SigProfilerExtractor 1.2.4__tar.gz → 1.2.6__tar.gz

{sigprofilerextractor-1.2.4/SigProfilerExtractor.egg-info → sigprofilerextractor-1.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.4
+Version: 1.2.6
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -16,7 +16,7 @@ Requires-Dist: pandas>=2.0.0
 Requires-Dist: nimfa>=1.1.0
 Requires-Dist: sigProfilerPlotting>=1.4.1
 Requires-Dist: SigProfilerMatrixGenerator>=1.3.5
-Requires-Dist: SigProfilerAssignment>=1.0.1
+Requires-Dist: SigProfilerAssignment>=1.1.0
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -149,7 +149,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **nmf_tolerance** | Float | Value defines the tolerance to achieve to converge (default: `1e-15`).|
 | **Execution** |  |  |  | 
 |  | **cpu** | Integer | The number of processors to be used to extract the signatures (default: all processors). |
-|  | **assignment_cpu** | Integer | The number of processors to be used for the final signature assignment step (default: all processors). This is independent of the `cpu` parameter. |
+|  | **assignment_cpu** | Integer | Number of processors to be used by SigProfilerAssignment for the final signature assignment step (default: all available). This is independent of the `cpu` parameter. |
 |  | **gpu** | Boolean | Defines if the GPU resource will used if available (default: `False`). If `True`, the GPU resources will be used in the computation. *Note: All available CPU processors are used by default, which may cause a memory error. This error can be resolved by reducing the number of CPU processes through the `cpu` parameter.*|
 |  | **batch_size** | Integer | Will be effective only if the GPU is used. Defines the number of NMF replicates to be performed by each CPU during the parallel processing (default: `1`). *Note: For `batch_size` values greater than 1, each NMF replicate will update until `max_nmf_iterations` is reached.*|
 | **Solution Estimation Thresholds** |  |  |  | 
@@ -158,7 +158,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **combined_stability** | Float | The cutoff thresh-hold of the combined stability (sum of average and minimum stability) (default: `1.0`). Solutions with combined stabilities below this thresh-hold will not be considered. |
 |  | **allow_stability_drop** | Boolean | Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered (default: `False`). |
 | **Decomposition** |  |  |  | 
-|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.4`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, and `3.4`.|
+|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.5`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, and `3.5`.|
 |  | **make_decomposition_plots** | Boolean | Generate de novo to COSMIC signature decomposition plots as part of the results (default: `True`). Set to `False` to skip generating these plots. |
 |  | **collapse_to_SBS96** | Boolean | If `True`, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: `True`). If `False`, those will be mapped to reference signatures of the same context.
 | **Others** |  |  |  | 

{sigprofilerextractor-1.2.4 → sigprofilerextractor-1.2.6}/README.md

@@ -116,7 +116,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **nmf_tolerance** | Float | Value defines the tolerance to achieve to converge (default: `1e-15`).|
 | **Execution** |  |  |  | 
 |  | **cpu** | Integer | The number of processors to be used to extract the signatures (default: all processors). |
-|  | **assignment_cpu** | Integer | The number of processors to be used for the final signature assignment step (default: all processors). This is independent of the `cpu` parameter. |
+|  | **assignment_cpu** | Integer | Number of processors to be used by SigProfilerAssignment for the final signature assignment step (default: all available). This is independent of the `cpu` parameter. |
 |  | **gpu** | Boolean | Defines if the GPU resource will used if available (default: `False`). If `True`, the GPU resources will be used in the computation. *Note: All available CPU processors are used by default, which may cause a memory error. This error can be resolved by reducing the number of CPU processes through the `cpu` parameter.*|
 |  | **batch_size** | Integer | Will be effective only if the GPU is used. Defines the number of NMF replicates to be performed by each CPU during the parallel processing (default: `1`). *Note: For `batch_size` values greater than 1, each NMF replicate will update until `max_nmf_iterations` is reached.*|
 | **Solution Estimation Thresholds** |  |  |  | 
@@ -125,7 +125,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **combined_stability** | Float | The cutoff thresh-hold of the combined stability (sum of average and minimum stability) (default: `1.0`). Solutions with combined stabilities below this thresh-hold will not be considered. |
 |  | **allow_stability_drop** | Boolean | Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered (default: `False`). |
 | **Decomposition** |  |  |  | 
-|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.4`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, and `3.4`.|
+|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.5`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, and `3.5`.|
 |  | **make_decomposition_plots** | Boolean | Generate de novo to COSMIC signature decomposition plots as part of the results (default: `True`). Set to `False` to skip generating these plots. |
 |  | **collapse_to_SBS96** | Boolean | If `True`, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: `True`). If `False`, those will be mapped to reference signatures of the same context.
 | **Others** |  |  |  | 

{sigprofilerextractor-1.2.4 → sigprofilerextractor-1.2.6}/SigProfilerExtractor/controllers/cli_controller.py

@@ -209,8 +209,8 @@ def parse_arguments_extractor(args: List[str], description: str) -> argparse.Nam
     parser.add_argument(
         "--cosmic_version",
         type=float,
-        default=3.4,
-        help="COSMIC version for reference signatures. Valid values are 1, 2, 3, 3.1, 3.2, 3.3, and 3.4 (default: 3.4).",
+        default=3.5,
+        help="COSMIC version for reference signatures. Valid values are 1, 2, 3, 3.1, 3.2, 3.3, 3.4, and 3.5 (default: 3.5).",
     )
     parser.add_argument(
         "--make_decomposition_plots",

{sigprofilerextractor-1.2.4 → sigprofilerextractor-1.2.6}/SigProfilerExtractor/sigpro.py

@@ -240,7 +240,7 @@ def sigProfilerExtractor(
     input_data,
     reference_genome="GRCh37",
     opportunity_genome="GRCh37",
-    cosmic_version=3.4,
+    cosmic_version=3.5,
     context_type="default",
     exome=False,
     minimum_signatures=1,

sigprofilerextractor-1.2.6/SigProfilerExtractor/version.py

@@ -0,0 +1,7 @@
+
+# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
+short_version = '1.2.6'
+version = '1.2.6'
+Update = 'v1.2.6: Update default COSMIC version to 3.5'
+    
+    

{sigprofilerextractor-1.2.4 → sigprofilerextractor-1.2.6/SigProfilerExtractor.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.4
+Version: 1.2.6
 Summary: Extracts mutational signatures from mutational catalogues
 Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
 Author: S Mishu Ashiqul Islam
@@ -16,7 +16,7 @@ Requires-Dist: pandas>=2.0.0
 Requires-Dist: nimfa>=1.1.0
 Requires-Dist: sigProfilerPlotting>=1.4.1
 Requires-Dist: SigProfilerMatrixGenerator>=1.3.5
-Requires-Dist: SigProfilerAssignment>=1.0.1
+Requires-Dist: SigProfilerAssignment>=1.1.0
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -149,7 +149,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **nmf_tolerance** | Float | Value defines the tolerance to achieve to converge (default: `1e-15`).|
 | **Execution** |  |  |  | 
 |  | **cpu** | Integer | The number of processors to be used to extract the signatures (default: all processors). |
-|  | **assignment_cpu** | Integer | The number of processors to be used for the final signature assignment step (default: all processors). This is independent of the `cpu` parameter. |
+|  | **assignment_cpu** | Integer | Number of processors to be used by SigProfilerAssignment for the final signature assignment step (default: all available). This is independent of the `cpu` parameter. |
 |  | **gpu** | Boolean | Defines if the GPU resource will used if available (default: `False`). If `True`, the GPU resources will be used in the computation. *Note: All available CPU processors are used by default, which may cause a memory error. This error can be resolved by reducing the number of CPU processes through the `cpu` parameter.*|
 |  | **batch_size** | Integer | Will be effective only if the GPU is used. Defines the number of NMF replicates to be performed by each CPU during the parallel processing (default: `1`). *Note: For `batch_size` values greater than 1, each NMF replicate will update until `max_nmf_iterations` is reached.*|
 | **Solution Estimation Thresholds** |  |  |  | 
@@ -158,7 +158,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **combined_stability** | Float | The cutoff thresh-hold of the combined stability (sum of average and minimum stability) (default: `1.0`). Solutions with combined stabilities below this thresh-hold will not be considered. |
 |  | **allow_stability_drop** | Boolean | Defines if solutions with a drop in stability with respect to the highest stable number of signatures will be considered (default: `False`). |
 | **Decomposition** |  |  |  | 
-|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.4`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, and `3.4`.|
+|  | **cosmic_version** | Float | Defines the version of the COSMIC reference signatures (default: `3.5`). Takes a positive float among `1`, `2`, `3`, `3.1`, `3.2`, `3.3`, `3.4`, and `3.5`.|
 |  | **make_decomposition_plots** | Boolean | Generate de novo to COSMIC signature decomposition plots as part of the results (default: `True`). Set to `False` to skip generating these plots. |
 |  | **collapse_to_SBS96** | Boolean | If `True`, SBS288 and SBS1536 de novo signatures will be mapped to SBS96 reference signatures (default: `True`). If `False`, those will be mapped to reference signatures of the same context.
 | **Others** |  |  |  | 

{sigprofilerextractor-1.2.4 → sigprofilerextractor-1.2.6}/SigProfilerExtractor.egg-info/requires.txt

@@ -5,7 +5,7 @@ pandas>=2.0.0
 nimfa>=1.1.0
 sigProfilerPlotting>=1.4.1
 SigProfilerMatrixGenerator>=1.3.5
-SigProfilerAssignment>=1.0.1
+SigProfilerAssignment>=1.1.0
 statsmodels>=0.9.0
 scikit-learn>=0.24.2
 psutil>=5.6.1

{sigprofilerextractor-1.2.4 → sigprofilerextractor-1.2.6}/setup.py

@@ -8,7 +8,7 @@ import subprocess
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.2.4"
+VERSION = "1.2.6"
 
 
 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 = 'v1.2.4: Added assignment_cpu parameter for SigProfilerAssignment v1.0.0 support.'
+Update = 'v1.2.6: Update default COSMIC version to 3.5'
     
     """
     fh = open(filename, "w")
@@ -42,7 +42,7 @@ requirements = [
     "nimfa>=1.1.0",
     "sigProfilerPlotting>=1.4.1",
     "SigProfilerMatrixGenerator>=1.3.5",
-    "SigProfilerAssignment>=1.0.1",
+    "SigProfilerAssignment>=1.1.0",
     "statsmodels>=0.9.0",
     "scikit-learn>=0.24.2",
     "psutil>=5.6.1",

sigprofilerextractor-1.2.4/SigProfilerExtractor/version.py

@@ -1,7 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
-short_version = '1.2.4'
-version = '1.2.4'
-Update = 'v1.2.4: Added assignment_cpu parameter for SigProfilerAssignment v1.0.0 support.'
-    
-