On Thu, May 28, 2009 at 02:34:13PM -0700, Christopher Lee wrote: -> On May 28, 2009, at 1:27 PM, C. Titus Brown wrote: -> -> > -> > -> >>>> al = blastmap(seq=some_sequence) -> > -> -> > -> Sure! -> > -> -> > -> >>>> -> > -> > -> > -> > OR -> > -> > -> > -> >>>> al = blastmap(queryDB=db) -> > -> -> > -> Sure! -> > -> > OK -- shall I make the appropriate changes? -> -> Yes, by all means!
Done. -> > -> Yes, as the Pygr docs discuss, the proper way of storing BLAST -> > results -> > -> in an NLMSA is to use bidirectional=False. I just looked at -> > blast.py, -> > -> and it appears we are not using that. This surprises me, since I -> > took -> > -> the trouble to implement that mode and document how that is the -> > proper -> > -> way to handle blast. I think we could use the bidirectional=False -> > -> option to eliminate these duplicates. -> > -> > OK. Shall I patch? -> -> Sure. Done. --- In git://github.com/ctb/pygr.git branch 'ctb_minor_changes', along with a few cleanup issues: http://github.com/ctb/pygr/commits/blast_minor_changes/ - modified blast.py to allow EITHER / OR seq= and queryDB= parameters - reformatted blast_test to get rid of > 80 char lines; - pulled apart some functions in blast_test.py to separate some tests; - bidirectional=False is now default for BlastMapping results; - use logger instead of stdout/stderr for warning & info messages in blast.py; --- Marek, note that I pulled apart some of the functions in blast_test so that I could get separate failures for blastall problems vs other issues. Having tests that may fail at multiple points makes it possible to run the test, have it fail at the first point, and then not run the remaining parts of the test. cheers, --titus -- C. Titus Brown, c...@msu.edu --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
