[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 #28 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-01 04:42 EST -------
In comment #26 Peter wrote:
>> Using shell=False [with subprocess.Popen] works while shell=True
>> fails on Windows (I tested on Windows XP with Python 2.5 from IDLE).
>> However, the opposite is true on Mac OS X with python 2.5 from IDLE.
>> This is a pain.

In comment #27 Patnaik  wrote:
> I tried the subprocess routine through a test.py file on a Mac OS X
> 10.5.5 with Python 2.5.2, but w/o using Biopython. I had to use
> 'shell=True', otherwise with 'shell=False',I get:
> 
>   File "/Lab/Laboratory/Libs/Python/lib/python2.5/subprocess.py", 
> ...
> _execute_child
>     raise child_exception
> 
> With 'shell=True', it works even when there is a space in the
> file-path/names of the BLAST executable, the database or the input
> sequence file (the escaping of the spaces needs to be properly done).

Good - at least that confirms the shell option differences I found between
Windows and Mac.  We'd need to check on Linux before we can write something
using subprocess which should work on all the main platforms.

Peter


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