Test adar1, not tested yet

Author: Jon Brenas

tests/integration/test_adar1.py

@@ -0,0 +1,77 @@
+import pytest
+
+from malariagen_data import Adar1, Region
+from malariagen_data.util import _locate_region, _resolve_region
+
+
+def setup_adar1(url="simplecache::gs://vo_adar_release_master_us_central1/", **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 Adar1(**kwargs)
+    if url.startswith("simplecache::"):
+        # configure the directory on the local file system to cache data
+        kwargs["simplecache"] = dict(cache_storage="gcs_cache")
+    return Adar1(url, **kwargs)
+
+
+def test_repr():
+    adar1 = setup_adar1(check_location=True)
+    assert isinstance(adar1, Adar1)
+    r = repr(adar1)
+    assert isinstance(r, str)
+
+
+@pytest.mark.parametrize(
+    "region_raw",
+    [
+        "2",
+        "gene-LOC125950257",
+        "2:4871446-4871535",
+        "2:2,630,355-2,633,221",
+        Region("2", 4871446, 4871535),
+    ],
+)
+def test_locate_region(region_raw):
+    # TODO Migrate this test.
+    adar1 = setup_adar1()
+    gene_annotation = adar1.geneset(attributes=["ID"])
+    region = _resolve_region(adar1, region_raw)
+    pos = adar1.snp_sites(region=region.contig, field="POS")
+    # Used by some code that has not been added yet
+    # ref = adar1.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 == "2":
+        assert region.contig == "2"
+        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 == "gene-LOC125950257":
+        gene = gene_annotation.query("ID == 'gene-LOC125950257'").squeeze()
+        assert region == Region(gene.contig, gene.start, gene.end)
+        assert pos[loc_region][0] == gene.start
+        assert pos[loc_region][-1] == gene.end
+        # To be checked
+        # assert (
+        #    ref[loc_region][:5].compute() == np.array(["T", "T", "G", "T", "T"])
+        # ).all()
+
+    # check string parsing
+    if region_raw == "2:4871446-4871535":
+        assert region == Region("2", 4871446, 4871535)
+    if region_raw == "2:2,630,355-2,633,221":
+        assert region == Region("2", 2630355, 2633221)