refactor: Save cluster tree with cluster prob (#190)

- Cluster probability instead of branch support

Co-authored-by: KARTIK KAKADIYA <[email protected]>

bin/rspr_heatmap.py

@@ -250,6 +250,34 @@ def generate_cluster_network(lst_tree_clusters, refer_tree):
     update_cluster_probability(refer_tree.root, dict_clstr_map, total_trees, leaf_mapping)
 
 
+#####################################################################
+### FUNCTION REPLACE_CLUSTER_PROBABILITY
+### Replace branch support with cluster probability
+### node: current node
+#####################################################################
+
+def replace_cluster_probability(node):
+    if not node:
+        return
+    node.comment = node.cluster_probability
+    if not node.is_terminal():
+        for child in node.clades:
+            replace_cluster_probability(child)
+
+
+#####################################################################
+### FUNCTION SAVE_CLUSTER_TREE
+### Save cluster network tree
+### cluster_file_path: path to store cliuster tree
+### refer_tree: reference tree
+#####################################################################
+
+def save_cluster_tree(cluster_file_path, refer_tree):
+    print("Saving cluster tree")
+    replace_cluster_probability(refer_tree.root)
+    Phylo.write(refer_tree, cluster_file_path, "newick")
+
+
 #####################################################################
 ### FUNCTION GENERATE_CLUSTER_HEATMAP
 ### Generate cluster heatmap
@@ -301,8 +329,6 @@ def read_tree(input_path):
         formatted = re.sub(r";[^:]+:", ":", tree_string)
         return Phylo.read(io.StringIO(formatted), "newick")
 
-def write_tree(output_path, data):
-    Phylo.write(data, output_path, "newick")
 
 def get_fig_size(refer_tree):
     max_fig_size = 100
@@ -350,7 +376,6 @@ def main(args=None):
     refer_tree = read_tree(refer_tree_path)
     if refer_tree:
         generate_cluster_network(lst_tree_clusters, refer_tree)
-        write_tree(cluster_file_path, refer_tree)
 
         plt.rcParams['font.size'] = '12'
         fig_size = get_fig_size(refer_tree)
@@ -361,5 +386,7 @@ def main(args=None):
         plt.title("Cluster network")
         plt.savefig(cluster_tree_path, format="png")
 
+        save_cluster_tree(cluster_file_path, refer_tree)
+
 if __name__ == "__main__":
     sys.exit(main())