Class Test_needleman_wunsch

source code

Unit tests for the lib.sequence_alignment.needleman_wunsch relax module.

Nested Classes

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Inherited from unittest.case.TestCase: failureException

Instance Methods

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test_needleman_wunsch_align_DNA(self)
Test the Needleman-Wunsch sequence alignment for two DNA sequences.

source code

test_needleman_wunsch_align_NUC_4_4(self)
Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.

source code

test_needleman_wunsch_align_NUC_4_4b(self)
Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.

source code

Inherited from unittest.case.TestCase: __call__, __eq__, __hash__, __init__, __ne__, __repr__, __str__, addCleanup, addTypeEqualityFunc, assertAlmostEqual, assertAlmostEquals, assertDictContainsSubset, assertDictEqual, assertEqual, assertEquals, assertFalse, assertGreater, assertGreaterEqual, assertIn, assertIs, assertIsInstance, assertIsNone, assertIsNot, assertIsNotNone, assertItemsEqual, assertLess, assertLessEqual, assertListEqual, assertMultiLineEqual, assertNotAlmostEqual, assertNotAlmostEquals, assertNotEqual, assertNotEquals, assertNotIn, assertNotIsInstance, assertNotRegexpMatches, assertRaises, assertRaisesRegexp, assertRegexpMatches, assertSequenceEqual, assertSetEqual, assertTrue, assertTupleEqual, assert_, countTestCases, debug, defaultTestResult, doCleanups, fail, failIf, failIfAlmostEqual, failIfEqual, failUnless, failUnlessAlmostEqual, failUnlessEqual, failUnlessRaises, id, run, setUp, shortDescription, skipTest, tearDown

Inherited from unittest.case.TestCase (private): _addSkip, _baseAssertEqual, _deprecate, _formatMessage, _getAssertEqualityFunc, _truncateMessage

Inherited from object: __delattr__, __format__, __getattribute__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Class Methods

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Inherited from unittest.case.TestCase: setUpClass, tearDownClass

Class Variables

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Inherited from unittest.case.TestCase: longMessage, maxDiff

Inherited from unittest.case.TestCase (private): _classSetupFailed, _diffThreshold

Properties

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Inherited from object: __class__

Method Details

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test_needleman_wunsch_align_NUC_4_4(self)

source code

Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.

From online servers, the results with a gap open penalty of 5 and gap extend of 1 should be:

   https://www.ebi.ac.uk/Tools/psa/emboss_needle/
   EMBOSS_001         1 GAAAAAAT      8
                        |    |||
   EMBOSS_001         1 G----AAT      4

test_needleman_wunsch_align_NUC_4_4b(self)

source code

Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.

From online servers, the results with a gap open penalty of 5 and gap extend of 1 should be:

   https://www.ebi.ac.uk/Tools/psa/emboss_needle/
   EMBOSS_001         1 GACAGAAT-      8
                            |||| 
   EMBOSS_001         1 ----GAATA      5