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  open(NPBXNUM1, ">npbxnum1");
  open(MYINPUTFILE, "npbxnum");

  open(NPBXNUM1, ">npbxnum1");
  open(MYINPUTFILE, "<npbxnum");

  open(NPBXNUM1, '>', "npbxnum1");
  open(MYINPUTFILE, '<', "npbxnum");

while (<MYINPUTFILE>) {
   my($line) = $_;
   chomp($line);

while (my $line = <MYINPUTFILE>) {
   chomp($line);

foreach my $inputData ($line) {
  my $outputData = $inputData;
...
  }
  print NPBXNUM1 "$outputData\n";
}

  my $outputData = $line;
  while (length($outputData) < 4) {
...
  }
  print NPBXNUM1 "$outputData\n";
}