changed struc of naming_dic, removed it

PyEED · Aug 14, 2024 · 68dea71 · 68dea71
1 parent 794030c
commit 68dea71
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Showing 3 changed files with 6 additions and 45 deletions.
diff --git a/docs/examples/network.ipynb b/docs/examples/network.ipynb
@@ -138,7 +138,6 @@
    "source": [
     "# create the network\n",
     "graph = SequenceNetwork(sequences=sequences)\n",
-    "graph.create_graph()\n",
     "graph.update_threshhold(0.4)\n",
     "\n",
     "# plot the network\n",
@@ -233,7 +232,7 @@
     "\n",
     "G = graph.network\n",
     "\n",
-    "# remove isolated nodes\n",
+    "# remove isolated node\n",
     "G.remove_node(\"NPA53530.1\")\n",
     "G.remove_node(\"O67275\")\n",
     "G.remove_nodes_from(list(nx.isolates(G)))\n",

diff --git a/pyeed/network/network.py b/pyeed/network/network.py
@@ -72,11 +72,14 @@ class Config:
         default="http://cytoscape:1234/v1",
     )
 
+    def post_init(self):
+        self.create_graph()
+
     def add_to_targets(self, target: SequenceRecord):
         if target.id not in self.targets:
             self.targets.append(target.id)
 
-    def create_graph(self, naming_dict=None):
+    def _create_graph(self):
         """
         Initializes the nx.Graph object and adds nodes and edges based on the sequences.
 
@@ -90,13 +93,6 @@ def create_graph(self, naming_dict=None):
         for sequence in self.sequences:
             seq_dict = sequence.to_dict()
             seq_id = seq_dict.pop("@id")
-            if naming_dict is not None:
-                seq_id = seq_id.split(".")[0]
-                if seq_id in naming_dict:
-                    seq_id = naming_dict[seq_id]
-                else:
-                    print(f"Sequence {seq_id} not found in the naming_dict")
-                    continue
             node_dict = seq_dict.pop("organism") if "organism" in seq_dict else {}
             node_dict["sequence"] = sequence.sequence
             node_dict["name"] = sequence.name if sequence.name else ""

diff --git a/tests/unit/network_tests/test_newtork_graph_build.py b/tests/unit/network_tests/test_newtork_graph_build.py
@@ -25,7 +25,6 @@ def test_general_build_networkx(self):
             sequences=mats,
             weight="identity",
         )
-        network.create_graph()
 
     def test_graph_build(self):
         mat_accessions = [
@@ -41,37 +40,4 @@ def test_graph_build(self):
             weight="identity",
         )
 
-        network.create_graph()
-
-        assert len(list(network.network.nodes)) == len(mats)
-
-    def test_graph_naming_dic(self):
-        mat_accessions = [
-            "MBP1912539.1",
-            "SEV92896.1",
-            "MBO8174569.1",
-            "WP_042680787.1",
-        ]
-
-        naming_dic = {
-            "MBP1912539": "MAT1",
-            "SEV92896": "MAT2",
-            "MBO8174569": "MAT3",
-            "WP_042680787": "MAT4",
-        }
-
-        mats = ProteinRecord.get_ids(mat_accessions)
-        # Create network
-        network = SequenceNetwork(
-            sequences=mats,
-            weight="identity",
-            naming_dict=naming_dic,
-        )
-
-        network.create_graph(naming_dict=naming_dic)
-
-        # convert networkx to pandas
-        data = dict(network.network.nodes(data=True))
-
-        assert len(list(network.network.nodes)) == len(mats)
-        assert 'MAT1' in list(data.keys())
+        assert len(list(network.network.nodes)) == len(mats)