Add tests for the new contig stitcher

cfe-lab · Nov 7, 2023 · 5041750 · 5041750
1 parent a42f4aa
commit 5041750
Showing 1 changed file with 46 additions and 0 deletions.
diff --git a/micall/tests/test_contig_stitcher.py b/micall/tests/test_contig_stitcher.py
@@ -15,3 +15,49 @@ def test_1():
     result = list(stitch_contigs(contigs))
     assert sorted(map(lambda x: x.seq, contigs)) \
         == sorted(map(lambda x: x.seq, result))
+
+
+def test_2():
+    ref_seq = 'A' * 100
+
+    contigs = [
+        GenotypedContig(name='a',
+                        seq=ref_seq,
+                        ref_name='testref',
+                        ref_seq=ref_seq,
+                        matched_fraction=0.5,
+                        ),
+        GenotypedContig(name='b',
+                        seq='C' * 100,
+                        ref_name='testref',
+                        ref_seq=ref_seq,
+                        matched_fraction=0.5,
+                        ),
+        ]
+
+    result = list(stitch_contigs(contigs))
+    assert sorted(map(lambda x: x.seq, contigs)) \
+        == sorted(map(lambda x: x.seq, result))
+
+
+def test_3():
+    ref_seq = 'A' * 100 + 'C' * 100
+
+    contigs = [
+        GenotypedContig(name='a',
+                        seq='A' * 50 + 'C' * 20,
+                        ref_name='testref',
+                        ref_seq=ref_seq,
+                        matched_fraction=0.5,
+                        ),
+        GenotypedContig(name='b',
+                        seq='A' * 20 + 'C' * 50,
+                        ref_name='testref',
+                        ref_seq=ref_seq,
+                        matched_fraction=0.5,
+                        ),
+        ]
+
+    result = list(stitch_contigs(contigs))
+    assert 100 == sum(len(x.seq) for x in result)
+    assert result[0].contig.name == 'a+overlap(a,b)+b'