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remove float (#4109)

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This commit is contained in:
mdehoon
2022-09-29 10:21:04 +09:00
committed by GitHub
parent dc6f1c1b1e
commit 8be16c3b5a
5 changed files with 20 additions and 45 deletions
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7
Tests/test_Affy.py
View File

@ -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)

14
Tests/test_Compass.py
View File

@ -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:

32
Tests/test_MarkovModel.py
View File

@ -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]))

4
Tests/test_ProtParam.py
View File

@ -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."""

8
Tests/test_SVDSuperimposer.py
View File

@ -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(