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A,B*,item2,,
A,B*item1,,,
A,B*,,,item4
C,D*item1,,,
C,D*,,item3,

sub merge {
      open(INFILE, "test.put");
...
  close INFILE;
  print Dumper(\%data);
}

$VAR1 = {
          'C,D' => {
...
                     'item1,,,' => 1
                   }
        };

C,D,item1,,item3,
A,B,item1,item2,,item4