my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    	-host => 'ensembldb.ensembl.org',
    	-user => 'anonymous'
);

my $home = $ENV{'HOME'};


my($ID, $query, $off, $idi, $subject, $ref, $st);


print "ID\tposition\tvariation\tRef Genome coordinates\n";
unless(open DATA, "Input_files/Contig_Alignment_Selected_3.txt"){die "Cannot open the file file $! \n";}
while(<DATA>) {
 chomp;

  if(m[^>]) { #Checks the start of the alignements 
  
   ($ID) = (split '\|',$_)[1];#splits the first line with '|' 
   ($ref) = $ID =~ /(\d+)\s+ref$/;
   
  }
 if(/^\s+Identities/){ #gets the percentage of identity
   
   my($identity, undef) = split/,/ ;
   ($idi) = $identity =~ /\sIdentities\s\=\s\d{3}\/\d{3}\s\((\d{2,3}\%)\)$/;
 } 
 
 if(/^\s+Strand/){ #check strands Plus/Minus
  
  ($st) = $_ =~/^\s\w+\=\w{4}\/(\w{4,5})$/;
  
 }

  

  if(m/^Query/) {
  ($query) = m[^Query\s+(\d+)];
  
   my $top = substr $_, 15;#substring the first 15 char
  
   my $pipes = substr <DATA>,15; #same,if the Sbjct is more than 5 numbers then this doesnt worx  
   my $subject = <DATA>;
   my($value) = $subject  =~ /^Sbjct\s+(\d+)/;
 
   my $bot = substr $subject, 15;#if the Sbjct is more than 5 numbers then this doesnt work
   my $p = 0 ;
   while ($p = 1+index $pipes,' ', $p) {
       
    my $pos1 = $value-$p;
 
    my $pos2 = $value+$p;
    my $var1 = substr( $top, $p-1, 1 );
    my $var2 = substr( $bot, $p-1, 1 );
   # my $genomref1 = 4900000 + $pos1;
    my $genomref2 = 4899999 + $pos2;
     if($st eq "Minus") {
      
     
      print join"\t", $ref,$pos1, $var1."/".$var2,$genomref2 ;
      
      snpdetails($genomref2);
      
      
      
     }else{
     print join "\t", $ref,$pos2, $var1."/".$var2,$genomref2;
     snpdetails($genomref2); 
     }
         
   }
  }
  
 #}