SigProfilerExtractor 1.2.0__tar.gz → 1.2.2__tar.gz

{sigprofilerextractor-1.2.0/SigProfilerExtractor.egg-info → sigprofilerextractor-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.0
+Version: 1.2.2
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -14,9 +14,9 @@ Requires-Dist: torch>=1.8.1
 Requires-Dist: numpy>=2.0.0
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: nimfa>=1.1.0
-Requires-Dist: sigProfilerPlotting>=1.4.0
-Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
-Requires-Dist: SigProfilerAssignment>=0.2.0
+Requires-Dist: sigProfilerPlotting>=1.4.1
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.5
+Requires-Dist: SigProfilerAssignment>=0.2.4
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -26,6 +26,7 @@ Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{sigprofilerextractor-1.2.0 → sigprofilerextractor-1.2.2}/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 @@ class CliController:
             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-1.2.0 → sigprofilerextractor-1.2.2}/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()

{sigprofilerextractor-1.2.0 → sigprofilerextractor-1.2.2}/SigProfilerExtractor/sigprofilerextractor_cli.py

@@ -11,7 +11,7 @@ def main_function():
 
     if len(sys.argv) < 2 or sys.argv[1].lower() not in commands:
         print_usage(commands)
-        sys.exit(1)
+        return
 
     command = sys.argv[1].lower()
     args = sys.argv[2:]

{sigprofilerextractor-1.2.0 → sigprofilerextractor-1.2.2}/SigProfilerExtractor/subroutines.py

@@ -1676,6 +1676,8 @@ def export_information(
                 "S" + str(i),
                 tmp_m,
                 True,
+                custom_text_upper=stability_list,
+                custom_text_middle=total_mutation_list,
             )
     else:
         custom_signatures_plot(processes, signature_subdirectory)

sigprofilerextractor-1.2.2/SigProfilerExtractor/version.py

@@ -0,0 +1,7 @@
+
+# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
+short_version = '1.2.2'
+version = '1.2.2'
+Update = 'v1.2.2: Add mutation count and stability to 4608 plots in All_Solutions and a stop parameter'
+    
+    

{sigprofilerextractor-1.2.0 → sigprofilerextractor-1.2.2/SigProfilerExtractor.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.0
+Version: 1.2.2
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -14,9 +14,9 @@ Requires-Dist: torch>=1.8.1
 Requires-Dist: numpy>=2.0.0
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: nimfa>=1.1.0
-Requires-Dist: sigProfilerPlotting>=1.4.0
-Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
-Requires-Dist: SigProfilerAssignment>=0.2.0
+Requires-Dist: sigProfilerPlotting>=1.4.1
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.5
+Requires-Dist: SigProfilerAssignment>=0.2.4
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -26,6 +26,7 @@ Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{sigprofilerextractor-1.2.0 → sigprofilerextractor-1.2.2}/SigProfilerExtractor.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 LICENSE.txt
 MANIFEST.in
 README.md
+pyproject.toml
 setup.py
 SigProfilerExtractor/__init__.py
 SigProfilerExtractor/estimate_best_solution.py

{sigprofilerextractor-1.2.0 → sigprofilerextractor-1.2.2}/SigProfilerExtractor.egg-info/requires.txt

@@ -3,9 +3,9 @@ torch>=1.8.1
 numpy>=2.0.0
 pandas>=2.0.0
 nimfa>=1.1.0
-sigProfilerPlotting>=1.4.0
-SigProfilerMatrixGenerator>=1.3.0
-SigProfilerAssignment>=0.2.0
+sigProfilerPlotting>=1.4.1
+SigProfilerMatrixGenerator>=1.3.5
+SigProfilerAssignment>=0.2.4
 statsmodels>=0.9.0
 scikit-learn>=0.24.2
 psutil>=5.6.1

sigprofilerextractor-1.2.2/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=61", "wheel", "build"]
+build-backend = "setuptools.build_meta"

{sigprofilerextractor-1.2.0 → sigprofilerextractor-1.2.2}/setup.py

@@ -8,7 +8,7 @@ import subprocess
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.2.0"
+VERSION = "1.2.2"
 
 
 with open("README.md") as f:
@@ -21,7 +21,7 @@ def write_version_py(filename="SigProfilerExtractor/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'Upgrade v1.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
+Update = 'v1.2.2: Add mutation count and stability to 4608 plots in All_Solutions and a stop parameter'
     
     """
     fh = open(filename, "w")
@@ -40,9 +40,9 @@ requirements = [
     "numpy>=2.0.0",
     "pandas>=2.0.0",
     "nimfa>=1.1.0",
-    "sigProfilerPlotting>=1.4.0",
-    "SigProfilerMatrixGenerator>=1.3.0",
-    "SigProfilerAssignment>=0.2.0",
+    "sigProfilerPlotting>=1.4.1",
+    "SigProfilerMatrixGenerator>=1.3.5",
+    "SigProfilerAssignment>=0.2.4",
     "statsmodels>=0.9.0",
     "scikit-learn>=0.24.2",
     "psutil>=5.6.1",

sigprofilerextractor-1.2.0/SigProfilerExtractor/version.py

@@ -1,7 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
-short_version = '1.2.0'
-version = '1.2.0'
-Update = 'Upgrade v1.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
-    
-