def test_google_freqs(self):
dist = distance.Distance(self.freqs, 'google')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.6078431 0.3809524',
'seq2 0.6078431 0.0000000 0.3949580',
'seq3 0.3809524 0.3949580 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_euclid_norm_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = distance.Distance(self.freqs, 'euclid_norm')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.3763512 0.2532387',
'seq2 0.3763512 0.0000000 0.2603008',
'seq3 0.2532387 0.2603008 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_euclid_norm_counts(self):
# The result of this method is identical to that from decaf+py.
dist = distance.Distance(self.counts, 'euclid_norm')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 7.5498344 5.4772256',
'seq2 7.5498344 0.0000000 4.3588989',
'seq3 5.4772256 4.3588989 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_euclid_squared_freqs(self):
# The result of this method is identical to that from decaf+py.
dist = distance.Distance(self.freqs, 'euclid_squared')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 0.1416402 0.0641298',
'seq2 0.1416402 0.0000000 0.0677565',
'seq3 0.0641298 0.0677565 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_euclid_squared_counts(self):
# The result of this method is identical to that from decaf+py.
dist = distance.Distance(self.counts, 'euclid_squared')
matrix = distmatrix.create(self.dna_records.id_list, dist)
data = [
' 3', 'seq1 0.0000000 57.0000000 30.0000000',
'seq2 57.0000000 0.0000000 19.0000000',
'seq3 30.0000000 19.0000000 0.0000000'
]
self.assertEqual(matrix.format(), "\n".join(data))
def test_set_disttypes_throws_exception(self):
dist = distance.Distance(self.freqs, 'google')
with self.assertRaises(Exception) as context:
dist.set_disttype('nonexistent')
self.assertIn('unknown disttype', str(context.exception))