reads an opentree summary tree annotated_supertree/annotations.json file and reports on the taxonomy-only nodes

find-taxonomy-only-from-annotations.py

#!/usr/bin/env python
import sys
try:
    annot_fp = sys.argv[1]
except:
    sys.exit("Expecting a path to an annotations.json file as the only argument.\n")
import json
import codecs
with codecs.open(annot_fp, 'rU', encoding='utf-8') as inp:
    obj = json.load(inp)
    nd_list = obj["nodes"]
    nabsent = 0
    for node_id, nd in nd_list.items():
        sb = nd.get("supported_by")
        if sb is None:
            nabsent += 1
            sys.stderr.write("taxonomy-only {}\n".format(node_id))
sys.stdout.write("{} taxonomy-only nodes\n".format(nabsent))

Note that this only reports on taxonomy-only internals. Thanks to @hyanwong for pointing that out!
See https://gist.github.com/mtholder/dc9c225dcda9a1d93859065d2245ecd0