[Biopython-dev] PAML yn00 under Windows

[Brandon Invergo]

Hi, 
Just got home and saw the emails. Yes, in the end it was good to do the
extra tests! So the path separator problem is solved, right?

That indexing is a weird one. I'll look at it now.

-brandon

On Wed, 2011-08-17 at 18:56 +0100, Peter Cock wrote:
> On Wed, Aug 17, 2011 at 6:02 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > Hi again,
> >
> > You may have noticed from the buildbot emails that there is a
> > separate issue with the PAML tests on Python (2.4 and) 2.5,
> > applying to executing all three binaries tried: yn00, baseml
> > and codeml, e.g.
> > ...
> > I can reproduce this at the terminal window, and it is specific
> > to Python (2.4 and) 2.5, using Python 2.6 and 2.7 is fine, as
> > are Python 3.1 and 3.2.
> 
> I'm getting -1 back from the subprocess.call(...)
> https://github.com/biopython/biopython/commit/2d94a24ca223851d9fd895a82780dd0f23dc2dca
> 
> Some debugging later I realised the paths in the control file
> were using Unix slashes rather than Windows slashes:
> https://github.com/biopython/biopython/commit/4125e55b291922053380b5fe688bd687c70035fa
> 
> That should now just leave the yn00 stats parsing for you
> to check (which offset should the fix use, assuming that
> is the right fix).
> 
> It was worth insisting on more tests and running them on Windows :)
> 
> Regards,
> 
> Peter