On Wed, Nov 30, 2011 at 12:28 PM, Christian Höner zu Siederdissen <choe...@tbi.univie.ac.at> wrote: > No, I didn't see it. I blame it on not having had breakfast yet (and yes > I'm still in Austria...). I'll take a look at your package. Can you > parse the complete Rfam.full.gz? If not, maybe I'll write an adaptor for > iteratee...
I've never tried, so I just did. Attached is my test program. With Rfam 10.1 seed: 41033 sequences, 1.7s, 10 MiB of memory With Rfam 9.1 seed: 27292 sequences, 1.1s, 9 MiB of memory With Rfam 9.1 full: stack overflow =D. So the answer right now is "no" =(. Given that it's a stack overflow, I guess it is a bug somewhere, not something inherent to lazy processing. >> Stuff about CMs is something that I still need to refactor. But now >> that you brought this subject, what do you feel about your stubs? I >> mean, is there any problem in changing them, or are you using them for >> something now? I'd like to change some bad design decisions of my >> code before merging it with BiobaseInfernal, and I'd like to know if >> I'm free to bend and break your code ;-). > > I can make available the old stuff. What I want to do is base > CM-handling on PrimitiveArray to be able to use CM's in high-performance > algorithms. As I have not started on this, feel free to do whatever you > want. Good =). >> And on a final note, I really miss a repository for BiobaseInfernal. >> Is there any somewhere? If "no", I'd like to suggest you either using >> darcs (because it rocks!) on patch-tag (not so much) or git (not so >> much) on github.com (because it rocks!). > > Yes, I have everything in git (used by most people at the TBI). Some old > stuff is still in darcs which I like a lot. > > I'll take a look at github, but this will take a while as I have ~ 40 > repositories and scripts that auto-update everything and I need to adapt > them. I'm looking forward to it then, I get uneasy programming without versioning =) Cheers, -- Felipe.
T.hs
Description: Binary data
_______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
