The reason is this portion of code:
foreach my $single (@sw) {

You don't have a closing bracket before:

for  $a (1 .. 2) { # a  has 2 levels:
 for  $t (1 .. 2) { # t has 2 levels:
  for  $g (1 .. 2) { # g has 2 levels:
   for  $c (1 .. 2) { # c has 2 levels: 

 $combi=sprintf($new_four,$a,$t,$g,$c,3-$a,3-$t,3-$g,3-$c); 
print"~$combi\n"; 
print $fh "~$combi\n";
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It's the way the loops are arranged, that's all. You can see this more easily by using the perl debugger or print statements to see the values of $new_four at each iteration, etc.