Stop parameter

SigProfilerExtractor/controllers/cli_controller.py

@@ -223,6 +223,21 @@ def parse_arguments_extractor(args: List[str], description: str) -> argparse.Nam
         help="Collapse to SBS288 and SBS1536 matrices to SBS96. If False, will map reference signatures to the same context as input (default: True).",
     )
 
+    parser.add_argument(
+        "--stop_after_extraction",
+        type=str2bool,
+        nargs="?",
+        const=True,
+        default=False,
+        help="Stop after de novo extraction (default: False).",
+    )
+
+    parser.add_argument(
+        "--volume",
+        default=None,
+        help="User specified directory for saving/loading template files.",
+    )
+
     return parser.parse_args(args)
 
 
@@ -263,4 +278,6 @@ def dispatch_sigProfilerExtractor(self, user_args: List[str]) -> None:
             cosmic_version=parsed_args.cosmic_version,
             make_decomposition_plots=parsed_args.make_decomposition_plots,
             collapse_to_SBS96=parsed_args.collapse_to_SBS96,
+            stop_after_extraction=parsed_args.stop_after_extraction,
+            volume=parsed_args.volume,
         )

SigProfilerExtractor/sigpro.py

@@ -269,6 +269,7 @@ def sigProfilerExtractor(
     combined_stability=1.0,
     allow_stability_drop=False,
     get_all_signature_matrices=False,
+    stop_after_extraction=False,
     volume=None,
 ):
     """
@@ -1115,23 +1116,23 @@ def sigProfilerExtractor(
             )
             sysdata.close()
             genome_build = "GRCh37"
-
-        decomp.spa_analyze(
-            allgenomes,
-            output,
-            signatures=processAvg,
-            genome_build=genome_build,
-            cosmic_version=cosmic_version,
-            exome=exome,
-            verbose=False,
-            decompose_fit_option=True,
-            denovo_refit_option=True,
-            cosmic_fit_option=False,
-            export_probabilities=export_probabilities,
-            devopts=devopts,
-            make_metadata=False,
-            volume=volume,
-        )
+        if not stop_after_extraction:
+            decomp.spa_analyze(
+                allgenomes,
+                output,
+                signatures=processAvg,
+                genome_build=genome_build,
+                cosmic_version=cosmic_version,
+                exome=exome,
+                verbose=False,
+                decompose_fit_option=True,
+                denovo_refit_option=True,
+                cosmic_fit_option=False,
+                export_probabilities=export_probabilities,
+                devopts=devopts,
+                make_metadata=False,
+                volume=volume,
+            )
 
     sysdata = open(out_put + "/JOB_METADATA.txt", "a")
     end_time = datetime.datetime.now()