Occasionally, you can't use just a /g to get all the changes to occur. Here are two common cases:


    # put commas in the right places in an integer
    1 while s/(.*\d)(\d\d\d)/$1,$2/g;      # perl4
    1 while s/(\d)(\d\d\d)(?!\d)/$1,$2/g;  # perl5

    # expand tabs to 8-column spacing
    1 while s/\t+/' ' x (length($&)*8 - length($`)%8)/e;

##</code><code>##

# patterns to search with are stored in @pattern Array
# patterns are strings of uc DNA (i.e. TTTAGT, etc)
# but can be interrupted by lc or non-DNA characters (i.e., html tags)

# searching for a needle in a haystack:
my $notNeedle = q{[^ACGTYRMKSWBDHVN]*};

 while ($g < $num) {  
   $needle[$g] = $pattern[$g];
   @{$parts[$g]} = split m/(\[|\]|\|)/, $needle[$g];
   my @array = @{$parts[$g]}; my @results;
   while (@array) {
     my $string = shift @array;
     if ($string eq '[') {
       $string .= (join "", splice(@array, 0, 2));
       }
     if ($string eq '|') {
       my $prev = pop @results;
       $string = (join "", $prev, $string, splice(@array, 0, 1));
       }
     push @results, $string;
     }
   @{$parts[$g]} = @results;
   $haystackPatt[$g] =  q{(} . join($notNeedle, @{$parts[$g]}) . q{)};
   $rxHaystack[$g]   = qr{$haystackPatt[$g]};   
   $g++;
   }

$text_seqs[$i] =~ s{$rxHaystack[$j]}{<span class=$class[$a]>$1</span>}gemx;