test: adjust testing to absence of sift and polyphen

opentargets · Dec 7, 2023 · 3dd52ed · 3dd52ed
1 parent de6f083
commit 3dd52ed
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Showing 2 changed files with 0 additions and 19 deletions.
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -338,11 +338,6 @@ def mock_variant_annotation(spark: SparkSession) -> VariantAnnotation:
             expr='array(named_struct("alleleFrequency", rand(), "populationName", cast(rand() as string)))',
             percentNulls=0.1,
         )
-        .withColumnSpec(
-            "cadd",
-            expr='named_struct("phred", cast(rand() as float), "raw", cast(rand() as float))',
-            percentNulls=0.1,
-        )
         .withColumnSpec("rsIds", expr="array(cast(rand() AS string))", percentNulls=0.1)
         .withColumnSpec(
             "vep",

diff --git a/tests/dataset/test_variant_annotation.py b/tests/dataset/test_variant_annotation.py
@@ -15,20 +15,6 @@ def test_variant_index_creation(mock_variant_annotation: VariantAnnotation) -> N
     assert isinstance(mock_variant_annotation, VariantAnnotation)
 
 
-def test_get_polyphen_v2g(
-    mock_variant_annotation: VariantAnnotation, mock_gene_index: GeneIndex
-) -> None:
-    """Test get_polyphen_v2g with mock variant annotation."""
-    assert isinstance(mock_variant_annotation.get_polyphen_v2g(mock_gene_index), V2G)
-
-
-def test_get_sift_v2g(
-    mock_variant_annotation: VariantAnnotation, mock_gene_index: GeneIndex
-) -> None:
-    """Test get_sift_v2g with mock variant annotation."""
-    assert isinstance(mock_variant_annotation.get_sift_v2g(mock_gene_index), V2G)
-
-
 def test_get_plof_v2g(
     mock_variant_annotation: VariantAnnotation, mock_gene_index: GeneIndex
 ) -> None: