Isn't it the formatdb that causes this probem? I think we need to print out format command to see whether there is quotation marks for every path. If not, we need to add them in order to process correctly in windows environment because windows path has a lot of *spaces*. Just a thought.
On Tue, May 12, 2009 at 10:25 AM, Christopher Lee <l...@chem.ucla.edu>wrote: > > Hi Marek, > this is odd. Assuming you are using a version of Python > 2.3, > FilePopen just uses Python subprocess.Popen, which presumably works on > Windows in a way that correctly supports Windows style paths. So it > is hard to see how this problem could happen. Also, we already showed > that FilePopen works on Windows and correctly handles Windows style > paths, because we use it to invoke the XMLRPC server process in our > tests on Windows... > > I'm afraid that to fix this, we'll need a bug report that specifies a > precise sequence of steps to reproduce the bug. > > On May 11, 2009, at 5:31 PM, Marek Szuba wrote: > > > While looking into something completely different I noticed today > > Pygr still has got problems with paths with spaces in them, at least > > under Windows: running blast_test.py yields multiple failures calling > > formatdb and blastall, with failures of the former quite clearly > > being caused by spaces in paths: > > Both run_formatdb() and start_blast() use FilePopen, which in turn > just uses Python's standard library subprocess.Popen. It's puzzling > that subprocess.Popen would screw up Windows paths... We will have to > catch the problem in the act in order to debug this. > > > > > > > INFO blast.run_formatdb: Building index: [...] > > [NULL_Caption] ERROR: Could not open C:\Documents > > who returns this message? Some part of Pygr? The external program > formatdb? > > -- 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 -~----------~----~----~----~------~----~------~--~---
