On Tue, Jun 09, 2009 at 07:21:19PM -0700, Marek Szuba wrote: -> On Mon, 8 Jun 2009 21:31:42 -0700 -> Christopher Lee <[email protected]> wrote: -> -> > that is already done. I got rid of the last few references to -> > pygr.Data from the reference docs. Unless someone has something -> > that must urgently go into this alpha, I will tag v0.8.0.alpha2. -> > Then we should generate and upload packages for our target platforms. -> Unfortunately it turns out we still haven't got rid of problems with -> BLAST tests... Since you fixed the bug I introduced into relaxed tests, -> Blast_Test.test_multiblast() has been failing again. It would, as I -> mentioned earlier, make sense to resolve this before releasing packages. -> -> Attached you will find a diff of expected and obtained results. -> Unfortunately, the problem cannot be solved by simply raising the -> identity-percentage threshold - while the vast majority of mismatches -> could indeed be eliminated this way, there are some on the "high" end -> as well. Moreover, I find the fact some hits are only present in one of -> the output samples, rather than appearing in both and only differing by -> the exact value of identity percentage, rather puzzling. What do you -> think we should do here?
How about separating the two types of tests? We can test BLAST running with some very simple and well-known sequence collections (see data/gapping.fa, for example) where we just check to make sure that a set of alignments exists between various sequences. We can test BLAST parsing itself against canned data. --titus --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
