[Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values

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http://bugzilla.open-bio.org/show_bug.cgi?id=2480





------- Comment #24 from drpatnaik at yahoo.com  2008-09-30 01:53 EST -------
[I myself do not need to work on a Windows machine, and I am following this bug
out of curiosity.]

I have tried the pywin32-short-path-name approach.

It seems I have to use win32api.GetShortPathName on the values for the BLAST
exe as well as the database and the input file. If I don't do so, the process
seems to hang: I see only a blinking cursor for 2-3 minutes when I just quit
the console application (I know the BLAST process itself takes less than a
second to finish). The error file has '^C' and the result file is empty.

But because the specified database ('mine') is really not a file,
GetShortPathName fails, unless I use code like:

  my_blast_db = win32api.GetShortPathName('C:/Documents and Settings/patnaik/My
Documents/blast/bin/mine.nin')[:-4]

Even then I see the hang, and get a similar as before [or empty] error file.

With a print command in NCBIStandalone.py, I can see that the value being
passed on to the system is:

  C:/DOCUME~1/patnaik/MYDOCU~1/blast/bin/blastall.exe -p blastn -d
C:/DOCUME~1/patnaik/MYDOCU~1/blast/bin/HAIRPI~1 -i
C:/DOCUME~1/patnaik/MYDOCU~1/blast/bin/30a.seq -m 7

This value is right as it works by itself.


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