#!/usr/bin/perl -w

use strict;


use CGI;  
use HTML::Template;

my $cgi = new CGI;
my $tmpl = HTML::Template->new (filename => 'tmpl/annotation.tmpl');

print "Content-type: text/html\n\n";

my $offgenes = 0;
my $prodgenes = 0;
my @offcordinates;
my @prodcordinates;
my $exactmatching = 0;
my $start;
my $stop;
my $start1;
my $stop1;
my $threeprimematch;
my %findgene;
my %findgene2;
my @officialannotation = ();
my @prodigalannotation = ();
my $hash_ref;
my $hash_ref2;

open(INFILE, "<", "genbankfile.txt") or die "cannot open file $!";
while(<INFILE>) {
  if ($_ =~ /\d+/) {
  $offgenes++;
}
  @offcordinates = split;
  $findgene = { "start" => $offcordinates[1], "stop" => $offcordinates[0] };


push @officialannotation, $findgene;
}

open(INFILE2, "<", "prodigalAnnotation.txt") or die "cannot open file $!";
while(<INFILE2>) {
   if($_ =~ /\d+/) {
      $prodgenes++;
   }
    @prodcordinates = split;
     $findgene2 = { "start1" => $prodcordinates[0], "stop1" => $prodcordinates[1] };
   
   
     push @prodigalannotation, $findgene2;


}


   foreach  $genes ( @officialannotation ) {
      my   %genes_= %$genes;
        foreach $genes2 ( @prodigalannotation ) {
            my    %genes2 = %$genes2; 
             if($genes{start} eq $genes2{start1}) {
                 $exactmatching++;
              }
          }
      }

print "$offgenes\n";
print "$prodgenes\n";
print "$exactmatching\n";


close(INFILE);
close(INFILE2);