[Biopython-dev] [Bug 3155] Some Phylip tools seem to fail on Jython

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3155





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2010-11-09 10:05 EST -------
(In reply to comment #2)
> (In reply to comment #1)
> > What version of Jython?
> 
> Jython 2.5.2rc2

Can you easily update to Jython 2.5.2 (actual release)?

> > What version of EMBOSS, and the phylipnew package?
> 
> EMBOSS 6.0.1
> Phylip seems 3.68

Your EMBOSS is a bit old, but should be fine.

> > Do these tests pass *on the same machine* if run in normal (C) Python?
> 
> Yep. This is the same machine as the one doing integration testing in C-Python
> 

Good - that means we can rule out EMBOSS being too old.

> > Alternately, do these four command line examples work when run by hand?
> 
> No. I've noticed that the example files do not exist! e.g. Phylip/opuntia.phy
> does not exist. Indeed this should not work, I think
> 

The unit tests create Phylip/opuntia.phy at runtime, converted from
Clustalw/opuntia.aln -- I'd forgotten about that and it does make testing the
individual commands harder. The point here is to ensure the PHYLIP likes what
we write out as PHYLIP format.


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