fix liftover test

conftest.py

@@ -11,6 +11,7 @@
 from pgscatalog_utils.download.download_scorefile import download_scorefile
 from pgscatalog_utils.match.preprocess import complement_valid_alleles
 from pgscatalog_utils.scorefile.combine_scorefiles import combine_scorefiles
+from pgscatalog_utils.scorefile.scorevariant import ScoreVariant
 
 from tests.data import combine
 
@@ -94,17 +95,57 @@ def chain_files(tmp_path_factory):
 
 @pytest.fixture(scope="session")
 def hg38_coords():
-    rs11903757 = {"rsid": "rs11903757", "chr_name": "2", "chr_position": 191722478}
-    rs6061231 = {"rsid": "rs6061231", "chr_name": "20", "chr_position": 62381861}
-    return [rs11903757, rs6061231]
+    rs11903757 = ScoreVariant(
+        **{
+            "rsid": "rs11903757",
+            "chr_name": "2",
+            "chr_position": 191722478,
+            "row_nr": 0,
+            "effect_weight": 1,
+            "accession": "test",
+            "effect_allele": "A",
+        }
+    )
+    rs6061231 = ScoreVariant(
+        **{
+            "rsid": "rs6061231",
+            "chr_name": "20",
+            "chr_position": 62381861,
+            "row_nr": 1,
+            "effect_weight": 1,
+            "accession": "test",
+            "effect_allele": "A",
+        }
+    )
+    return (x for x in [rs11903757, rs6061231])
 
 
 @pytest.fixture(scope="session")
 def hg19_coords():
     # hg38_coords in GRCh37, from dbSNP
-    rs11903757 = {"rsid": "rs11903757", "chr_name": "2", "chr_position": 192587204}
-    rs6061231 = {"rsid": "rs6061231", "chr_name": "20", "chr_position": 60956917}
-    return [rs11903757, rs6061231]
+    rs11903757 = ScoreVariant(
+        **{
+            "rsid": "rs11903757",
+            "chr_name": "2",
+            "chr_position": 192587204,
+            "row_nr": 0,
+            "effect_weight": 1,
+            "accession": "test",
+            "effect_allele": "A",
+        }
+    )
+    rs6061231 = ScoreVariant(
+        **{
+            "rsid": "rs6061231",
+            "chr_name": "20",
+            "chr_position": 60956917,
+            "row_nr": 1,
+            "effect_weight": 1,
+            "accession": "test",
+            "effect_allele": "A",
+        }
+    )
+    return (x for x in [rs11903757, rs6061231])
 
 
 @pytest.fixture(scope="session")

tests/test_liftover.py

@@ -10,32 +10,30 @@ def test_liftover(hg38_coords, hg19_coords, chain_files):
     Config.chain_dir = chain_files
     Config.lo = create_liftover()
     Config.min_lift = 0.95
-
-    hg38 = copy.deepcopy(hg38_coords)
+    hg38 = list(hg38_coords)
+    hg19 = list(hg19_coords)
+    hg19_ = copy.deepcopy(hg19)
+    hg38_ = copy.deepcopy(hg38)
     lifted = list(
         liftover(
-            hg38,
+            (x for x in hg38),
             harmonised=False,
             current_build=GenomeBuild.GRCh38,
             target_build=GenomeBuild.GRCh37,
         )
     )
 
-    assert [x["chr_position"] for x in lifted] == [
-        x["chr_position"] for x in hg19_coords
-    ]
-    assert [x["chr_name"] for x in lifted] == [x["chr_name"] for x in hg19_coords]
+    assert [x.chr_position for x in lifted] == [x.chr_position for x in hg19_]
+    assert [x.chr_name for x in lifted] == [x.chr_name for x in hg19_]
 
-    hg19 = copy.deepcopy(hg19_coords)
+    hg19 = copy.deepcopy(hg19)
     lift_back = list(
         liftover(
-            hg19,
+            (x for x in hg19),
             harmonised=False,
             current_build=GenomeBuild.GRCh37,
             target_build=GenomeBuild.GRCh38,
         )
     )
-    assert [x["chr_position"] for x in lift_back] == [
-        x["chr_position"] for x in hg38_coords
-    ]
-    assert [x["chr_name"] for x in lift_back] == [x["chr_name"] for x in hg38_coords]
+    assert [x.chr_position for x in lift_back] == [x.chr_position for x in hg38_]
+    assert [x.chr_name for x in lift_back] == [x.chr_name for x in hg38_]