diff --git a/Tests/test_Affy.py b/Tests/test_Affy.py index d49c08152..21a06eb6c 100644 --- a/Tests/test_Affy.py +++ b/Tests/test_Affy.py @@ -320,9 +320,6 @@ class AffyTest(unittest.TestCase): *(preHeaders[header] for header in preHeadersOrder), ) - def packData(intensity, sdev, pixel): - return struct.pack("< f f h", intensity, sdev, pixel) - f.write(headersEncoded) for header in headers: try: @@ -334,9 +331,9 @@ class AffyTest(unittest.TestCase): f.write(prePadding) f.write(b"\x00" * 15) for i in range(25): - f.write(packData(float(i), float(-i), 9)) + f.write(struct.pack("< f f h", i, -i, 9)) # intensity, sdev, pixel if __name__ == "__main__": - runner = unittest.TextTestRunner(verbosity=0) + runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner) diff --git a/Tests/test_Compass.py b/Tests/test_Compass.py index 468aa3271..5a928757d 100644 --- a/Tests/test_Compass.py +++ b/Tests/test_Compass.py @@ -26,7 +26,7 @@ class CompassTest(unittest.TestCase): self.assertEqual("60456.blo.gz.aln", com_record.query) self.assertEqual("60456.blo.gz.aln", com_record.hit) - self.assertEqual(0.5, com_record.gap_threshold) + self.assertAlmostEqual(0.5, com_record.gap_threshold) self.assertEqual(388, com_record.query_length) self.assertEqual(386, com_record.query_filtered_length) @@ -34,12 +34,12 @@ class CompassTest(unittest.TestCase): self.assertEqual(386, com_record.hit_filtered_length) self.assertEqual(399, com_record.query_nseqs) - self.assertEqual(12.972, com_record.query_neffseqs) + self.assertAlmostEqual(12.972, com_record.query_neffseqs) self.assertEqual(399, com_record.hit_nseqs) - self.assertEqual(12.972, com_record.hit_neffseqs) + self.assertAlmostEqual(12.972, com_record.hit_neffseqs) self.assertEqual(2759, com_record.sw_score) - self.assertEqual(float("0.00e+00"), com_record.evalue) + self.assertAlmostEqual(0.0, com_record.evalue) def testCompassParser(self): with open(self.test_files[0]) as handle: @@ -60,15 +60,15 @@ class CompassTest(unittest.TestCase): com_record = next(records) self.assertEqual("allscop//14982.blo.gz.aln", com_record.hit) - self.assertEqual(float("1.01e+03"), com_record.evalue) + self.assertAlmostEqual(1.01e03, com_record.evalue) com_record = next(records) self.assertEqual("allscop//14983.blo.gz.aln", com_record.hit) - self.assertEqual(float("1.01e+03"), com_record.evalue) + self.assertAlmostEqual(1.01e03, com_record.evalue) com_record = next(records) self.assertEqual("allscop//14984.blo.gz.aln", com_record.hit) - self.assertEqual(float("5.75e+02"), com_record.evalue) + self.assertAlmostEqual(5.75e02, com_record.evalue) def testAlignmentParsingOne(self): with open(self.test_files[1]) as handle: diff --git a/Tests/test_MarkovModel.py b/Tests/test_MarkovModel.py index 877d3a4f8..adcb0af8f 100644 --- a/Tests/test_MarkovModel.py +++ b/Tests/test_MarkovModel.py @@ -468,17 +468,14 @@ class TestMarkovModel(unittest.TestCase): lp_transition = log([[0.7, 0.3], [0.5, 0.5]]) lp_emission = log([[0.6, 0.1, 0.3], [0.1, 0.7, 0.2]]) - output1 = [0, 1, 0] - output2 = -3.968593356916541 - viterbi_output = MarkovModel._viterbi( len(states), lp_initial, lp_transition, lp_emission, outputs ) self.assertEqual(len(viterbi_output[0][0]), 3) - self.assertEqual(viterbi_output[0][0][0], output1[0]) - self.assertEqual(viterbi_output[0][0][1], output1[1]) - self.assertEqual(viterbi_output[0][0][2], output1[2]) - self.assertEqual(float(f"{viterbi_output[0][1]:.3f}"), float(f"{output2:.3f}")) + self.assertEqual(viterbi_output[0][0][0], 0) + self.assertEqual(viterbi_output[0][0][1], 1) + self.assertEqual(viterbi_output[0][0][2], 0) + self.assertAlmostEqual(viterbi_output[0][1], -3.968593356916541) def test_normalize_and_copy_and_check(self): matrix_in1 = array([[1.1, 2.2, 3.3], [4.4, 5.5, 6.6], [7.7, 8.8, 9.9]]) @@ -559,23 +556,10 @@ class TestMarkovModel(unittest.TestCase): matrix = array([[1.1, 2.2, 3.3], [4.4, 5.5, 6.6], [7.7, 8.8, 9.9]]) matrix1 = array([1, 2, 3]) - output = 10.304721798 - output1 = 3.40760596444 - self.assertEqual( - float(f"{MarkovModel._logsum(matrix):.3f}"), float(f"{output:.3f}") - ) - self.assertEqual( - float(f"{MarkovModel._logsum(matrix1):.3f}"), float(f"{output1:.3f}") - ) - - output2 = 29873.342245 - output3 = 30.1928748506 - self.assertEqual( - float(f"{MarkovModel._exp_logsum(matrix):.3f}"), float(f"{output2:.3f}") - ) - self.assertEqual( - float(f"{MarkovModel._exp_logsum(matrix1):.3f}"), float(f"{output3:.3f}") - ) + self.assertAlmostEqual(MarkovModel._logsum(matrix), 10.304721798) + self.assertAlmostEqual(MarkovModel._logsum(matrix1), 3.40760596444) + self.assertAlmostEqual(MarkovModel._exp_logsum(matrix), 29873.342245) + self.assertAlmostEqual(MarkovModel._exp_logsum(matrix1), 30.1928748506) def test_logvecadd(self): vec1 = log(array([1, 2, 3, 4])) diff --git a/Tests/test_ProtParam.py b/Tests/test_ProtParam.py index a61754c7d..8ddff65a6 100644 --- a/Tests/test_ProtParam.py +++ b/Tests/test_ProtParam.py @@ -42,9 +42,7 @@ class ProtParamTest(unittest.TestCase): percent_dict = analysis.get_amino_acids_percent() seq_len = len(self.text) for i in percent_dict: - self.assertAlmostEqual( - percent_dict[i], self.text.count(i) / float(seq_len) - ) + self.assertAlmostEqual(percent_dict[i], self.text.count(i) / seq_len) def test_get_molecular_weight(self): """Calculate protein molecular weight.""" diff --git a/Tests/test_SVDSuperimposer.py b/Tests/test_SVDSuperimposer.py index 3700e85a8..9e8db047d 100644 --- a/Tests/test_SVDSuperimposer.py +++ b/Tests/test_SVDSuperimposer.py @@ -51,10 +51,7 @@ class SVDSuperimposerTest(unittest.TestCase): y = array([[1.91, 1.82, 1.73], [1.64, 1.55, 1.46], [1.37, 1.28, 1.19]]) self.sup.set(x, y) self.assertIsNone(self.sup.init_rms) - init_rms = 0.8049844719 - self.assertTrue( - float(f"{self.sup.get_init_rms():.3f}"), float(f"{init_rms:.3f}") - ) + self.assertAlmostEqual(self.sup.get_init_rms(), 0.8049844719) def test_oldTest(self): self.assertTrue( @@ -98,8 +95,7 @@ class SVDSuperimposerTest(unittest.TestCase): self.assertIsNone(self.sup.rms) self.assertIsNone(self.sup.init_rms) - rms = 0.00304266526014 - self.assertEqual(float(f"{self.sup.get_rms():.3f}"), float(f"{rms:.3f}")) + self.assertAlmostEqual(self.sup.get_rms(), 0.00304266526014) rot_get, tran_get = self.sup.get_rotran() self.assertTrue(