for (1..6){
  $line = <$input_file>;
  print $output_file $line;
}

##</code><code>##

my $M = 5;  # constant multiplier
my $T = 0.1 # negative number threshold
my $al = 0; # alternator

while(<$input_file>){
  s|([-.\d]+)|
    if($1 == -9999){
       $1;                    # leave -9999 alone
    } elsif( $1 < 0 and abs($1) < $T ){
       $al++ % 2 ? 0 : -9999;  # replace small negative with 0 or -9999
    } else {
       $1 * $M;  # multiply other numbers by constant
    }
  |ge;
  print $output_file;
}