On May 12, 2009, at 1:21 PM, Marek Szuba wrote: >> >>> [NULL_Caption] ERROR: Could not open C:\Documents >> who returns this message? Some part of Pygr? The external program >> formatdb? > This one actually comes from formatfb. Moreover, I have run formatdb > by > hand with exactly the same options: > - with quotation marks in place I got the aforementioned message;
Are you saying that even with correctly quoted path strings passed to formatdb, it fails with the above error message? Then it is a NCBI formatdb bug and there is nothing Pygr can do to make formatdb properly handle paths containing whitespace... > > - without them, I got > [NULL_Caption] ERROR: Arguments must start with '-' (the > offending argument #3 was: 'and') > I also get the 'Arguments must start...' error from blastall if I > omit quotation marks so since we don't see it in test output, the > failure is caused by something else. Sorry, I didn't quite understand. Have you found any way of getting blastall to run properly on a database path containing whitespace, running it by hand? I guess if formatdb failed, the necessary blast index files will be missing and blast will not be able to run anyway. > > This suggests it's formatdb and not Pygr which has got problems with > spaces this time... Whew, false alarm. I've reported the problem to > BLAST developers - but even if they do fix it soon, for the sake of > users of old versions we may want to add a warning about this to > either > our BLAST code or our documentation. Perhaps we can do better than that. Pygr has a nice mechanism in place for specifying a search path in which to find / create blast index files -- they don't need to be in the same directory as the original fasta file. I guess the main issue is that we would have to decide on a standard location to use specifically for windows (with no whitespace in the path), then create a symbolic link from there to the fasta file (otherwise we'd have to copy the whole fasta file to the standard location). And we would probably add support for the user to specify an environment variable to set the blast index search path. And we should add some totally clear error messages for this situation on Windows. -- Chris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
