Merge branch 'master' of https://gitlab.binets.fr/etienne.morice/bioinf588

alignementseq_tests.py

@@ -123,6 +123,49 @@ class AlignmentSeqTestCase(unittest.TestCase):
                     print(ex_r1)
                     print(ex_r2)
                     raise
+    
+    def test_blosum_align2steps(self):
+        """Tests alignments with blosum and gap extension.
+        """
+        from alignementseq import align2steps
+        
+        for s1, s2, filename in self.get_dataset_heads():
+            (ex_r1, ex_r2, exp_score, *_) = Bio.pairwise2.align.globaldd(
+                s1.seq, s2.seq, blosum62, -8, -4, -8, -4, one_alignment_only=True)[0]
+            score, r1, r2 = align2steps(s1, s2)
+            try:
+                self.assertSameResidues(r1.seq, s1.seq)
+                self.assertSameResidues(r2.seq, s2.seq)
+                calc_score = 0   # score calculated from r1 and r2
+                gap1, gap2 = False, False
+                for a,b in zip(r1.seq, r2.seq):
+                    if a == '-':
+                        if not gap1:
+                            gap1 = True
+                            gap2 = False   # suppose 2 gaps are never aligned
+                            calc_score -= 8
+                        else:
+                            calc_score -= 4
+                    elif b == '-':
+                        if not gap2:
+                            gap2 = True
+                            gap1 = False
+                            calc_score -= 8
+                        else:
+                            calc_score -= 4
+                    else:
+                        gap1, gap2 = False, False
+                        calc_score += blosum62[a,b] if (a,b) in blosum62 else blosum62[b,a]
+                self.assertEqual(score, calc_score)
+                self.assertEqual(score, exp_score)
+            except AssertionError:
+                print('from', filename, "with", align2steps, ":")
+                print(r1.seq)
+                print(r2.seq)
+                print('')
+                print(ex_r1)
+                print(ex_r2)
+                raise
 
 class PerformanceTestCase(AlignmentSeqTestCase):
     """Performance tests, slow.