use Bio::Tools::Run::RepeatMasker;

  my @params=("mam" => 1,"noint"=>1);
  my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
  $in  = Bio::SeqIO->new(-file => "contig1.fa",
                         -format => 'fasta');
  my $seq = $in->next_seq();

  #return an array of Bio::SeqFeature::FeaturePair objects
  my @feats = $factory->run($seq); 

  # or

  $factory->run($seq);
  my @feats = $factory->repeat_features;

  #return the masked sequence, a Bio::SeqI object
  my $masked_seq = $factory->run;

 1. Make sure the RepeatMasker executable is in your path.
 2. Define an environmental variable REPEATMASKERDIR which is a 
    directory which contains the RepeatMasker executable:
    In bash:

    export REPEATMASKERDIR=/home/username/RepeatMasker/

    In csh/tcsh:

    setenv REPEATMASKERDIR /home/username/RepeatMasker/

 3. Include a definition of an environmental variable REPEATMASKERDIR in
    every script that will use this RepeatMasker wrapper module, e.g.:

    BEGIN { $ENV{REPEATMASKERDIR} = '/home/username/RepeatMasker/' }
    use Bio::Tools::Run::RepeatMasker;

    @RM_PARAMS = qw(DIR DIV LIB CUTOFF PARALLEL GC FRAG SPECIES MAXSIZE );

    @RM_SWITCHES = qw(NOLOW LOW L NOINT INT NORNA ALU M MUS ROD 
		      RODENT MAM MAMMAL COW AR 
		      ARABIDOPSIS DR DROSOPHILA EL ELEGANS 
		      IS_ONLY IS_CLIP NO_IS RODSPEC E EXCLN 
                      NO_ID FIXED XM U GFF ACE POLY X XSMALL SMALL
                      INV A ALIGNMENTS 
		      PRIMSPEC W WUBLAST S Q QQ GCCALC NOCUT); 
    @OTHER_SWITCHES = qw(NOISY QUIET SILENT);

    # Authorize attribute fields
    foreach my $attr ( @RM_PARAMS, @RM_SWITCHES,
                       @OTHER_SWITCHES) { $OK_FIELD{$attr}++;

  return 'RepeatMasker';

  return Bio::Root::IO->catfile($ENV{REPEATMASKERDIR}) if $ENV{REPEATMASKERDIR};

    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};

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

  my ($attr, $value);
  # Need to check that filehandle is not left open here...
  while (@args) { 
    $attr =   shift @args;
    $value =  shift @args;
    next if( $attr =~ /^-/ ); # don't want named parameters
    $self->$attr($value);
  }
  unless ($self->executable()) {
    if( $self->verbose >= 0 ) {
      warn "RepeatMasker program not found as ".($self->executable||'').
	  " or not executable.\n "; 
    }
  }  
  return $self;

    my ($self) = @_;
    return $self->{'_version'} if( defined $self->{'_version'} );
    my $exe = $self->executable;
    return undef unless $exe;
    my $string = `$exe -- ` ;    
    if( $string =~ /\(([\d.]+)\)/ ||
	$string =~ /RepeatMasker\s+version\s+(\S+)/ ) { 
	return $self->{'_version'} = $1;
    } else {
	return $self->{'_version'} = undef;
    }

  my ($self,$seq) = @_;
  my ($infile);
  $infile = $self->_setinput($seq);

  my $param_string = $self->_setparams();
  my @repeat_feats = $self->_run($infile,$param_string);

  return @repeat_feats;

	return shift->run(@_);

  my ($self,$infile,$param_string) = @_;
  my $instring;
  $self->debug( "Program ".$self->executable."\n");

  my $outfile = $infile.".out";
  my $cmd_str = $self->executable." $param_string ". $infile;
  $self->debug("repeat masker command = $cmd_str");
  if ($self->quiet || $self->verbose <=0){
      $cmd_str.=" 2> /dev/null 1>/dev/null";
  }
  my $status = system($cmd_str);
  $self->throw("Repeat Masker Call($cmd_str) crashed: $?\n") 
      unless $status == 0;
  unless (open (RM, $outfile)) {
      $self->throw("Cannot open RepeatMasker outfile for parsing");
  }
  my $rpt_parser = Bio::Tools::RepeatMasker->new(-fh=>\*RM);
  my @rpt_feat;
  while(my $rpt_feat = $rpt_parser->next_result){
      push @rpt_feat, $rpt_feat;
  }
  $self->repeat_features(\@rpt_feat);

  #get masked sequence
  my $masked = $infile.".masked";
  my $seqio = Bio::SeqIO->new(-file=>$masked,-format=>'FASTA');
  $self->masked_seq($seqio->next_seq);

  return @rpt_feat;

  my ($self,$seq) = @_;
  if($seq){
    $self->{'_masked_seq'} = $seq;
  }
  return $self->{'_masked_seq'};

  my ($self,$rf) = @_;
  if($rf) {
    $self->{'_rf'} = $rf;
  }
  return @{$self->{'_rf'}};

    my ($attr, $value, $self);

    $self = shift;

    my $param_string = "";
    for  $attr ( @RM_PARAMS ) {
      $value = $self->$attr();
      next unless (defined $value);

      my $attr_key = lc $attr; #put params in format expected by dba

      $attr_key = ' -'.$attr_key;
      $param_string .= $attr_key.' '.$value;
    }

    for  $attr ( @RM_SWITCHES) {
      $value = $self->$attr();
      next unless ($value);
      my $attr_key = lc $attr; #put switches in format expected by dba
      $attr_key = ' -'.$attr_key;
      $param_string .= $attr_key ;
    }


    return $param_string;

  my ($self,$seq) = @_;
  $seq->isa("Bio::PrimarySeqI") || 
      $self->throw("Need a Bio::PrimarySeq compliant object for RepeatMasker");
#  my  $in  = Bio::SeqIO->new(-file => $infilename , '-format' => 'Fasta');
  my ($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
  my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'fasta');
  $out1->write_seq($seq);
  close($tfh1);
  undef $tfh1;
  return ($outfile1);

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

 
Please direct usage questions or support issues to the mailing list:
  
bioperl-l@bioperl.org
  
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

  http://bugzilla.open-bio.org/

 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values  
 Returns : value of no_param_checks
 Args    : newvalue (optional)

 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)

 Title   : outfile_name
 Usage   : my $outfile = $codeml->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to

 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none

 Title   : cleanup
 Usage   : $codeml->cleanup();
 Function: Will cleanup the tempdir directory
 Returns : none
 Args    : none

 Title   : io
 Usage   : $obj->io($newval)
 Function:  Gets a Bio::Root::IO object
 Returns : Bio::Root::IO
 Args    : none