Reimplement tree shape kernel as C shared library

[ArtPoon]

Rosemary's written an implementation in C, so it should just be matter of writing the hooks from this code into Python as a shared library.

[rmcclosk]

It might not be that simple: the C version represents the trees as igraph_t objects from the igraph library, but the python version uses the BioPython Phylo objects. It's probably easiest to just call the treekernel binary using Popen.

[ArtPoon]

A shared library would be more elegant. Can't we just pass the trees as serialized representations, i.e., Newick strings?

On Oct 13, 2015, at 11:38 AM, Rosemary McCloskey [email protected] wrote:

It might not be that simple: the C version represents the trees as igraph_t objects from the igraph library, but the python version uses the BioPython Phylo objects. It's probably easiest to just call the treekernel binary using Popen.

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[rmcclosk]

Okay, I can write a wrapper around the kernel function which operates on two Newick strings. I'll add it to my todo list.