def test_probs_for_vars_mut_wts(self):
mut_wt, mut_max = 0.10, 0.50
hvb = preprocess.HapVarBaseMatrix(self.ref, self.phy, mut_wt, mut_max)
obs_I = zip(range(9), "GAAAAAAAA")
self.assertEqual(str(hvb.prob_for_vars('I', obs_I)),
str(math.log((0.9**7) * (0.8**2))))
self.assertEqual(str(hvb.prob_for_vars('C', obs_I)),
str(math.log((0.9**5) * (0.8**2) * ((0.1 / 3)**2))))
def test_probs_for_vars(self):
mut_wt, mut_max = 0.10, 0.10
hvb = preprocess.HapVarBaseMatrix(self.ref, self.phy, mut_wt, mut_max)
obs_I = list(zip(list(range(9)), "GAAAAAAAA"))
self.assertAlmostEqual(hvb.prob_for_vars('I', obs_I),
math.log(0.9 ** 9))
self.assertAlmostEqual(hvb.prob_for_vars('C', obs_I),
math.log((0.9 ** 7) * ((0.1 / 3) ** 2)))
self.assertAlmostEqual(hvb.prob_for_vars('D', obs_I),
math.log((0.9 ** 5) * ((0.1 / 3) ** 4)))
def test_probs(self):
mut_wt, mut_max = 0.10, 0.10
hvb = preprocess.HapVarBaseMatrix(self.ref, self.phy, mut_wt, mut_max)
# hits
self.assertEqual(hvb._prob(hvb.markers['I'], 0, 'G'), 1.0 - 0.1)
self.assertEqual(hvb._prob(hvb.markers['I'], 4, 'A'), 1.0 - 0.1)
self.assertEqual(hvb._prob(hvb.markers['I'], 3, 'A'), 1.0 - 0.1)
# misses
self.assertEqual(hvb._prob(hvb.markers['I'], 0, 'A'), 0.1 / 3.0)
self.assertEqual(hvb._prob(hvb.markers['I'], 4, 'T'), 0.1 / 3.0)
self.assertEqual(hvb._prob(hvb.markers['I'], 3, 'T'), 0.1 / 3.0)
def test_hapvarbasematrix_init(self):
mut_wt, mut_max = 0.02, 0.6
hvb = preprocess.HapVarBaseMatrix(self.ref, self.phy, mut_wt, mut_max)
self.assertEqual(hvb.refseq, self.ref)
self.assertEqual(hvb.phylo, self.phy)
self.assertEqual(hvb.mut_wt, mut_wt)
self.assertEqual(hvb.mut_max, mut_max)
markers = {'A':{1:'T', 3:'T', 0:'G'},
'B':{0:'G', 2:'T', 4:'T', 5:'T', 7:'T'},
'C':{0:'G', 2:'T', 5:'T'},
'D':{0:'G', 2:'T', 4:'T', 6:'T', 8:'T'},
'E':{0:'G', 2:'T', 3:'T', 4:'T', 6:'T'},
'F':{0:'G', 2:'T', 4:'T', 5:'T'},
'G':{0:'G', 2:'T', 4:'T', 6:'T'},
'H':{0:'G', 2:'T', 4:'T'},
'I':{0:'G'}}
self.assertEqual(hvb.markers, markers)