refactor: drop plasmodium.py and test_plasmodium.py changes from this PR

Author: khushthecoder

malariagen_data/plasmodium.py

@@ -232,22 +232,17 @@ def _resolve_region(self, region):
     def _subset_genome_sequence_region(
         self, genome, region, inline_array=True, chunks="native"
     ):
-        """Subset reference genome sequence."""
+        """Sebset reference genome sequence."""
         region = self._resolve_region(region)
         z = genome[region.contig]
 
         d = _da_from_zarr(z, inline_array=inline_array, chunks=chunks)
 
-        if region.start is not None:
-            if region.start < 1:
-                raise ValueError("Region start must be >= 1 or None.")
+        if region.start:
             slice_start = region.start - 1
         else:
             slice_start = None
-
-        if region.end is not None:
-            if region.end < 1:
-                raise ValueError("Region end must be >= 1 or None.")
+        if region.end:
             slice_stop = region.end
         else:
             slice_stop = None

tests/test_plasmodium.py

@@ -690,37 +690,6 @@ def test_subset_genome_sequence_contig2(self):
         assert sequence.shape == (15,)
         assert sequence.ndim == 1
 
-    def test_subset_genome_sequence_region_slice(self):
-        from malariagen_data.util import Region
-
-        # contig1 is np.arange(10)
-        # Valid slice 1-3 -> indices 0,1,2 (length 3)
-        region = Region("contig1", 1, 3)
-        sequence = self.test_plasmodium_class._subset_genome_sequence_region(
-            genome=self.test_ref_zarr, region=region
-        )
-        assert isinstance(sequence, da.Array)
-        assert sequence.shape == (3,)
-        assert sequence.compute().tolist() == [0, 1, 2]
-
-    def test_subset_genome_sequence_region_invalid_start_0(self):
-        from malariagen_data.util import Region
-
-        region = Region("contig1", 0, 3)
-        with self.assertRaises(ValueError):
-            self.test_plasmodium_class._subset_genome_sequence_region(
-                genome=self.test_ref_zarr, region=region
-            )
-
-    def test_subset_genome_sequence_region_invalid_end_0(self):
-        from malariagen_data.util import Region
-
-        region = Region("contig1", 1, 0)
-        with self.assertRaises(ValueError):
-            self.test_plasmodium_class._subset_genome_sequence_region(
-                genome=self.test_ref_zarr, region=region
-            )
-
 
 if __name__ == "__main__":
     unittest.main()