Merge branch 'main' into 1076-grm-skipna

docs/changelog.rst

@@ -35,7 +35,7 @@ New Features
 - Add :func:`sgkit.io.vcf.read_vcf` convenience function.
   (:user:`tomwhite`, :pr:`1052`, :issue:`1004`)
 
-- Add :func:`sgkit.hybrid_relationship`, :func:`sgkit.hybrid_inverse_relationship` 
+- Add :func:`sgkit.hybrid_relationship`, :func:`sgkit.hybrid_inverse_relationship`
   and :func:`invert_relationship_matrix` methods.
   (:user:`timothymillar`, :pr:`1053`, :issue:`993`)
 
@@ -45,6 +45,9 @@ New Features
 - Add ``skipna`` option to :func:`genomic_relationship` function.
   (:user:`timothymillar`, :pr:`1078`, :issue:`1076`)
 
+- Add `additional_variant_fields` to :func:`sgkit.simulate_genotype_call_dataset` function.
+  (:user:`benjeffery`, :pr:`1056`)
+
 Bug fixes
 ~~~~~~~~~
 

sgkit/testing.py

@@ -18,6 +18,7 @@ def simulate_genotype_call_dataset(
     seed: Optional[int] = 0,
     missing_pct: Optional[float] = None,
     phased: Optional[bool] = None,
+    additional_variant_fields: Optional[dict] = None,
 ) -> Dataset:
     """Simulate genotype calls and variant/sample data.
 
@@ -50,6 +51,9 @@ def simulate_genotype_call_dataset(
         The percentage of missing calls, must be within [0.0, 1.0], optional
     phased
         Whether genotypes are phased, default is unphased, optional
+    additional_variant_fields
+        Additional variant fields to add to the dataset as a dictionary of
+        {field_name: field_dtype}, optional
 
     Returns
     -------
@@ -62,6 +66,7 @@ def simulate_genotype_call_dataset(
     - :data:`sgkit.variables.call_genotype_spec` (variants, samples, ploidy)
     - :data:`sgkit.variables.call_genotype_mask_spec` (variants, samples, ploidy)
     - :data:`sgkit.variables.call_genotype_phased_spec` (variants, samples), if ``phased`` is not None
+    - Those specified in ``additional_variant_fields``, if provided
     """
     if missing_pct and (missing_pct < 0.0 or missing_pct > 1.0):
         raise ValueError("missing_pct must be within [0.0, 1.0]")
@@ -87,7 +92,7 @@ def simulate_genotype_call_dataset(
         ["A", "C", "G", "T"], size=(n_variant, n_allele)
     ).astype("S")
     sample_id = np.array([f"S{i}" for i in range(n_sample)])
-    return create_genotype_call_dataset(
+    ds = create_genotype_call_dataset(
         variant_contig_names=contig_names,
         variant_contig=contig,
         variant_position=position,
@@ -96,3 +101,18 @@ def simulate_genotype_call_dataset(
         call_genotype=call_genotype,
         call_genotype_phased=call_genotype_phased,
     )
+    # Add in each of the additional variant fields, if provided with random data
+    if additional_variant_fields is not None:
+        for field_name, field_dtype in additional_variant_fields.items():
+            if field_dtype in (np.float32, np.float64):
+                field = rs.rand(n_variant).astype(field_dtype)
+            elif field_dtype in (np.int8, np.int16, np.int32, np.int64):
+                field = rs.randint(0, 100, n_variant, dtype=field_dtype)
+            elif field_dtype is np.bool:
+                field = rs.rand(n_variant) > 0.5
+            elif field_dtype is np.str:
+                field = np.arange(n_variant).astype("S")
+            else:
+                raise ValueError(f"Unrecognized dtype {field_dtype}")
+            ds[field_name] = (("variants",), field)
+    return ds

sgkit/tests/test_testing.py

@@ -29,3 +29,35 @@ def test_simulate_genotype_call_dataset__phased(tmp_path):
     ds = simulate_genotype_call_dataset(n_variant=10, n_sample=10, phased=False)
     assert "call_genotype_phased" in ds
     assert not np.any(ds["call_genotype_phased"])
+
+
+def test_simulate_genotype_call_dataset__additional_variant_fields():
+    ds = simulate_genotype_call_dataset(
+        n_variant=10,
+        n_sample=10,
+        phased=True,
+        additional_variant_fields={
+            "variant_id": np.str,
+            "variant_filter": np.bool,
+            "variant_quality": np.int8,
+            "variant_yummyness": np.float32,
+        },
+    )
+    assert "variant_id" in ds
+    assert np.all(ds["variant_id"] == np.arange(10).astype("S"))
+    assert "variant_filter" in ds
+    assert ds["variant_filter"].dtype == np.bool
+    assert "variant_quality" in ds
+    assert ds["variant_quality"].dtype == np.int8
+    assert "variant_yummyness" in ds
+    assert ds["variant_yummyness"].dtype == np.float32
+
+    with pytest.raises(ValueError, match="Unrecognized dtype"):
+        simulate_genotype_call_dataset(
+            n_variant=10,
+            n_sample=10,
+            phased=True,
+            additional_variant_fields={
+                "variant_id": None,
+            },
+        )