CLS_S3_Contig100_st CLS_S3_Contig100  53      10      0.3717
CLS_S3_Contig100_at CLS_S3_Contig100  55      11      0.4321
CLS_S3_Contig100_st CLS_S3_Contig100  57      10      0.3223
CLS_S3_Contig100_at CLS_S3_Contig100  59      11      0.4055
CLS_S3_Contig100_st CLS_S3_Contig100  61      11      0.4511
CLS_S3_Contig100_at CLS_S3_Contig100  63      11      0.474
.
.
.
CLS_S3_Contig10031_st CLS_S3_Contig10031 53   12      0.5548
CLS_S3_Contig10031_st CLS_S3_Contig10031 57   10      0.4871
CLS_S3_Contig10031_st CLS_S3_Contig10031 61   12      0.547
CLSS3627.b1_F19.ab1   CLS_S3_Contig10031 62   11      0.5129
CLSS3627.b1_F19.ab1   CLS_S3_Contig10031 64   11      0.5789

##</code><code>##

my %hash_F2_1 =(); my %hash_F2_2 =(); my %hash_F2_3 = ();my %hash_F2_4= ();
while(<INPUT2>){
         (my $probeset_id, my $origin, my $probeseq, my $pip, my $gc, my $affyscore) = split("\t", $_);

         push (@{$hash_F2_1{$origin}}, $pip); # This makes a hash of multiple value for each probeset ID
                                             
}


#clculate the max and put into hash (origin and max of pip)
for (sort keys %hash_F2_1){
     #print RESULTS "$_", "\t", max(@{$hash_F2_1{$_}}), "\n";


     $hash_F2_2{$_} =  max(@{$hash_F2_1{$_}});
}

# then go thorough $hash_F2_2 and that has the key (origin) # and max as value and make a multivalue hash as follows:

for my $k (sort keys %hash_F2_2){
          my $v = $hash_F2_2{$k};
           #print RESULTS "$k\t$v\n";
              for (my $i=1; $i <= $v; $i++){
              push (@{$hash_F2_3{$k}}, $i);
# this hash (%hash_F2_3) is the hash of origins and PIPs from 1 to max
    }
}


LOOP1: foreach my $key(sort keys %hash_F2_3){
         LOOP2:            foreach my $position (@{$hash_F2_3{$key}}){

LOOP3: foreach my $key1(sort keys %hash_F2_1){
         LOOP4:            foreach my $position1(@{$hash_F2_1{$key1}}){

LOOP1: foreach my $key(sort keys %hash_F2_3){
         LOOP2:            foreach my $position (@{$hash_F2_3{$key}}){

LOOP3: foreach my $key1(sort keys %hash_F2_1){
         LOOP4:            foreach my $position1(@{$hash_F2_1{$key1}}){

         if ($key =~ m/$key1/ && $position==$position1 ) {
         print "$key\t$position\t1\n";
        
         }
        else {
        print "$key\t$position\t0\n";
         }
        }
       }
      }
     }