Other packages in the module: Bio::EnsEMBL::Analysis::Runnable::BestTargetted

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Bio::EnsEMBL::Analysis::Runnable::BaseExonerate

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Methods code

sub parse_results {

  my ($self, $fh) = @_;

  my $score = 0;
  my $perc_id = 0;
  
  # my $basic_options = "--showsugar false --showvulgar false --showalignment false --ryo \"RESULT: %S %pi %ql %tl %g %V\\n\" ";
  while (<$fh>){
    if ($_=~/^RESULT:/){
      my @tmp = split/\s+/, $_;
      print "exonerate results @tmp ";
      print "\n";
#     my (
#        $tag, $q_id, $q_start, $q_end, $q_strand,
#        $t_id, $t_start, $t_end, $t_strand, $score,
#        $perc_id, $q_length, $t_length, $gene_orientation,
#        @vulgar_blocks
#        ) = split;
#     my($match_type, $query_match_length, $target_match_length,@rest_of_vulgar) = @vulgar_blocks;
      if ($score < $tmp[9]){
        $score = $tmp[9]; #return the best score
        $perc_id = $tmp[10];
      }
    }
  }  

  $self->output([$score, $perc_id]);

}


1;

}

sub query_type {

  my ($self) = @_;
  
  return 'protein';

}

sub target_type {

  my ($self) = @_;

  return 'protein';

}

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