[Biopython-dev] [biopython] Bugfix in test_Phylo; branch length formatter for Newick trees (#7)

[Eric Talevich]

On Fri, May 27, 2011 at 9:48 AM, Erick Matsen <matsen at fhcrc.org> wrote:

> Hello everyone--
>
>
> Hope you don't mind my chiming into this discussion.
>
> > Good to know. The format for confidences is also hard-coded ("%1.2f"), do
> > you suppose that should be given the same treatment?
>
> I think this would be entirely appropriate. There are some cases (eg
> bootstrap) where the confidence is actually a count, and being able to
> express it as such might be convenient.
>
> I have one related point to discuss if you don't mind. In
>
>
> https://github.com/biopython/biopython/blob/master/Bio/Phylo/NewickIO.py#L246
>
> trees without confidence values get written out as trees with confidence
> values of zero. These are of course two different things.
>
> I realize that if we want to write out a tree without confidence values
> we can specify branchlengths_only, but it would seem to me that the most
> natural behavior would be to just write out confidence values when they
> are specified.
>
>
Hi Erick & folks,

This commit should fix both those issues:
https://github.com/biopython/biopython/commit/4ce56619cb13e27659927707e2979807d37b26b0

There's an issue with naming -- I called the argument "format_support"
because all the other arguments refer to confidence as "support", since they
were all copied from Bio.Nexus. The Bio.Phylo Clade attribute this affects
is called "confidence", though. It's confusing either way. Thoughts &
suggestions?

-E