Just as a note, using both $file and $FILE for variable names is going to cause pain. Why not name them $filename and $iFH/$oFH or something else unique?

Also, a nicer way to close a filehandle is to allow the variable to go out of scope. Just my $filehandle it inside the outer loop, and use next FILE; with an appropriate "FILE" label on the outer loop instead of closing it manually. The filehandle will get closed for you when you leave, and $filehandle won't exist after the file is closed so you can't accidentally try to do operations on the closed filehandle.

That's a bit nicer than closing the file in order to make your read throw an error in the while loop, thus breaking out to the outer loop.

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