[BioPython] BLAST subprocess problem with a GUI

[Stefanie Lück]

Thanks! That's was!

Stefanie
----- Original Message ----- 
From: "Peter" <biopython at maubp.freeserve.co.uk>
To: "Stefanie Lück" <lueck at ipk-gatersleben.de>
Cc: <biopython at lists.open-bio.org>
Sent: Monday, February 09, 2009 5:06 PM
Subject: Re: [BioPython] BLAST subprocess problem with a GUI


On Mon, Feb 9, 2009 at 3:21 PM, Stefanie Lück <lueck at ipk-gatersleben.de> 
wrote:
>
> Never ending story...
>
> After compilation and changing in the
> Application/__init__.py file, unfortunatly Primer3 don't work and gives 
> this
> Error:
>
> Traceback (most recent call last):
> File "primer3.pyc", line 208, in get_2
> File "Bio\Application\__init__.pyc", line 29, in generic_run
> File "subprocess.pyc", line 593, in __init__
> File "subprocess.pyc", line 793, in _execute_child
>
> WindowsError: [Error 2] Das System kann die angegebene Datei nicht finden

In English that's something like "The system cannot find the indicated
file", which suggests that you don't have the primer3 path specified
correctly (and this this isn't the pipe problem we had before with
BLAST).  Try adding check on the primer3 executable filename:

import os
primer3_exe = r"C:\Program Files\EMBOSS\primer3.exe"
assert os.path.isfile(primer3_exe)
cline = Primer3Commandline(primer3_exe)
...

Note that you can create the Primer3Commandline object without
specifying the location of the executable file.  On Unix, this will
then try and locate the tool from the path environment variable.  On
Windows, I find it best to always be explicit and provide the full
path to the filename.

Peter