add initial tests for adir1

Author: tristanpwdennis

tests/integration/test_adir1.py

@@ -0,0 +1,79 @@
+import numpy as np
+import pytest
+
+from malariagen_data import Adir1, Region
+from malariagen_data.util import locate_region, resolve_region
+
+
+def setup_adir1(
+    url="simplecache::gs://vo_adir_production_us_central1/release/", **kwargs
+):
+    kwargs.setdefault("check_location", False)
+    kwargs.setdefault("show_progress", False)
+    if url is None:
+        # test default URL
+        # This only tests the setup_af1 default url, not the Af1 default.
+        # The test_anopheles setup_subclass tests true defaults.
+        return Adir1(**kwargs)
+    if url.startswith("simplecache::"):
+        # configure the directory on the local file system to cache data
+        kwargs["simplecache"] = dict(cache_storage="gcs_cache")
+    return Adir1(url, **kwargs)
+
+
+def test_repr():
+    adir1 = setup_adir1(check_location=True)
+    assert isinstance(adir1, Adir1)
+    r = repr(adir1)
+    assert isinstance(r, str)
+
+
+@pytest.mark.parametrize(
+    "region_raw",
+    [
+        "ADIR015707",
+        "KB672490",
+        "KB672490:4871446-4871535",
+        "KB672490:2,630,355-2,633,221",
+        Region("KB672490", 4871446, 4871535),
+    ],
+)
+def test_locate_region(region_raw):
+    # TODO Migrate this test.
+    adir1 = setup_adir1()
+    gene_annotation = adir1.geneset(attributes=["ID"])
+    region = resolve_region(adir1, region_raw)
+    pos = adir1.snp_sites(region=region.contig, field="POS")
+    ref = adir1.snp_sites(region=region.contig, field="REF")
+    loc_region = locate_region(region, pos)
+
+    # check types
+    assert isinstance(loc_region, slice)
+    assert isinstance(region, Region)
+
+    # check Region with contig
+    if region_raw == "KB672490":
+        assert region.contig == "KB672490"
+        assert region.start is None
+        assert region.end is None
+
+    # check that Region goes through unchanged
+    if isinstance(region_raw, Region):
+        assert region == region_raw
+
+    # check that gene name matches coordinates from the geneset and matches gene sequence
+    if region_raw == "ADIR015707":
+        gene = gene_annotation.query("ID == 'ADIR015707'").squeeze()
+        assert region == Region(gene.contig, gene.start, gene.end)
+        assert pos[loc_region][0] == gene.start
+        assert pos[loc_region][-1] == gene.end
+        assert (
+            ref[loc_region][:5].compute()
+            == np.array(["T", "T", "T", "C", "T"], dtype="S1")
+        ).all()
+
+    # check string parsing
+    if region_raw == "KB672490:4871446-4871535":
+        assert region == Region("KB672490", 4871446, 4871535)
+    if region_raw == "KB672490:2,630,355-2,633,221":
+        assert region == Region("KB672490", 2630355, 2633221)