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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for psw module."""
import doctest
import unittest
import random
import sys
from Bio.Wise import psw
if "requires_wise" in sys.modules:
del sys.modules["requires_wise"]
import requires_wise # noqa: E402
class TestPSW(unittest.TestCase):
def test_Alignment_normal(self):
a = psw.Alignment()
a.append(psw.ColumnUnit(0, 98, "SEQUENCE"))
a.append(psw.ColumnUnit(1, 200, "SEQUENCE"))
a.append(psw.ColumnUnit(0, 98, "INSERT"))
a.append(psw.ColumnUnit(1, 201, "SEQUENCE"))
a.append(psw.ColumnUnit(0, 98, "END"))
a.append(psw.ColumnUnit(1, 201, "END"))
self.assertEqual(str(a), "[SEQUENCE(98, 200), INSERT(98, 201), END(98, 201)]")
def test_Alignment_assertions(self):
a = psw.Alignment()
self.assertRaises(AssertionError, a.append, psw.ColumnUnit(1, 200, "SEQUENCE"))
a.append(psw.ColumnUnit(0, 98, "SEQUENCE"))
self.assertRaises(AssertionError, a.append, psw.ColumnUnit(0, 200, "SEQUENCE"))
a.append(psw.ColumnUnit(1, 200, "SEQUENCE"))
self.assertRaises(AssertionError, a.append, psw.ColumnUnit(1, 200, "SEQUENCE"))
def test_AlignmentColumn_kinds(self):
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "INSERT"))
self.assertEqual(ac.kind, "INSERT")
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "INSERT"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "SEQUENCE"))
self.assertEqual(ac.kind, "INSERT")
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "SEQUENCE"))
self.assertEqual(ac.kind, "SEQUENCE")
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "END"))
self.assertEqual(ac.kind, "END")
def test_AlignmentColumn_repr(self):
ac = psw.AlignmentColumn(psw.ColumnUnit(0, 34, "SEQUENCE"))
ac.append(psw.ColumnUnit(1, 55, "END"))
self.assertEqual(repr(ac), "END(34, 55)")
def test_AlignmentColumn_full(self):
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "END"))
self.assertRaises(
psw.AlignmentColumnFullException,
ac.append,
psw.ColumnUnit(1, random.randint(0, 9999), "END"),
)
def test_AlignmentColumn_assertions(self):
self.assertRaises(
AssertionError,
psw.AlignmentColumn,
psw.ColumnUnit(1, random.randint(0, 9999), "SEQUENCE"),
)
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
self.assertRaises(
AssertionError,
ac.append,
psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"),
)
def test_ColumnUnit(self):
self.assertEqual(
repr(psw.ColumnUnit(0, 33, "SEQUENCE")),
"ColumnUnit(unit=0, column=33, kind='SEQUENCE')",
)
self.assertEqual(
repr(psw.ColumnUnit(1, 33, "INSERT")),
"ColumnUnit(unit=1, column=33, kind='INSERT')",
)
self.assertEqual(
repr(psw.ColumnUnit(1, 33, "END")),
"ColumnUnit(unit=1, column=33, kind='END')",
)
PARSED = (
"[SEQUENCE(39, 22), SEQUENCE(40, 23), SEQUENCE(41, 24), "
"SEQUENCE(42, 25), SEQUENCE(43, 26), SEQUENCE(44, 27), END(0, 27)]"
)
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity=2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests."""
unittest_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = "test_"
tests = [TestPSW]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
unittest_suite.addTest(cur_suite)
doctest_suite = doctest.DocTestSuite(psw)
big_suite = unittest.TestSuite((unittest_suite, doctest_suite))
return big_suite
if __name__ == "__main__":
unittest_suite = unittest.TestLoader().loadTestsFromName("test_psw")
doctest_suite = doctest.DocTestSuite(psw)
suite = unittest.TestSuite((unittest_suite, doctest_suite))
runner = unittest.TextTestRunner(sys.stdout, verbosity=2)
runner.run(suite)
|
