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

[Stefanie Lück]

Hi!

Sorry I mixed up things. It's should be windows (as in your setup.py) and not console to get no black screen!

Sorry again, I think I need holidays ;-)
Stefanie
  ----- Original Message ----- 
  From: Joaquin Abian Monux 
  To: lueck at ipk-gatersleben.de ; biopython at maubp.freeserve.co.uk ; biopython at lists.open-bio.org 
  Sent: Tuesday, April 21, 2009 7:15 PM
  Subject: RE: [BioPython]blastall produces a black console screen with biopython 1.49 and up‏


  Hi Stefanie,

  It is a normal, minimal setup.py for windows and single file executables:

  # exWx/setup.py
  from distutils.core import setup
  import py2exe

  setup(
      windows=[
              {'script': "blast_main_205.pyw",
               'icon_resources':[(0,'blast.ico')]
              }
              ],
              
      options={
              'py2exe': {
                          #'packages' :    [],
                          #'includes':     [],
                          'excludes':     [
                                           'Tkconstants','Tkinter', 'tcl'
                                          ],
                          'ignores':       ['wxmsw26uh_vc.dll'],
                          'dll_excludes': ['libgdk_pixbuf-2.0-0.dll',
                                           'libgdk-win32-2.0-0.dll',
                                           'libgobject-2.0-0.dll'
                                          ],
                          'compressed': 1,
                          'optimize':2,
                          'bundle_files': 1
                          }
              },
      zipfile = None,
      data_files= [
                  ]
      )


  I think I understand the logic of your question. I will try with 'console' and let you know what happens. Here at work I have 1.48 installed and 1.50 at home.

  Currently, with biopython 1.50, I can produce py2exe single file executables of GUI programs based on wxpython that work perfectly after:

  a) I set console=True in the subprocess call in _invoke_blast (NCBIStandalone.py). Otherwise I have the Blast.exe console popping when I make a search.

  b) I modify a line in the addRule function in spark.py: rules = doc.split() ---to-->  rules = doc.split() if doc else []. Otherwise the executable is produced but gives an exception when ran saying that can not split 'None'.

  Best regards

  Joaquin  





  > From: lueck at ipk-gatersleben.de
  > To: biopython at maubp.freeserve.co.uk; gatoygata at hotmail.com; biopython at lists.open-bio.org
  > Subject: Re: [BioPython]blastall produces a black console screen with biopython 1.49 and up‏
  > Date: Mon, 20 Apr 2009 13:07:20 +0200
  > 
  > Hi!
  > 
  > How does your py2exe setup.py file looks?
  > 
  > from distutils.core import setup
  > import py2exe
  > 
  > #python setup.py py2exe
  > 
  > setup(
  > windows = [
  > {
  > "script": "nb_psst.py", ### Main Python 
  > script
  > "icon_resources": [(0, "Icon.ico")] ### Icon to embed into 
  > the PE file.
  > }
  > ],
  > )
  > 
  > If you use console instead of windows in setup() will the black screen 
  > dissapear?
  > 
  > Kind regards
  > Stefanie
  > 
  > 
  > ----- Original Message ----- 
  > From: "Peter" <biopython at maubp.freeserve.co.uk>
  > To: "Joaquin Abian Monux" <gatoygata at hotmail.com>; "BioPython Mailing List" 
  > <biopython at lists.open-bio.org>
  > Sent: Friday, April 17, 2009 5:38 PM
  > Subject: Re: [BioPython]blastall produces a black console screen with 
  > biopython 1.49 and up‏
  > 
  > 
  > On Fri, Apr 17, 2009 at 4:24 PM, Joaquin Abian Monux
  > <gatoygata at hotmail.com> wrote:
  > > Dear Peter,
  > >
  > > Thanks, I fixed it. I'm not sure how.
  > >
  > > In:
  > >
  > > blast_process = subprocess.Popen(cmd_string,
  > > stdout=subprocess.PIPE,
  > > stderr=subprocess.PIPE,
  > > stdin=subprocess.PIPE,
  > > shell= (sys.platform!="win32"))
  > >
  > > (sys.platform!="win32") is False for my winXP computer. But if I set the
  > > parameter shell=True, then the problem disappears, either in the py2exe
  > > executables and in the scripts. Everything works perfect as usual.
  > >
  > > if shell=True in windows the shell used is the one set in COMSPEC. In my
  > > case it is the normal windows shell (cmd.exe). If shell=False I am not 
  > > sure
  > > what happens in windows. Obviously no cmd shell should be 
  > > expected...still,
  > > blast.exe opens his.
  > > ...
  > > Done! (Although it would be nice someone could explain why the 'shell'
  > > parameter must be 'True' for the program to behave properly)...
  > 
  > >From memory, with subprocess using the shell argument in this way was
  > deliberate on to get things to work cross platform. I looks like when
  > running from the command line you need the *opposite* shell setting to
  > running from py2exe.
  > 
  > Could you put together a trivial python GUI application that calls
  > BLAST that we could use for testing?
  > 
  > Peter
  > 
  > _______________________________________________
  > Biopython mailing list - Biopython at lists.open-bio.org
  > http://lists.open-bio.org/mailman/listinfo/biopython
  > 


------------------------------------------------------------------------------
  ¿Quieres estar al día de la últimas novedades? ¡Apúntate gratis aquí!