[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 #20 from biopython-bugzilla at maubp.freeserve.co.uk  2008-09-18 06:58 EST -------
I think I've fixed some of this in CVS.  Biopython should now cope with a blast
exe or input file with spaces in the name - but thus far I have only tested
this on Mac OS X.

See Bio/Blast/NCBIStandalone.py revision 1.77 in CVS.  You will be able to look
at the changes and download them via the following URL shortly:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py?cvsroot=biopython

Dealing with database(s) where the path(s) contain spaces is trickier.  I think
the best solution here is to setup BLAST so that it knows where to find your
databases, and then you can refer to them by name only (no paths, therefore no
spaces).


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