little enhancement

src/snipe/cli/cli_qc.py

@@ -16,6 +16,7 @@
 
 import signal
 
+
 def validate_sig_input(ctx, param, value: tuple) -> str:
     supported_extensions = ['.zip', '.sig']
     for path in value:
@@ -24,10 +25,10 @@ def validate_sig_input(ctx, param, value: tuple) -> str:
         if not any(path.lower().endswith(ext) for ext in supported_extensions):
             raise click.BadParameter(f"Unsupported file format: {path}, supported formats: {', '.join(supported_extensions)}")
 
-def process_sample(sample_path: str, ref_path: str, amplicon_path: Optional[str],
+def process_sample(sample_path: str, reference_sig: SnipeSig, amplicon_sig: Optional[SnipeSig],
                   advanced: bool, roi: bool, debug: bool,
-                  ychr: Optional[str] = None,
-                  vars_paths: Optional[Union[List[str], List[SnipeSig]]] = None) -> Dict[str, Any]:
+                  ychr_sig: Optional[SnipeSig] = None,
+                  var_sigs: Optional[List[SnipeSig]] = None) -> Dict[str, Any]:
     """
     Process a single sample for QC.
 
@@ -59,16 +60,6 @@ def process_sample(sample_path: str, ref_path: str, amplicon_path: Optional[str]
         sample_sig = SnipeSig(sourmash_sig=sample_path, sig_type=SigType.SAMPLE, enable_logging=debug)
         logger.debug(f"Loaded sample signature: {sample_sig.name}")
 
-        # Load reference signature
-        reference_sig = SnipeSig(sourmash_sig=ref_path, sig_type=SigType.GENOME, enable_logging=debug)
-        logger.debug(f"Loaded reference signature: {reference_sig.name}")
-
-        # Load amplicon signature if provided
-        amplicon_sig = None
-        if amplicon_path:
-            amplicon_sig = SnipeSig(sourmash_sig=amplicon_path, sig_type=SigType.AMPLICON, enable_logging=debug)
-            logger.debug(f"Loaded amplicon signature: {amplicon_sig.name}")
-
         # Instantiate ReferenceQC
         qc_instance = ReferenceQC(
             sample_sig=sample_sig,
@@ -78,28 +69,17 @@ def process_sample(sample_path: str, ref_path: str, amplicon_path: Optional[str]
         )
 
         # Load variable signatures if provided
-        if vars_paths:
-            qc_instance.logger.debug(f"Loading {len(vars_paths)} variable signature(s).")
-            vars_dict: Dict[str, SnipeSig] = {sig.name: sig for sig in vars_paths} if isinstance(vars_paths[0], SnipeSig) else {}
+        if var_sigs:
+            qc_instance.logger.debug(f"Loading {len(var_sigs)} variable signature(s).")
+            vars_dict: Dict[str, SnipeSig] = {sig.name: sig for sig in var_sigs}
             qc_instance.logger.debug(f"vars_dict: {vars_dict}")
-            qc_instance.logger.debug(f"vars_paths: {vars_paths}")
             vars_order: List[str] = []
-
-            if not vars_dict:
-                qc_instance.logger.debug("Loading variable signature(s) from file paths.")
-                for path in vars_paths:
-                    qc_instance.logger.debug(f"Loading variable signature from: {path}")
-                    var_sig = SnipeSig(sourmash_sig=path, sig_type=SigType.AMPLICON, enable_logging=debug)
-                    var_name = var_sig.name if var_sig.name else os.path.basename(path)
-                    vars_order.append(var_name)
-                    vars_dict[var_name] = var_sig
+
+            qc_instance.logger.debug("Loading variable signature(s) from SnipeSig objects.")
+            for snipe_name in vars_dict.keys():
+                vars_order.append(snipe_name)
+                qc_instance.logger.debug(f"Loaded variable signature: {snipe_name}")
 
-            else:
-                qc_instance.logger.debug("Loading variable signature(s) from SnipeSig objects.")
-                for snipe_name in vars_dict.keys():
-                    vars_order.append(snipe_name)
-                    qc_instance.logger.debug(f"Loaded variable signature: {snipe_name}")
-
             # log keys of vars_dict and vars_order
             qc_instance.logger.debug(f"vars_dict keys: {vars_dict.keys()}")
             qc_instance.logger.debug(f"vars_order: {vars_order}")
@@ -111,8 +91,7 @@ def process_sample(sample_path: str, ref_path: str, amplicon_path: Optional[str]
         # Calculate chromosome metrics
         # genome_chr_to_sig: Dict[str, SnipeSig] = qc_instance.load_genome_sig_to_dict(zip_file_path = ref_path)
         chr_to_sig = reference_sig.chr_to_sig.copy()
-        if ychr:
-            ychr_sig = SnipeSig(sourmash_sig=ychr, sig_type=SigType.GENOME, enable_logging=debug)
+        if ychr_sig:
             chr_to_sig['y'] = ychr_sig
 
         qc_instance.calculate_chromosome_metrics(chr_to_sig)
@@ -492,6 +471,17 @@ def qc(ref: str, sample: List[str], samples_from_file: Optional[str],
         except Exception as e:
             logger.error(f"Failed to load amplicon signature from {amplicon}: {e}")
             sys.exit(1)
+
+    # Load Y chromosome signature if provided
+    ychr_sig = None
+    if ychr:
+        logger.info(f"Loading Y chromosome signature from: {ychr}")
+        try:
+            ychr_sig = SnipeSig(sourmash_sig=ychr, sig_type=SigType.GENOME, enable_logging=debug)
+            logger.debug(f"Loaded Y chromosome signature: {ychr_sig.name}")
+        except Exception as e:
+            logger.error(f"Failed to load Y chromosome signature from {ychr}: {e}")
+            sys.exit(1)
 
     # Prepare variable signatures if provided
     vars_paths = []
@@ -517,15 +507,15 @@ def qc(ref: str, sample: List[str], samples_from_file: Optional[str],
     for sample_path in valid_samples:
         dict_process_args.append({
             "sample_path": sample_path,
-            "ref_path": ref,
-            "amplicon_path": amplicon,
+            "reference_sig": reference_sig,
+            "amplicon_sig": amplicon_sig,
             "advanced": advanced,
             "roi": roi,
             "debug": debug,
-            "ychr": ychr,
-            "vars_paths": vars_snipesigs #vars_paths
+            "ychr_sig": ychr_sig,
+            "var_sigs": vars_snipesigs #vars_paths
         })
-
+        
     results = []
 
     # Define a handler for graceful shutdown