Merge branch 'master' into master

Author: jonbrenas

malariagen_data/anoph/genome_features.py

@@ -552,5 +552,5 @@ def _transcript_to_parent_name(self, transcript):
             return self._gene_name_overrides[parent_id]
         except KeyError:
             rec_parent = df_genome_features.loc[parent_id]
-            # Try to access "Name" attribute, fall back to "ID" if not present.
-            return rec_parent.get("Name", parent_id)
+            # Try to access gene name attribute, fall back to "ID" if not present.
+            return rec_parent.get(self._gff_gene_name_attribute, parent_id)

tests/anoph/test_genome_features.py

@@ -169,7 +169,9 @@ def test_plot_genes_with_gene_labels(fixture, api: AnophelesGenomeFeaturesData):
     # For each contig in the fixture...
     for contig in fixture.contigs:
         # Get the genes for this contig.
-        genes_df = api.genome_features(region=contig).query("type == 'gene'")
+        genes_df = api.genome_features(region=contig).query(
+            f"type == '{api._gff_gene_type}'"
+        )
 
         # If there are no genes, we cannot label them.
         if not genes_df.empty:
@@ -181,7 +183,10 @@ def test_plot_genes_with_gene_labels(fixture, api: AnophelesGenomeFeaturesData):
 
             # Put the random gene "ID" and its "Name" in a dictionary.
             random_gene_labels = dict(
-                zip(random_sample_genes_df["ID"], random_sample_genes_df["Name"])
+                zip(
+                    random_sample_genes_df["ID"],
+                    random_sample_genes_df[api._gff_gene_name_attribute],
+                )
             )
 
             # Check that we get a Bokeh figure from plot_genes() with these gene_labels.