Eleos special case

packages/df-wiki-cli/df_wiki_cli/content/main.py

@@ -304,44 +304,82 @@ def system_operon_structure(
             in_exchangeables = False
             current_gene = {}
             exchangeables = []
-            with open(def_path["path"]) as file:
-                for event, elem in ET.iterparse(file, events=("start", "end")):
-                    if event == "start":
-                        if (
-                            elem.tag == "gene"
-                            and not in_exchangeables
-                            and elem.attrib["presence"] != "forbidden"
-                        ):
-                            current_gene = {
-                                "system": system,
-                                "subsystem": subsystem,
-                                "gene": elem.attrib["name"],
-                                "version": def_path["version"],
-                                "exchangeables": None,
-                            }
-
-                            # get hmm definition to extract the size
-                            base_path_list = def_path["path"].parts[0:-4]
-                            profile_path = (
-                                Path(*base_path_list)
-                                / f"profiles/{current_gene['gene']}.hmm"
-                            )
-                            with open(profile_path) as profile_file:
-                                for line in profile_file:
-                                    if line.startswith("LENG"):
-                                        size = int(re.split(r"\s+", line)[1])
-                                        current_gene["size"] = size
-                            system_genes.append(current_gene)
-                        if elem.tag == "gene" and in_exchangeables:
-                            exchangeables.append(elem.attrib["name"])
-                        if elem.tag == "exchangeables":
-                            in_exchangeables = True
-                            exchangeables = []
-                    elif event == "end":
-                        if elem.tag == "exchangeables":
-                            in_exchangeables = False
-                            current_gene["exchangeables"] = ",".join(exchangeables)
-                            exchangeables = []
+
+            # <model inter_gene_max_space="5" min_mandatory_genes_required="2" min_genes_required="2" vers="2.0">
+
+            # <gene name="Eleos__LeoA" presence="mandatory">
+            # <exchangeables>
+            # <gene name="Eleos__LeoA2"/>
+            # </exchangeables>
+            # </gene>
+
+            # <gene name="Eleos__LeoBC" presence="mandatory"/>
+
+            # <gene name="Eleos__LeoB" presence="mandatory"/>
+
+            # <gene name="Eleos__LeoC" presence="mandatory"/>
+
+            # </model>
+            if system == 'Eleos':
+                eleos_struct = [
+                    {
+                        "system": system,
+                        "subsystem": "Eleos",
+                        "gene": "Eleos__LeoA",
+                        "version": "1.2.4",
+                        "exchangeables": "Eleos__LeoA2",
+                        "size": 559,
+                    },
+                    {
+                        "system": system,
+                        "subsystem": "Eleos",
+                        "gene": "Eleos__LeoBC",
+                        "version": "1.2.4",
+                        "exchangeables": None,
+                        "size": 601,
+                    },
+
+                ]
+                system_genes += eleos_struct
+            else:
+                with open(def_path["path"]) as file:
+                    for event, elem in ET.iterparse(file, events=("start", "end")):
+                        if event == "start":
+                            if (
+                                elem.tag == "gene"
+                                and not in_exchangeables
+                                and elem.attrib["presence"] != "forbidden"
+                            ):
+                                current_gene = {
+                                    "system": system,
+                                    "subsystem": subsystem,
+                                    "gene": elem.attrib["name"],
+                                    "version": def_path["version"],
+                                    "exchangeables": None,
+                                }
+
+                                # get hmm definition to extract the size
+                                base_path_list = def_path["path"].parts[0:-4]
+                                profile_path = (
+                                    Path(*base_path_list)
+                                    / f"profiles/{current_gene['gene']}.hmm"
+                                )
+                                with open(profile_path) as profile_file:
+                                    for line in profile_file:
+                                        if line.startswith("LENG"):
+                                            size = int(re.split(r"\s+", line)[1])
+                                            current_gene["size"] = size
+                                system_genes.append(current_gene)
+                            if elem.tag == "gene" and in_exchangeables:
+                                exchangeables.append(elem.attrib["name"])
+                            if elem.tag == "exchangeables":
+                                in_exchangeables = True
+                                exchangeables = []
+                        elif event == "end":
+                            if elem.tag == "exchangeables":
+                                in_exchangeables = False
+                                current_gene["exchangeables"] = ",".join(exchangeables)
+                                exchangeables = []
 
     with open(output, "w") as f:
         fieldnames = [