Permalink
Cannot retrieve contributors at this time
Fetching contributors…
Cannot retrieve contributors at this time
| #!/usr/bin/env python | |
| # 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. | |
| import doctest | |
| import unittest | |
| import random | |
| import sys | |
| if 'requires_wise' in sys.modules: | |
| del sys.modules['requires_wise'] | |
| import requires_wise | |
| from Bio.Wise import psw | |
| 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, SEQUENCE)") | |
| self.assertEqual(repr(psw.ColumnUnit(1, 33, "INSERT")), | |
| "ColumnUnit(unit=1, column=33, INSERT)") | |
| self.assertEqual(repr(psw.ColumnUnit(1, 33, "END")), | |
| "ColumnUnit(unit=1, column=33, END)") | |
| PARSED = "[SEQUENCE(39, 22), SEQUENCE(40, 23), SEQUENCE(41, 24), SEQUENCE(42, 25), SEQUENCE(43, 26), SEQUENCE(44, 27), END(0, 27)]" | |
| # def test_align(self): | |
| # self.assertEqual(repr(psw.align(("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), "introns.bla", 23, 5, quiet=True)), self.PARSED) | |
| 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) |