def multistatise(nexus_obj, charlabel=None):
"""
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
"""
charlabel = charlabel or getattr(nexus_obj, 'short_filename', 1) or 1
states = {}
for taxon in nexus_obj.data.matrix:
states[taxon] = []
sequence = nexus_obj.data.matrix[taxon]
for site_idx, value in enumerate(sequence):
if site_idx > 26:
raise ValueError(
"Too many characters to handle! - run out of A-Z")
assert value == str(value), "%r is not a string" % value
if value == '1':
states[taxon].append(chr(65 + site_idx))
nexout = NexusWriter()
for taxon in states:
if not states[taxon]:
nexout.add(taxon, charlabel, '?')
else:
for s in states[taxon]:
nexout.add(taxon, charlabel, s)
return nexout._convert_to_reader()
def multistatise(nexus_obj, charlabel=None):
"""
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'])
if not charlabel:
charlabel = getattr(nexus_obj, 'short_filename', 1)
states = {}
for taxon in nexus_obj.data.matrix:
states[taxon] = []
sequence = nexus_obj.data.matrix[taxon]
for site_idx, value in enumerate(sequence):
if site_idx > 26:
raise ValueError(
"Too many characters to handle! - run out of A-Z"
)
assert value == str(value), "%r is not a string" % value
if value == '1':
states[taxon].append(chr(65 + site_idx))
nexout = NexusWriter()
for taxon in states:
if len(states[taxon]) == 0:
nexout.add(taxon, charlabel, '?')
else:
for s in states[taxon]:
nexout.add(taxon, charlabel, s)
return nexout._convert_to_reader()
