# @gene_pairs contains the pairs of numbers e.g, 1304  1509
# @rep1_pids, @rep2_pids and @rep3_pids are where the numbers came from.

foreach my $pair (@gene_pairs)   {
        my @pair = $pair;
        my $p = join ('', @pair);
        @pair = split (/\t/, $pair);                                                                                                                                                                                    

      for (my $i=0; $i<@rep1_pids; $i++)  {
                 if ($pair[0] == $rep1_pids[$i])  {
                           push @locations, "rep1 ";
                           push @new_gp, "$rep1_pids[$i] ";
                 }
                                                                                                                                                                                    
                 if ($pair[1] == $rep1_pids[$i])  {
                           push @locations, "rep1 ";
                           push @new_gp, "$rep1_pids[$i] ";
                 }
      }
      for (my $i=0; $i<@rep2_pids; $i++)  {
                 if ($pair[0] == $rep2_pids[$i])  {
                           push @locations, "rep2 ";
                           push @new_gp, "$rep2_pids[$i] ";
                 }
                 if ($pair[1] == $rep2_pids[$i])  {
                           push @locations, "rep2 ";
                           push @new_gp, "$rep2_pids[$i] ";
                 }
      }
      for (my $i=0; $i<@rep3_pids; $i++)  {
                 if ($pair[0] == $rep3_pids[$i])  {
                           push @locations, "rep3 ";
                           push @new_gp, "$rep3_pids[$i] ";
                 }
                 if ($pair[1] == $rep3_pids[$i])  {
                           push @locations, "rep3 ";
                           push @new_gp, "$rep3_pids[$i] ";
                 }
      }
}

print "@new_gp\n";

my (@paired_genes1, @paired_genes2);
my @pairs2 = @new_gp;
print "@pairs2\n";
while (my ($one, $two) = splice(@pairs2,0,2)) {
   #print "$one ---- $two\n";
   push @paired_genes1, "$one ";
   push @paired_genes2, "$two ";
}