There's about a million variations of this problem. It would help if you could submit some code and/or data that demonstrated how it is that you're sending the temporary data to the database and which (may) illuminate possible solutions.
Presently, it feels like there is no solution; but that seems to be false since you have some way to "shell out" to produce the temp table.
UPDATE: No, no, you miss my point entirely. If you can find a way to "shell out" and do what you want, then there's almost certainly a way to do it in perl. I still don't think I know enough about the problem or what you're doing when you "shell out" to be able to provide more information.
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