Fixed linting issues

bin/input_assure.py

@@ -5,57 +5,60 @@
 import csv
 import gzip
 
+
 def open_file(file_path, mode):
     # Open a file based on the file extension
-    if file_path.endswith('.gz'):
+    if file_path.endswith(".gz"):
         return gzip.open(file_path, mode)
     else:
         return open(file_path, mode)
 
+
 def check_inputs(json_file, sample_id, address, output_error_file):
     with open_file(json_file, "rt") as f:
         json_data = json.load(f)
 
     # Define a variable to store the match_status (True or False)
     match_status = sample_id in json_data
-    
-    keys = list (json_data.keys())
+
+    keys = list(json_data.keys())
     original_key = keys[0]
 
     # Initialize the error message
-    error_message = None 
-    
+    error_message = None
+
     # Check for multiple keys in the JSON file and define error message
     if len(keys) > 1:
         # Check if sample_id matches any key
         if not match_status:
             error_message = f"No key in the MLST JSON file ({json_file}) matches the specified sample ID '{sample_id}'. The first key '{original_key}' has been forcefully changed to '{sample_id}' and all other keys have been removed."
-            # Retain only the specified sample ID 
+            # Retain only the specified sample ID
             json_data = {sample_id: json_data.pop(original_key)}
         else:
             error_message = f"MLST JSON file ({json_file}) contains multiple keys: {keys}. The MLST JSON file has been modified to retain only the '{sample_id}' entry"
             # Remove all keys expect the one matching sample_id
-            json_data = {sample_id: json_data[sample_id]} 
+            json_data = {sample_id: json_data[sample_id]}
     elif not match_status:
-    # Define error message based on meta.address (query or reference)
+        # Define error message based on meta.address (query or reference)
         if address == "null":
             error_message = f"Query {sample_id} ID and JSON key in {json_file} DO NOT MATCH. The '{original_key}' key in {json_file} has been forcefully changed to '{sample_id}': User should manually check input files to ensure correctness."
         else:
             error_message = f"Reference {sample_id} ID and JSON key in {json_file} DO NOT MATCH. The '{original_key}' key in {json_file} has been forcefully changed to '{sample_id}': User should manually check input files to ensure correctness."
         # Update the JSON file with the new sample ID
         json_data[sample_id] = json_data.pop(original_key)
-   
+
     # Write file containing relevant error messages
     if error_message:
         with open(output_error_file, "w", newline="") as f:
             writer = csv.writer(f)
             writer.writerow(["sample", "JSON_key", "error_message"])
             writer.writerow([sample_id, keys, error_message])
 
-    # Write the updated JSON data back to the original file 
+    # Write the updated JSON data back to the original file
     with open_file(json_file, "wt") as f:
         json.dump(json_data, f, indent=4)
 
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         description="Check sample inputs, force change if ID ≠ KEY, and generate an error report."
@@ -73,6 +76,4 @@ def check_inputs(json_file, sample_id, address, output_error_file):
 
     args = parser.parse_args()
 
-    check_inputs(
-        args.input, args.sample_id, args.address, args.output_error
-    )
+    check_inputs(args.input, args.sample_id, args.address, args.output_error)