Forget about doing everything in one regexp. It just makes it hard to read and hard to maintain.

while (<DATA>) {
   chomp;
   my ($host, $domain, $test) = /^([^,]+),([^.]+)\.(.+)$/;
   next if not defined $host;
   $domain =~ s/,/./g;
   next if substr($domain, -4) eq '.net';
   print("Host: $host   Test: $test\n");
}
[download]

Update: This should be faster:

while (<DATA>) {
   print("Host: $1   Test: $2\n")
      if /^([^,]+),[^.]+(?<!,net)\.(.+)$/;
}
[download]

• No need to chomp since . won't match newline without the s modifier. (The $ will absorb it.)
• No need to convert the commas to periods since we don't care about the domain.
• No need for two conditions. We can check for .com domains name right in the regexp.
• No need to assign the return values of the regexp to variables.

Update: I just realized you said it needs to process 6000 files a minute. That's 100 files a second! That seems excessive. You way want to rethink your design.

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