def __test(self, hmm, seq):
hmm = create_hmm('inputs/' + hmm + '.hmm')
seq = create_seq('inputs/' + seq + '.seq')
xseq = ZipSequence.from_sequence(seq, hmm.state_count)
expect = seq_to_string(seq)
actual = seq_to_string(xseq.iterate_original_sequence())
self.assertEqual(expect, actual)
def test_from_file(self):
seq = create_seq('inputs/test2.seq')
self.assertEqual(20, len(seq))
self.assertEqual(4, seq.alphabet_size)
self.assertEqual('0 2 3 1 0 2 0 2 2 1 0 2 3 0 2 1 0 3 2 1',
seq_to_string(seq))
def test_from_sequence(self):
hmm = create_hmm("inputs/test0.hmm")
seq = create_seq("inputs/test0.seq")
xseq = ZipSequence.from_sequence(seq, hmm.state_count)
self.assertEqual('0 1 4 4', seq_to_string(xseq))
self.assertEqual(5, xseq.alphabet_size)
self.assertEqual(3, xseq.extended_alphabet_size)
self.assertEqual(2, xseq.original_alphabet_size)
self.assertEqual(2, xseq.state_count)
self.assertEqual((3, 3), xseq.get_substitute(4))
self.assertEqual((2, 2), xseq.get_substitute(3))
self.assertEqual((0, 1), xseq.get_substitute(2))
self.assertIsNone(xseq.get_substitute(1))
self.assertEqual('0 1 2 3 4', seq_to_string(xseq.iterate_alphabet()))
self.assertEqual('2 3 4',
seq_to_string(xseq.iterate_extended_alphabet()))
self.assertEqual('0 1',
seq_to_string(xseq.iterate_original_alphabet()))
self.assertEqual('0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1',
seq_to_string(xseq.iterate_original_sequence()))
self.assertEqual(
'2 0 1 ; 3 2 2 ; 4 3 3', ' ; '.join(
map(lambda (a, (b, c)): ' '.join(map(str, [a, b, c])),
xseq.iterate_substitutes())))
def __test(self, hmm, seq):
hmm = create_hmm('inputs/' + hmm + '.hmm')
seq = create_seq('inputs/' + seq + '.seq')
xseq = ZipSequence.from_sequence(seq, hmm.state_count)
expect = seq_to_string(seq)
actual = seq_to_string(xseq.iterate_original_sequence())
self.assertEqual(expect, actual)
def test_from_file(self):
seq = create_seq('inputs/test2.seq')
self.assertEqual(20, len(seq))
self.assertEqual(4, seq.alphabet_size)
self.assertEqual(
'0 2 3 1 0 2 0 2 2 1 0 2 3 0 2 1 0 3 2 1',
seq_to_string(seq))
def __test(self, hmm_name, seq_name, expected_value):
def fix(n, digits=4):
if n is None:
return None
fmt = '{0:.' + str(digits) + 'f}'
return fmt.format(round(n, digits))
hmm = create_hmm('inputs/' + hmm_name + '.hmm')
seq = create_seq('inputs/' + seq_name + '.seq')
actual_value = _mann.evaluate(hmm, seq)
self.assertEqual(fix(expected_value), fix(actual_value))
def __test(self, hmm_name, seq_name, expected_value):
def fix(n, digits=4):
if n is None:
return None
fmt = '{0:.' + str(digits) + 'f}'
return fmt.format(round(n, digits))
hmm = create_hmm('inputs/' + hmm_name + '.hmm')
seq = create_seq('inputs/' + seq_name + '.seq')
actual_value = _mann.evaluate(hmm, seq)
self.assertEqual(fix(expected_value), fix(actual_value))
def __test(self, hmm_name, seq_name, expected_value):
def fix(n, digits=4):
if n is None:
return None
fmt = '{0:.' + str(digits) + 'f}'
return fmt.format(round(n, digits))
hmm = create_hmm('inputs/' + hmm_name + '.hmm')
seq = create_seq('inputs/' + seq_name + '.seq')
xseq = ZipSequence.from_sequence(seq, hmm.state_count)
actual_value = compute_lle(hmm, xseq)
self.assertEqual(fix(expected_value), fix(actual_value))
def __test(self, hmm_name, seq_name, expected_value):
def fix(n, digits=4):
if n is None:
return None
fmt = '{0:.' + str(digits) + 'f}'
return fmt.format(round(n, digits))
hmm = create_hmm('inputs/' + hmm_name + '.hmm')
seq = create_seq('inputs/' + seq_name + '.seq')
xseq = ZipSequence.from_sequence(seq, hmm.state_count)
actual_value = compute_lle(hmm, xseq)
self.assertEqual(fix(expected_value), fix(actual_value))
def __test(self, hmm_name, seq_name, expected_value):
def compute_lle(hmm, seq):
le = _rabiner.evaluate(hmm, seq)
return None if le == 0.0 else math.log(le)
def fix(n, digits=4):
if n is None:
return None
fmt = '{0:.' + str(digits) + 'f}'
return fmt.format(round(n, digits))
hmm = create_hmm('inputs/' + hmm_name + '.hmm')
seq = create_seq('inputs/' + seq_name + '.seq')
actual_value = compute_lle(hmm, seq)
self.assertEqual(fix(expected_value), fix(actual_value))
def __test(self, hmm_name, seq_name, expected_value):
def compute_lle(hmm, seq):
le = _rabiner.evaluate(hmm, seq)
return None if le == 0.0 else math.log(le)
def fix(n, digits=4):
if n is None:
return None
fmt = '{0:.' + str(digits) + 'f}'
return fmt.format(round(n, digits))
hmm = create_hmm('inputs/' + hmm_name + '.hmm')
seq = create_seq('inputs/' + seq_name + '.seq')
actual_value = compute_lle(hmm, seq)
self.assertEqual(fix(expected_value), fix(actual_value))
def test_from_sequence(self):
hmm = create_hmm("inputs/test0.hmm")
seq = create_seq("inputs/test0.seq")
xseq = ZipSequence.from_sequence(seq, hmm.state_count)
self.assertEqual('0 1 4 4', seq_to_string(xseq))
self.assertEqual(5, xseq.alphabet_size)
self.assertEqual(3, xseq.extended_alphabet_size)
self.assertEqual(2, xseq.original_alphabet_size)
self.assertEqual(2, xseq.state_count)
self.assertEqual((3, 3), xseq.get_substitute(4))
self.assertEqual((2, 2), xseq.get_substitute(3))
self.assertEqual((0, 1), xseq.get_substitute(2))
self.assertIsNone(xseq.get_substitute(1))
self.assertEqual(
'0 1 2 3 4',
seq_to_string(xseq.iterate_alphabet()))
self.assertEqual(
'2 3 4',
seq_to_string(xseq.iterate_extended_alphabet()))
self.assertEqual(
'0 1',
seq_to_string(xseq.iterate_original_alphabet()))
self.assertEqual(
'0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1',
seq_to_string(xseq.iterate_original_sequence()))
self.assertEqual(
'2 0 1 ; 3 2 2 ; 4 3 3',
' ; '.join(map(lambda (a, (b, c)): ' '.join(
map(str, [a, b, c])), xseq.iterate_substitutes())))