def new_nexus_without_sites(nexus_obj, sites_to_remove):
"""
Returns a new NexusReader instance with the sites in
`sites_to_remove` removed.
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param sites_to_remove: A list of site numbers
:type sites_to_remove: List
:return: A NexusWriter 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'])
# make new nexus
nexout = NexusWriter()
nexout.add_comment(
"Removed %d sites: %s" %
(len(sites_to_remove), ",".join(["%s" % s for s in sites_to_remove])))
new_sitepos = 0
for sitepos in range(nexus_obj.data.nchar):
if sitepos in sites_to_remove:
continue # skip!
for taxon, data in nexus_obj.data:
nexout.add(taxon, new_sitepos, data[sitepos])
new_sitepos += 1
return nexout
def find_constant_sites(nexus_obj):
"""
Returns a list of the constant sites in a nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A list of constant site positions.
: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'])
const = []
for i in range(0, nexus_obj.data.nchar):
states = []
for taxa, data in nexus_obj.data:
c = data[i]
if c in ('?', '-'):
continue # pragma: no cover
elif c not in states:
states.append(c)
if len(states) == 1:
const.append(i)
return const
def count_binary_set_size(nexus_obj):
"""
Counts the number of sites by their size (i.e. how many sites have two
members, etc)
Returns a dictionary of the set size and count
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A Dictionary
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
e.g. {
0: 0,
1: 100,
2: 20,
}
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = Counter()
for char_id in nexus_obj.data.characters:
char = nexus_obj.data.characters[char_id]
tally[len([v for v in char.values() if v == '1'])] += 1
return tally
def tally_by_site(nexus_obj):
"""
Counts the number of taxa per state per site (i.e. site 1 has three taxa
coded as "A", and 1 taxa coded as "G")
Returns a dictionary of the cognate sets by members in the nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A Dictionary
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
e.g. {
'site1': {'state1': ['taxon1', 'taxon2'], 'state0': ['taxon3'], }
'site2': {'state1': ['taxon2'], 'state0': ['taxon1', 'taxon3'], }
}
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = {}
for site, data in nexus_obj.data.characters.items():
tally[site] = tally.get(site, {})
for taxon, state in data.items():
tally[site][state] = tally[site].get(state, [])
tally[site][state].append(taxon)
return tally
def find_unique_sites(nexus_obj):
"""
Returns a list of the unique sites in a binary nexus
i.e. sites with only one taxon belonging to them.
(this only really makes sense if the data is coded as presence/absence)
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A list of unique site positions.
: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'])
unique = []
for i in range(0, nexus_obj.data.nchar):
members = {}
missing = 0
for taxa, characters in nexus_obj.data:
c = characters[i]
if c in ('?', '-'):
missing += 1
else:
members[c] = members.get(c, 0) + 1
# a character is unique if there's only two states
# AND there's a state with 1 member
# AND the state with 1 member is NOT the 0 (absence) state
if len(members) == 2:
for state, count in members.items():
if state != '0' and count == 1:
unique.append(i)
return unique
def count_site_values(nexus_obj, characters=('-', '?')):
"""
Counts the number of sites with values in `characters` in a nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param characters: An iterable of the characters to count
:type characters: tuple
:return: (A dictionary of taxa and missing counts, and a log)
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
if not isinstance(characters, Iterable):
raise TypeError("characters should be iterable")
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = {}
for taxon, sites in nexus_obj.data:
tally[taxon] = tally.get(taxon, 0)
for site in sites:
if site in characters:
tally[taxon] += 1
return tally
def count_site_values(nexus_obj, characters=('-', '?')):
"""
Counts the number of sites with values in `characters` in a nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param characters: An iterable of the characters to count
:type characters: tuple
:return: (A dictionary of taxa and missing counts, and a log)
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
if not isinstance(characters, Iterable):
raise TypeError("characters should be iterable")
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = {}
for taxon, sites in nexus_obj.data:
tally[taxon] = tally.get(taxon, 0)
for site in sites:
if site in characters:
tally[taxon] += 1
return tally
def find_unique_sites(nexus_obj):
"""
Returns a list of the unique sites in a binary nexus
i.e. sites with only one taxon belonging to them.
(this only really makes sense if the data is coded as presence/absence)
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A list of unique site positions.
: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'])
unique = []
for i in range(0, nexus_obj.data.nchar):
members = {}
missing = 0
for taxa, characters in nexus_obj.data:
c = characters[i]
if c in ('?', '-'):
missing += 1
else:
members[c] = members.get(c, 0) + 1
# a character is unique if there's only two states
# AND there's a state with 1 member
# AND the state with 1 member is NOT the 0 (absence) state
if len(members) == 2:
for state, count in members.items():
if state != '0' and count == 1:
unique.append(i)
return unique
def find_constant_sites(nexus_obj):
"""
Returns a list of the constant sites in a nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A list of constant site positions.
: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'])
const = []
for i in range(0, nexus_obj.data.nchar):
states = []
for taxa, data in nexus_obj.data:
c = data[i]
if c in ('?', '-'):
continue # pragma: no cover
elif c not in states:
states.append(c)
if len(states) == 1:
const.append(i)
return const
def count_binary_set_size(nexus_obj):
"""
Counts the number of sites by their size (i.e. how many sites have two
members, etc)
Returns a dictionary of the set size and count
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A Dictionary
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
e.g. {
0: 0,
1: 100,
2: 20,
}
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = Counter()
for char_id in nexus_obj.data.characters:
char = nexus_obj.data.characters[char_id]
tally[len([v for v in char.values() if v == '1'])] += 1
return tally
def tally_by_taxon(nexus_obj):
"""
Counts the number of states per site that each taxon has (i.e. taxon 1
has three sites coded as "A" and 1 coded as "G")
Returns a dictionary of the cognate sets by members in the nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A Dictionary
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
e.g. {
'taxon1': {'state1': ['site1', 'site2'], 'state0': ['site3'], }
'taxon2': {'state1': ['site2'], 'state0': ['site1', 'site3'], }
}
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = {}
for taxon, characters in nexus_obj.data:
tally[taxon] = {}
for pos, char in enumerate(characters):
label = nexus_obj.data.charlabels.get(pos, pos)
tally[taxon][char] = tally[taxon].get(char, [])
tally[taxon][char].append(label)
return tally
def tally_by_site(nexus_obj):
"""
Counts the number of taxa per state per site (i.e. site 1 has three taxa
coded as "A", and 1 taxa coded as "G")
Returns a dictionary of the cognate sets by members in the nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A Dictionary
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
e.g. {
'site1': {'state1': ['taxon1', 'taxon2'], 'state0': ['taxon3'], }
'site2': {'state1': ['taxon2'], 'state0': ['taxon1', 'taxon3'], }
}
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = {}
for site, data in nexus_obj.data.characters.items():
tally[site] = tally.get(site, {})
for taxon, state in data.items():
tally[site][state] = tally[site].get(state, [])
tally[site][state].append(taxon)
return tally
def tally_by_taxon(nexus_obj):
"""
Counts the number of states per site that each taxon has (i.e. taxon 1
has three sites coded as "A" and 1 coded as "G")
Returns a dictionary of the cognate sets by members in the nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:return: A Dictionary
:raises AssertionError: if nexus_obj is not a nexus
:raises NexusFormatException: if nexus_obj does not have a `data` block
e.g. {
'taxon1': {'state1': ['site1', 'site2'], 'state0': ['site3'], }
'taxon2': {'state1': ['site2'], 'state0': ['site1', 'site3'], }
}
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
tally = {}
for taxon, characters in nexus_obj.data:
tally[taxon] = {}
for pos, char in enumerate(characters):
label = nexus_obj.data.charlabels.get(pos, pos)
tally[taxon][char] = tally[taxon].get(char, [])
tally[taxon][char].append(label)
return tally
def new_nexus_without_sites(nexus_obj, sites_to_remove):
"""
Returns a new NexusReader instance with the sites in
`sites_to_remove` removed.
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param sites_to_remove: A list of site numbers
:type sites_to_remove: List
:return: A NexusWriter 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'])
# make new nexus
nexout = NexusWriter()
nexout.add_comment(
"Removed %d sites: %s" %
(len(sites_to_remove), ",".join(["%s" % s for s in sites_to_remove]))
)
new_sitepos = 0
for sitepos in range(nexus_obj.data.nchar):
if sitepos in sites_to_remove:
continue # skip!
for taxon, data in nexus_obj.data:
nexout.add(taxon, new_sitepos, data[sitepos])
new_sitepos += 1
return nexout
def binarise(nexus_obj, one_nexus_per_block=False, keep_zero=False):
"""
Returns a binary variant of the given `nexus_obj`.
If `one_nexus_per_block` then we return a list of NexusWriter instances.
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param one_nexus_per_block: Whether to return a single NexusWriter, or a
list of NexusWriter's (one per character)
:type one_nexus_per_block: Boolean
:param keep_zero: A boolean flag denoting whether to
treat '0' as a missing state or not. The default
(False) is to ignore '0' as a trait absence.
Setting this to True will treat '0' as a unique
state.
:type keep_zero: Boolean
:return: A NexusWriter instance or a list of NexusWriter instances.
: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'])
nexuslist = []
n = NexusWriter()
for i in sorted(nexus_obj.data.charlabels):
label = nexus_obj.data.charlabels[i] # character label
char = nexus_obj.data.characters[label] # character dict
recoding = _recode_to_binary(char, keep_zero) # recode
new_char_length = len(recoding[list(recoding.keys())[0]])
# loop over recoded data
for j in range(new_char_length):
for taxon, state in recoding.items():
# make new label
new_label = "%s_%d" % (str(label), j)
# add to nexus
n.add(taxon, new_label, state[j])
if one_nexus_per_block:
nexuslist.append(n)
n = NexusWriter()
if one_nexus_per_block:
return nexuslist
else:
return n
def shufflenexus(nexus_obj, resample=False):
"""
Shuffles the characters between each taxon to create a new nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param resample: The number of characters to resample. If set to False,
then the number of characters will equal the number of characters
in the original data file.
:type resample: Integer
:return: A shuffled NexusReader instance
:raises AssertionError: if nexus_obj is not a nexus
:raises ValueError: if resample is not False or a positive Integer
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
if resample is False:
resample = nexus_obj.data.nchar
try:
resample = int(resample)
except ValueError:
raise ValueError('resample must be a positive integer or False!')
if resample < 1:
raise ValueError('resample must be a positive integer or False!')
newnexus = NexusWriter()
newnexus.add_comment(
"Randomised Nexus generated from %s" % nexus_obj.filename
)
for i in range(resample):
# pick existing character
character = randrange(0, nexus_obj.data.nchar)
chars = nexus_obj.data.characters[character]
site_values = [chars[taxon] for taxon in nexus_obj.data.taxa]
shuffle(site_values)
for taxon in nexus_obj.data.taxa:
newnexus.add(taxon, i, site_values.pop(0))
return newnexus
def shufflenexus(nexus_obj, resample=False):
"""
Shuffles the characters between each taxon to create a new nexus
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param resample: The number of characters to resample. If set to False,
then the number of characters will equal the number of characters
in the original data file.
:type resample: Integer
:return: A shuffled NexusReader instance
:raises AssertionError: if nexus_obj is not a nexus
:raises ValueError: if resample is not False or a positive Integer
:raises NexusFormatException: if nexus_obj does not have a `data` block
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
if resample is False:
resample = nexus_obj.data.nchar
try:
resample = int(resample)
except ValueError:
raise ValueError('resample must be a positive integer or False!')
if resample < 1:
raise ValueError('resample must be a positive integer or False!')
newnexus = NexusWriter()
newnexus.add_comment("Randomised Nexus generated from %s" %
nexus_obj.filename)
for i in range(resample):
# pick existing character
character = randrange(0, nexus_obj.data.nchar)
chars = nexus_obj.data.characters[character]
site_values = [chars[taxon] for taxon in nexus_obj.data.taxa]
shuffle(site_values)
for taxon in nexus_obj.data.taxa:
newnexus.add(taxon, i, site_values.pop(0))
return newnexus
def combine_nexuses(nexuslist):
"""
Combines a list of NexusReader instances into a single nexus
:param nexuslist: A list of NexusReader instances
:type nexuslist: List
:return: A NexusWriter instance
:raises TypeError: if nexuslist is not a list of NexusReader instances
:raises IOError: if unable to read an file in nexuslist
:raises NexusFormatException: if a nexus file does not have a `data` block
"""
out = NexusWriter()
charpos = 0
for nex_id, nex in enumerate(nexuslist, 1):
check_for_valid_NexusReader(nex, required_blocks=['data'])
if hasattr(nex, 'short_filename'):
nexus_label = os.path.splitext(nex.short_filename)[0]
elif hasattr(nex, 'label'):
nexus_label = nex.label
else:
nexus_label = str(nex_id)
out.add_comment(
"%d - %d: %s" %
(charpos, charpos + nex.data.nchar - 1, nexus_label)
)
for site_idx, site in enumerate(sorted(nex.data.characters), 0):
data = nex.data.characters.get(site)
charpos += 1
# work out character label
charlabel = nex.data.charlabels.get(site_idx, site_idx + 1)
label = '%s.%s' % (nexus_label, charlabel)
for taxon, value in data.items():
out.add(taxon, label, value)
return out
def check_zeros(nexus_obj, absences=None, missing=None):
"""
Checks for sites in the nexus that are coded as all empty.
Returns a list of sites that are completely empty. Note that
this is zero-indexed (i.e. the first site is site 0 not 1)
to enable indexing of nexus.data.matrix/.character lists
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param absences: A list of values to be marked as absent.
Default = ["0"]
:type char: list
:param missing: A list of values to be marked as missing.
Default = ["-", "?"]
:type char: list
:return: A list of site indexes
:raises ValueError: if any of the states in the
`char` dictionary is not a string (i.e.
integer or None values)
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
absences = absences if absences else ['0']
missing = missing if missing else ['-', '?']
bad = []
for site_idx in range(0, nexus_obj.data.nchar):
states = Counter([nexus_obj.data.matrix[t][site_idx] for t in nexus_obj.data.matrix])
zeros = sum([
states[k] for k in states if k in absences or k in missing
])
total = sum(states.values())
if zeros == total:
bad.append(site_idx)
return bad
def check_zeros(nexus_obj, absences=None, missing=None):
"""
Checks for sites in the nexus that are coded as all empty.
Returns a list of sites that are completely empty. Note that
this is zero-indexed (i.e. the first site is site 0 not 1)
to enable indexing of nexus.data.matrix/.character lists
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param absences: A list of values to be marked as absent.
Default = ["0"]
:type char: list
:param missing: A list of values to be marked as missing.
Default = ["-", "?"]
:type char: list
:return: A list of site indexes
:raises ValueError: if any of the states in the
`char` dictionary is not a string (i.e.
integer or None values)
"""
check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
absences = absences if absences else ['0']
missing = missing if missing else ['-', '?']
bad = []
for site_idx in range(0, nexus_obj.data.nchar):
states = Counter([nexus_obj.data.matrix[t][site_idx] for t in nexus_obj.data.matrix])
zeros = sum([
states[k] for k in states if k in absences or k in missing
])
total = sum(states.values())
if zeros == total:
bad.append(site_idx)
return bad
def binarise(nexus_obj, keep_zero=False):
"""
Returns a binary variant of the given `nexus_obj`.
If `one_nexus_per_block` then we return a list of NexusWriter instances.
:param nexus_obj: A `NexusReader` instance
:type nexus_obj: NexusReader
:param keep_zero: A boolean flag denoting whether to
treat '0' as a missing state or not. The default
(False) is to ignore '0' as a trait absence.
Setting this to True will treat '0' as a unique
state.
:type keep_zero: Boolean
:return: A NexusWriter instance or a list of NexusWriter instances.
: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'])
n = NexusWriter()
for i in sorted(nexus_obj.data.charlabels):
label = nexus_obj.data.charlabels[i] # character label
char = nexus_obj.data.characters[label] # character dict
recoding = _recode_to_binary(char, keep_zero) # recode
new_char_length = len(recoding[list(recoding.keys())[0]])
# loop over recoded data
for j in range(new_char_length):
for taxon, state in recoding.items():
# make new label
new_label = "%s_%d" % (str(label), j)
# add to nexus
n.add(taxon, new_label, state[j])
return n
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()
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 not states[taxon]:
nexout.add(taxon, charlabel, '?')
else:
for s in states[taxon]:
nexout.add(taxon, charlabel, s)
return nexout._convert_to_reader()
def combine_nexuses(nexuslist):
"""
Combines a list of NexusReader instances into a single nexus
:param nexuslist: A list of NexusReader instances
:type nexuslist: List
:return: A NexusWriter instance
:raises TypeError: if nexuslist is not a list of NexusReader instances
:raises IOError: if unable to read an file in nexuslist
:raises NexusFormatException: if a nexus file does not have a `data` block
"""
out = NexusWriter()
charpos = 0
for nex_id, nex in enumerate(nexuslist, 1):
check_for_valid_NexusReader(nex, required_blocks=['data'])
if hasattr(nex, 'short_filename'):
nexus_label = os.path.splitext(nex.short_filename)[0]
else:
nexus_label = str(nex_id)
out.add_comment("%d - %d: %s" %
(charpos, charpos + nex.data.nchar - 1, nexus_label))
for site_idx, site in enumerate(sorted(nex.data.characters), 0):
data = nex.data.characters.get(site)
charpos += 1
# work out character label
charlabel = nex.data.charlabels.get(site_idx, site_idx + 1)
label = '%s.%s' % (nexus_label, charlabel)
for taxon, value in data.items():
out.add(taxon, label, value)
return out
def test_failure_on_required_block_two(self):
nexus_obj = NexusReader(os.path.join(EXAMPLE_DIR, 'example2.nex'))
with self.assertRaises(NexusFormatException):
check_for_valid_NexusReader(nexus_obj, ['r8s'])
def test_valid_with_required_block_two(self):
nexus_obj = NexusReader(os.path.join(EXAMPLE_DIR, 'example2.nex'))
check_for_valid_NexusReader(nexus_obj, ['data', 'taxa'])
def test_valid_with_required_block_two(self):
nexus_obj = NexusReader(os.path.join(EXAMPLE_DIR, 'example2.nex'))
check_for_valid_NexusReader(nexus_obj, ['data', 'taxa'])
def test_failure_on_required_block_two(self):
nexus_obj = NexusReader(os.path.join(EXAMPLE_DIR, 'example2.nex'))
with self.assertRaises(NexusFormatException):
check_for_valid_NexusReader(nexus_obj, ['r8s'])
def test_valid_NexusReader(self):
check_for_valid_NexusReader(NexusReader())
def test_valid_NexusReader(self):
check_for_valid_NexusReader(NexusReader())
