I recently did something similar comparing items that were in two different files using hashes. Each hash had a primary key that was the list name with a value of 1 if it exixted in the first file, 2 if it existed in both files, and 3 if it was only in the secoond file.

my $file1 = "/home/scott/file1"; 
  my $file2 = "/home/scott/file2"; 
  my $hashOfLists; 
  my %hashOfLists; 

  open (FILE1, "$file1") or die "Could not open $file1 $!"; 
  open (FILE2, "$file2") or die "Could not open $file2 $!"; 


  ######################################################
  #####This block reads all of the items of the file into 
  #####a hash with the item being the key. Since I
  ##### was comparing 2 files each key received a 
  #####value of 1 if it was in the first file, 2 if 
  #####it was in both , and 3 if it was only in file 2 
  ###################################################### 

  foreach (<FILE1>) 
  { 
  chomp $_; 
  $hashOfLists{$_} =1; 
  } 


  foreach (<FILE2>) 
  { 
  chomp $_; 
  ###################################################### 
  #####if exists checks the hash to see if $_ exists.
  ##### If true $_'s value becomes 2, 
  #####if false, $_ gets a value of three
  ######################################################
  if (exists $hashOfLists{$_}) 
  { 
  ($hashOfLists{$_}) =2; 
  } 
  else 
  { 
  ($hashOfLists{$_})=3; 
  } 
  } 


  close FILE1 or die "Could not close $file1 $!"; 
  close FILE2 or die "Could not close $file2 $!";
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