features = @{$runnable->output};

Description

tRNAscan_SE expects to run the program tRNAscan-SE and produces
SimpleFeature which can be stored in the simple_feature table in the
core database

Methods

Methods description

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE
  Function  : produce a tRNAscan_SE runnable and set the options
  and program if undefined
  Returntype: Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE
  Exceptions: 
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE
  Arg [2]   : string, filename
  Function  : to open and parse the results file
  Returntype: none
  Exceptions: throws on failure to open or close the results file
  or if the results file doesnt exist
  Example   :

Methods code

sub new {

  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);

  ######################
  #SETTING THE DEFAULTS#
  ######################
  if(!$self->options){
    $self->options('-q');
  }
  if(!$self->program){
    $self->program('tRNAscan-SE');
  }
  ######################
  return $self;

}

sub parse_results {

  my ($self, $results) = @_;

  if(!$results){
    $results = $self->resultsfile;
  }
  if(!-e $results){
    throw("Can't parse an no existance results file ".$results.
          " tRNAscan_SE:parse_results");
  }
  my $ff = $self->feature_factory;
  my @output;
  open(CPG, $results) or throw("FAILED to open ".$results.
                               " tRNAscan_SE:parse_results");
 LINE:while(<CPG>){
    next LINE if(/^Sequence/ ||/^Name/ || /^---/); 
    #ignore introductory lines
    my @element = split (/\s+/, $_); 
    my ($name, $start, $end, $display_label, $score) 
      = @element[0, 2, 3, 4, 8];
    my $strand = 1;
    if($start > $end){
      $strand = -1;
      my $temp_end = $start;
      $start = $end;
      $end = $temp_end;
    }
    my $sf = $ff->create_simple_feature($start, $end, $strand, $score,
                                        $display_label, 
                                        $name, $self->query);
    push(@output, $sf)
  }
  $self->output(\@output);
  close(CPG) or throw("FAILED to close ".$results.
                      " tRNAscan_SE:parse_results");
}


1;

}

General documentation

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