Added tests

Author: jonbrenas

malariagen_data/anoph/karyotype.py

@@ -8,15 +8,11 @@
 from . import base_params
 from typing import Optional
 
-from .genome_features import AnophelesGenomeFeaturesData
-from .genome_sequence import AnophelesGenomeSequenceData
-from .sample_metadata import AnophelesSampleMetadata
+from .snp_data import AnophelesSnpData
 from .karyotype_params import inversion_param
 
 
-class AnophelesKaryotypeData(
-    AnophelesSampleMetadata, AnophelesGenomeFeaturesData, AnophelesGenomeSequenceData
-):
+class AnophelesKaryotypeData(AnophelesSnpData):
     def __init__(
         self,
         **kwargs,

tests/integration/test_af1.py

@@ -75,3 +75,24 @@ def test_locate_region(region_raw):
         assert region == Region("2RL", 48714463, 48715355)
     if region_raw == "2RL:24,630,355-24,633,221":
         assert region == Region("2RL", 24630355, 24633221)
+
+
+@pytest.mark.parametrize(
+    "inversion",
+    ["2La", "2Rb", "2Rc_col", "X_x"],
+)
+def test_karyotyping(inversion):
+    af1 = setup_af1()
+
+    if inversion == "X_x":
+        with pytest.raises(TypeError):
+            af1.karyotype(
+                inversion=inversion, sample_sets="AG1000G-GH", sample_query=None
+            )
+    else:
+        with pytest.raises(ValueError):
+            af1.karyotype(
+                inversion=inversion,
+                sample_sets="1229-VO-GH-DADZIE-VMF00095",
+                sample_query=None,
+            )

tests/integration/test_ag3.py

@@ -159,19 +159,30 @@ def test_xpehh_gwss():
     assert_allclose(xpehh[:, 2][100], 0.4817561326426265)
 
 
-def test_karyotyping():
+@pytest.mark.parametrize(
+    "inversion",
+    ["2La", "2Rb", "2Rc_col", "X_x"],
+)
+def test_karyotyping(inversion):
     ag3 = setup_ag3(cohorts_analysis="20230516")
 
-    df = ag3.karyotype(inversion="2La", sample_sets="AG1000G-GH", sample_query=None)
-
-    assert isinstance(df, pd.DataFrame)
-    expected_cols = [
-        "sample_id",
-        "inversion",
-        "karyotype_2La_mean",
-        "karyotype_2La",
-        "total_tag_snps",
-    ]
-    assert set(df.columns) == set(expected_cols)
-    assert all(df["karyotype_2La"].isin([0, 1, 2]))
-    assert all(df["karyotype_2La_mean"].between(0, 2))
+    if inversion == "X_x":
+        with pytest.raises(TypeError):
+            ag3.karyotype(
+                inversion=inversion, sample_sets="AG1000G-GH", sample_query=None
+            )
+    else:
+        df = ag3.karyotype(
+            inversion=inversion, sample_sets="AG1000G-GH", sample_query=None
+        )
+        assert isinstance(df, pd.DataFrame)
+        expected_cols = [
+            "sample_id",
+            "inversion",
+            f"karyotype_{inversion}_mean",
+            f"karyotype_{inversion}",
+            "total_tag_snps",
+        ]
+        assert set(df.columns) == set(expected_cols)
+        assert all(df[f"karyotype_{inversion}"].isin([0, 1, 2]))
+        assert all(df[f"karyotype_{inversion}_mean"].between(0, 2))