Merge pull request #246 from labgem/fix_proksee_module

Fix proksee module
labgem · Jul 3, 2024 · 5173797 · 5173797
2 parents e94b151 + 32c1f3c
commit 5173797
Showing 1 changed file with 17 additions and 13 deletions.
diff --git a/ppanggolin/formats/write_proksee.py b/ppanggolin/formats/write_proksee.py
@@ -51,7 +51,7 @@ def write_legend_items(features: List[str], module_to_color: Dict[Module, str] =
 
     if module_to_color is not None and ("modules" in features or "all" in features):
         for mod, color in sorted(module_to_color.items(), key=lambda x: x[0].ID):
-            legend_data["items"].append({"name": f"module_{mod.ID}",
+            legend_data["items"].append({"name": str(mod),
                                          "decoration": "arc",
                                          "swatchColor": color,
                                          "visible": False})
@@ -324,23 +324,27 @@ def write_modules(organism: Organism, gf2genes: Dict[str, List[Gene]], metadata_
 
         if gf_intersection:
             # Calculate the completion percentage
-            completion = round(100 * len(gf_intersection) / len(set(module.families)), 1)
-
+            metadata_for_proksee = {'completion': round(100 * len(gf_intersection) / len(set(module.families)), 1)}
+
+            metadata_for_proksee.update(module.formatted_metadata_dict(metadata_sep))
             # Create module data entries for genes within intersecting gene families
             for gf in gf_intersection:
                 for gene in gf2genes[gf.name]:
-                    modules_data_list.append({
-                        "name": f"Module_{module.ID}",
-                        "presence": "Module",
-                        "start": gene.start,
-                        "stop": gene.stop,
-                        "contig": gene.contig.name,
-                        "legend": f"module_{module.ID}",
-                        "source": "Module",
-                        "tags": [f'{completion}% complete'],
-                        "meta": module.formatted_metadata_dict(metadata_sep)
+                    for start, stop in gene.coordinates:
+                        modules_data_list.append({
+                            "name": str(module),
+                            "presence": "Module",
+                            "start": start,
+                            "stop": stop,
+                            "contig": gene.contig.name,
+                            "legend": str(module),
+                            "source": "Module",
+                            "tags": [],
+                            "meta": metadata_for_proksee
                     })
 
+
+
     return modules_data_list