feat: required changes in variant index

opentargets · Dec 7, 2023 · 0d1b387 · 0d1b387
1 parent f208d60
commit 0d1b387
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Showing 3 changed files with 58 additions and 12 deletions.
diff --git a/src/otg/assets/schemas/variant_index.json b/src/otg/assets/schemas/variant_index.json
@@ -76,26 +76,72 @@
       "metadata": {}
     },
     {
-      "name": "cadd",
+      "name": "inSilicoPredictors",
+      "nullable": false,
+      "metadata": {},
       "type": {
         "type": "struct",
         "fields": [
           {
-            "name": "phred",
-            "type": "float",
+            "name": "cadd",
+            "nullable": true,
+            "metadata": {},
+            "type": {
+              "type": "struct",
+              "fields": [
+                {
+                  "name": "raw",
+                  "type": "float",
+                  "nullable": true,
+                  "metadata": {}
+                },
+                {
+                  "name": "phred",
+                  "type": "float",
+                  "nullable": true,
+                  "metadata": {}
+                }
+              ]
+            }
+          },
+          {
+            "name": "revelMax",
+            "type": "double",
             "nullable": true,
             "metadata": {}
           },
           {
-            "name": "raw",
+            "name": "spliceaiDsMax",
             "type": "float",
             "nullable": true,
             "metadata": {}
+          },
+          {
+            "name": "pangolinLargestDs",
+            "type": "double",
+            "nullable": true,
+            "metadata": {}
+          },
+          {
+            "name": "phylop",
+            "type": "double",
+            "nullable": true,
+            "metadata": {}
+          },
+          {
+            "name": "siftMax",
+            "type": "double",
+            "nullable": true,
+            "metadata": {}
+          },
+          {
+            "name": "polypheMax",
+            "type": "double",
+            "nullable": true,
+            "metadata": {}
           }
         ]
-      },
-      "nullable": true,
-      "metadata": {}
+      }
     },
     {
       "name": "mostSevereConsequence",

diff --git a/src/otg/dataset/variant_index.py b/src/otg/dataset/variant_index.py
@@ -58,7 +58,7 @@ def from_variant_annotation(
             "positionB37",
             "alleleType",
             "alleleFrequencies",
-            "cadd",
+            "inSilicoPredictors",
         ]
         va_slimmed = variant_annotation.filter_by_variant_df(
             study_locus.unique_variants_in_locus()

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -354,13 +354,13 @@ def mock_variant_annotation(spark: SparkSession) -> VariantAnnotation:
             expr='named_struct("cadd", named_struct("phred", cast(rand() as float), "raw_score", cast(rand() as float)), "revelMax", cast(rand() as double), "spliceaiDsMax", cast(rand() as float), "pangolinLargestDs", cast(rand() as double), "phylop", cast(rand() as double), "polyphenMax", cast(rand() as double), "siftMax", cast(rand() as double))',
             percentNulls=0.1,
         )
-
     )
     return VariantAnnotation(_df=data_spec.build(), _schema=va_schema)
 
+
 @pytest.fixture()
 def mock_variant_index(spark: SparkSession) -> VariantIndex:
-    """Mock gene index."""
+    """Mock variant index."""
     vi_schema = VariantIndex.get_schema()
 
     data_spec = (
@@ -383,8 +383,8 @@ def mock_variant_index(spark: SparkSession) -> VariantIndex:
             percentNulls=0.1,
         )
         .withColumnSpec(
-            "cadd",
-            expr='named_struct("phred", cast(rand() AS float), "raw", cast(rand() AS float))',
+            "inSilicoPredictors",
+            expr='named_struct("cadd", named_struct("phred", cast(rand() as float), "raw_score", cast(rand() as float)), "revelMax", cast(rand() as double), "spliceaiDsMax", cast(rand() as float), "pangolinLargestDs", cast(rand() as double), "phylop", cast(rand() as double), "polyphenMax", cast(rand() as double), "siftMax", cast(rand() as double))',
             percentNulls=0.1,
         )
         .withColumnSpec("rsIds", expr="array(cast(rand() AS string))", percentNulls=0.1)