Update H1 references for titer plots

Updates H1 references, includes comments to note which clade each
reference comes from, and adds support for comments in the plotting
script.

config/references_for_titer_plots_h1n1pdm.txt

@@ -1,17 +1,17 @@
-A/Ghana/2711/2022
-A/Norway/25089/2022
-A/SouthAfrica/R05722/2022
-A/Wisconsin/67/2022
-A/Victoria/4897/2022
-A/Wisconsin/47/2022
-A/Sydney/44/2023
-A/Washington/22/2023
-A/SouthAustralia/59/2023
-A/Darwin/23/2023
-A/Victoria/2570/2019-egg
-A/Sydney/5/2021-egg
-A/Sydney/173/2022-egg
-A/Norway/31694/2022-egg
-A/SouthAfrica/R05722/2022-egg
-A/Victoria/4897/2022-egg
-A/Darwin/7/2023-egg
+A/Sydney/604/2023 # C.1
+A/Victoria/650/2023 # C.1
+A/Wisconsin/67/2022 # C.1.1, vaccine strain
+A/Norway/25089/2022 # C.1.1
+A/Victoria/4897/2022 # C.1.1.1
+A/Wisconsin/47/2022 # C.1.1.1
+A/Maine/10/2022 # C.1.2
+A/Washington/22/2023 # C.1.3
+A/Darwin/7/2023 # C.1.6
+A/SouthAustralia/59/2023 # C.1.6
+A/Darwin/23/2023 # C.1.7
+A/Sydney/5/2021-egg # C.1
+A/Norway/31694/2022-egg # C.1.1
+A/SouthAfrica/R05722/2022-egg # C.1.1
+A/Victoria/4897/2022-egg # C.1.1.1, vaccine strain
+A/Sydney/44/2023-egg # C.1.3
+A/Darwin/7/2023-egg # C.1.6

scripts/plot_antigenic_distances_between_strains.py

@@ -86,7 +86,10 @@
     if args.references:
         # If references are given in order, we take these as they are.
         with open(args.references, "r") as fh:
-            references_to_use = [line.strip() for line in fh]
+            # We allow comments following each strain in the form of "strain #
+            # comment", so split lines on whitespace and keep only the leading
+            # text to ignore any comments.
+            references_to_use = [line.split(" ")[0].strip() for line in fh]
 
         record_by_strain = df.loc[
             :,