Merge branch 'master' into fix/invalid-param-error-messages

Author: jonbrenas

malariagen_data/anoph/genome_sequence.py

@@ -16,6 +16,8 @@
 
 
 class AnophelesGenomeSequenceData(AnophelesBase):
+    _cache_genome: Optional[zarr.hierarchy.Group]
+
     def __init__(
         self, virtual_contigs: Optional[Mapping[str, Sequence[str]]] = None, **kwargs
     ):
@@ -29,9 +31,6 @@ def __init__(
             virtual_contigs = dict()
         self._virtual_contigs = virtual_contigs
 
-        # Initialize cache attributes.
-        self._cache_genome = None
-
     @property
     def contigs(self) -> Tuple[str, ...]:
         """Contigs in the reference genome."""
@@ -62,13 +61,9 @@ def _genome_ref_id(self) -> str:
     def _genome_ref_name(self) -> str:
         return self.config["GENOME_REF_NAME"]
 
-    @_check_types
-    @doc(
-        summary="Open the reference genome zarr.",
-        returns="Zarr hierarchy containing the reference genome sequence.",
-    )
     def open_genome(self) -> zarr.hierarchy.Group:
-        if self._cache_genome is None:
+        """Open the reference genome zarr."""
+        if not hasattr(self, "_cache_genome") or self._cache_genome is None:
             path = f"{self._base_path}/{self._genome_zarr_path}"
             store = _init_zarr_store(fs=self._fs, path=path)
             self._cache_genome = zarr.open_consolidated(store=store)

malariagen_data/anoph/snp_frq.py

@@ -1,3 +1,4 @@
+from functools import cached_property
 from typing import Optional, Dict, Union, Callable, List
 import warnings
 
@@ -40,9 +41,6 @@ def __init__(
         # to the superclass constructor.
         super().__init__(**kwargs)
 
-        # Set up cache variables.
-        self._cache_annotator = None
-
     def _snp_df_melt(self, *, ds_snp: xr.Dataset) -> pd.DataFrame:
         """Set up a dataframe with SNP site and filter data,
         melting each alternate allele into a separate row."""
@@ -81,13 +79,12 @@ def _snp_df_melt(self, *, ds_snp: xr.Dataset) -> pd.DataFrame:
 
         return df_snps
 
+    @cached_property
     def _snp_effect_annotator(self):
         """Set up variant effect annotator."""
-        if self._cache_annotator is None:
-            self._cache_annotator = veff.Annotator(
-                genome=self.open_genome(), genome_features=self.genome_features()
-            )
-        return self._cache_annotator
+        return veff.Annotator(
+            genome=self.open_genome(), genome_features=self.genome_features()
+        )
 
     @_check_types
     @doc(
@@ -112,7 +109,7 @@ def snp_effects(
         df_snps = self._snp_df_melt(ds_snp=ds_snp)
 
         # Setup variant effect annotator.
-        ann = self._snp_effect_annotator()
+        ann = self._snp_effect_annotator
 
         # Add effects to the dataframe.
         ann.get_effects(transcript=transcript, variants=df_snps)
@@ -249,7 +246,7 @@ def snp_allele_frequencies(
 
         if effects:
             # Add effect annotations.
-            ann = self._snp_effect_annotator()
+            ann = self._snp_effect_annotator
             ann.get_effects(
                 transcript=transcript, variants=df_snps, progress=self._progress
             )
@@ -586,7 +583,7 @@ def snp_allele_frequencies_advanced(
             frequency = np.compress(loc_variant, frequency, axis=0)
 
         # Set up variant effect annotator.
-        ann = self._snp_effect_annotator()
+        ann = self._snp_effect_annotator
 
         # Add effects to the dataframe.
         ann.get_effects(
@@ -832,7 +829,7 @@ def snp_genotype_allele_counts(
         df_snps = pd.concat([df_snps, df_counts], axis=1)
 
         # Add effect annotations.
-        ann = self._snp_effect_annotator()
+        ann = self._snp_effect_annotator
         ann.get_effects(
             transcript=transcript, variants=df_snps, progress=self._progress
         )