use Bio::Tools::Signalp;
 my $parser = new Bio::Tools::Signalp(-fh =>$filehandle );
 while( my $sp_feat = $parser->next_result ) {
       #do something
       #eg
       push @sp_feat, $sp_feat;
 }

 Parser for Signalp output

      my($class,@args) = @_;

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

      return $self;

        my ($self) = @_;
        
        my $line;
        # parse
        my $id;
        my ( $fact1, $fact2, $end);
        while ($_=$self->_readline()) {
           $line = $_;
           chomp $line;
           
           if ($line=~/^\>(\S+)/) {
              $id = $1;
              $self->seqname($id);
              next;
           }
           elsif ($line=~/max\.\s+Y\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
              $fact1 = $2;
              $self->fact1($fact1);
              next;
           }
           elsif ($line=~/mean\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
              $fact2 = $2;
                 $fact1 = $self->fact1;
                 $id = $self->seqname;
              
              if ($fact1 eq "YES" && $fact2 eq "YES") {
                  
                  my $line = $self->_readline();
              
                  if ($line =~ /Most likely cleavage site between pos\.\s+(\d+)/) {
                      $end = $1;
                  }
                  else {
                      $self->throw ("parsing problem in signalp");
                  }
                  my (%feature);
                  $feature{name} = $id;
                  $feature{start} = 1;
                  $feature{end} = $end;
                  $feature{source} = 'Signalp';
                  $feature{primary}= 'signal_peptide';
                  $feature{program} = 'Signalp';
                  $feature{logic_name} = 'signal_peptide';
                  $self->_parse_hmm_result(\%feature);
                  my $new_feat = $self->create_feature (\%feature);
                  return $new_feat;
                  
              }
               next;
               
           }
        
           next;
        
        }

    my ($self, $feature_hash) = @_;
    while(my $line = $self->_readline){
        chomp $line;
        if($line =~ /Prediction: (.+)$/){
            $feature_hash->{hmmProdiction} = $1;
        }elsif($line =~ /Signal peptide probability: ([0-9\.]+)/){
            $feature_hash->{peptideProb} = $1;
        }elsif($line =~ /Signal anchor probability: ([0-9\.]+)/){
            $feature_hash->{anchorProb} = $1;
            last;
        }
    }

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


       # create feature object
       my $feature = Bio::SeqFeature::Generic->new(
            -seq_id=>$feat->{name},
            -start       => $feat->{start},
            -end         => $feat->{end},
            -score       => $feat->{score},
            -source      => $feat->{source},
            -primary     => $feat->{primary},
            -logic_name  => $feat->{logic_name}, 
       );
           
    $feature->score($feat->{peptideProb});
    $feature->add_tag_value('peptideProb', $feat->{peptideProb});
    $feature->add_tag_value('anchorProb', $feat->{anchorProb});
    $feature->add_tag_value('evalue',$feat->{anchorProb});
    $feature->add_tag_value('percent_id','NULL');
    $feature->add_tag_value("hid",$feat->{primary});
    $feature->add_tag_value('SignalpProediction', $feat->{hmmProdiction});
    return $feature;

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

    if (defined$seqname){

        $self->{'seqname'}=$seqname;
    }

    return $self->{'seqname'};

    my ($self,$fact1)=@_;

    if (defined$fact1){

       $self->{'fact1'}=$fact1;
    }

    return $self->{'fact1'};

 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to
 the Bioperl mailing list.  Your participation is much appreciated.

 bioperl-l@bioperl.org              - General discussion
 http://bioperl.org/MailList.shtml  - About the mailing lists

 Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via
 email or the web:

 bioperl-bugs@bio.perl.org
 http://bugzilla.bioperl.org/

 Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
 originally written by Marc Sohrmann (ms2@sanger.ac.uk)
 Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
 Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)

 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _