[Biopython-dev] Code review request for phyloxml branch

[Eric Talevich]

Hi Brad, I hope the holidays treated you well.

On Mon, Jan 4, 2010 at 5:16 AM, Brad Chapman <chapmanb at 50mail.com> wrote:

>
> Are the annotations often used in real life cases or is this more of
> a fringe problem? I'm not as familiar with tree work, but know this
> is a pain in sequence space. A good goal is to capture the most
> common use cases and then integrate the other issues as feasible.
>

The data that TreeIO preserves round-trip are:

 - Branching structure (topology)
 - Branch lengths
 - Clade/taxon names
 - Rooted-ness (for the whole tree)
 - Tree ID

The troublesome parts are:

 - The "confidences" attribute in PhyloXML trees should map onto the
"support" attribute in Nexus trees, but that's tricky -- the original Nexus
attribute seemed content with a little ambiguity in what that attribute's
numerical value actually meant (relative/absolute support), while PhyloXML
uses a list of Confidence objects containing both a numerical value and a
"type" string such as "bootstrap". Currently that information is dropped
when converting between PhyloXML and Nexus/Newick trees.
 - Nexus also has a "comment" attribute for each node, while PhyloXML
doesn't directly support that.
 - The branch length of the root node/clade is None in PhyloXML, but 0.0 in
Nexus. I prefer None because there is no meaningful branch leading to that
node, but there might be a reason 0.0 was chosen for Nexus that I'm not
aware of.
  - The names of unlabeled internal nodes might change from None to "" in
some cases, since None is the PhyloXML default and "" is the Nexus default.
 - Since PhyloXML supports more structured taxonomic information on each
node than Newick, it's possible to have a PhyloXML tree where a Clade has no
name, but instead one or more Taxonomy objects containing the scientific
name, common names, etc. -- so when this tree is converted to Newick format
the taxonomy info is lost for those nodes. I could squash the Taxonomy
object into a string for the sake of Nexus labels, but I think it would be
safer (less surprising) to just write a cookbook entry on how to collapse
PhyloXML Taxonomies into Clade names to aid format conversions.

If the support-vs-confidence issue can be resolved, then we can treat
PhyloXML as a rough superset of Newick, in terms of annotation, and then it
shouldn't be surprising to lose some annotation data in converting PhyloXML
to Newick.

Cheers,
Eric