while (<$IN_FILE>) {
     chomp;
     next if /[^ACTG]/; # removes lines with other letters
     next if length != 19; # removes lines not 19 char long
     # I just made up the next rule for the example
     next if /(.)\1\1/; # removes lines where the same letter comes three times in a row
     # etc.
     # now start doing the real processing
     # ...
}