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

[bugzilla-daemon at portal.open-bio.org]

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





------- Comment #19 from robert.cadena at gmail.com  2008-09-17 23:15 EST -------
A quick fix to this might be to call a .bat file that calls the blastall
executable.  For example:

blastall_wrapper.bat:
"c:/Documents and Settings/maldoror/My Documents/blast/bin/blastall.exe" %1 %2
%3 %4 %5 %6 %7 %8 %9

All arguments containing spaces should be escaped with "\"[arg]".  For example:

my_blast_db should be r"\"\\\"c:/documents and settings/maldoror/my
documents/blast/bin/mine\""

When the above value is printed out it should look like:
"\"c:/documents ...."

finally, set my_blastall_exe to the batch file:

"\"c:/documents and settings .../blastall_wrapper.bat\""

You still have to deal with the problem that os.path.exists and os.system
expect the command with and without quotes.  but, at least the batch file
wrapper method should pass the arguments properly.

hope it works on your system.  best of luck.


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