[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 #31 from drpatnaik at yahoo.com  2008-10-02 01:03 EST -------
 > For any documentation I would want to recommend using the
> win32api.GetShortPathName() function to avoid the spaces, with an example
> showing how to do this for the database name(s).  To me this seems much simpler
> than the complex quoting solution.

To me it seems win32api.GetShortPathName() will not work for database paths
because the specified values are not really files (e.g., BLAST uses the
/data/mouse.db value to look for /data/mouse.db.nin, etc.), and
win32api.GetShortPathName works only on files.

For BLAST's 'd' argument, to specify multiple databases, one uses the space
separator, and double-quotes the entire argument value ("Db1 Db2"). If a
database value has spaces within, one backslash-double-quotes that database
value (\"Db 3\") and BLAST is supplied with "Db1 Db2 \"Db 3\"".

The following BLAST 2.2.18 console command, using multiple databases with
spaces in the pointers, e.g., work on Windows XP SP2:

  "C:/Documents and Settings/patnaik/My Documents/blast/bin/blastall.exe" -p
blastn -d "\"C:\Documents and Settings\patnaik\My Documents\blast\data\db 1\"
\"C:\Documents and Settings\patnaik\My Documents\blast\data\db 2\"" -i
"C:/Documents and Settings/patnaik/My Documents/blast/data/My 30a.seq" -m 7


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