There are some benchmarks of Perl and Java for reading files on this site. The main things they will tell you is that Perl is plenty fast, and it takes tons more code to do a decent job of it in Java. You already said that the performance of the application is irrelevant in this case, so it comes down to the cost of development and maintenance. If you can build and maintain this app twice as fast in Perl as in Java, you will save your company money. It's that simple.
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