On Wed, Jun 03, 2009 at 10:15:23AM -0700, Christopher Lee wrote: -> On Jun 3, 2009, at 7:16 AM, C. Titus Brown wrote: -> -> > - 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? -> -> I think just raising a clear error message (see below) is all that's -> needed. formatdb is a one-time operation, not an inner loop, so I -> don't think this is a performance bottleneck that justifies the added -> complexity of caching.
OK -- I may have to go re-check the code, but is it true that if formatdb fails, the database does not exist? -> > - the run_formatdb code looks in a number of locations. So we should -> > probably only raise OSError if all of the locations fail. -> -> Yes, that's what I meant. In the case where run_formatdb fails in all -> locations, raise an exception, with an error message like "formatdb -> failed. Either formatdb is not in your PATH, you had insufficient -> privileges or diskspace in all the locations specified by -> blast.BlastMapping.blastIndexDirs, or your NCBI tools are -> misconfigured." -> -> What do you think? sounds good. I'll put that in and submit a patch. --t -- 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 -~----------~----~----~----~------~----~------~--~---
