[BioRuby] BioRuby, performance, cut_with_enzyme

[Maciej Łopatka]

Hello,

I've got a big problem with performance of BioRuby. I need to cut sequence
(about 5MB <  < 17MB) with restriction enzymes. It takes ages to cut it with
just one enzyme, it just doesn't stop, and I have no idea what is going on.
My friend for the same task used BioPython and it took just 2 minutes for 20
enzymes.

I know that Ruby is slower than Python, but it doesn't explain this. Has
anyone had similar problems?

I've tested this on Ubuntu 9.04 and Windows 7 with Ruby 1.8.7 on Linux, and
Ruby 1.9.2 on Windows.

Thanks,
Maciek Lopatka