out = codecs.open(outfn, mode='w', encoding='utf-8')
except:
sys.exit('validate_ot_nexson: Could not open output filepath "{fn}"\n'.format(fn=outfn))
else:
out = codecs.getwriter('utf-8')(sys.stdout)
try:
nexson = read_as_json(inp_filepath)
except ValueError as vx:
_LOG.error('Not valid JSON.')
if args.verbose:
raise vx
else:
sys.exit(1)
except Exception as nx:
_LOG.error(nx.value)
sys.exit(1)
convert_nexson_format(nexson, BY_ID_HONEY_BADGERFISH)
trees = extract_tree_nexson(nexson, tree_id=args.tree_id)
if len(trees) == 0:
trees = extract_tree_nexson(nexson, tree_id=None)
if trees:
v = '", "'.join([i[0] for i in trees])
sys.exit('Tree ID {i} not found. Valid IDs for this file are "{l}"\n'.format(i=args.tree_id, l=v))
else:
sys.exit('This NexSON has not trees.\n')
ott = OTT()
for tree_id, tree, otus in trees:
tree_proxy = NexsonTreeProxy(tree=tree, tree_id=tree_id, otus=otus)
evaluate_tree_rooting(nexson, ott, tree_proxy)
def testTaxoRooting(self):
ott = OTT()
phylo = self.np.get_tree(tree_id='tree324')
evaluate_tree_rooting(self.nexson, ott, phylo)
def testTaxoRooting(self):
ott = OTT()
phylo = self.np.get_tree(tree_id='tree324')
evaluate_tree_rooting(self.nexson, ott, phylo)