test_suite.unit_tests._lib._sequence_alignment.test_msa.Test

Class Test_msa

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

Nested Classes

Inherited from unittest.case.TestCase: failureException

Instance Methods

test_central_star(self)
Test the central star multiple sequence alignment function lib.sequence_alignment.msa.central_star().

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

[hide private]

Inherited from unittest.case.TestCase: setUpClass, tearDownClass

Class Variables

[hide private]

Inherited from unittest.case.TestCase: longMessage, maxDiff

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

Properties

[hide private]

Inherited from object: __class__

test_central_star(self)

source code

Test the central star multiple sequence alignment function lib.sequence_alignment.msa.central_star().

This uses the sequences:

'TEEQVDADGGT',
'ADQLTEEQVDADGNGTIDFPEFLTMMARKM',
'LTEEQMINEVDAGNGTIDFPEFLTMMAR'.

The result should be:

   Pairwise protein alignment.
   Substitution matrix:           BLOSUM62
   Gap opening penalty:           5.0
   Gap extend penalty:            1.0
   
   Input sequence 1:              TEEQVDADGGT
   Input sequence 2:              ADQLTEEQVDADGNGTIDFPEFLTMMARKM
   
   Aligned sequence 1:            ----TEEQVDADG-GT--------------
   Aligned sequence 2:            ADQLTEEQVDADGNGTIDFPEFLTMMARKM
                                      ********* **              
   
   
   Pairwise protein alignment.
   Substitution matrix:           BLOSUM62
   Gap opening penalty:           5.0
   Gap extend penalty:            1.0
   
   Input sequence 1:              TEEQVDADGGT
   Input sequence 2:              LTEEQMINEVDAGNGTIDFPEFLTMMAR
   
   Aligned sequence 1:            -TEEQ----VDADGGT------------
   Aligned sequence 2:            LTEEQMINEVDAGNGTIDFPEFLTMMAR
                                   ****    ***  **            

   ----TEEQ----VDADG-GT--------------
   ADQLTEEQ----VDADGNGTIDFPEFLTMMARKM
   ---LTEEQMINEVDA-GNGTIDFPEFLTMMAR--