def multistatise(nexus_obj):
"""
Returns a multistate variant of the given `nexus_obj`.
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A NexusReader instance
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
site_idx = 0
nexout = NexusWriter()
missing = []
charlabel = getattr(nexus_obj, 'short_filename', 1)
for site, data in nexus_obj.data.characters.items():
multistate_value = chr(65 + site_idx)
for taxon, value in data.items():
assert value == str(value)
if value in ('?', '-'):
missing.append(taxon)
if value == '1':
nexout.add(taxon, charlabel, multistate_value)
if taxon in missing: # remove taxon if we've seen a non-? entry
missing.remove(taxon)
site_idx += 1
assert site_idx < 26, "Too many characters to handle! - run out of A-Z"
# add missing state for anything that is all missing, and has not been
# observed anywhere
for taxon in nexus_obj.data.taxa:
if taxon not in nexout.data[str(charlabel)]:
nexout.add(taxon, charlabel, '?')
return nexout._convert_to_reader()
