def testAmbiguity2(self):
msa = array([list('AB'), list('BZ')], dtype='|S1')
expect = array([[0., 2.], [2., 0.]])
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testAmbiguity7(self):
msa = array([list("bx"), list("xb")], dtype="|S1")
expect = array([[0.0, 162.0 / 121], [162.0 / 121, 0.0]])
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testAmbiguity7(self):
msa = array([list('bx'), list('xb')], dtype='|S1')
expect = array([[0., 162. / 121], [162. / 121, 0.]])
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testNoAmbiguity(self):
msa = array([list('OX'), list('XO')], dtype='|S1')
expect = array([[0., 2.], [2., 0.]])
result = buildOMESMatrix(msa, ambiquity=False)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, ambiquity=False, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testAmbiguity3(self):
msa = array([list('XX')], dtype='|S1')
expect = zeros((2, 2))
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testAmbiguity4(self):
msa = array([list("Bb"), list("jJ"), list("Zz")], dtype="|S1")
expect = array([[0.0, 6.0], [6.0, 0.0]])
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testAmbiguity3(self):
msa = array([list("XX")], dtype="|S1")
expect = zeros((2, 2))
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testNoAmbiguity(self):
msa = array([list("OX"), list("XO")], dtype="|S1")
expect = array([[0.0, 2.0], [2.0, 0.0]])
result = buildOMESMatrix(msa, ambiquity=False)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, ambiquity=False, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testFourSequences(self):
msa = array([list("ACCA"), list("ACDA"), list("ACDC"), list("ACDC")], dtype="|S1")
expect = array([[0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 4.0 / 3], [0.0, 0.0, 4.0 / 3, 0.0]])
result = buildOMESMatrix(msa)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testTwentyReversed(self):
seq = 'ACDEFGHIKLMNPQRSTVWY'
msa = array([[s, seq[-i - 1]] for i, s in enumerate(seq)], dtype='|S1')
expect = array([[0., 380.], [380., 0.]])
result = buildOMESMatrix(msa)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testTwenty(self):
seq = 'ACDEFGHIKLMNPQRSTVWY'
msa = array([[s, s] for s in seq], dtype='|S1')
expect = array([[0., 380.], [380., 0.]])
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testTwenty(self):
seq = "ACDEFGHIKLMNPQRSTVWY"
msa = array([[s, s] for s in seq], dtype="|S1")
expect = array([[0.0, 380.0], [380.0, 0.0]])
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testTwentyReversed(self):
seq = "ACDEFGHIKLMNPQRSTVWY"
msa = array([[s, seq[-i - 1]] for i, s in enumerate(seq)], dtype="|S1")
expect = array([[0.0, 380.0], [380.0, 0.0]])
result = buildOMESMatrix(msa)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testInf(self):
msa = zeros((500, 10), "|S1")
msa.fill(".")
msa[95, 8] = "s"
msa[95, 9] = "i"
expect = zeros((10, 10))
expect[8, 9] = expect[9, 8] = 500.0
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg="turbo failed")
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg="w/out turbo failed")
def testInf(self):
msa = zeros((500, 10), '|S1')
msa.fill('.')
msa[95, 8] = 's'
msa[95, 9] = 'i'
expect = zeros((10, 10))
expect[8, 9] = expect[9, 8] = 500.
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testAmbiguity5(self):
expect = array([[0.0, 0.0], [0.0, 0.0]])
for seq in ["bx", "Xb", "jX", "Xj", "xz", "ZX", "bj", "jb", "bz", "zb", "jz", "zj"]:
msa = array([list(seq)], dtype="|S1")
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg=seq + " failed")
def testAmbiguity6(self):
expect = zeros((2, 2))
for seq in ['bb', 'jj', 'zz']:
msa = array([list(seq)], dtype='|S1')
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg=seq + ' failed')
def testAmbiguity6(self):
expect = zeros((2, 2))
for seq in ["bb", "jj", "zz"]:
msa = array([list(seq)], dtype="|S1")
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg=seq + " failed")
def testFourSequences(self):
msa = array([list('ACCA'),
list('ACDA'),
list('ACDC'),
list('ACDC')],
dtype='|S1')
expect = array([
[0., 0., 0., 0.],
[0., 0., 0., 0.],
[0., 0., 0., 4. / 3],
[0., 0., 4. / 3, 0.],
])
result = buildOMESMatrix(msa)
assert_array_almost_equal(expect, result, err_msg='turbo failed')
result = buildOMESMatrix(msa, turbo=False)
assert_array_almost_equal(expect, result, err_msg='w/out turbo failed')
def testAmbiguity5(self):
expect = array([[0., 0.], [0., 0.]])
for seq in [
'bx', 'Xb', 'jX', 'Xj', 'xz', 'ZX', 'bj', 'jb', 'bz', 'zb',
'jz', 'zj'
]:
msa = array([list(seq)], dtype='|S1')
result = buildOMESMatrix(msa, debug=False)
assert_array_almost_equal(expect, result, err_msg=seq + ' failed')
