r27259 - /trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py -- January 21, 2015 - 15:52

Author: bugman
Date: Wed Jan 21 15:52:03 2015
New Revision: 27259

URL: http://svn.gna.org/viewcvs/relax?rev=27259&view=rev
Log:
Created a unit test for lib.sequence_alignment.align_protein.align_pairwise().

This is to test the pairwise alignment of two protein sequences using the 
Needleman-Wunsch sequence
alignment algorithm, BLOSUM62 substitution matrix, and gap penalty of 10.0.


Added:
    trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
      - copied, changed from r27254, 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py

Copied: 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py 
(from r27254, 
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_align_protein.py?p2=trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py&p1=trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py&r1=27254&r2=27259&rev=27259&view=diff
==============================================================================
--- 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py 
      (original)
+++ 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py  
Wed Jan 21 15:52:03 2015
@@ -20,39 +20,62 @@
 
###############################################################################
 
 # Python module imports.
+from numpy import int16, zeros
 from unittest import TestCase
 
 # relax module imports.
-from lib.sequence_alignment.needleman_wunsch import needleman_wunsch_align
+from lib.sequence_alignment.align_protein import align_pairwise
 
 
-class Test_needleman_wunsch(TestCase):
-    """Unit tests for the lib.sequence_alignment.needleman_wunsch relax 
module."""
+class Test_align_protein(TestCase):
+    """Unit tests for the lib.sequence_alignment.align_protein relax 
module."""
 
-    def test_needleman_wunsch_align_DNA(self):
-        """Test the Needleman-Wunsch sequence alignment for two DNA 
sequences."""
+    def test_align_pairwise(self):
+        """Test the Needleman-Wunsch sequence alignment for two protein 
sequences.
+
+        This uses the sequences:
+
+            - 
'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
+            - 
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.
+
+        From online servers, the results 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
+                                  *** *** *** ** * *   ********** *    * * 
******** **  *  *  * * **
+        """
 
         # The sequences.
-        seq1 = 'GCATGCU'
-        seq2 = 'GATTACA'
+        seq1 = 
'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla'
+        seq2 = 
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'
         print(seq1)
         print(seq2)
 
         # Perform the alignment. 
-        align1, align2, gaps = needleman_wunsch_align(seq1, seq2)
+        align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62', 
gap_penalty=10.0)
         print(align1)
         print(align2)
         print(gaps)
 
         # Check the alignment.
-        self.assertEqual(align1, 'GCA-TGCU')
-        self.assertEqual(align2, 'G-ATTACA')
+        self.assertEqual(align1, 
'IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA')
+        self.assertEqual(align2, 
'LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-')
 
         # The gap matrix.
-        real_gaps = [
-                [0, 0, 0, 1, 0, 0, 0, 0],
-                [0, 1, 0, 0, 0, 0, 0, 0]
-        ]
+        real_gaps = zeros((2, 68), int16)
+        real_gaps[0, 15] = 1
+        real_gaps[0, 17] = 1
+        real_gaps[0, 19] = 1
+        real_gaps[0, 20] = 1
+        real_gaps[0, 21] = 1
+        real_gaps[0, 36] = 1
+        real_gaps[1, 67] = 1
         for i in range(2):
-            for j in range(8):
+            for j in range(68):
                 self.assertEqual(gaps[i, j], real_gaps[i][j])