use Bio::Tools::Blat;
  my $blat_parser = new Bio::Tools::Blat(-fh =>$filehandle );
  while( my $blat_feat = $blat_parser->next_result ) {
        push @bllat_feat, $blat_feat;
  }

 Parser for Blat  program

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

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

      return $self;

    my ($self) = @_;
    my $filehandle;
    
 my $line;

    my $id;
 while ($_=$self->_readline()){
   
    # first split on spaces:
    $line = $_;
    chomp $line;
   # chomp;
   
    my (
            $matches,      $mismatches,    $rep_matches, $n_count, $q_num_insert, $q_base_insert,
            $t_num_insert, $t_base_insert, $strand,      $q_name,  $q_length,     $q_start,
            $q_end,        $t_name,        $t_length,    $t_start, $t_end,        $block_count,
            $block_sizes,  $q_starts,      $t_starts
          )
          = split;

   
    my $superfeature = Bio::SeqFeature::Generic->new();
   
    # ignore any preceeding text
    unless ( $matches =~/^\d+$/ ){
      next;
    }
   
    # create as many features as blocks there are in each output line
    my (%feat1, %feat2);
    $feat1{name} = $t_name;
    $feat2{name} = $q_name;
   
    $feat2{strand} = 1;
    $feat1{strand} = $strand;
   
   
    my $percent_id = sprintf "%.2f", ( 100 * ($matches + $rep_matches)/( $matches + $mismatches + $rep_matches )
);
   
   
    unless ( $q_length ){
      $self->warn("length of query is zero, something is wrong!");
      next;
    }
    my $score   = sprintf "%.2f", ( 100 * ( $matches + $mismatches + $rep_matches ) / $q_length );
   
    # size of each block of alignment (inclusive)
    my @block_sizes     = split ",",$block_sizes;
   
    # start position of each block (you must add 1 as psl output is off by one in the start coordinate)
    my @q_start_positions = split ",",$q_starts;
    my @t_start_positions = split ",",$t_starts;
   
    $superfeature->seq_id($q_name);
    $superfeature->score( $score );
    #$superfeature->percent_id( $percent_id );
    $superfeature->add_tag_value('percent_id',$percent_id);
    # each line of output represents one possible entire aligment of the query (feat1) and the target(feat2)
    for (my $i=0; $i<$block_count; $i++ ){
   

      my ($query_start,$query_end);

      if ( $strand eq '+' ){
        $query_start = $q_start_positions[$i] + 1;
        $query_end   = $query_start + $block_sizes[$i] - 1;
      }
      else{
        $query_end   = $q_length  - $q_start_positions[$i];
        $query_start = $query_end - $block_sizes[$i] + 1;
      }
   
      #$feat2 {start} = $q_start_positions[$i] + 1;
      #$feat2 {end}   = $feat2{start} + $block_sizes[$i] - 1;
      $feat2 {start} = $query_start;
      $feat2 {end}   = $query_end;
      if ( $query_end <  $query_start ){
        $self->warn("dodgy feature coordinates: end = $query_end, start = $query_start. Reversing...");
        $feat2 {end}   = $query_start;
        $feat2 {start} = $query_end;
      }

      $feat1 {start} = $t_start_positions[$i] + 1;
      $feat1 {end}   = $feat1{start} + $block_sizes[$i] - 1;
   
      # we put all the features with the same score and percent_id
      $feat2 {score}   = $score;
      $feat1 {score}   = $feat2 {score};
      $feat2 {percent} = $percent_id;
      $feat1 {percent} = $feat2 {percent};
   
      # other stuff:
      $feat1 {db}         = undef;
      $feat1 {db_version} = undef;
      $feat1 {program}    = 'blat';
      $feat1 {p_version}  = '1';
      $feat1 {source}     = 'blat';
      $feat1 {primary}    = 'similarity';
      $feat2 {source}     = 'blat';
      $feat2 {primary}    = 'similarity';
   
      my $feature_pair = $self->create_feature(\%feat1,\% feat2);
      $superfeature->add_sub_SeqFeature( $feature_pair,'EXPAND');
    }
    #push(@features_within_features, $superfeature);
    return $superfeature; 
  }

    my ($self, $feat1,$feat2) = @_;



    my $feature1= Bio::SeqFeature::Generic->new( -seq_id     =>$feat1->{name},
                                                 -start      =>$feat1->{start},
                                                 -end        =>$feat1->{end},
                                                 -strand     =>$feat1->{strand},
                                                 -score      =>$feat1->{score},
                                                 -source     =>$feat1->{source},
                                                 -primary    =>$feat1->{primary},
                                                   );
    


    my $feature2= Bio::SeqFeature::Generic->new( -seq_id     =>$feat2->{name}, 
                                                 -start      =>$feat2->{start},
                                                 -end        =>$feat2->{end},
                                                 -strand     =>$feat2->{strand},
                                                 -score      =>$feat2->{score},
                                                 -source     =>$feat2->{source},
                                                 -primary    =>$feat2->{primary},
                                                  );




    my $featurepair = Bio::SeqFeature::FeaturePair->new;
    $featurepair->feature1 ($feature1);
    $featurepair->feature2 ($feature2);
   
   $featurepair->add_tag_value('evalue',$feat2->{p});
   $featurepair->add_tag_value('percent_id',$feat2->{percent});
   $featurepair->add_tag_value("hid",$feat2->{primary});
    return  $featurepair;

 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.

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 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
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 bioperl-bugs@bioperl.org
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 Email: bala@tll.org.sg

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