A little more legible (if not as elegant) version of what the previous post is doing:

#! perl

my $str = '.,a..A,,C..+4ACGTG.,-2TG,,...,a.';

print replace($str);

sub replace {
    my $str = shift;
    if ($str =~ m/([+-])(\d*)/) {
        $str =~ s/\Q$1\E$2.{$2}//;
        return replace($str);
    }
    return $str;
}
[download]