def hamming_distance(s1, s2):
s1 = BiologicalSequence(s1)
s2 = BiologicalSequence(s2)
return s1.distance(s2)
class BiologicalSequenceTests(TestCase):
def setUp(self):
self.b1 = BiologicalSequence('GATTACA')
self.b2 = BiologicalSequence(
'ACCGGTACC', id="test-seq-2",
description="A test sequence")
self.b3 = BiologicalSequence(
'GREG', id="test-seq-3", description="A protein sequence")
self.b4 = BiologicalSequence(
'PRTEIN', id="test-seq-4")
self.b5 = BiologicalSequence(
'LLPRTEIN', description="some description")
self.b6 = BiologicalSequence('ACGTACGTACGT')
self.b7 = BiologicalSequence('..--..')
self.b8 = BiologicalSequence('HE..--..LLO')
def test_init_varied_input(self):
# init as string
b = BiologicalSequence('ACCGGXZY')
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "")
self.assertEqual(b.description, "")
# init as string with optional values
b = BiologicalSequence(
'ACCGGXZY', 'test-seq-1', 'The first test sequence')
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "test-seq-1")
self.assertEqual(b.description, "The first test sequence")
# test init as a different string
b = BiologicalSequence('WRRTY')
self.assertEqual(str(b), 'WRRTY')
# init as list
b = BiologicalSequence(list('ACCGGXZY'))
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "")
self.assertEqual(b.description, "")
# init as tuple
b = BiologicalSequence(tuple('ACCGGXZY'))
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "")
self.assertEqual(b.description, "")
def test_init_with_validation(self):
self.assertRaises(BiologicalSequenceError, BiologicalSequence, "ACC",
validate=True)
try:
# no error raised when only allow characters are passed
BiologicalSequence("..--..", validate=True)
except BiologicalSequenceError:
self.assertTrue(False)
def test_contains(self):
self.assertTrue('G' in self.b1)
self.assertFalse('g' in self.b1)
def test_eq(self):
self.assertTrue(self.b1 == self.b1)
self.assertTrue(self.b2 == self.b2)
self.assertTrue(self.b3 == self.b3)
self.assertTrue(self.b1 != self.b3)
self.assertTrue(self.b1 != self.b2)
self.assertTrue(self.b2 != self.b3)
# identicial sequences of the same type are equal, even if they have
# different ids and/or descriptions
self.assertTrue(
BiologicalSequence('ACGT') == BiologicalSequence('ACGT'))
self.assertTrue(
BiologicalSequence('ACGT', id='a') ==
BiologicalSequence('ACGT', id='b'))
self.assertTrue(
BiologicalSequence('ACGT', description='c') ==
BiologicalSequence('ACGT', description='d'))
self.assertTrue(
BiologicalSequence('ACGT', id='a', description='c') ==
BiologicalSequence('ACGT', id='b', description='d'))
# different type causes sequences to not be equal
self.assertFalse(
BiologicalSequence('ACGT') == NucleotideSequence('ACGT'))
def test_getitem(self):
self.assertEqual(self.b1[0], BiologicalSequence('G'))
self.assertEqual(self.b1[:], BiologicalSequence('GATTACA'))
self.assertEqual(self.b1[::-1], BiologicalSequence('ACATTAG'))
def test_getitem_out_of_range(self):
with self.assertRaises(IndexError):
self.b1[42]
def test_hash(self):
self.assertTrue(isinstance(hash(self.b1), int))
def test_iter(self):
b1_iter = iter(self.b1)
for actual, expected in zip(b1_iter, "GATTACA"):
self.assertEqual(actual, expected)
self.assertRaises(StopIteration, lambda: next(b1_iter))
def test_k_words(self):
# overlapping = True
self.assertEqual(list(self.b1.k_words(1, overlapping=True)),
['G', 'A', 'T', 'T', 'A', 'C', 'A'])
self.assertEqual(list(self.b1.k_words(2, overlapping=True)),
['GA', 'AT', 'TT', 'TA', 'AC', 'CA'])
self.assertEqual(list(self.b1.k_words(3, overlapping=True)),
['GAT', 'ATT', 'TTA', 'TAC', 'ACA'])
self.assertEqual(list(self.b1.k_words(7, overlapping=True)),
['GATTACA'])
self.assertEqual(list(self.b1.k_words(8, overlapping=True)),
[])
# overlapping = False
self.assertEqual(list(self.b1.k_words(1, overlapping=True)),
['G', 'A', 'T', 'T', 'A', 'C', 'A'])
self.assertEqual(list(self.b1.k_words(2, overlapping=False)),
['GA', 'TT', 'AC'])
self.assertEqual(list(self.b1.k_words(3, overlapping=False)),
['GAT', 'TAC'])
self.assertEqual(list(self.b1.k_words(7, overlapping=False)),
['GATTACA'])
self.assertEqual(list(self.b1.k_words(8, overlapping=False)),
[])
# error on invalid k
self.assertRaises(ValueError, list, self.b1.k_words(0))
self.assertRaises(ValueError, list, self.b1.k_words(-42))
# tests with different sequences
self.assertEqual(list(self.b8.k_words(3, overlapping=False)),
['HE.', '.--', '..L'])
b = BiologicalSequence('')
self.assertEqual(list(b.k_words(3)), [])
def test_k_word_counts(self):
# overlapping = True
expected = Counter('GATTACA')
self.assertEqual(self.b1.k_word_counts(1, overlapping=True),
expected)
expected = Counter(['GAT', 'ATT', 'TTA', 'TAC', 'ACA'])
self.assertEqual(self.b1.k_word_counts(3, overlapping=True),
expected)
# overlapping = False
expected = Counter(['GAT', 'TAC'])
self.assertEqual(self.b1.k_word_counts(3, overlapping=False),
expected)
expected = Counter(['GATTACA'])
self.assertEqual(self.b1.k_word_counts(7, overlapping=False),
expected)
def test_k_word_frequencies(self):
# overlapping = True
expected = defaultdict(int)
expected['A'] = 3/7.
expected['C'] = 1/7.
expected['G'] = 1/7.
expected['T'] = 2/7.
self.assertEqual(self.b1.k_word_frequencies(1, overlapping=True),
expected)
expected = defaultdict(int)
expected['GAT'] = 1/5.
expected['ATT'] = 1/5.
expected['TTA'] = 1/5.
expected['TAC'] = 1/5.
expected['ACA'] = 1/5.
self.assertEqual(self.b1.k_word_frequencies(3, overlapping=True),
expected)
# overlapping = False
expected = defaultdict(int)
expected['GAT'] = 1/2.
expected['TAC'] = 1/2.
self.assertEqual(self.b1.k_word_frequencies(3, overlapping=False),
expected)
expected = defaultdict(int)
expected['GATTACA'] = 1.0
self.assertEqual(self.b1.k_word_frequencies(7, overlapping=False),
expected)
expected = defaultdict(int)
empty = BiologicalSequence('')
self.assertEqual(empty.k_word_frequencies(1, overlapping=False),
expected)
def test_len(self):
self.assertEqual(len(self.b1), 7)
self.assertEqual(len(self.b2), 9)
self.assertEqual(len(self.b3), 4)
def test_repr(self):
self.assertEqual(repr(self.b1),
"<BiologicalSequence: GATTACA (length: 7)>")
self.assertEqual(repr(self.b6),
"<BiologicalSequence: ACGTACGTAC... (length: 12)>")
def test_reversed(self):
b1_reversed = reversed(self.b1)
for actual, expected in zip(b1_reversed, "ACATTAG"):
self.assertEqual(actual, expected)
self.assertRaises(StopIteration, lambda: next(b1_reversed))
def test_str(self):
self.assertEqual(str(self.b1), "GATTACA")
self.assertEqual(str(self.b2), "ACCGGTACC")
self.assertEqual(str(self.b3), "GREG")
def test_alphabet(self):
self.assertEqual(self.b1.alphabet(), set())
def test_description(self):
self.assertEqual(self.b1.description, "")
self.assertEqual(self.b2.description, "A test sequence")
self.assertEqual(self.b3.description, "A protein sequence")
def test_gap_alphabet(self):
self.assertEqual(self.b1.gap_alphabet(), set('-.'))
def test_id(self):
self.assertEqual(self.b1.id, "")
self.assertEqual(self.b2.id, "test-seq-2")
self.assertEqual(self.b3.id, "test-seq-3")
def test_count(self):
self.assertEqual(self.b1.count('A'), 3)
self.assertEqual(self.b1.count('T'), 2)
self.assertEqual(self.b1.count('TT'), 1)
def test_degap(self):
self.assertEqual(self.b1.degap(), self.b1)
self.assertEqual(self.b7.degap(), BiologicalSequence(''))
self.assertEqual(self.b8.degap(), BiologicalSequence('HELLO'))
def test_distance(self):
# note that test_hamming_distance covers default behavior more
# extensively
self.assertEqual(self.b1.distance(self.b1), 0.0)
self.assertEqual(self.b1.distance(BiologicalSequence('GATTACC')), 1./7)
def dumb_distance(x, y):
return 42
self.assertEqual(
self.b1.distance(self.b1, distance_fn=dumb_distance), 42)
def test_distance_unequal_length(self):
# Hamming distance (default) requires that sequences are of equal
# length
with self.assertRaises(BiologicalSequenceError):
self.b1.distance(self.b2)
# alternate distance functions don't have that requirement (unless
# it's implemented within the provided distance function)
def dumb_distance(x, y):
return 42
self.assertEqual(
self.b1.distance(self.b2, distance_fn=dumb_distance), 42)
def test_fraction_diff(self):
self.assertEqual(self.b1.fraction_diff(self.b1), 0., 5)
self.assertEqual(
self.b1.fraction_diff(BiologicalSequence('GATTACC')), 1. / 7., 5)
def test_fraction_same(self):
self.assertAlmostEqual(self.b1.fraction_same(self.b1), 1., 5)
self.assertAlmostEqual(
self.b1.fraction_same(BiologicalSequence('GATTACC')), 6. / 7., 5)
def test_gap_maps(self):
# in sequence with no gaps, the gap_maps are identical
self.assertEqual(self.b1.gap_maps(),
([0, 1, 2, 3, 4, 5, 6], [0, 1, 2, 3, 4, 5, 6]))
# in sequence with all gaps, the map of degapped to gapped is the empty
# list (bc its length is 0), and the map of gapped to degapped is all
# None
self.assertEqual(self.b7.gap_maps(),
([], [None, None, None, None, None, None]))
self.assertEqual(self.b8.gap_maps(),
([0, 1, 8, 9, 10],
[0, 1, None, None, None, None, None, None, 2, 3, 4]))
# example from the gap_maps doc string
self.assertEqual(BiologicalSequence('-ACCGA-TA-').gap_maps(),
([1, 2, 3, 4, 5, 7, 8],
[None, 0, 1, 2, 3, 4, None, 5, 6, None]))
def test_gap_vector(self):
self.assertEqual(self.b1.gap_vector(),
[False] * len(self.b1))
self.assertEqual(self.b7.gap_vector(),
[True] * len(self.b7))
self.assertEqual(self.b8.gap_vector(),
[False, False, True, True, True, True,
True, True, False, False, False])
def test_unsupported_characters(self):
self.assertEqual(self.b1.unsupported_characters(), set('GATC'))
self.assertEqual(self.b7.unsupported_characters(), set())
def test_has_unsupported_characters(self):
self.assertTrue(self.b1.has_unsupported_characters())
self.assertFalse(self.b7.has_unsupported_characters())
def test_index(self):
""" index functions as expected """
self.assertEqual(self.b1.index('G'), 0)
self.assertEqual(self.b1.index('A'), 1)
self.assertEqual(self.b1.index('AC'), 4)
self.assertRaises(ValueError, self.b1.index, 'x')
def test_is_gap(self):
self.assertTrue(self.b1.is_gap('.'))
self.assertTrue(self.b1.is_gap('-'))
self.assertFalse(self.b1.is_gap('A'))
self.assertFalse(self.b1.is_gap('x'))
self.assertFalse(self.b1.is_gap(' '))
self.assertFalse(self.b1.is_gap(''))
def test_is_gapped(self):
self.assertFalse(self.b1.is_gapped())
self.assertFalse(self.b2.is_gapped())
self.assertTrue(self.b7.is_gapped())
self.assertTrue(self.b8.is_gapped())
def test_is_valid(self):
self.assertFalse(self.b1.is_valid())
self.assertTrue(self.b7.is_valid())
def test_to_fasta(self):
self.assertEqual(self.b1.to_fasta(), ">\nGATTACA\n")
self.assertEqual(self.b1.to_fasta(terminal_character=""), ">\nGATTACA")
self.assertEqual(self.b2.to_fasta(),
">test-seq-2 A test sequence\nACCGGTACC\n")
self.assertEqual(self.b3.to_fasta(),
">test-seq-3 A protein sequence\nGREG\n")
self.assertEqual(self.b4.to_fasta(),
">test-seq-4\nPRTEIN\n")
self.assertEqual(self.b5.to_fasta(),
"> some description\nLLPRTEIN\n")
# alt parameters
self.assertEqual(self.b2.to_fasta(field_delimiter=":"),
">test-seq-2:A test sequence\nACCGGTACC\n")
self.assertEqual(self.b2.to_fasta(terminal_character="!"),
">test-seq-2 A test sequence\nACCGGTACC!")
self.assertEqual(
self.b2.to_fasta(field_delimiter=":", terminal_character="!"),
">test-seq-2:A test sequence\nACCGGTACC!")
def test_upper(self):
b = NucleotideSequence('GAt.ACa-', id='x', description='42')
expected = NucleotideSequence('GAT.ACA-', id='x',
description='42')
self.assertEqual(b.upper(), expected)
def test_lower(self):
b = NucleotideSequence('GAt.ACa-', id='x', description='42')
expected = NucleotideSequence('gat.aca-', id='x',
description='42')
self.assertEqual(b.lower(), expected)
def hamming_distance(s1, s2):
s1 = BiologicalSequence(s1)
s2 = BiologicalSequence(s2)
return s1.distance(s2)
class BiologicalSequenceTests(TestCase):
def setUp(self):
self.b1 = BiologicalSequence('GATTACA')
self.b2 = BiologicalSequence('ACCGGTACC',
id="test-seq-2",
description="A test sequence")
self.b3 = BiologicalSequence('GREG',
id="test-seq-3",
description="A protein sequence")
self.b4 = BiologicalSequence('PRTEIN', id="test-seq-4")
self.b5 = BiologicalSequence('LLPRTEIN',
description="some description")
self.b6 = BiologicalSequence('ACGTACGTACGT')
self.b7 = BiologicalSequence('..--..')
self.b8 = BiologicalSequence('HE..--..LLO')
def test_init_varied_input(self):
# init as string
b = BiologicalSequence('ACCGGXZY')
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "")
self.assertEqual(b.description, "")
# init as string with optional values
b = BiologicalSequence('ACCGGXZY', 'test-seq-1',
'The first test sequence')
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "test-seq-1")
self.assertEqual(b.description, "The first test sequence")
# test init as a different string
b = BiologicalSequence('WRRTY')
self.assertEqual(str(b), 'WRRTY')
# init as list
b = BiologicalSequence(list('ACCGGXZY'))
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "")
self.assertEqual(b.description, "")
# init as tuple
b = BiologicalSequence(tuple('ACCGGXZY'))
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.id, "")
self.assertEqual(b.description, "")
def test_init_with_validation(self):
self.assertRaises(BiologicalSequenceError,
BiologicalSequence,
"ACC",
validate=True)
# no error raised when only allow characters are passed
BiologicalSequence("..--..", validate=True)
def test_contains(self):
self.assertTrue('G' in self.b1)
self.assertFalse('g' in self.b1)
def test_eq(self):
self.assertTrue(self.b1 == self.b1)
self.assertTrue(self.b2 == self.b2)
self.assertTrue(self.b3 == self.b3)
self.assertTrue(self.b1 != self.b3)
self.assertTrue(self.b1 != self.b2)
self.assertTrue(self.b2 != self.b3)
# identicial sequences of the same type are equal, even if they have
# different ids and/or descriptions
self.assertTrue(
BiologicalSequence('ACGT') == BiologicalSequence('ACGT'))
self.assertTrue(
BiologicalSequence('ACGT', id='a') == BiologicalSequence('ACGT',
id='b'))
self.assertTrue(
BiologicalSequence('ACGT', description='c') == BiologicalSequence(
'ACGT', description='d'))
self.assertTrue(
BiologicalSequence('ACGT', id='a', description='c') ==
BiologicalSequence('ACGT', id='b', description='d'))
# different type causes sequences to not be equal
self.assertFalse(
BiologicalSequence('ACGT') == NucleotideSequence('ACGT'))
def test_getitem(self):
self.assertEqual(self.b1[0], BiologicalSequence('G'))
self.assertEqual(self.b1[:], BiologicalSequence('GATTACA'))
self.assertEqual(self.b1[::-1], BiologicalSequence('ACATTAG'))
def test_iter(self):
b1_iter = iter(self.b1)
for actual, expected in zip(b1_iter, "GATTACA"):
self.assertEqual(actual, expected)
self.assertRaises(StopIteration, lambda: next(b1_iter))
def test_k_words(self):
# overlapping = True
self.assertEqual(list(self.b1.k_words(1, overlapping=True)),
['G', 'A', 'T', 'T', 'A', 'C', 'A'])
self.assertEqual(list(self.b1.k_words(2, overlapping=True)),
['GA', 'AT', 'TT', 'TA', 'AC', 'CA'])
self.assertEqual(list(self.b1.k_words(3, overlapping=True)),
['GAT', 'ATT', 'TTA', 'TAC', 'ACA'])
self.assertEqual(list(self.b1.k_words(7, overlapping=True)),
['GATTACA'])
self.assertEqual(list(self.b1.k_words(8, overlapping=True)), [])
# overlapping = False
self.assertEqual(list(self.b1.k_words(1, overlapping=True)),
['G', 'A', 'T', 'T', 'A', 'C', 'A'])
self.assertEqual(list(self.b1.k_words(2, overlapping=False)),
['GA', 'TT', 'AC'])
self.assertEqual(list(self.b1.k_words(3, overlapping=False)),
['GAT', 'TAC'])
self.assertEqual(list(self.b1.k_words(7, overlapping=False)),
['GATTACA'])
self.assertEqual(list(self.b1.k_words(8, overlapping=False)), [])
# error on invalid k
self.assertRaises(ValueError, list, self.b1.k_words(0))
self.assertRaises(ValueError, list, self.b1.k_words(-42))
# tests with different sequences
self.assertEqual(list(self.b8.k_words(3, overlapping=False)),
['HE.', '.--', '..L'])
b = BiologicalSequence('')
self.assertEqual(list(b.k_words(3)), [])
def test_k_word_counts(self):
# overlapping = True
expected = Counter('GATTACA')
self.assertEqual(self.b1.k_word_counts(1, overlapping=True), expected)
expected = Counter(['GAT', 'ATT', 'TTA', 'TAC', 'ACA'])
self.assertEqual(self.b1.k_word_counts(3, overlapping=True), expected)
# overlapping = False
expected = Counter(['GAT', 'TAC'])
self.assertEqual(self.b1.k_word_counts(3, overlapping=False), expected)
expected = Counter(['GATTACA'])
self.assertEqual(self.b1.k_word_counts(7, overlapping=False), expected)
def test_k_word_frequencies(self):
# overlapping = True
expected = defaultdict(int)
expected['A'] = 3 / 7.
expected['C'] = 1 / 7.
expected['G'] = 1 / 7.
expected['T'] = 2 / 7.
self.assertEqual(self.b1.k_word_frequencies(1, overlapping=True),
expected)
expected = defaultdict(int)
expected['GAT'] = 1 / 5.
expected['ATT'] = 1 / 5.
expected['TTA'] = 1 / 5.
expected['TAC'] = 1 / 5.
expected['ACA'] = 1 / 5.
self.assertEqual(self.b1.k_word_frequencies(3, overlapping=True),
expected)
# overlapping = False
expected = defaultdict(int)
expected['GAT'] = 1 / 2.
expected['TAC'] = 1 / 2.
self.assertEqual(self.b1.k_word_frequencies(3, overlapping=False),
expected)
expected = defaultdict(int)
expected['GATTACA'] = 1.0
self.assertEqual(self.b1.k_word_frequencies(7, overlapping=False),
expected)
expected = defaultdict(int)
empty = BiologicalSequence('')
self.assertEqual(empty.k_word_frequencies(1, overlapping=False),
expected)
def test_len(self):
self.assertEqual(len(self.b1), 7)
self.assertEqual(len(self.b2), 9)
self.assertEqual(len(self.b3), 4)
def test_repr(self):
self.assertEqual(repr(self.b1),
"<BiologicalSequence: GATTACA (length: 7)>")
self.assertEqual(repr(self.b6),
"<BiologicalSequence: ACGTACGTAC... (length: 12)>")
def test_reversed(self):
b1_reversed = reversed(self.b1)
for actual, expected in zip(b1_reversed, "ACATTAG"):
self.assertEqual(actual, expected)
self.assertRaises(StopIteration, lambda: next(b1_reversed))
def test_str(self):
self.assertEqual(str(self.b1), "GATTACA")
self.assertEqual(str(self.b2), "ACCGGTACC")
self.assertEqual(str(self.b3), "GREG")
def test_alphabet(self):
self.assertEqual(self.b1.alphabet(), set())
def test_description(self):
self.assertEqual(self.b1.description, "")
self.assertEqual(self.b2.description, "A test sequence")
self.assertEqual(self.b3.description, "A protein sequence")
def test_gap_alphabet(self):
self.assertEqual(self.b1.gap_alphabet(), set('-.'))
def test_id(self):
self.assertEqual(self.b1.id, "")
self.assertEqual(self.b2.id, "test-seq-2")
self.assertEqual(self.b3.id, "test-seq-3")
def test_count(self):
self.assertEqual(self.b1.count('A'), 3)
self.assertEqual(self.b1.count('T'), 2)
self.assertEqual(self.b1.count('TT'), 1)
def test_degap(self):
self.assertEqual(self.b1.degap(), self.b1)
self.assertEqual(self.b7.degap(), BiologicalSequence(''))
self.assertEqual(self.b8.degap(), BiologicalSequence('HELLO'))
def test_distance(self):
# note that test_hamming_distance covers default behavior more
# extensively
self.assertEqual(self.b1.distance(self.b1), 0.0)
self.assertEqual(self.b1.distance(BiologicalSequence('GATTACC')),
1. / 7)
def dumb_distance(x, y):
return 42
self.assertEqual(self.b1.distance(self.b1, distance_fn=dumb_distance),
42)
def test_fraction_diff(self):
self.assertEqual(self.b1.fraction_diff(self.b1), 0., 5)
self.assertEqual(self.b1.fraction_diff(BiologicalSequence('GATTACC')),
1. / 7., 5)
def test_fraction_same(self):
self.assertAlmostEqual(self.b1.fraction_same(self.b1), 1., 5)
self.assertAlmostEqual(
self.b1.fraction_same(BiologicalSequence('GATTACC')), 6. / 7., 5)
def test_gap_maps(self):
# in sequence with no gaps, the gap_maps are identical
self.assertEqual(self.b1.gap_maps(),
([0, 1, 2, 3, 4, 5, 6], [0, 1, 2, 3, 4, 5, 6]))
# in sequence with all gaps, the map of degapped to gapped is the empty
# list (bc its length is 0), and the map of gapped to degapped is all
# None
self.assertEqual(self.b7.gap_maps(),
([], [None, None, None, None, None, None]))
self.assertEqual(self.b8.gap_maps(),
([0, 1, 8, 9, 10],
[0, 1, None, None, None, None, None, None, 2, 3, 4]))
# example from the gap_maps doc string
self.assertEqual(
BiologicalSequence('-ACCGA-TA-').gap_maps(),
([1, 2, 3, 4, 5, 7, 8], [None, 0, 1, 2, 3, 4, None, 5, 6, None]))
def test_gap_vector(self):
self.assertEqual(self.b1.gap_vector(), [False] * len(self.b1))
self.assertEqual(self.b7.gap_vector(), [True] * len(self.b7))
self.assertEqual(self.b8.gap_vector(), [
False, False, True, True, True, True, True, True, False, False,
False
])
def test_unsupported_characters(self):
self.assertEqual(self.b1.unsupported_characters(), set('GATC'))
self.assertEqual(self.b7.unsupported_characters(), set())
def test_has_unsupported_characters(self):
self.assertTrue(self.b1.has_unsupported_characters())
self.assertFalse(self.b7.has_unsupported_characters())
def test_index(self):
""" index functions as expected """
self.assertEqual(self.b1.index('G'), 0)
self.assertEqual(self.b1.index('A'), 1)
self.assertEqual(self.b1.index('AC'), 4)
self.assertRaises(ValueError, self.b1.index, 'x')
def test_is_gap(self):
self.assertTrue(self.b1.is_gap('.'))
self.assertTrue(self.b1.is_gap('-'))
self.assertFalse(self.b1.is_gap('A'))
self.assertFalse(self.b1.is_gap('x'))
self.assertFalse(self.b1.is_gap(' '))
self.assertFalse(self.b1.is_gap(''))
def test_is_gapped(self):
self.assertFalse(self.b1.is_gapped())
self.assertFalse(self.b2.is_gapped())
self.assertTrue(self.b7.is_gapped())
self.assertTrue(self.b8.is_gapped())
def test_is_valid(self):
self.assertFalse(self.b1.is_valid())
self.assertTrue(self.b7.is_valid())
def test_to_fasta(self):
self.assertEqual(self.b1.to_fasta(), ">\nGATTACA\n")
self.assertEqual(self.b1.to_fasta(terminal_character=""), ">\nGATTACA")
self.assertEqual(self.b2.to_fasta(),
">test-seq-2 A test sequence\nACCGGTACC\n")
self.assertEqual(self.b3.to_fasta(),
">test-seq-3 A protein sequence\nGREG\n")
self.assertEqual(self.b4.to_fasta(), ">test-seq-4\nPRTEIN\n")
self.assertEqual(self.b5.to_fasta(), "> some description\nLLPRTEIN\n")
# alt parameters
self.assertEqual(self.b2.to_fasta(field_delimiter=":"),
">test-seq-2:A test sequence\nACCGGTACC\n")
self.assertEqual(self.b2.to_fasta(terminal_character="!"),
">test-seq-2 A test sequence\nACCGGTACC!")
self.assertEqual(
self.b2.to_fasta(field_delimiter=":", terminal_character="!"),
">test-seq-2:A test sequence\nACCGGTACC!")
def test_upper(self):
b = NucleotideSequence('GAt.ACa-', id='x', description='42')
expected = NucleotideSequence('GAT.ACA-', id='x', description='42')
self.assertEqual(b.upper(), expected)
def test_lower(self):
b = NucleotideSequence('GAt.ACa-', id='x', description='42')
expected = NucleotideSequence('gat.aca-', id='x', description='42')
self.assertEqual(b.lower(), expected)
class BiologicalSequenceTests(TestCase):
""" Tests of the BiologicalSequence class """
def setUp(self):
""" Initialize values to be used in tests
"""
self.b1 = BiologicalSequence('GATTACA')
self.b2 = BiologicalSequence(
'ACCGGTACC', identifier="test-seq-2",
description="A test sequence")
self.b3 = BiologicalSequence(
'GREG', identifier="test-seq-3", description="A protein sequence")
self.b4 = BiologicalSequence(
'PRTEIN', identifier="test-seq-4")
self.b5 = BiologicalSequence(
'LLPRTEIN', description="some description")
self.b6 = BiologicalSequence('ACGTACGTACGT')
self.b7 = BiologicalSequence('..--..')
self.b8 = BiologicalSequence('HE..--..LLO')
def test_init(self):
""" Initialization functions as expected with varied input types
"""
# init as string
b = BiologicalSequence('ACCGGXZY')
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.identifier, "")
self.assertEqual(b.description, "")
# init as string with optional values
b = BiologicalSequence(
'ACCGGXZY', 'test-seq-1', 'The first test sequence')
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.identifier, "test-seq-1")
self.assertEqual(b.description, "The first test sequence")
# test init as a different string
b = BiologicalSequence('WRRTY')
self.assertEqual(str(b), 'WRRTY')
# init as list
b = BiologicalSequence(list('ACCGGXZY'))
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.identifier, "")
self.assertEqual(b.description, "")
# init as tuple
b = BiologicalSequence(tuple('ACCGGXZY'))
self.assertEqual(str(b), 'ACCGGXZY')
self.assertEqual(b.identifier, "")
self.assertEqual(b.description, "")
def test_init_validate(self):
""" initialization with validation functions as expected
"""
self.assertRaises(BiologicalSequenceError, BiologicalSequence, "ACC",
validate=True)
# no error raised when only allow characters are passed
BiologicalSequence("..--..", validate=True)
def test_contains(self):
""" contains functions as expected
"""
self.assertTrue('G' in self.b1)
self.assertFalse('g' in self.b1)
def test_eq(self):
""" equality functions as expected
"""
self.assertTrue(self.b1 == self.b1)
self.assertTrue(self.b2 == self.b2)
self.assertTrue(self.b3 == self.b3)
self.assertTrue(self.b1 != self.b3)
self.assertTrue(self.b1 != self.b2)
self.assertTrue(self.b2 != self.b3)
# identicial sequences of the same type are equal, even if they have
# different identifiers and/or descriptions
self.assertTrue(
BiologicalSequence('ACGT') == BiologicalSequence('ACGT'))
self.assertTrue(
BiologicalSequence('ACGT', identifier='a') ==
BiologicalSequence('ACGT', identifier='b'))
self.assertTrue(
BiologicalSequence('ACGT', description='c') ==
BiologicalSequence('ACGT', description='d'))
self.assertTrue(
BiologicalSequence('ACGT', identifier='a', description='c') ==
BiologicalSequence('ACGT', identifier='b', description='d'))
# different type causes sequences to not be equal
self.assertFalse(
BiologicalSequence('ACGT') == NucleotideSequence('ACGT'))
def test_getitem(self):
""" getitem functions as expected
"""
self.assertEqual(self.b1[0], BiologicalSequence('G'))
self.assertEqual(self.b1[:], BiologicalSequence('GATTACA'))
self.assertEqual(self.b1[::-1], BiologicalSequence('ACATTAG'))
def test_iter(self):
""" iter functions as expected
"""
b1_iter = iter(self.b1)
for actual, expected in zip(b1_iter, "GATTACA"):
self.assertEqual(actual, expected)
self.assertRaises(StopIteration, b1_iter.next)
def test_len(self):
""" len functions as expected
"""
self.assertEqual(len(self.b1), 7)
self.assertEqual(len(self.b2), 9)
self.assertEqual(len(self.b3), 4)
def test_repr(self):
""" repr functions as expected
"""
self.assertEqual(repr(self.b1),
"<BiologicalSequence: GATTACA (length: 7)>")
self.assertEqual(repr(self.b6),
"<BiologicalSequence: ACGTACGTAC... (length: 12)>")
def test_reversed(self):
""" reversed functions as expected
"""
b1_reversed = reversed(self.b1)
for actual, expected in zip(b1_reversed, "ACATTAG"):
self.assertEqual(actual, expected)
self.assertRaises(StopIteration, b1_reversed.next)
def test_str(self):
""" str functions as expected
"""
self.assertEqual(str(self.b1), "GATTACA")
self.assertEqual(str(self.b2), "ACCGGTACC")
self.assertEqual(str(self.b3), "GREG")
def test_alphabet(self):
""" alphabet property functions as expected
"""
self.assertEqual(self.b1.alphabet(), set())
def test_description(self):
""" description property functions as expected
"""
self.assertEqual(self.b1.description, "")
self.assertEqual(self.b2.description, "A test sequence")
self.assertEqual(self.b3.description, "A protein sequence")
def test_gap_alphabet(self):
""" gap_alphabet property functions as expected
"""
self.assertEqual(self.b1.gap_alphabet(), set('-.'))
def test_identifier(self):
""" identifier property functions as expected
"""
self.assertEqual(self.b1.identifier, "")
self.assertEqual(self.b2.identifier, "test-seq-2")
self.assertEqual(self.b3.identifier, "test-seq-3")
def test_count(self):
""" count functions as expected
"""
self.assertEqual(self.b1.count('A'), 3)
self.assertEqual(self.b1.count('T'), 2)
self.assertEqual(self.b1.count('TT'), 1)
def test_degap(self):
""" degap functions as expected
"""
self.assertEqual(self.b1.degap(), self.b1)
self.assertEqual(self.b7.degap(), BiologicalSequence(''))
self.assertEqual(self.b8.degap(), BiologicalSequence('HELLO'))
def test_distance(self):
""" distance functions as expected
"""
# note that test_hamming_distance covers default behavior more
# extensively
self.assertEqual(self.b1.distance(self.b1), 0.0)
self.assertEqual(self.b1.distance(BiologicalSequence('GATTACC')), 1./7)
def dumb_distance(x, y):
return 42
self.assertEqual(
self.b1.distance(self.b1, distance_fn=dumb_distance), 42)
def test_fraction_diff(self):
""" fraction_diff functions as expected
"""
self.assertEqual(self.b1.fraction_diff(self.b1), 0., 5)
self.assertEqual(
self.b1.fraction_diff(BiologicalSequence('GATTACC')), 1. / 7., 5)
def test_fraction_same(self):
""" fraction_same functions as expected
"""
self.assertAlmostEqual(self.b1.fraction_same(self.b1), 1., 5)
self.assertAlmostEqual(
self.b1.fraction_same(BiologicalSequence('GATTACC')), 6. / 7., 5)
def test_gap_maps(self):
""" gap_maps functions as expected
"""
# in sequence with no gaps, the gap_maps are identical
self.assertEqual(self.b1.gap_maps(),
([0, 1, 2, 3, 4, 5, 6], [0, 1, 2, 3, 4, 5, 6]))
# in sequence with all gaps, the map of degapped to gapped is the empty
# list (bc its length is 0), and the map of gapped to degapped is all
# None
self.assertEqual(self.b7.gap_maps(),
([], [None, None, None, None, None, None]))
self.assertEqual(self.b8.gap_maps(),
([0, 1, 8, 9, 10],
[0, 1, None, None, None, None, None, None, 2, 3, 4]))
# example from the gap_maps doc string
self.assertEqual(BiologicalSequence('-ACCGA-TA-').gap_maps(),
([1, 2, 3, 4, 5, 7, 8],
[None, 0, 1, 2, 3, 4, None, 5, 6, None]))
def test_gap_vector(self):
""" gap_vector functions as expected
"""
self.assertEqual(self.b1.gap_vector(),
[False] * len(self.b1))
self.assertEqual(self.b7.gap_vector(),
[True] * len(self.b7))
self.assertEqual(self.b8.gap_vector(),
[False, False, True, True, True, True,
True, True, False, False, False])
def test_unsupported_characters(self):
""" unsupported_characters functions as expected
"""
self.assertEqual(self.b1.unsupported_characters(), set('GATC'))
self.assertEqual(self.b7.unsupported_characters(), set())
def test_has_unsupported_characters(self):
""" has_unsupported_characters functions as expected
"""
self.assertTrue(self.b1.has_unsupported_characters())
self.assertFalse(self.b7.has_unsupported_characters())
def test_index(self):
""" index functions as expected """
self.assertEqual(self.b1.index('G'), 0)
self.assertEqual(self.b1.index('A'), 1)
self.assertEqual(self.b1.index('AC'), 4)
self.assertRaises(ValueError, self.b1.index, 'x')
def test_is_gap(self):
""" is_gap functions as expected """
self.assertTrue(self.b1.is_gap('.'))
self.assertTrue(self.b1.is_gap('-'))
self.assertFalse(self.b1.is_gap('A'))
self.assertFalse(self.b1.is_gap('x'))
self.assertFalse(self.b1.is_gap(' '))
self.assertFalse(self.b1.is_gap(''))
def test_is_gapped(self):
""" is_gapped functions as expected """
self.assertFalse(self.b1.is_gapped())
self.assertFalse(self.b2.is_gapped())
self.assertTrue(self.b7.is_gapped())
self.assertTrue(self.b8.is_gapped())
def test_is_valid(self):
""" is_valid functions as expected
"""
self.assertFalse(self.b1.is_valid())
self.assertTrue(self.b7.is_valid())
def test_to_fasta(self):
""" to_fasta functions as expected
"""
self.assertEqual(self.b1.to_fasta(), ">\nGATTACA\n")
self.assertEqual(self.b1.to_fasta(terminal_character=""), ">\nGATTACA")
self.assertEqual(self.b2.to_fasta(),
">test-seq-2 A test sequence\nACCGGTACC\n")
self.assertEqual(self.b3.to_fasta(),
">test-seq-3 A protein sequence\nGREG\n")
self.assertEqual(self.b4.to_fasta(),
">test-seq-4\nPRTEIN\n")
self.assertEqual(self.b5.to_fasta(),
"> some description\nLLPRTEIN\n")
# alt parameters
self.assertEqual(self.b2.to_fasta(field_delimiter=":"),
">test-seq-2:A test sequence\nACCGGTACC\n")
self.assertEqual(self.b2.to_fasta(terminal_character="!"),
">test-seq-2 A test sequence\nACCGGTACC!")
self.assertEqual(
self.b2.to_fasta(field_delimiter=":", terminal_character="!"),
">test-seq-2:A test sequence\nACCGGTACC!")
def test_upper(self):
""" upper functions as expected
"""
b = NucleotideSequence('GAt.ACa-', identifier='x', description='42')
expected = NucleotideSequence('GAT.ACA-', identifier='x',
description='42')
self.assertEqual(b.upper(), expected)
def test_lower(self):
""" lower functions as expected
"""
b = NucleotideSequence('GAt.ACa-', identifier='x', description='42')
expected = NucleotideSequence('gat.aca-', identifier='x',
description='42')
self.assertEqual(b.lower(), expected)