Bio::EnsEMBL::Analysis::Runnable Dust
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Summary
Bio::EnsEMBL::Analysis::Runnable::Dust
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Runnable
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Analysis::Runnable
Synopsis
  my $dust = Bio::EnsEMBL::Analysis::Runnable::Dust->
  new(
      -query => $slice,
      -program => 'tcdust',
     );
  $dust->run;
  my @repeats = @{$dust->output};
Description
Dust is a wrapper for the tcdust program which runs the dust algorithm
to identify and mask simple repeats
Methods
level
No description
Code
newDescriptionCode
parse_resultsDescriptionCode
run_analysisDescriptionCode
window_size
No description
Code
word_size
No description
Code
Methods description
newcode    nextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::Dust
  Arg [2]   : int, masking threshold
  Arg [3]   : int, word size
  Arg [4]   : int, window size
  Function  : create a new  Bio::EnsEMBL::Analysis::Runnable::Dust
  Returntype: Bio::EnsEMBL::Analysis::Runnable::Dust
  Exceptions: 
  Example   :
parse_resultscodeprevnextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::Dust
  Arg [2]   : string, filename
  Function  : open and parse the results file into repeat
  features
  Returntype: none 
  Exceptions: throws on failure to open or close output file
  Example   :
run_analysiscodeprevnextTop
  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::Dust
  Arg [2]   : string, program name
  Function  : constructs a commandline and runs the program passed
  in, the generic method in Runnable isnt used as Dust doesnt
  fit this module
  Returntype: none
  Exceptions: throws if run failed because system doesnt
  return 0
  Example   :
Methods code
leveldescriptionprevnextTop
sub level {
  my $self = shift;
  $self->{'min_length'} = shift if(@_);
  return $self->{'min_length'};
}
newdescriptionprevnextTop
sub new {
  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);

  my ($level, $word_size, $window_size) = rearrange(['MASKING_THRESHOLD',
                                                     'WORD_SIZE', 
                                                     'WINDOW_SIZE',
                                                    ], @args);
  ##################
  #SETTING DEFAULTS#
  ##################
  $self->program('tcdust') if(!$self->program);
  ##################

  $self->level($level) if($level);
  $self->word_size($word_size) if($word_size);
  $self->window_size($window_size) if($window_size);
  return $self;
}

#container methods
}
parse_resultsdescriptionprevnextTop
sub parse_results {
  my ($self, $results) = @_;
  if(!$results){
    $results = $self->resultsfile;
  }
  my $ff = $self->feature_factory;
  my @output;
  open(DUST, $results) or throw("FAILED to open ".$results);
 LINE:while(<DUST>){
    chomp;
    next LINE if(/^>/);
    if (/(\d+)\.\.(\d+)/) {
      my ($start, $end) = ($1, $2);
      $start++;
      $end++;
      my $rc = $ff->create_repeat_consensus('dust', 'dust', 'simple', 'N');
      my $rf = $ff->create_repeat_feature($start, $end, 0, 0, $start,
                                          $end, $rc, $self->query->name,
                                          $self->query);
      push(@output, $rf);
    }
  }
  $self->output(\@output);
  close(DUST) or throw("FAILED to close ".$results);
}
run_analysisdescriptionprevnextTop
sub run_analysis {
  my ($self, $program) = @_;
  if(!$program){
    $program = $self->program;
  }
  throw($program." is not executable Dust::run_analysis ") 
    unless($program && -x $program);
  my $command = $self->program;
  $command .= " -l ".$self->level if($self->level);
  $command .= " -k ".$self->word_size if($self->word_size);
  $command .= " -w ".$self->window_size if($self->window_size);
  $command .= " -x ".$self->queryfile." > ".$self->resultsfile;
  print "Running analysis ".$command."\n";
  system($command) == 0 or throw("FAILED to run ".$command);
}
window_sizedescriptionprevnextTop
sub window_size {
  my $self = shift;
  $self->{'min_gc_content'} = shift if(@_);
  return $self->{'min_gc_content'};
}
word_sizedescriptionprevnextTop
sub word_size {
  my $self = shift;
  $self->{'min_oe'} = shift if(@_);
  return $self->{'min_oe'};
}



#utility methods
}
General documentation
CONTACTTop
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
containersTop
  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::Dust
  Arg [2]   : int for specified value (for more info see tcdust)
  Function  : container for specified variable. This pod refers to the
  three methods below level, window size and word size. These are simple 
  containers which dont do more than hold and return an given value
  nothing is defined
  Returntype: int
  Exceptions: 
  Example   :