Merge pull request #35 from didillysquat/master

check for no root decomposition when updating toplogy
merenlab · Mar 9, 2021 · aaa0b89 · aaa0b89
2 parents 2b9c774 + 7e82e7c
commit aaa0b89
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git a/Oligotyping/lib/decomposer.py b/Oligotyping/lib/decomposer.py
@@ -389,11 +389,11 @@ def _generate_raw_topology(self):
         self.progress.new('Raw Topology')
         # main loop
         while 1:
-            self.decomposition_depth += 1
+
             if not len(self.node_ids_to_analyze):
                 self.progress.end()
                 break
-
+            self.decomposition_depth += 1
             # following for loop will go through all nodes that are stored in
             # self.node_ids_to_analyze list. while those nodes are being decomposed,
             # new nodes will appear and need to be analyzed next round. following
@@ -564,7 +564,7 @@ def _generate_raw_topology(self):
 
         #finally:
         self.progress.end()
-        self.topology.update_final_nodes()
+        self.topology.update_final_nodes(decomposition_depth=self.decomposition_depth)
 
         self.run.info('num_raw_nodes', utils.pretty_print(len(self.topology.final_nodes)))
 
@@ -575,7 +575,7 @@ def _refresh_topology(self):
         self.progress.new('Refreshing the topology')
         self.progress.update('Updating final nodes...')
 
-        self.topology.update_final_nodes()
+        self.topology.update_final_nodes(decomposition_depth=self.decomposition_depth)
 
         dirty_nodes = []
         for node_id in self.topology.final_nodes:

diff --git a/Oligotyping/lib/topology.py b/Oligotyping/lib/topology.py
@@ -228,11 +228,14 @@ def get_parent_node(self, node_id):
         return self.nodes[self.nodes[node_id].parent]
 
 
-    def update_final_nodes(self):
+    def update_final_nodes(self, decomposition_depth):
         self.alive_nodes = [n for n in sorted(self.nodes.keys()) if not self.nodes[n].killed]
 
         # get final nodes sorted by abundance        
-        final_nodes_tpls = [(self.nodes[n].size, n) for n in self.alive_nodes if not self.nodes[n].children]
+        final_nodes_tpls = [
+            (self.nodes[n].size, n) for n in self.alive_nodes if not self.nodes[n].children or (
+                    decomposition_depth == 0 and
+                    n == 'root')]
         final_nodes_tpls.sort(reverse = True)
         self.final_nodes = [n[1] for n in final_nodes_tpls]