On Tue, Jul 28, 2009 at 10:36:25AM -0700, Christopher Lee wrote: -> -> Hi Titus, -> Thanks for all your work on simpleframe and the blast tutorial! I -> have a couple questions about your simpleframe fixes. -> -> - commit 56a0699: -> for trans_seq in tdb.annodb: -> This loops over all sequences in the annotation db, and then tries -> them to see if they're in the alignment. If the annotation db is -> large, that could get really slow. I think we could clean this up by -> simply adding a SeqTranslator method that iterates over all six of its -> frames. We would then just use that iterator on our query sequence -> instead of looping over all sequences in the annotation db.
Huh, good point. Yes, that sounds better, thanks. -> - what is the status of your simpleframe_ctb branch, which provides -> the translation() method that you said you wanted? Should this be -> merged to master? No, it's not ready or tested... I'm both busy and waiting for the simpleframe and silencio branches to get merged, so that we can cut a beta, and then I'll do some polishing on the beta (which will include this minor method). cheers, --titus -- C. Titus Brown, [email protected] --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
