use Bio::Tools::Genewise;
  my $gw = Bio::Tools::Genewise(-file=>"genewise.out");

  while (my $gene = $gw->next_prediction){
    my @transcripts = $gene->transcripts;
      foreach my $t(@transcripts){
        my @exons =  $t->exons;
        foreach my $e(@exons){
            print $e->start." ".$e->end."\n";
        }
      }
  }

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

  my ($self,$start,$end) = @_;
  $start || $self->throw("Need a start");
  $end   || $self->throw("Need an end");
  my $strand;
  if ($start > $end) {
    my $tmp = $start;
    $start = $end;
    $end = $tmp;
    $strand = -1;
  }
  else {
    $strand = 1;
  }
  return ($start,$end,$strand);

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

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

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

    my ($self) = @_;

    my $genes = new Bio::SeqFeature::Gene::GeneStructure(-source => $Srctag);
    my $transcript = new Bio::SeqFeature::Gene::Transcript(-source => $Srctag);

    local ($/) = "//";
    my $score;
    my $prot_id;
    my $target_id;
    while ( defined($_ = $self->_readline) ) {
	$self->debug( $_ ) if( $self->verbose > 0);
        ($score) = $_=~m/Score\s+(\d+[\.][\d]+)/;
        $self->_score($score) unless defined $self->_score;
        ($prot_id) = $_=~m/Query protein:\s+(\S+)/;
        $self->_prot_id($prot_id) unless defined $self->_prot_id;
        ($target_id) = $_=~m/Target Sequence\s+(\S+)/;	
        $self->_target_id($target_id) unless defined $self->_target_id;
        next unless /Gene\s+\d+\n/;

        #grab exon + supporting feature info
        my @exons;
	
	unless ( @exons = $_ =~ m/(Exon .+\s+Supporting .+)/g ) {
	    @exons = $_ =~ m/(Exon .+\s+)/g;

	}
        my $nbr = 1;

        #loop through each exon-supporting feature pair
        foreach my $e (@exons){
	    my ($e_start,$e_end,$phase) = $e =~ m/Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/;
	    my $e_strand;
	    ($e_start,$e_end,$e_strand) = $self->_get_strand($e_start,$e_end);
	    $transcript->strand($e_strand) unless $transcript->strand != 0;
	    
	    my $exon = new Bio::SeqFeature::Gene::Exon
		(-seq_id=>$self->_target_id,
		 -source => $Srctag,
		 -start=>$e_start, 
		 -end=>$e_end, 
		 #-frame => $phase,
		 -strand=>$e_strand);
	    $exon->add_tag_value('phase',$phase);
	    if( $self->_prot_id ) {
		$exon->add_tag_value('Sequence',"Protein:".$self->_prot_id);
	    }
	    $exon->add_tag_value("Exon",$nbr++);

	    if( $e =~ m/Supporting\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/) {
		my ($geno_start,$geno_end,
		    $prot_start,
		    $prot_end) = ($1,$2,$3,$4);
          
		my $prot_strand;
		($prot_start,$prot_end,
		 $prot_strand) = $self->_get_strand($prot_start,$prot_end);
		
		my $pf = new Bio::SeqFeature::Generic
		    ( -start   => $prot_start,
		      -end     => $prot_end,
		      -seq_id  => $self->_prot_id,
		      -score   => $self->_score,
		      -strand  => $prot_strand,
		      -source  => $Srctag,
		      -primary=> 'supporting_protein_feature',
		      );
		my $geno_strand;
		($geno_start,$geno_end,
		 $geno_strand) = $self->_get_strand($geno_start,$geno_end);
		my $gf = new Bio::SeqFeature::Generic
		    ( -start   => $geno_start,
		      -end     => $geno_end,
		      -seq_id  => $self->_target_id,
		      -score   => $self->_score,
		      -strand  => $geno_strand,
		      -source  => $Srctag,
		      -primary => 'supporting_genomic_feature',
		      );
		my $fp = new Bio::SeqFeature::FeaturePair(-feature1=>$gf,
							  -feature2=>$pf);
	  
		$exon->add_tag_value( 'supporting_feature' => $fp );
	    }
          $transcript->add_exon($exon);
        }
	$transcript->seq_id($self->_target_id);
	$genes->add_transcript($transcript);
	$genes->seq_id($self->_target_id);
	return $genes;
    }

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

 Email: fugui@worf.fugu-sg.org

 Title   : score
 Usage   : $obj->score
 Function: get/set for score info
 Example :
 Returns : a score value