Package test_suite :: Package unit_tests :: Package _lib :: Package _sequence_alignment :: Module test_align_protein :: Class Test_align_protein
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Class Test_align_protein

source code


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

Nested Classes [hide private]

Inherited from unittest.case.TestCase: failureException

Instance Methods [hide private]
 
test_align_pairwise(self)
Test the Needleman-Wunsch sequence alignment for two protein sequences.
source code
 
test_align_pairwise_PAM250(self)
Test the Needleman-Wunsch sequence alignment for two protein sequences using the PAM250 substitution 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 [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__

Method Details [hide private]

test_align_pairwise(self)

source code 

Test the Needleman-Wunsch sequence alignment for two protein sequences.

This uses the sequences:

  • 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
  • 'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.

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           IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA
                        :|||:|||:|||:|| | |   ||||||||||:|.. .|:|:||||||||:||:.|::|.:|:|.||
   EMBOSS_001           LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-

   http://web.expasy.org/cgi-bin/sim/sim.pl?prot
   UserSeq1             IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKL
   UserSeq2             LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL
                         *** *** *** ** * *   ********** *    * * ******** **  *  *  * * **

test_align_pairwise_PAM250(self)

source code 

Test the Needleman-Wunsch sequence alignment for two protein sequences using the PAM250 substitution matrix.

This uses the sequences:

  • 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
  • 'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.

From online servers, the results with a gap open penalty of 5 and gap extend of 0.5 should be:

   https://www.ebi.ac.uk/Tools/psa/emboss_needle/
   EMBOSS_001          IHAAEEKDWKTAYSYb--g---FYEAFEGYdsidspk--aitslkymllckimlntpedvqalvsgkla
                       :|||:|||.|||:||.  |   ||||||||||:|. |  |:|:||||||||:||:.|::|::|:|:|| 
   EMBOSS_001          LHAADEKDFKTAFSYabiggapFYEAFEGYdsvde-kvsaltalkymllckvmldlpdevnsllsakl-

   http://web.expasy.org/cgi-bin/sim/sim.pl?prot
   UserSeq1            IHAAEEKDWKTAYSYBG-----FYEAFEGYDSIDSPK--AITSLKYMLLCKIMLNTPEDVQALVSGKL
   UserSeq2            LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDE-KVSALTALKYMLLCKVMLDLPDEVNSLLSAKL
                        *** *** *** **       ********** *  *  * * ******** **  *  *  * * **