feat: now creating a hub_plasmids.csv file when running the plasnet type command explicitly listing each hub plasmid

plasnet/hub_graph.py

@@ -55,14 +55,17 @@ def _get_hub_plasmids(self, use_cached: bool = False) -> list[str]:
 
         return self._hub_plasmids
 
-    def remove_hub_plasmids(self) -> None:
+    def remove_hub_plasmids(self) -> set[str]:
+        all_hub_plasmids = set()
         while True:
             hub_plasmids = self._get_hub_plasmids()
+            all_hub_plasmids.update(hub_plasmids)
             there_are_still_hub_plasmids = len(hub_plasmids) > 0
             if there_are_still_hub_plasmids:
                 self.remove_nodes_from(hub_plasmids)
             else:
                 break
+        return all_hub_plasmids
 
     def _get_filters_HTML(self) -> str:
         nb_of_hubs = len(self._get_hub_plasmids(use_cached=True))

plasnet/plasnet_main.py

@@ -205,8 +205,10 @@ def type(
 
     logging.info("Typing communities (i.e. splitting them into subcommunities)")
     all_subcommunities = Subcommunities()
+    all_hub_plasmids = set()
     for community in communities:
-        community.remove_hub_plasmids()
+        hub_plasmids = community.remove_hub_plasmids()
+        all_hub_plasmids.update(hub_plasmids)
         subcommunities = community.split_graph_into_subcommunities(
             small_subcommunity_size_threshold
         )
@@ -229,6 +231,10 @@ def type(
     original_communities.save(objects_dir / "communities.pkl")
     all_subcommunities.save(objects_dir / "subcommunities.pkl")
     all_subcommunities.save_classification(objects_dir / "typing.tsv", "plasmid\ttype")
+    with open(objects_dir / "hub_plasmids.csv", "w") as hub_plasmids_fh:
+        print("hub_plasmids", file=hub_plasmids_fh)
+        for plasmid in all_hub_plasmids:
+            print(plasmid, file=hub_plasmids_fh)
 
     logging.info("All done!")
 

tests/data/hub/hub_plasmids.csv

@@ -0,0 +1,4 @@
+hub_plasmids
+pKPC_CAV1320
+pCAV1492-6393
+pCAV1374-6538

tests/test_integration_tests.py

@@ -113,3 +113,11 @@ def test_remove_hub_plasmids_iteratively(self) -> None:
                 sort=True,
             )
         )
+
+        self.assertTrue(
+            check_if_files_are_equal(
+                Path("tests/data/hub/out/type_out/objects/hub_plasmids.csv"),
+                Path("tests/data/hub/hub_plasmids.csv"),
+                sort=True,
+            )
+        )