On Wed, Jun 03, 2009 at 12:12:02AM -0700, Christopher Lee wrote: -> On Jun 2, 2009, at 6:49 AM, C. Titus Brown wrote: -> -> > http://github.com/ctb/pygr/commits/blast_skip -> -> Thanks, Titus! Pushed to master.
great! -> > Finally, I don't entirely understand how the formatdb stuff is -> > working; -> -> I think you're right, it should raise an error if all the formatdb -> attempts fail. Which do you prefer, IOError or OSError? I'm not sure I agree; if it were that simple I'd have just made the change ;). Three issues -- - formatdb (as currently run) could fail for a bunch of reasons, not just that it's not installed. Should we test to see if a 'formatdb' executable can be run, much like we test that blastall exists in testutil.py? And should this be cached? - what if the database already exists and we don't need to run formatdb, e.g. the database is in a location specified in the BLASTDB variable or .ncbirc file? - the run_formatdb code looks in a number of locations. So we should probably only raise OSError if all of the locations fail. --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 -~----------~----~----~----~------~----~------~--~---
