Re^6: Bioinformatic task

[BrowserUk]

True. I took the OP at face value. Just as I did with you and your timings in the db/sort case.

However, after the I first became aware of the performance problem, I did eventually get (parts of) BioPerl installed on my own (old) machine and verified that the problem existed. I also tried to hunt down the cause.

One possibility that was muted for this was the use of $`, $& or $'. Although I suggested to the OP that he try Devel::SawAmpersand, there was no follow up, so I hacked my way to installing Bio::SeqIO::fasta and all the required support packages, manually. (The full package has never installed for me.) I didn't detect that particular problem, but saw the machinations the module went through (back then; I see quite a lot of it is now commented out), to read a text file, and attributed the (at that point, quite extreme) slowness to that. I also attempted to track the module changes for a while, but that went out the window when I got my current machine.

Long story short, when the OP reports "half an hour" for 200MB, that fit with my prior experiences, and I took him at his word. As your reply in that thread was not to me, I probably never saw it. So, if you are responsible for the performance improvements in the module, I congratulate you.

All of that said, performance was only one of the issues I raised above.