I'd really like to understand this script
That's probably a bad idea. Either you just want to understand how it works, and you've already seen by yourself that it's probably not the good way to do it, so you shouldn't learn from it ; or you want to use it as a base for custom modifications, and I'm pretty sure that writing from scratch will be easier (there's only 78 lines of code, it's like a lot of work went into it).

The thread that poj referenced contains a link to the Bio::SeqIO::fastq module, which might be the best starting point for you if you want to reuse something that works. Or if you want to rewrite the whole thing (that's one way to learn), it will be easier for us to help you on specific blocking points rather than this quite obscure script.

In reply to Re: explanation of passages of a Perl script by Eily
in thread explanation of passages of a Perl script by uuuiii

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