🐛 refactored files

Author: marcoreverenna

src/instanexus/assembly.py

@@ -28,7 +28,7 @@
 import Bio
 
 from . import helpers
-from . import mapping as map
+from . import visualization as viz
 
 from tqdm import tqdm
 from pathlib import Path
@@ -778,13 +778,13 @@ def main(
         stats_path = output_path.parent / "statistics"
         stats_path.mkdir(parents=True, exist_ok=True)
 
-        mapped_scaffolds = map.process_protein_contigs_scaffold(
+        mapped_scaffolds = viz.process_protein_contigs_scaffold(
             assembled_contigs=scaffolds,
             target_protein=protein_norm,
             max_mismatches=max_mismatches,
             min_identity=min_identity, 
         )
-        df_scaffolds_mapped = map.create_dataframe_from_mapped_sequences(
+        df_scaffolds_mapped = viz.create_dataframe_from_mapped_sequences(
             data=mapped_scaffolds
         )
         helpers.compute_assembly_statistics(

src/instanexus/clustering.py

@@ -11,7 +11,7 @@
  ██████████      █████    ░░████████  
 ░░░░░░░D░░      ░░░░░      ░░░░░░░░   
      
-__authors__ = Marco Reverenna
+__authors__ = Marco Reverenna & Konstantinos Kalogeropoulus
 __copyright__ = Copyright 2025-2026
 __research-group__ = DTU Biosustain (Multi-omics Network Analytics) and DTU Bioengineering
 __date__ = 14 Nov 2025
@@ -22,7 +22,6 @@
 
 import argparse
 import logging
-import os
 import shutil
 import subprocess
 import pandas as pd