Fix missing num tips in ushertools (#130)

* Fix missing num tips in ushertools

* Prettified Code!

Co-authored-by: theosanderson <[email protected]>

taxonium_data_handling/filtering.js

@@ -144,8 +144,6 @@ function searchFiltering({ data, spec, mutations, node_to_mut, all_data }) {
         .filter((line) => line !== "")
     );
 
-
-
     filtered = data.filter((node) => {
       const to_test = node[spec.type].toLowerCase().trim();
       //console.log(to_test);
@@ -165,17 +163,18 @@ function searchFiltering({ data, spec, mutations, node_to_mut, all_data }) {
         );
       })
       .map((mutation) => mutation.mutation_id);
-    //console.log("relevant_mutations:", relevant_mutations);
+    console.log("relevant_mutations:", relevant_mutations);
     const relevant_mutations_set = new Set(relevant_mutations);
     //console.log("node_to_mut:", node_to_mut);
+    console.log("NODE", data[0]);
 
     filtered = data.filter(
       (node) =>
         node_to_mut[node.node_id].some((mutation_id) =>
           relevant_mutations_set.has(mutation_id)
         ) && node.num_tips > spec.min_tips
     );
-    //console.log("filtered:", filtered);
+    console.log("filtered:", filtered);
     return filtered;
   } else if (spec.method === "revertant") {
     if (!all_data) {

taxonium_data_handling/importing.js

@@ -132,23 +132,23 @@ export const processJsonl = async (jsonl, sendStatusMessage) => {
 
   const scale_x = 10;
   const scale_y = 24e2 / new_data.nodes.length;
-  console.log("Scaling")
+  console.log("Scaling");
   for (const node of new_data.nodes) {
     node.x_dist = node.x_dist * scale_x;
     node.x = node.x_dist;
     node.y = node.y * scale_y;
   }
-  console.log("Calculating y positions")
+  console.log("Calculating y positions");
   const y_positions = new_data.nodes.map((node) => node.y);
 
-  console.log("Calculating coord extremes")
+  console.log("Calculating coord extremes");
 
   const overallMaxY = reduceMaxOrMin(new_data.nodes, (node) => node.y, "max");
   const overallMinY = reduceMaxOrMin(new_data.nodes, (node) => node.y, "min");
   const overallMaxX = reduceMaxOrMin(new_data.nodes, (node) => node.x, "max");
   const overallMinX = reduceMaxOrMin(new_data.nodes, (node) => node.x, "min");
 
-console.log("Creating output obj")
+  console.log("Creating output obj");
   const output = {
     nodes: new_data.nodes,
     overallMaxX,

taxonium_web_client/src/components/NodeHoverTip.jsx

@@ -5,7 +5,6 @@ const fixName = (name) => {
   return name.replace("hCoV-19/", "hCoV-19/\n");
 };
 
-
 const NodeHoverTip = ({
   hoverInfo,
   hoverDetails,

taxonium_web_client/src/hooks/useSearch.js

@@ -16,13 +16,11 @@ const useSearch = (
     return JSON.parse(query.srch);
   }, [query.srch]);
 
-  console.log("spec", searchSpec);
-
   const [zoomToSearch, setZoomToSearch] = useState(
     query.zoomToSearch ? { index: query.zoomToSearch } : null
   );
   const searchesEnabled = query.enabled ? JSON.parse(query.enabled) : {};
-  console.log("searchesEnabled", searchesEnabled);
+
   const setEnabled = (key, enabled) => {
     console.log("setEnabled", key, enabled);
     const newSearchesEnabled = { ...searchesEnabled, [key]: enabled };

taxoniumtools/src/taxoniumtools/usher_to_taxonium.py

@@ -195,6 +195,8 @@ def get_node_object(node, node_to_index, metadata, aa_mut_tuple_to_index,
             node.parent] if node.parent else node_to_index[node]
         object['node_id'] = node_to_index[
             node]  # We don't strictly need this, but it doesn't add much to the space
+
+        object['num_tips'] = node.num_tips
         return object
 
 

taxoniumtools/src/taxoniumtools/ushertools.py

@@ -144,6 +144,7 @@ def __init__(self, tree_file, genbank_file=None):
         if genbank_file:
             self.load_genbank_file(genbank_file)
             self.perform_aa_analysis()
+        self.assign_num_tips()
 
     def perform_aa_analysis(self):
         seq = str(self.genbank.seq)
@@ -197,3 +198,10 @@ def get_condensed_nodes_dict(self, condensed_nodes_dict):
             output_dict[
                 condensed_node.node_name] = condensed_node.condensed_leaves
         return output_dict
+
+    def assign_num_tips(self):
+        for node in self.tree.traverse_postorder():
+            if node.is_leaf():
+                node.num_tips = 1
+            else:
+                node.num_tips = sum(child.num_tips for child in node.children)