#!/usr/bin/perl -w
use strict;

my $s1 ='CCCATCTGTCCTTATTTGCTG';  my @a1 = qw(ATCTG ATTTG);
my $s2 ='ACCCATCTGTCCTTGGCCAT';   my @a2 = qw(CCATC);
my $s3 ='CCACCAGCACCTGTC';        my @a3 = qw(CCACC CCAGC GCACC);
my $s4 ='CCCAACACCTGCTGCCT';      my @a4 = qw(CCAAC ACACC);

put_bracket($s1,\@a1);
put_bracket($s2,\@a2);

put_bracket($s3,\@a3);
put_bracket($s4,\@a4);

sub put_bracket
{
    my( $str, $ar ) = @_;

    foreach my $subs ( @$ar  )
    {
      # Construct a regexp with [\[\]] between all the letters
      my $newsub = join '[\[\]]?', split //, $subs;
      $str =~ s/($newsub)/[$1]/g;
    }

    # Now de-nest the brackets in the string
    my $depth = 0;
    my $newstr = '';
    foreach my $c ( split //, $str )
    {
      if ( $c eq '[' ) {
        $newstr .= $c
          if $depth++ == 0;
      }
      elsif ( $c eq ']' ) {
        $newstr .= $c
          if --$depth == 0;
      }
      else {
        $newstr .= $c;
      }
    }


    return $newstr;
}