def test_read_blosum(self):
f = data.data_stream("blosum80")
mat = SubMatrix.read(f)
self.assertEqual(mat[0, 10], -3)
f.close()
f = data.data_stream("blosum62")
mat = SubMatrix.read(f)
self.assertEqual(mat[4, 5], -4)
f.close()
def test_read_pam(self):
f = data.data_stream("pam250")
mat = SubMatrix.read(f)
self.assertEqual(mat[0, 0], 2.0)
f.close()
f = data.data_stream("pam120")
mat = SubMatrix.read(f)
self.assertEqual(mat[4, 5], -7)
f.close()
def test_read_alphabets(self):
# incompatable alphabets
f = StringIO(test_matrix3)
self.assertRaises(ValueError, SubMatrix.read, f)
f = StringIO(test_matrix3)
SubMatrix.read(f, alphabet=Alphabet('ARNDCQEGHILKMFPSTWYV'))
f2 = StringIO(test_matrix1)
self.assertRaises(ValueError, SubMatrix.read, f2,
unambiguous_protein_alphabet)
def test_get(self):
ab = Alphabet('ABCD')
ar = np.asarray([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12],
[13, 14, 15, 16]])
s = SubMatrix(ab, ar)
s1 = 'DCCBBBAAA'
s2 = 'BA'
v = s.index((s1, s2))
# print v
for m, i in enumerate(s1):
for n, j in enumerate(s2):
assert s[i, j] == v[m, n]
def test_get_subMatrix(self):
ab = Alphabet('ABCD')
ar = np.asarray([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12],
[13, 14, 15, 16]])
mat = SubMatrix(ab, ar)
mat2 = mat.reindex('ABC')
assert np.all(
mat2.array == np.asarray([[1, 2, 3], [5, 6, 7], [9, 10, 11]]))
mat2 = mat.reindex('BA')
assert np.all(mat2.array == np.asarray([[6, 5], [2, 1]]))
mat2 = mat.reindex(Alphabet('BA'))
assert np.all(mat2.array == np.asarray([[6, 5], [2, 1]]))
def test_repr(self):
ab = Alphabet('ABCD')
ar = np.asarray([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12],
[13, 14, 15, 16]])
s = SubMatrix(ab, ar)
repr(s)
def test_read_blast(self):
# New style blast matrices have letters at beginning of lines and a '*'
f = data_stream("blosum35.blast.new")
mat = SubMatrix.read(f)
self.assertEqual(mat[4, 5], -3)
f.close()
# Matrices formatted for old blast have a '*' (stop)
# column and no letters at the beggining of lines
f = data_stream("blosum35.blast")
mat = SubMatrix.read(f)
self.assertEqual(mat[0, 10], -2)
self.assertEqual(mat.array.shape, (23, 23))
f.close()
# For comparison, we'll also parse a matrix without '*'
f = data_stream("pam250.mat")
mat = SubMatrix.read(f)
self.assertEqual(mat[4, 5], -5)
f.close()
def test_fail_get(self):
ab = Alphabet('ABCD')
ar = np.asarray([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12],
[13, 14, 15, 16]])
s = SubMatrix(ab, ar)
self.assertRaises(IndexError, s.__getitem__, ('E', 'A'))
self.assertRaises(IndexError, s.__getitem__, ('5', '6'))
# FIXME
self.assertRaises(IndexError, s.index, ('E', 'A'))
def test_create(self):
ab = 'ABCD'
ar = np.asarray([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12],
[13, 14, 15, 16]])
s = SubMatrix(ab, ar)
assert s[0, 0] == 1
assert s['A', 'A'] == 1
assert s['B', 'C'] == 7
s['B', 'C'] = -1
assert s['B', 'C'] == -1
def test_fail_get(self):
ab = Alphabet("ABCD")
ar = np.asarray([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12],
[13, 14, 15, 16]])
s = SubMatrix(ab, ar)
self.assertRaises(IndexError, s.__getitem__, ("E", "A"))
self.assertRaises(IndexError, s.__getitem__, ("5", "6"))
# FIXME
self.assertRaises(IndexError, s.index, ("E", "A"))
def test_create(self):
ab = "ABCD"
ar = np.asarray([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12],
[13, 14, 15, 16]])
s = SubMatrix(ab, ar)
assert s[0, 0] == 1
assert s["A", "A"] == 1
assert s["B", "C"] == 7
s["B", "C"] = -1
assert s["B", "C"] == -1
def test_read(self):
f = StringIO(test_matrix1)
mat = SubMatrix.read(f)
assert mat['a', 'a'] == 4
def test_read(self):
f = StringIO(test_matrix1)
mat = SubMatrix.read(f)
assert mat["a", "a"] == 4