There are a number of things you can improve. The two most important are:

1. If you do foreach $unit(<PFAMDB>) { } it reads the whole file into memory first, then iterates over it. If you instead write while ($unit = <PFAMDB>) { ... }, the file is read line by line.

2.Instead of doing a nested loop, read the IDs into a hash first, and then extract the IDs from the second file, and look them up in the hash. That will greatly speed up things.

Perl 6 - second systems done right

In reply to Re: Using less memory with BIG files by moritz
in thread Using less memory with BIG files by jemswira

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