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

[Joaquin Abian Monux]

Dear Peter,

I already had seen that issue.  I though it was not  related with my problem because my program didn't hang (it had been also compiled with py2exe). The program works perfect. It runs the searches and shows the output, but each time I  make a search I get the /Blast/bin/blastall.exe console popping. I have tried right now with 1.50b (I upgraded to 1.50b).

Now, If I execute the main script from the system console (>python
blast_main_205.pyw) the black screen does not appear when I send a
Blast query. Neither If I execute from within the Stani's Python Editor
IDE: it does not appear. It seems that this has been solved: before, with biopython 1.49 I was getting a console flash.

But if I execute by double clicking on the main script, then it appears (!?)

I compiled with py2exe (after fixing some problems in spark.py, see below) and the single file executable worked perfectly but I still get the nasty console when I make a blast query.

So, still looking for help

Joaquin

Note: I got and error log when trying to execute the single file executable produced by py2exe:

Traceback (most recent call last):
  File "blast_main_205.pyw", line 23, in <module>
  File "zipextimporter.pyo", line 82, in load_module
 ......etc
   File "Bio\Parsers\spark.pyo", line 129, in collectRules
  File "Bio\Parsers\spark.pyo", line 101, in addRule
AttributeError: 'NoneType' object has no attribute 'split'

I fixed it by modifying spark.py in biopython 1.50b:
original:
def addRule(self, doc, func):

     rules = doc.split()

fixed:
def addRule(self, doc, func):
     rules = doc.split() if doc else []



> Date: Fri, 17 Apr 2009 13:14:22 +0100
> Subject: Re: [BioPython] blastall produces a black console screen with biopython 1.49 and up‏
> From: biopython at maubp.freeserve.co.uk
> To: gatoygata at hotmail.com
> CC: biopython at lists.open-bio.org
> 
> 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

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