use Bio::SearchIO;
  my $in = new Bio::SearchIO(-file   => 'result.blast',
                             -format => 'blast');
  my $out = new Bio::SearchIO(-output_format  => 'GbrowseGFF',
                              -file           => ">result.gff");
  while( my $r = $in->next_result ) {
    $out->write_result($r);
  }

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

  my $self = $class->SUPER::new(@args);
  my ($evalue) = $self->_rearrange(["E_VALUE"], @args);
  $self->{_evalue} = $evalue > 0?$evalue:10;
  return $self;

    my ($self, $result, @args) = @_;
    my $GFF;
    while( my $hit = $result->next_hit ) {
        my $significance = $hit->significance;
        next unless (($significance < $self->{_evalue}) &&  ($self->{_evalue} > 0)); 
        my $refseq = $hit->name;
        my $seqname = $result->query_name;  # hopefully this will be a simple identifier without a full description line!!
        my $score = $hit->raw_score;
        $self->throw("No reference sequence name found in hit; required for GFF (this may not be your fault if your report type does not include reference sequence names)\n") unless $refseq;
        my $source = $hit->algorithm;
        $self->throw("No algorithm name found in hit; required for GFF (this may not be your fault if your report type does not include algorithm names)\n") unless $refseq;
        $self->throw("This module only works on BLASTN reports at this time.  Sorry.\n") unless $source eq "BLASTN";
        
        my @plus_hsps;
        my @minus_hsps;
        
        # pre-process the HSP's because we later need to know
        # the extents of the plus and munus strand
        # on both the subject and query strands individually
        my ($qpmin, $qpmax, $qmmin, $qmmax, $spmin, $spmax, $smmin, $smmax); # variables for the plus/minus strand min start and max end to know the full extents of the hit
        while( my $hsp = $hit->next_hsp ) {
            next unless (($hsp->significance < $self->{_evalue}) && ($self->{_evalue} > 0));
            if ($hsp->strand('subject') eq "1"){
                push @plus_hsps, $hsp;
                if (defined $qpmin){  # set or reset the minimum and maximum extent of the plus-strand hit
                    $qpmin = $hsp->start('query') if $hsp->start('query') < $qpmin;
                    $qpmax = $hsp->end('query') if $hsp->end('query') > $qpmax;
                    $spmin = $hsp->start('subject') if $hsp->start('subject') < $spmin;
                    $spmax = $hsp->end('subject') if $hsp->end('subject') > $spmax;                    
                } else {
                    $qpmin = $hsp->start('query');
                    $qpmax = $hsp->end('query');
                    $spmin = $hsp->start('subject');
                    $spmax = $hsp->end('subject');
                }
            } 
            if ($hsp->strand('subject') eq "-1"){
                push @minus_hsps, $hsp;
                if (defined $qmmin){ # set or reset the minimum and maximum extent of the minus-strand hit
                    $qmmin = $hsp->start('query') if $hsp->start('query') < $qmmin;
                    $qmmax = $hsp->end('query') if $hsp->end('query') > $qmmax;
                    $smmin = $hsp->start('subject') if $hsp->start('subject') < $smmin;
                    $smmax = $hsp->end('subject') if $hsp->end('subject') > $smmax;                    
                } else {
                    $qmmin = $hsp->start('query');
                    $qmmax = $hsp->end('query');
                    $smmin = $hsp->start('subject');
                    $smmax = $hsp->end('subject');
                }
            }
            #else next if there is no strand, but that makes no sense..??
        }
        next unless (scalar(@plus_hsps) + scalar(@minus_hsps));  # next if no hsps (??)
        # okay, write out the index line for the entire hit before processing HSP's
        if (scalar(@plus_hsps)){
            $GFF .= "$refseq\t$source\tmatch\t$spmin\t$spmax\t$score\t+\t.\tTarget EST:$seqname ; tstart $qpmin ; tend $qpmax\n";
        }
        if (scalar(@minus_hsps)){
            $GFF .= "$refseq\t$source\tmatch\t$smmin\t$smmax\t$score\t-\t.\tTarget EST:$seqname ; tstart $qmmax ; tend $qmmin\n";  # note reversal of max and min in column 9, as per the spec
        }
        # process + strand hsps
        my $strand = "+";
        foreach my $hsp(@plus_hsps){
            my $qstart = $hsp->start('query');
            my $qend = $hsp->end('query');
            my $sstart = $hsp->start('subject');
            my $send = $hsp->end('subject');
            my $score = $hsp->score;
            $GFF .= "$refseq\t$source\tHSP\t$sstart\t$send\t$score\t+\t.\tTarget EST:$seqname ; tstart $qstart ; tend $qend\n";
        }
        foreach my $hsp(@minus_hsps){
            my $qstart = $hsp->start('query');
            my $qend = $hsp->end('query');
            my $sstart = $hsp->start('subject');
            my $send = $hsp->end('subject');
            my $score = $hsp->score;
            $GFF .= "$refseq\t$source\tHSP\t$sstart\t$send\t$score\t-\t.\tTarget EST:$seqname ; tstart $qend ; tend $qstart\n";  # note reversal of qstart/qend as per spec
        }
    }
    return $GFF;

 return ''

  return ''

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

  http://bugzilla.bioperl.org/

 Title   : filter
 Usage   : $writer->filter('hsp', \&hsp_filter);
 Function: Filter out either at HSP,Hit,or Result level
 Returns : none
 Args    : string => data type,
           CODE reference
 Note    : GbrowseGFF.pm makes no changes to the default filter code