my %hash;
open file1...
while (<$file1>)
{
  ... do something to get the id
  $hash{$id}++;  
}
close file1
open file 2
while (<$file2>)
{
  ... do something to get the id
  $hash{$id}+=3;
}
close file 2
open 3 output files: 
    the both file, file1 only and file2 only
loop back thru file1 and file2
for each line decide where it goes
  if hash value of the id ==1 file one only
  if hash value of the id ==3 file two only
  if hash value of the id ==4 both files
  negate the hash value to signal that this id
  has already been dealt with - each id should only
  appear in one of the 3 output files.