[Biopython-dev] Tests for Emboss Phylip wrappers

[Eric Talevich]

On Fri, Sep 18, 2009 at 5:26 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Fri, Sep 18, 2009 at 4:52 AM, David Winter
> <winda002 at student.otago.ac.nz> wrote:
>
> > One possibly foolish thing I did was use TreeIO to test the trees that
> came
> > out of these programs made sense, thinking that module would be part of
> the
> > next release. If the plan is for a new release soon and having a test for
> > these wrappers is important the tests could be done with Nexus.Trees but
> I
> > found that was difficult to use for files with multiple newick trees.
>
> Hmm. In the short term we can either comment out those bits of the test
> pending the inclusion of TreeIO in the next release, or add a quick tiny
> parser in the test itself to load the trees, split them on the ";" and pass
> them one by one to Bio.Nexus.Trees for parsing.
>
>
That's all TreeIO does. The relevant loop is in NewickIO.parse(), if you'd
like to copy it verbatim:
http://github.com/etal/biopython/blob/phyloxml/Bio/TreeIO/NewickIO.py

-Eric