🎨 format using black

Author: enryH

src/instanexus/__main__.py

@@ -2,6 +2,7 @@
 import argparse
 from . import script_dbg, script_greedy
 
+
 def main():
     banner = r"""
      ______                   __             __  __                                   
@@ -15,8 +16,9 @@ def main():
 
     parser = argparse.ArgumentParser(
         prog="instanexus",
-        description=(banner + "\n"
-            "InstaNexus CLI: de novo protein sequencing based on InstaNovo,\n\n" \
+        description=(
+            banner + "\n"
+            "InstaNexus CLI: de novo protein sequencing based on InstaNovo,\n\n"
             "an end-to-end workflow from de novo peptides to proteins\n\n"
             "Usage:\n"
             "  instanexus <command> [options]\n\n"
@@ -30,8 +32,8 @@ def main():
         ),
         formatter_class=argparse.RawTextHelpFormatter,
     )
-    
-    parser.add_argument('--version', action='version', version='InstaNexus 0.1.0'),
+
+    parser.add_argument("--version", action="version", version="InstaNexus 0.1.0"),
 
     subparsers = parser.add_subparsers(dest="command", help="subcommands")
 
@@ -50,5 +52,6 @@ def main():
     else:
         parser.print_help()
 
+
 if __name__ == "__main__":
     main()

src/instanexus/alignment.py

@@ -3,14 +3,14 @@
 r"""Alignment module for clustered scaffolds.
 
  ██████████   ███████████ █████  █████
-░░███░░░░███ ░█░░░███░░░█░░███  ░░███ 
- ░███   ░░███░   ░███  ░  ░███   ░███ 
- ░███    ░███    ░███     ░███   ░███ 
- ░███    ░███    ░███     ░███   ░███ 
- ░███    ███     ░███     ░███   ░███ 
- ██████████      █████    ░░████████  
-░░░░░░░░░░      ░░░░░      ░░░░░░░░   
-                          
+░░███░░░░███ ░█░░░███░░░█░░███  ░░███
+ ░███   ░░███░   ░███  ░  ░███   ░███
+ ░███    ░███    ░███     ░███   ░███
+ ░███    ░███    ░███     ░███   ░███
+ ░███    ███     ░███     ░███   ░███
+ ██████████      █████    ░░████████
+░░░░░░░░░░      ░░░░░      ░░░░░░░░
+
 __authors__ = Marco Reverenna
 __copyright__ = Copyright 2025-2026
 __research-group__ = DTU Biosustain (Multi-omics Network Analytics) and DTU Bioengineering
@@ -28,7 +28,9 @@
 from pathlib import Path
 from Bio import SeqIO
 
-logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s] %(message)s")
+logging.basicConfig(
+    level=logging.INFO, format="%(asctime)s [%(levelname)s] %(message)s"
+)
 logger = logging.getLogger(__name__)
 
 
@@ -49,16 +51,29 @@ def align_or_copy_fasta(fasta_file, output_file):
         logger.debug(f"Copied single-sequence file: {Path(fasta_file).name}")
     elif len(sequences) > 1:
         # Multiple sequences, run clustalo
-        logger.debug(f"Aligning {len(sequences)} sequences from {Path(fasta_file).name}...")
+        logger.debug(
+            f"Aligning {len(sequences)} sequences from {Path(fasta_file).name}..."
+        )
         try:
             subprocess.run(
-                ["clustalo", "-i", fasta_file, "-o", output_file, "--outfmt", "fa", "--force"],
+                [
+                    "clustalo",
+                    "-i",
+                    fasta_file,
+                    "-o",
+                    output_file,
+                    "--outfmt",
+                    "fa",
+                    "--force",
+                ],
                 check=True,
-                capture_output=True, # Suppress clustalo stdout
-                text=True
+                capture_output=True,  # Suppress clustalo stdout
+                text=True,
             )
         except FileNotFoundError:
-            logger.error("clustalo command not found. Please ensure it is in your system's PATH.")
+            logger.error(
+                "clustalo command not found. Please ensure it is in your system's PATH."
+            )
             raise
         except subprocess.CalledProcessError as e:
             logger.error(f"Clustalo failed for {fasta_file}: {e.stderr}")
@@ -71,39 +86,39 @@ def align_or_copy_fasta(fasta_file, output_file):
 def process_alignment(input_dir: str, output_dir: str):
     """
     Align all FASTA files from input_dir and save results in output_dir.
-    
+
     Args:
         input_dir (str): Path to the .../cluster_fasta/ directory.
         output_dir (str): Path to the .../alignment/ directory.
     """
     cluster_fasta_folder = Path(input_dir)
     alignment_folder = Path(output_dir)
-    
+
     alignment_folder.mkdir(parents=True, exist_ok=True)
 
     if not cluster_fasta_folder.exists():
         logger.error(f"Cluster FASTA folder not found: {cluster_fasta_folder}")
-        raise FileNotFoundError(f"Cluster FASTA folder not found: {cluster_fasta_folder}")
+        raise FileNotFoundError(
+            f"Cluster FASTA folder not found: {cluster_fasta_folder}"
+        )
 
     fasta_files_to_align = [
-        f for f in sorted(os.listdir(cluster_fasta_folder))
-        if f.endswith(".fasta")
+        f for f in sorted(os.listdir(cluster_fasta_folder)) if f.endswith(".fasta")
     ]
 
     logger.info(f"Found {len(fasta_files_to_align)} cluster FASTA files to align.")
 
     for fasta_file in fasta_files_to_align:
         fasta_path = cluster_fasta_folder / fasta_file
         # Save output as .afa (alignment FASTA)
-        output_path = alignment_folder / fasta_file.replace(".fasta", "_aligned.afa") 
-        
+        output_path = alignment_folder / fasta_file.replace(".fasta", "_aligned.afa")
+
         align_or_copy_fasta(fasta_path, output_path)
 
     logger.info("All alignment tasks completed.")
 
 
-def main(input_cluster_fasta_folder: str, 
-    output_alignment_folder: str):
+def main(input_cluster_fasta_folder: str, output_alignment_folder: str):
     """
     Main function to run the alignment script.
     """
@@ -113,10 +128,9 @@ def main(input_cluster_fasta_folder: str,
     logger.info(f"Output Folder (Alignments): {output_alignment_folder}")
 
     process_alignment(
-        input_dir=input_cluster_fasta_folder,
-        output_dir=output_alignment_folder
+        input_dir=input_cluster_fasta_folder, output_dir=output_alignment_folder
     )
-    
+
     logger.info("--- Step 4: Alignment Completed ---")
 
 
@@ -127,30 +141,31 @@ def cli():
     parser = argparse.ArgumentParser(
         description="Alignment script for clustered scaffolds."
     )
-    
+
     parser.add_argument(
         "--input-folder",
         type=str,
         required=True,
-        help="Path to the folder containing cluster FASTA files (e.g., .../cluster_fasta)."
+        help="Path to the folder containing cluster FASTA files (e.g., .../cluster_fasta).",
     )
     parser.add_argument(
         "--output-folder",
         type=str,
         required=True,
-        help="Path to the folder to save aligned .afa files (e.g., .../alignment)."
+        help="Path to the folder to save aligned .afa files (e.g., .../alignment).",
     )
-    
+
     args = parser.parse_args()
 
-    main(input_cluster_fasta_folder=args.input_folder,
-         output_alignment_folder=args.output_folder
-         )
+    main(
+        input_cluster_fasta_folder=args.input_folder,
+        output_alignment_folder=args.output_folder,
+    )
 
 
 if __name__ == "__main__":
     cli()
 
 # python -m instanexus.alignment \
 #     --input-folder outputs/bsa/scaffolds/clustering/cluster_fasta \
-#     --output-folder outputs/bsa/scaffolds/alignment
+#     --output-folder outputs/bsa/scaffolds/alignment