[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 #21 from drpatnaik at yahoo.com  2008-09-28 20:57 EST -------
I have tried the latest 'NCBIStandalone.py' file, from CVS (version 1.77). The
variable values are as mentioned in comment #16.

I no longer get the error from 'os.path.exists'. However, I still get the
'C:/Documents' is not recognized...' error in the error file.

By adding a print command to the 'NCBIStandalone.py' file, I can see that the
system command being initiated by Python is:

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

This command works as such if run outside Python. If I put it directly inside
the 'os.popen3' call in the 'NCBIStandalone.py' file, I still get the
'C:/Documents' is not recognized...'. Same happens if I run a Python file with
this code:

 import os
 my_cmd = r'"C:/Documents and Settings/patnaik/My
Documents/blast/bin/blastall.exe" -p blastn -d "\"C:\Documents and
Settings\patnaik\My Documents\blast\bin\hairpin.fa.db\"" -i "C:\Documents and
Settings\patnaik\My Documents\blast\bin\30a.seq" -m 7'
 w, r, e = os.popen3(my_cmd)
 print e.read()

It seems that using the 'subprocess' module is the only way around this.


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