No nexus reading/writing

[hyanwong]

The README mentions NEXUS, but there are no functions that help to read or write this format in this repo.

However, you can grab the newick(s) from within the nexus and convert them using

with open("myfile.nexus") as nex:
    tags = "begin trees;", "end;"
    newicks = None
    for line in nex:
        line = line.strip()
        if newicks is not None:
            if line[:len(tags[1])].lower().startswith(tags[1]):
                break
            p = line.find("=")
            if p >= 0:
                newicks[line[:p].strip()] = line[p+1:] if line.endswith(";") else f"{line[p+1:]};"
        elif line[:len(tags[0])].lower().startswith(tags[0]):
            newicks = {}

tree_seqs = {k: tsconvert.from_newick(line, min_edge_length=1e-10) for k, line in newicks.items()}