r27273 - /trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py -- January 22, 2015 - 17:00

Author: bugman
Date: Thu Jan 22 17:00:03 2015
New Revision: 27273

URL: http://svn.gna.org/viewcvs/relax?rev=27273&view=rev
Log:
Created a unit test for demonstrating a failure in the Needleman-Wunsch 
sequence alignment algorithm.

The test is Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4b from 
the
_lib._sequence_alignment.test_needleman_wunsch module.  The problem is that 
the start of the
alignment is truncated if any gaps are present.


Modified:
    
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py

Modified: 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py?rev=27273&r1=27272&r2=27273&view=diff
==============================================================================
--- 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py 
      (original)
+++ 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py 
      Thu Jan 22 17:00:03 2015
@@ -100,3 +100,43 @@
         for i in range(2):
             for j in range(8):
                 self.assertEqual(gaps[i, j], real_gaps[i][j])
+
+
+    def test_needleman_wunsch_align_NUC_4_4b(self):
+        """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
+        """
+
+        # The sequences.
+        seq1 = 'GACAGAAT'
+        seq2 = 'GAATA'
+        print("\nIn:")
+        print(seq1)
+        print(seq2)
+
+        # Perform the alignment. 
+        align1, align2, gaps = needleman_wunsch_align(seq1, seq2, 
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5, 
gap_extend_penalty=1)
+        print("\nOut:")
+        print(align1)
+        print(align2)
+        print(gaps)
+        print("\n")
+
+        # Check the alignment.
+        self.assertEqual(align1, 'GACAGAAT-')
+        self.assertEqual(align2, '----GAATA')
+
+        # The gap matrix.
+        real_gaps = [
+                [0, 0, 0, 0, 0, 0, 0, 0, 1],
+                [1, 1, 1, 1, 0, 0, 0, 0, 0]
+        ]
+        for i in range(2):
+            for j in range(8):
+                self.assertEqual(gaps[i, j], real_gaps[i][j])