Bio::Tools::Blat - parser for Blat program

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

 Parser for Blat program

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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 _

 Title   : new
 Usage   : my $obj = Bio::Tools::Blat->new(-fh=>$filehandle);
 Function: Builds a new Bio::Tools::Blat object
 Returns : Bio::Tools::Blat
 Args    : -filename
           -fh (filehandle)

 Title   : next_result
 Usage   : my $feat = $blat_parser->next_result
 Function: Get the next result set from parser data
 Returns : L<Bio::SeqFeature::Generic>
 Args    : none

 Title   : create_feature
 Usage   : my $feat=$blat_parser->create_feature($feature,$seqname)
 Function: creates a SeqFeature Generic object
 Returns : L<Bio::SeqFeature::Generic>
 Args    :

#
# BioPerl module for Bio::Tools::Blat
#
# Written by Balamurugan Kumarasamy
#
# You may distribute this module under the same terms as perl itself
#

package Bio::Tools::Blat;
use strict;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root Bio::Root::IO);

sub new {
      my($class,@args) = @_;

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

      return $self;
}

sub next_result {
	my ($self) = @_;
	my $filehandle;
	my $line;
	my $id;

	while ($_=$self->_readline()){
		# first split on spaces:
		$line = $_;
		chomp $line;

		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
		next unless ( $matches =~/^\d+$/ );

		# create as many features as blocks there are in each output line
		my (%feat1, %feat2);
		$feat1{name} = $t_name;
		$feat2{name} = $q_name;

		$strand = $1 if ($strand =~/([+-])[+-]/);

		$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 );
		$superfeature->add_tag_value('percent_id',$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');
		}
		return $superfeature;
	}
}

sub create_feature {
    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;
}

1;