Source Code for Module test_suite.unit_tests._lib._sequence_alignment.test_needleman_wunsch

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  2  #                                                                             # 
  3  # Copyright (C) 2015 Edward d'Auvergne                                        # 
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 21   
 22  # Python module imports. 
 23  from unittest import TestCase 
 24   
 25  # relax module imports. 
 26  from lib.sequence_alignment.needleman_wunsch import needleman_wunsch_align 
 27  from lib.sequence_alignment.substitution_matrices import NUC_4_4, NUC_4_4_SEQ, SIMILARITY_DNA, SIMILARITY_DNA_SEQ 
 28   
 29   
 30 -class Test_needleman_wunsch(TestCase): 
 31      """Unit tests for the lib.sequence_alignment.needleman_wunsch relax module.""" 
 32   
 33 -    def test_needleman_wunsch_align_DNA(self): 
 34          """Test the Needleman-Wunsch sequence alignment for two DNA sequences.""" 
 35   
 36          # The sequences. 
 37          seq1 = 'GCATTACT' 
 38          seq2 = 'GATTACT' 
 39          print("\nIn:") 
 40          print(seq1) 
 41          print(seq2) 
 42   
 43          # Perform the alignment.  
 44          score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2, sub_matrix=SIMILARITY_DNA, sub_seq=SIMILARITY_DNA_SEQ, gap_open_penalty=1, gap_extend_penalty=1) 
 45          print("\nOut:") 
 46          print(score) 
 47          print(align1) 
 48          print(align2) 
 49          print(gaps) 
 50          print("\n") 
 51   
 52          # Check the alignment. 
 53          self.assertEqual(align1, 'GCATTACT') 
 54          self.assertEqual(align2, 'G-ATTACT') 
 55   
 56          # The gap matrix. 
 57          real_gaps = [ 
 58                  [0, 0, 0, 0, 0, 0, 0, 0], 
 59                  [0, 1, 0, 0, 0, 0, 0, 0] 
 60          ] 
 61          for i in range(2): 
 62              for j in range(8): 
 63                  self.assertEqual(gaps[i, j], real_gaps[i][j]) 
 64   
 65   
 66 -    def test_needleman_wunsch_align_NUC_4_4(self): 
 67          """Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix. 
 68   
 69          From online servers, the results with a gap open penalty of 5 and gap extend of 1 should be:: 
 70   
 71              https://www.ebi.ac.uk/Tools/psa/emboss_needle/ 
 72              EMBOSS_001         1 GAAAAAAT      8 
 73                                   |    ||| 
 74              EMBOSS_001         1 G----AAT      4 
 75          """ 
 76   
 77          # The sequences. 
 78          seq1 = 'GAAAAAAT' 
 79          seq2 = 'GAAT' 
 80          print("\nIn:") 
 81          print(seq1) 
 82          print(seq2) 
 83   
 84          # Perform the alignment.  
 85          score, 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) 
 86          print("\nOut:") 
 87          print(score) 
 88          print(align1) 
 89          print(align2) 
 90          print(gaps) 
 91          print("\n") 
 92   
 93          # Check the alignment. 
 94          self.assertEqual(align1, 'GAAAAAAT') 
 95          self.assertEqual(align2, 'G----AAT') 
 96   
 97          # The gap matrix. 
 98          real_gaps = [ 
 99                  [0, 0, 0, 0, 0, 0, 0, 0], 
100                  [0, 1, 1, 1, 1, 0, 0, 0] 
101          ] 
102          for i in range(2): 
103              for j in range(8): 
104                  self.assertEqual(gaps[i, j], real_gaps[i][j]) 
105   
106   
107 -    def test_needleman_wunsch_align_NUC_4_4b(self): 
108          """Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix. 
109   
110          From online servers, the results with a gap open penalty of 5 and gap extend of 1 should be:: 
111   
112              https://www.ebi.ac.uk/Tools/psa/emboss_needle/ 
113              EMBOSS_001         1 GACAGAAT-      8 
114                                       ||||  
115              EMBOSS_001         1 ----GAATA      5 
116          """ 
117   
118          # The sequences. 
119          seq1 = 'GACAGAAT' 
120          seq2 = 'GAATA' 
121          print("\nIn:") 
122          print(seq1) 
123          print(seq2) 
124   
125          # Perform the alignment.  
126          score, 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) 
127          print("\nOut:") 
128          print(score) 
129          print(align1) 
130          print(align2) 
131          print(gaps) 
132          print("\n") 
133   
134          # Check the alignment. 
135          self.assertEqual(align1, 'GACAGAAT-') 
136          self.assertEqual(align2, '----GAATA') 
137   
138          # The gap matrix. 
139          real_gaps = [ 
140                  [0, 0, 0, 0, 0, 0, 0, 0, 1], 
141                  [1, 1, 1, 1, 0, 0, 0, 0, 0] 
142          ] 
143          for i in range(2): 
144              for j in range(8): 
145                  self.assertEqual(gaps[i, j], real_gaps[i][j]) 
146