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";

[download]
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.

Bioinformatics

In reply to Re: How can one get all possible combinations of a string without changing positions & using window size? by bioinformatics
in thread How can one get all possible combinations of a string without changing positions & using window size? by supriyoch_2008

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.