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# $Id: Blat.pm 11480 2007-06-14 14:16:21Z sendu $
#
# BioPerl module for Bio::Tools::Blat
#
# Written by Balamurugan Kumarasamy
#
# You may distribute this module under the same terms as perl itself
#
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=head1 NAME
Bio::Tools::Blat - parser for Blat program
=head1 SYNOPSIS
  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;
  }
=head1 DESCRIPTION
 Parser for Blat program
=head1 FEEDBACK
=head2 Mailing Lists
 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/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
 Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted the
 web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Balamurugan Kumarasamy
 Email: bala@tll.org.sg
=head1 APPENDIX
 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _
=cut
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);
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=head2 new
 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)
=cut
sub new {
      my($class,@args) = @_;
      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);
      return $self;
}
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=head2 next_result
 Title   : next_result
 Usage   : my $feat = $blat_parser->next_result
 Function: Get the next result set from parser data
 Returns : L<Bio::SeqFeature::Generic>
 Args    : none
=cut
sub next_result {
        my ($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;
        }
}
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=head2 create_feature
 Title   : create_feature
 Usage   : my $feat=$blat_parser->create_feature($feature,$seqname)
 Function: creates a SeqFeature Generic object
 Returns : L<Bio::SeqFeature::Generic>
 Args    :
=cut
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;