Check for mutations and clades before removing

Fixes a bug in the fix_tree script when trying to remove mutations or
clades from lists where those values don't exist. The short-term fix is
to check for the presence of the values in the lists before trying to
remove them. The long term fix is to use a different tree builder than
eliminates the need for a "fix tree" script.

phylogenetic/scripts/fix_tree.py

@@ -57,10 +57,14 @@
                             print(f"Below {clade}: {mut_child} in {child.name} reverted in {grandchild.name}")
 
     for reversion in reversions:
-        # Remove reversion from grandchild
-        reversion["grandchild"].relevant_mutations.remove(reversion["mut_grandchild"])
-        # Remove grandchild from child
-        reversion["child"].clades.remove(reversion["grandchild"])
+        if reversion["mut_grandchild"] in reversion["grandchild"].relevant_mutations:
+            # Remove reversion from grandchild
+            reversion["grandchild"].relevant_mutations.remove(reversion["mut_grandchild"])
+
+        if reversion["grandchild"] in reversion["child"].clades:
+            # Remove grandchild from child
+            reversion["child"].clades.remove(reversion["grandchild"])
+
         # If there are mutations, add grandchild as child of parent
         if reversion["grandchild"].relevant_mutations != reversion["parent"].relevant_mutations:
             reversion["parent"].clades.append(reversion["grandchild"])