[BioPython] blastall produces a black console screen with biopython 1.49 and up‏

[Peter]

On Fri, Apr 17, 2009 at 12:25 PM, Joaquin Abian Monux
<gatoygata at hotmail.com> wrote:
>
> Dear all,
>
>  I coded a GUI utility to perform local blast searches
> on lists of peptides using NCBIStandalone.blastall().
>
> I work on windows XP with python 2.5
>
> After I updated from biopython1.48 to 1.49,  when I
> make a search, NCBIStandalone.blastall()  produces
> a black screen (a windows system console produced
> by the execution of ..\bin\blastall.exe) that pops up and
> rapidly disappears as blastall.exe is executed.  Nothing
> more has been changed in the application and the
> screen does not appears if I downgrade to 1.48.
>
> This black window is very annoying (it appears in
> front of all other open windows) and in fact it is
> preventing me from upgrading my biopython installation.
>
> This problem occurs both with biopyton 1.49 an 1.50.
> With biopython 1.48 and below NCBIStandalone.blastall
> works silently.
>
> I have seen looking at the code that 1.49 uses preferently
> subprocess.popen() (in function _invoke_blast) to execute
> blast while in 1.48 it was os.popen3() (in function blastall).
> I have been playing with this but I got nothing clear
>
> Is this something already known? I could not found any hint
> by googling. Is there some way to get rid of this screen?.

Stefanie Lück had some issues with BLAST and subprocess on
her Windows GUI program, which we traced to a bug in Python itself,
http://bugs.python.org/issue1124861

See:
http://lists.open-bio.org/pipermail/biopython/2009-January/004896.html
http://lists.open-bio.org/pipermail/biopython/2009-February/004898.html

We were able to resolve this for Stefanie, and the fix was included in
Biopython 1.50 beta.  Have you tried this yet?

If that doesn't work could you show as a short GUI example that fails?
Details of how you are running your program could also help.  This may
also make a difference - e.g. is it started from the command line with
"python my_gui.py", or run from IDLE?

Thanks

Peter