[BioPython] blastall directory problem

[Peter]

On Tue, Jan 13, 2009 at 7:38 AM, Stefanie Lück <lueck at ipk-gatersleben.de> wrote:
> I was a little bit to optimistic...
>
> After compilation with py2exe, blast hangs. In the log file of py2exe
> I get the following error message:
>
>  Traceback (most recent call last):
>  File "prim_search.pyc", line 464, in make_xml
>
>  File "Bio\Blast\NCBIStandalone.pyc", line 1668, in blastall
>  File "Bio\Blast\NCBIStandalone.pyc", line 1992, in _invoke_blast
>  File "subprocess.pyc", line 586, in __init__
>  File "subprocess.pyc", line 681, in _get_handles
>  File "subprocess.pyc", line 722, in _make_inheritable
>  TypeError: an integer is required
>
> Any ideas?
> Stefanie

Are you using Biopython 1.49?

What version of Python are you using here?  (Python 2.3 is handled a
little differently, as it does not have the subprocess module).

Can you confirm the exact same code works fine run from Python
directly (via IDLE or the commandline?), but fails via py2exe?

Are you running the py2exe compiled version from the Windows command
line?  Can you try that, even thought you said it was a GUI program.
This might be related to the following python bug on Windows to do
with pipe redirection, http://bugs.python.org/issue1124861
If so, I think there is a suggested work around we can try (this will
require a change to the Biopython code).

Peter