More matching tests

Author: jeromekelleher

tests/test_inference.py

@@ -576,44 +576,99 @@ def test_exact_matches(
         assert len(s.path) == 1
         assert s.path[0].parent == parent
 
-    # def test_stuff(
-    #     self, tmp_path, fx_ts_2020_02_10, fx_alignment_store, fx_metadata_db
-    # ):
-    #     # SRR11597207 0 42 0
-    #     # SRR11597218 1 10 1
-
-    #     # date = "2020-02-11" # 2 samples
-    #     date = "2020-02-13"  # 4 samples
-    #     samples = sc2ts.preprocess(
-    #         date,
-    #         metadata_db=fx_metadata_db,
-    #         alignment_store=fx_alignment_store,
-    #         base_ts=fx_ts_2020_02_10,
-    #     )
-    #     # print(samples)
-
-    #     num_mismatches = 3
-    #     sc2ts.match_tsinfer(
-    #         samples=samples,
-    #         ts=fx_ts_2020_02_10,
-    #         num_mismatches=3,
-    #         precision=12,
-    #         num_threads=0,
-    #     )
-    #     for sample in samples:
-    #         print(
-    #             sample.strain,
-    #             sample.get_hmm_cost(num_mismatches),
-    #             sample.path[0].parent,
-    #             len(sample.mutations),
-    #         )
-
-    #     # match_db = sc2ts.MatchDb.initialise(tmp_path / "match.db")
-    #     # ts = sc2ts.extend(
-    #     #     alignment_store=fx_alignment_store,
-    #     #     metadata_db=fx_metadata_db,
-    #     #     base_ts=fx_ts_2020_02_10,
-    #     #     date="2020-02-11",
-    #     #     match_db=match_db,
-    #     #     min_group_size=2,
-    #     # )
+    @pytest.mark.parametrize(
+        ("strain", "parent", "position", "derived_state"),
+        [("SRR11597218", 10, 289, "T"), ("ERR4206593", 62, 26994, "T")],
+    )
+    @pytest.mark.parametrize("num_mismatches", [1, 2, 3, 4])
+    @pytest.mark.parametrize("precision", [0, 1, 2, 12])
+    def test_one_mismatch(
+        self,
+        fx_ts_2020_02_10,
+        fx_alignment_store,
+        fx_metadata_db,
+        strain,
+        parent,
+        position,
+        derived_state,
+        num_mismatches,
+        precision,
+    ):
+        samples = sc2ts.preprocess(
+            [fx_metadata_db[strain]], fx_ts_2020_02_10, "2020-02-20", fx_alignment_store
+        )
+        sc2ts.match_tsinfer(
+            samples=samples,
+            ts=fx_ts_2020_02_10,
+            num_mismatches=num_mismatches,
+            precision=precision,
+            num_threads=0,
+        )
+        s = samples[0]
+        assert len(s.mutations) == 1
+        assert s.mutations[0].site_position == position
+        assert s.mutations[0].derived_state == derived_state
+        assert len(s.path) == 1
+        assert s.path[0].parent == parent
+
+    @pytest.mark.parametrize("num_mismatches", [2, 3, 4])
+    @pytest.mark.parametrize("precision", [0, 1, 2, 12])
+    def test_two_mismatches(
+        self,
+        fx_ts_2020_02_10,
+        fx_alignment_store,
+        fx_metadata_db,
+        num_mismatches,
+        precision,
+    ):
+        strain = "ERR4204459"
+        samples = sc2ts.preprocess(
+            [fx_metadata_db[strain]], fx_ts_2020_02_10, "2020-02-20", fx_alignment_store
+        )
+        sc2ts.match_tsinfer(
+            samples=samples,
+            ts=fx_ts_2020_02_10,
+            num_mismatches=num_mismatches,
+            precision=precision,
+            num_threads=0,
+        )
+        s = samples[0]
+        assert len(s.path) == 1
+        assert s.path[0].parent == 5
+        assert len(s.mutations) == 2
+        # assert s.mutations[0].site_position == position
+        # assert s.mutations[0].derived_state == derived_state
+
+
+#     def test_stuff(
+#         self,
+#         fx_ts_2020_02_10,
+#         fx_alignment_store,
+#         fx_metadata_db):
+
+#         # date = "2020-02-11" # 2 samples
+#         date = "2020-02-13"  # 4 samples
+
+#         # metadata_matches =
+#         samples = sc2ts.preprocess(
+#             list(fx_metadata_db.get(date)),
+#             fx_ts_2020_02_10,
+#             date, fx_alignment_store
+#         )
+#         # print(samples)
+
+#         num_mismatches = 3
+#         sc2ts.match_tsinfer(
+#             samples=samples,
+#             ts=fx_ts_2020_02_10,
+#             num_mismatches=3,
+#             precision=12,
+#             num_threads=0,
+#         )
+#         for sample in samples:
+#             print(
+#                 sample.strain,
+#                 sample.get_hmm_cost(num_mismatches),
+#                 sample.path[0].parent,
+#                 len(sample.mutations),
+#             )