On Mon, 11 May 2009 18:25:37 -0700
Christopher Lee <l...@chem.ucla.edu> wrote:
> I'm afraid that to fix this, we'll need a bug report that specifies
> a precise sequence of steps to reproduce the bug.
This is pretty easy to reproduce:
1. Get a Windows machine;
2. Install BLAST on it somewhere and add the relevant path to PATH so
that Pygr can find it;
3. Build Pygr in a directory with spaces in names, e.g. your Windows
home directory;
4. Enter tests/;
5. Make sure no old formatdb output is present;
6. Run blast_test.py.
> > [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;
- 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.
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.
--
MS
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