Fix sorting of measurements by subclade y axis position instead of clade position

Author: huddlej

scripts/generate_collection_config_json.py

@@ -78,14 +78,14 @@ def calc_row(clade):
 
     # Find minimum y-axis position for reference strains within each clade. This
     # position represents the earliest instance of the clade in the tree.
-    min_y_axis_position_by_reference_clade = collection_df.groupby("clade_reference")["y_axis_position_in_phylogeny"].min().reset_index().rename(
+    min_y_axis_position_by_reference_clade = collection_df.groupby("subclade_reference")["y_axis_position_in_phylogeny"].min().reset_index().rename(
         columns={"y_axis_position_in_phylogeny": "min_y_axis_position_in_phylogeny"}
     )
 
     # Annotate min y-axis position per clade to collection.
     collection_df = collection_df.merge(
         min_y_axis_position_by_reference_clade,
-        on="clade_reference",
+        on="subclade_reference",
         how="left",
     )
 

workflow/snakemake_rules/titer_models.smk

@@ -125,7 +125,7 @@ rule generate_collection_config_json:
         groupings=[
             "reference_strain",
             "reference_strain_source",
-            "clade_reference",
+            "subclade_reference",
             "emerging_haplotype_reference",
             "derived_haplotype_reference",
             "source",
@@ -141,8 +141,8 @@ rule generate_collection_config_json:
             "source",
             "test_date",
             "reference_date",
-            "clade_test",
-            "clade_reference",
+            "subclade_test",
+            "subclade_reference",
             "emerging_haplotype_test",
             "emerging_haplotype_reference",
             "derived_haplotype_test",
@@ -185,7 +185,7 @@ rule export_measurements:
         filters=[
             "reference_strain",
             "reference_strain_source",
-            "clade_reference",
+            "subclade_reference",
             "emerging_haplotype_reference",
             "derived_haplotype_reference",
             "source",
@@ -201,8 +201,8 @@ rule export_measurements:
             "source",
             "test_date",
             "reference_date",
-            "clade_test",
-            "clade_reference",
+            "subclade_test",
+            "subclade_reference",
             "emerging_haplotype_test",
             "emerging_haplotype_reference",
             "derived_haplotype_test",