Merge pull request #1602 from SynBioHub/updateSO

Updated sequence ontology file

lib/ontologies/obo2js.py

@@ -0,0 +1,82 @@
+import re
+import sys
+
+def parse_obo(file_path):
+    """
+    Parses an OBO file to extract terms with their IDs, names, and definitions.
+    """
+    terms = {}
+    with open(file_path, 'r') as obo_file:
+        term = {}
+        for line in obo_file:
+            line = line.strip()
+            if line == '[Term]':
+                if 'id' in term and 'name' in term:
+                    if 'def' in term:
+                        term['def'] = format_definition(term['def'])
+                    terms[term['id']] = {
+                        'name': term['name'],
+                        'def': term.get('def', '')
+                    }
+                term = {}
+            elif line.startswith('id: '):
+                term['id'] = line[4:]
+            elif line.startswith('name: '):
+                term['name'] = line[6:]
+            elif line.startswith('def: '):
+                term['def'] = line[5:].strip()
+        # Add the last term in the file if it's valid
+        if 'id' in term and 'name' in term:
+            if 'def' in term:
+                term['def'] = format_definition(term['def'])
+                terms[term['id']] = {
+                    'name': term['name'],
+                    'def': term.get('def', '')
+                }
+    return terms
+
+def format_definition(def_text):
+    """
+    Reformats the definition text to match the required format.
+    Removes enclosing double quotes from the definition if present.
+    """
+    if def_text.startswith('"') and def_text.endswith('"'):
+        def_text = def_text[1:-1]
+    parts = def_text.rsplit('[', 1)
+    if len(parts) == 2:
+        definition, source = parts
+        if definition.startswith('"') and definition.startswith('"'):
+            definition = definition[1:-2]
+        return f"{definition.strip()} [{source.strip()}"
+    return def_text.strip()
+
+def generate_js(terms, output_file):
+    """
+    Generates a JavaScript file exporting the terms as a module.
+    """
+    with open(output_file, 'w') as js_file:
+        js_file.write("module.exports = {\n")
+        for term_id, details in terms.items():
+            js_file.write(f"  '{term_id}': {{\n")
+            js_file.write(f"    'name': '{details['name']}'")
+            if details['def']:
+                if "'" in details['def']:
+                    js_file.write(f",\n    'def': \"{details['def']}\"\n")
+                else:
+                    js_file.write(f",\n    'def': '{details['def']}'\n")
+            else:
+                js_file.write(f"\n")
+            js_file.write("  },\n")
+        js_file.write("};\n")
+
+if __name__ == "__main__":
+    if len(sys.argv) != 3:
+        print("Usage: python obo_to_js.py <input_obo_file> <output_js_file>")
+        sys.exit(1)
+
+    input_file = sys.argv[1]
+    output_file = sys.argv[2]
+
+    terms = parse_obo(input_file)
+    generate_js(terms, output_file)
+    print(f"JavaScript file '{output_file}' has been created successfully.")