* Felipe Almeida Lessa <felipe.le...@gmail.com> [30.11.2011 15:22]: > On Wed, Nov 30, 2011 at 12:07 PM, Christian Höner zu Siederdissen > <choe...@tbi.univie.ac.at> wrote: > > Hi, > > > > newest BiobaseInfernal is up, now with partial biocore and a whole lot > > of newtypes in Biobase.Infernal.Types. If you want shorter names and > > have good ones, please say so ;-) > > Nice! I can't take a look at it now, but I'll do so ASAP. > > > Stuff on Stockholm files is still missing, and the CM modules are just > > stubs, as both parts will change a lot. > > > > Felipe, didn't you have some stuff on Stockholm? and CMs? Could you make > > that available? Or tell me what you would expect / like to see? > > About Stockholm files, did you see the biostockholm package [1]? Or > do you mean something else? I'm pretty happy with my own package haha > ;-). >
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... > 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. > > 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. Gruss, Christian > > Cheers, =D > > [1] http://hackage.haskell.org/package/biostockholm > -- > Felipe.
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