while(<FILE>)
{
#  chomp;
    #@_=split(',');
  foreach $line (<FILE>) {
      @_=split(',');
  $Data->{$_[1]}->{$_[3]}++;
  }
}
[download]

to

while(<FILE>)
{
  chomp;
  @_=split(',');
  $Data->{$_[1]}->{$_[3]}++;
}
[download]

The "chomp" will get rid of that pesky newline you are seeing in the output. Also, the "while(<FILE>)" will process each line of your file (one at a time) and will assign each line to $_. This means your "foreach $line (<FILE>)" is not needed.

Note: The foreach loop in your code would assign data to the $line variable. Your split is splitting $_ (nothing specified mean you get to use the default $_)... if you were to use your foreach, you would want to change your split to "@_=split(',',$line);"