I have edited the script above as follows (below): it writes out a temporary file that I will use while running my second script. The second script will now take the temporary file which I will delete afterwards. Please critisize as it must be 100% accurate.

#!/usr/bin/perl
use strict;
use warnings;

my $file = 'my_data_file.txt';

my %seen = ();

{
      local @ARGV = ($file);

#remove all previous re-organized files
my $remove = "my.txt.tmp";
    if (unlink($remove) == 1) {
                        print "Existing \"$remove\" file was removed\n
+";
                              }
  
      while(<>){
            
  #now make a file for the ouput
       my $outputfile = "my.txt.tmp";
           if (! open(POS, ">>$outputfile") ) {
            print "Cannot open file \"$outputfile\" to write to!!\n\n"
+;
                exit;
        }
   
      $seen{$_}++;
      
  if($seen{$_} !~/-/g){
      
      next if $seen{$_} > 1;

      print POS;
      }
    }
  }
  
  print "\n\nfinished processing file.\n";
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