Source Code for Module test_suite.unit_tests._data_store.test_seq_align

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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 data_store.seq_align import Sequence_alignments 
 27   
 28   
 29 -class Test_seq_align(TestCase): 
 30      """Unit tests for the data.seq_align relax module.""" 
 31   
 32   
 33 -    def setUp(self): 
 34          """Set 'self.seq_align' to an empty instance of the Sequence_alignments class.""" 
 35   
 36          self.seq_align = Sequence_alignments() 
 37   
 38   
 39 -    def generate_ids(self, object_ids, models, molecules): 
 40          """Generate the expected IDs.""" 
 41   
 42          # Generate the IDs. 
 43          ids = [] 
 44          for i in range(len(object_ids)): 
 45              ids.append("Object '%s'" % object_ids[i]) 
 46              if models[i] != None: 
 47                  ids[-1] += "; Model %i" % models[i] 
 48              ids[-1] += "; Molecule '%s'" % molecules[i] 
 49   
 50          # Return the IDs. 
 51          return ids 
 52   
 53   
 54 -    def return_align_data(self): 
 55          """Return a data set for alignment testing.""" 
 56   
 57          # The data. 
 58          object_ids = ['frame_order', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble'] 
 59          models = [None, 1, 1, 1, 1, 1, 1, 1] 
 60          molecules = [ 
 61              'N-dom', 
 62              'ensemble 4M A', 
 63              'ensemble 4M B', 
 64              'ensemble 4M C', 
 65              'ensemble 4M D', 
 66              'CaM-IQ A', 
 67              'CaM-IQ B', 
 68              'CaM-IQ C' 
 69          ] 
 70          sequences = [ 
 71              'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK*****', 
 72              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****', 
 73              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****', 
 74              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****', 
 75              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****', 
 76              '                                                                                                                           QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****', 
 77              '                                                                                                                           LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****', 
 78              '                                                                                                                           LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****', 
 79   
 80              'TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG', 
 81              'ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKM', 
 82              'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR' 
 83          ] 
 84          strings = [ 
 85              '---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK------------------------------------------------------------------------*****----------------------------------------------------------------------------', 
 86              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----------------------------------------------------------------------------MKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****', 
 87              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------', 
 88              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------', 
 89              '*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------', 
 90              '--QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------', 
 91              '---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------', 
 92              '---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK-------EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------', 
 93          ] 
 94          gaps = [] 
 95          for i in range(len(strings)): 
 96              gaps.append([]) 
 97              for j in range(len(strings[0])): 
 98                  if strings[i][j] == '-': 
 99                      gaps[i].append(1) 
100                  else: 
101                      gaps[i].append(0) 
102          msa_algorithm = 'Central Star' 
103          pairwise_algorithm = 'NW70' 
104          matrix = 'BLOSUM62' 
105          gap_open_penalty = 10.0 
106          gap_extend_penalty = 1.0 
107          end_gap_open_penalty = 0.0 
108          end_gap_extend_penalty = 0.0 
109   
110          # Return the data. 
111          return object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty 
112   
113   
114 -    def test_alignment_addition(self): 
115          """Test the creation of a new sequence alignment object.""" 
116   
117          # The data. 
118          object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data() 
119   
120          # Add the alignment. 
121          self.seq_align.add(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, strings=strings, gaps=gaps, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty) 
122   
123          # Generate the expected IDs. 
124          ids = self.generate_ids(object_ids, models, molecules) 
125   
126          # Check the data. 
127          for i in range(8): 
128              print("Checking \"%s\"" % ids[i]) 
129              self.assertEqual(self.seq_align[0].ids[i], ids[i]) 
130              self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i]) 
131              self.assertEqual(self.seq_align[0].models[i], models[i]) 
132              self.assertEqual(self.seq_align[0].molecules[i], molecules[i]) 
133              self.assertEqual(self.seq_align[0].sequences[i], sequences[i]) 
134              self.assertEqual(self.seq_align[0].strings[i], strings[i]) 
135              self.assertEqual(self.seq_align[0].gaps[i], gaps[i]) 
136              self.assertEqual(self.seq_align[0].msa_algorithm, msa_algorithm) 
137              self.assertEqual(self.seq_align[0].pairwise_algorithm, pairwise_algorithm) 
138              self.assertEqual(self.seq_align[0].matrix, matrix) 
139              self.assertEqual(self.seq_align[0].gap_open_penalty, gap_open_penalty) 
140              self.assertEqual(self.seq_align[0].gap_extend_penalty, gap_extend_penalty) 
141              self.assertEqual(self.seq_align[0].end_gap_open_penalty, end_gap_open_penalty) 
142              self.assertEqual(self.seq_align[0].end_gap_extend_penalty, end_gap_extend_penalty) 
143   
144   
145 -    def test_find_alignment(self): 
146          """Test the retrieval of pre-existing alignment.""" 
147   
148          # Execute the body of the test_alignment_addition() unit test to set up the object. 
149          self.test_alignment_addition() 
150   
151          # The identifying data. 
152          object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data() 
153   
154          # Retrieve the alignment. 
155          align = self.seq_align.find_alignment(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty) 
156   
157          # Check that something was returned. 
158          self.assertNotEqual(align, None) 
159   
160          # Generate the expected IDs. 
161          ids = self.generate_ids(object_ids, models, molecules) 
162   
163          # Check some of the data. 
164          for i in range(8): 
165              print("Checking \"%s\"" % ids[i]) 
166              self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i]) 
167              self.assertEqual(self.seq_align[0].models[i], models[i]) 
168              self.assertEqual(self.seq_align[0].molecules[i], molecules[i]) 
169   
170   
171 -    def test_find_missing_alignment(self): 
172          """Test the retrieval of non-existent alignment.""" 
173   
174          # Execute the body of the test_alignment_addition() unit test to set up the object. 
175          self.test_alignment_addition() 
176   
177          # The identifying data. 
178          object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data() 
179   
180          # Change a gap penalty. 
181          gap_open_penalty = 0.5 
182   
183          # Retrieve the alignment. 
184          align = self.seq_align.find_alignment(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty) 
185   
186          # Check that nothing was returned. 
187          self.assertEqual(align, None) 
188