Changed the error for Af

Author: jonbrenas

malariagen_data/af1.py

@@ -123,6 +123,7 @@ def __init__(
             taxon_colors=TAXON_COLORS,
             virtual_contigs=None,
             gene_names=None,
+            inversion_tag_path=None,
         )
 
     def __repr__(self):

malariagen_data/ag3.py

@@ -7,7 +7,6 @@
 import malariagen_data
 from .anopheles import AnophelesDataResource
 
-from typing import Literal, Annotated, TypeAlias
 
 # silence dask performance warnings
 dask.config.set(**{"array.slicing.split_native_chunks": False})  # type: ignore
@@ -29,6 +28,7 @@
 GENE_NAMES = {
     "AGAP004707": "Vgsc/para",
 }
+INVERSION_TAG_PATH = "karyotype_tag_snps.csv"
 
 
 def _setup_aim_palettes():
@@ -77,12 +77,6 @@ def _setup_aim_palettes():
 }
 
 
-inversion_param: TypeAlias = Annotated[
-    Literal["2La", "2Rb", "2Rc_gam", "2Rc_col", "2Rd", "2Rj"],
-    "Name of inversion to infer karyotype for.",
-]
-
-
 class Ag3(AnophelesDataResource):
     """Provides access to data from Ag3.x releases.
 
@@ -197,6 +191,7 @@ def __init__(
             taxon_colors=TAXON_COLORS,
             virtual_contigs=VIRTUAL_CONTIGS,
             gene_names=GENE_NAMES,
+            inversion_tag_path=INVERSION_TAG_PATH,
         )
 
         # set up caches

malariagen_data/anoph/karyotype.py

@@ -15,13 +15,18 @@
 class AnophelesKaryotypeData(AnophelesSnpData):
     def __init__(
         self,
+        inversion_tag_path: Optional[str] = None,
         **kwargs,
     ):
         # N.B., this class is designed to work cooperatively, and
         # so it's important that any remaining parameters are passed
         # to the superclass constructor.
         super().__init__(**kwargs)
 
+        # If provided, this analysis version will override the
+        # default value provided in the release configuration.
+        self._inversion_tag_path = inversion_tag_path
+
     @check_types
     @doc(
         summary="Load tag SNPs for a given inversion in Ag.",
@@ -31,7 +36,7 @@ def load_inversion_tags(self, inversion: inversion_param) -> pd.DataFrame:
         import importlib.resources
         from .. import resources
 
-        with importlib.resources.path(resources, "karyotype_tag_snps.csv") as path:
+        with importlib.resources.path(resources, self._inversion_tag_path) as path:
             df_tag_snps = pd.read_csv(path, sep=",")
         return df_tag_snps.query(f"inversion == '{inversion}'").reset_index()
 

malariagen_data/anopheles.py

@@ -140,6 +140,7 @@ def __init__(
         taxon_colors: Optional[Mapping[str, str]],
         virtual_contigs: Optional[Mapping[str, Sequence[str]]],
         gene_names: Optional[Mapping[str, str]],
+        inversion_tag_path: Optional[str],
     ):
         super().__init__(
             url=url,
@@ -173,6 +174,7 @@ def __init__(
             taxon_colors=taxon_colors,
             virtual_contigs=virtual_contigs,
             gene_names=gene_names,
+            inversion_tag_path=inversion_tag_path,
         )
 
     @property

tests/integration/test_af1.py

@@ -90,7 +90,7 @@ def test_karyotyping(inversion):
                 inversion=inversion, sample_sets="AG1000G-GH", sample_query=None
             )
     else:
-        with pytest.raises(ValueError):
+        with pytest.raises(FileNotFoundError):
             af1.karyotype(
                 inversion=inversion,
                 sample_sets="1229-VO-GH-DADZIE-VMF00095",