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

[Peter Cock]

On Fri, May 27, 2011 at 2:48 PM, 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.
>
> In particular, it surprises me that reading a tree and then writing it
> with the default settings changes the meaning of the tree.
>
> I realize that changing the behavior like this might not be possible
> because this is a large group project, but I thought I would point it
> out.
>
> Thank you for your great work here!
>
> Erick

That is a very good point. Can we use None for no confidence value?

Peter