def test_notimplemented_exception(self):
with self.assertRaises(NotImplementedError):
nex = NexusReader()
nex.read_string("""Begin something;
Dimensions ntax=5 nchar=1;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 1
;""")
anonymise(nex)
def test_notimplemented_exception(self):
with self.assertRaises(NotImplementedError):
nex = NexusReader()
nex.read_string(
"""Begin something;
Dimensions ntax=5 nchar=1;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 1
;""")
anonymise(nex)
def test_anonymise_data_with_interleave(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example3.nex'))
nex = anonymise(nex)
for old_taxon in ['Harry', 'Simon']:
assert old_taxon not in nex.data.matrix, '%s should have been anonymised' % old_taxon
assert nex.data.matrix['6eb7148a2d4155085e517979410b9f23'] == ['0', '1', '2', '3', '4', '5']
assert nex.data.matrix['698de77f637e7fae18ead22f2172102a'] == ['0', '1', '2', '3', '4', '5']
def test_anonymise_translated_trees(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example-translated.trees'))
nex = anonymise(nex)
expected = ['Chris', 'Bruce', 'Tom', 'Henry', 'Timothy', 'Mark', 'Simon', 'Fred', 'Kevin', 'Roger', 'Michael', 'Andrew', 'David']
assert len(nex.trees.taxa) == len(expected)
for taxon in expected:
hashtaxon = hash(os.path.join(EXAMPLE_DIR, 'example-translated.trees'), taxon)
assert hashtaxon in nex.trees.taxa
def test_anonymise_data(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
nex = anonymise(nex)
for old_taxon in ['Harry', 'Simon', 'Betty', 'Louise']:
assert old_taxon not in nex.data.matrix, '%s should have been anonymised' % old_taxon
assert nex.data.matrix['894a76c65225a9812d31ff75edf38feb'] == ['1', '0']
assert nex.data.matrix['a0434190848c0d64332dce12a8a27961'] == ['0', '0']
assert nex.data.matrix['bbf0da40d536d862e184a6eccb433a73'] == ['0', '1']
assert nex.data.matrix['d24eb4091c14b87b6cd0bd94fd0704be'] == ['1', '1']
def test_anonymise_data_with_interleave(self):
filename = os.path.join(EXAMPLE_DIR, 'example3.nex')
nex = anonymise(NexusReader(filename), salt="test")
for old_taxon in ['Harry', 'Simon']:
assert old_taxon not in nex.data.matrix, \
'%s should have been anonymised' % old_taxon
h = hash("test", old_taxon)
assert h in nex.data.matrix
assert h in nex.data.taxa
assert nex.data.matrix[h] == ['0', '1', '2', '3', '4', '5']
def test_anonymise_data_with_interleave(self):
filename = os.path.join(EXAMPLE_DIR, 'example3.nex')
nex = anonymise(NexusReader(filename), salt="test")
for old_taxon in ['Harry', 'Simon']:
assert old_taxon not in nex.data.matrix, \
'%s should have been anonymised' % old_taxon
h = hash("test", old_taxon)
assert h in nex.data.matrix
assert h in nex.data.taxa
assert nex.data.matrix[h] == ['0', '1', '2', '3', '4', '5']
def test_anonymise_data_with_labels(self):
filename = os.path.join(EXAMPLE_DIR, 'example2.nex')
nex = anonymise(NexusReader(filename), salt="test")
for old_taxon in ['John', 'Paul', 'George', 'Ringo']:
assert old_taxon not in nex.data.matrix, \
'%s should have been anonymised' % old_taxon
h = hash("test", old_taxon)
# check data block
assert h in nex.data.matrix, "Missing %s" % h
assert nex.data.matrix[h] == ['a', 'c', 't', 'g']
# check taxa block
assert h in nex.taxa.taxa
def test_anonymise_data_with_labels(self):
filename = os.path.join(EXAMPLE_DIR, 'example2.nex')
nex = anonymise(NexusReader(filename), salt="test")
for old_taxon in ['John', 'Paul', 'George', 'Ringo']:
assert old_taxon not in nex.data.matrix, \
'%s should have been anonymised' % old_taxon
h = hash("test", old_taxon)
# check data block
assert h in nex.data.matrix, "Missing %s" % h
assert nex.data.matrix[h] == ['a', 'c', 't', 'g']
# check taxa block
assert h in nex.taxa.taxa
def test_anonymise_taxa(self):
filename = os.path.join(EXAMPLE_DIR, 'example.nex')
nex = anonymise(NexusReader(filename), salt="test")
for old_taxon in ['Harry', 'Simon', 'Betty', 'Louise']:
assert old_taxon not in nex.data.matrix, \
'%s should have been anonymised' % old_taxon
assert nex.data.matrix[hash("test", "Betty")] == \
['1', '0']
assert nex.data.matrix[hash("test", "Harry")] == \
['0', '0']
assert nex.data.matrix[hash("test", "Simon")] == \
['0', '1']
assert nex.data.matrix[hash("test", "Louise")] == \
['1', '1']
def test_anonymise_taxa(self):
filename = os.path.join(EXAMPLE_DIR, 'example.nex')
nex = anonymise(NexusReader(filename), salt="test")
for old_taxon in ['Harry', 'Simon', 'Betty', 'Louise']:
assert old_taxon not in nex.data.matrix, \
'%s should have been anonymised' % old_taxon
assert nex.data.matrix[hash("test", "Betty")] == \
['1', '0']
assert nex.data.matrix[hash("test", "Harry")] == \
['0', '0']
assert nex.data.matrix[hash("test", "Simon")] == \
['0', '1']
assert nex.data.matrix[hash("test", "Louise")] == \
['1', '1']
def test_anonymise_characters(self):
filename = os.path.join(EXAMPLE_DIR, 'example-characters.nex')
nex = anonymise(NexusReader(filename), salt="test")
expected_taxa = ['A', 'B', 'C', 'D', 'E']
for taxon in expected_taxa:
h = hash("test", taxon)
# check taxa block
assert taxon not in nex.taxa.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.taxa.taxa
# check characters block
assert taxon not in nex.data.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.data.taxa
def test_anonymise_characters(self):
filename = os.path.join(EXAMPLE_DIR, 'example-characters.nex')
nex = anonymise(NexusReader(filename), salt="test")
expected_taxa = ['A', 'B', 'C', 'D', 'E']
for taxon in expected_taxa:
h = hash("test", taxon)
# check taxa block
assert taxon not in nex.taxa.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.taxa.taxa
# check characters block
assert taxon not in nex.data.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.data.taxa
def test_anonymise_characters(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example-characters.nex'))
nex = anonymise(nex)
expected_taxa = ['A', 'B', 'C', 'D', 'E']
# check taxa block
for taxon in expected_taxa:
assert taxon not in nex.taxa.taxa, '%s should have been anonymised' % taxon
hashtaxon = hash(os.path.join(EXAMPLE_DIR, 'example-characters.nex'), taxon)
assert hashtaxon in nex.taxa.taxa
# check characters block
for taxon in expected_taxa:
assert taxon not in nex.data.taxa, '%s should have been anonymised' % taxon
hashtaxon = hash(os.path.join(EXAMPLE_DIR, 'example-characters.nex'), taxon)
assert hashtaxon in nex.data.taxa
def test_anonymise_data_with_labels(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example2.nex'))
nex = anonymise(nex)
for old_taxon in ['John', 'Paul', 'George', 'Ringo']:
assert old_taxon not in nex.data.matrix, '%s should have been anonymised' % old_taxon
# check data block
assert nex.data.matrix['e5b17eef97cc46782008af612450c650'] == ['a', 'c', 't', 'g']
assert nex.data.matrix['fc38854f2edead0c7a799a35de58bd60'] == ['a', 'c', 't', 'g']
assert nex.data.matrix['c12b8557f6be8a49aef5fcee99c40724'] == ['a', 'c', 't', 'g']
assert nex.data.matrix['de57ceacb7eb62511210794be2cff5ab'] == ['a', 'c', 't', 'g']
# check taxa block
assert 'e5b17eef97cc46782008af612450c650' in nex.taxa.taxa
assert 'fc38854f2edead0c7a799a35de58bd60' in nex.taxa.taxa
assert 'c12b8557f6be8a49aef5fcee99c40724' in nex.taxa.taxa
assert 'de57ceacb7eb62511210794be2cff5ab' in nex.taxa.taxa
def test_anonymise_beast_treefile(self):
filename = os.path.join(EXAMPLE_DIR, 'example-beast.trees')
nex = anonymise(NexusReader(filename), salt="test")
expected = [
"R1", "B2", "S3", "T4", "A5", "E6", "U7", "T8", "T9", "F10", "U11",
"T12", "N13", "F14", "K15", "N16", "I17", "L18", "S19", "T20",
"V21", "R22", "M23", "H24", "M25", "M26", "M27", "R28", "T29",
"M30", "P31", "T32", "R33", "P34", "R35", "W36", "F37", "F38"
]
for taxon in expected:
h = hash("test", taxon)
# check taxa block
assert taxon not in nex.taxa.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.taxa.taxa
# check trees block
assert taxon not in nex.trees.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.trees.taxa
def test_anonymise_beast_treefile(self):
filename = os.path.join(EXAMPLE_DIR, 'example-beast.trees')
nex = anonymise(NexusReader(filename), salt="test")
expected = [
"R1", "B2", "S3", "T4", "A5", "E6", "U7", "T8", "T9", "F10", "U11",
"T12", "N13", "F14", "K15", "N16", "I17", "L18", "S19", "T20",
"V21", "R22", "M23", "H24", "M25", "M26", "M27", "R28", "T29",
"M30", "P31", "T32", "R33", "P34", "R35", "W36", "F37", "F38"
]
for taxon in expected:
h = hash("test", taxon)
# check taxa block
assert taxon not in nex.taxa.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.taxa.taxa
# check trees block
assert taxon not in nex.trees.taxa, \
'%s should have been anonymised' % taxon
assert h in nex.trees.taxa
def test_anonymise_beast_treefile(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example-beast.trees'))
nex = anonymise(nex)
expected = [
"R1", "B2", "S3", "T4", "A5", "E6", "U7", "T8", "T9", "F10", "U11",
"T12", "N13", "F14", "K15", "N16", "I17", "L18", "S19", "T20", "V21",
"R22", "M23", "H24", "M25", "M26", "M27", "R28", "T29", "M30", "P31",
"T32", "R33", "P34", "R35", "W36", "F37", "F38"
]
# check taxa block
for taxon in expected:
assert taxon not in nex.taxa.taxa, '%s should have been anonymised' % taxon
hashtaxon = hash(os.path.join(EXAMPLE_DIR, 'example-beast.trees'), taxon)
assert hashtaxon in nex.taxa.taxa
# check trees block
for taxon in expected:
assert taxon not in nex.trees.taxa, '%s should have been anonymised' % taxon
hashtaxon = hash(os.path.join(EXAMPLE_DIR, 'example-beast.trees'), taxon)
assert hashtaxon in nex.trees.taxa
def test_notimplemented_exception_untranslated_trees(self):
with self.assertRaises(NotImplementedError):
anonymise(NexusReader(os.path.join(EXAMPLE_DIR, 'example.trees')))
def test_notimplemented_exception_untranslated_trees(self):
with self.assertRaises(NotImplementedError):
anonymise(NexusReader(os.path.join(EXAMPLE_DIR, 'example.trees')))