Rerun analyses for submission.

CholGen · Nov 15, 2024 · c0163a8 · c0163a8
1 parent edafa6f
commit c0163a8
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Showing 33 changed files with 1,090,330 additions and 1,089,412 deletions.
diff --git a/analyses/estimate-introductions/estimate-introductions.py b/analyses/estimate-introductions/estimate-introductions.py
@@ -72,7 +72,7 @@ def _identity_func( node ):
             node_dict["earliest_date"] = min( children_dates )
             node_dict["latest_date"] = max( children_dates )
             inclusion_dates = [date for child, date in zip( node_dict["children.names"], children_dates ) if
-                               not inclusion_dict[child]]
+                               not inclusion_dict.get( child, True )]   # Some taxa might be missing from the dictionary/metadata because they were removed as duplicates after the beast run. However, these are all workshop sequences so we can set missing to True. 
             try:
                 node_dict["earliest_date_ncg"] = min( inclusion_dates )
                 node_dict["latest_date_ncg"] = max( inclusion_dates )
@@ -139,4 +139,4 @@ def parse_lineages( trees, burnin, trait, states, metadata, output ):
     args = parser.parse_args()
 
     print( f"Parsing lineages for states: {args.states}")
-    parse_lineages( args.trees, args.burnin, args.trait, args.states, args.metadata, args.output )
+    parse_lineages( args.trees, args.burnin, args.trait, args.states, args.metadata, args.output )