def test_scoring_blossum(self):
"""Testing score calculation using Blossum62 + Gap Penalty = -11, gap extend = -1"""
print("######### Testing calculation of scoring matrix. ###########")
got = Gotoh(substitution_matrix=MatrixInfo.blosum62,
gap_penalty=-11,
gap_extend=-1)
print("############# Case 1 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "A"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(got.scoring_matrix_D,
np.array([[0., -12.0], [-12., 4.]]))
print("############# FINISH ##############")
print("############# Case 2 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "AT"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(
got.scoring_matrix_D, np.array([[0., -12., -13.], [-12., 4.,
-8.]]))
print("############# FINISH ##############")
print("############# Case 3 ##############")
print("############# START ##############")
seq1 = "RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT"
seq2 = "ISDTEADIGSNLRWGCAAAGKPRPMVRWLRNGEPLASQNRVEVLA"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % pprint.pformat(got.scoring_matrix_D))
self.assertAlmostEqual(got.scoring_matrix_D[-1][-1], -5.0)
print("############# FINISH ##############")
def test_scoring_pam(self):
"""Testing score calculation using PAM250 + Gap Penalty = -11, gap extend = -1"""
print("######### Testing calculation of scoring matrix. ###########")
got = Gotoh(substitution_matrix=MatrixInfo.pam250,
gap_penalty=-11,
gap_extend=-1)
print("############# Case 1 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "A"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(got.scoring_matrix_D,
np.array([[0., -12.], [-12., 2.]]))
print("############# FINISH ##############")
print("############# Case 2 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "AT"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(
got.scoring_matrix_D, np.array([[0., -12., -13.], [-12., 2.,
-10.]]))
print("############# FINISH ##############")
print("############# Case 3 ##############")
print("############# START ##############")
seq1 = "ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN"
seq2 = "RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % pprint.pformat(got.scoring_matrix_D))
self.assertAlmostEqual(got.scoring_matrix_D[-1][-1], 33)
print("############# FINISH ##############")