SigProfilerExtractor 1.2.2__tar.gz → 1.2.4__tar.gz

{sigprofilerextractor-1.2.2/SigProfilerExtractor.egg-info → sigprofilerextractor-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.2
+Version: 1.2.4
 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>=0.2.4
+Requires-Dist: SigProfilerAssignment>=1.0.1
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -130,7 +130,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **output** | String | The name of the output folder. The output folder will be generated in the current working directory.  |
 |  | **input_data** | String | <br>Path to input folder for input_type:<ul><li>`vcf`</li><li>`bedpe`</li></ul>Path to file for input_type:<ul><li>`matrix`</li><li>`seg:TYPE`</li></ul> |
 |  | **reference_genome** | String | The name of the reference genome (default: `"GRCh37"`). This parameter is applicable only if the `input_type` is `"vcf"`. |
-|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, and `rn6`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
+|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, `mm39`, `rn6`, and `rn7`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
 |  | **context_type** | String | Mutation context name(s), separated by commas (`,`), that define the mutational contexts for signature extraction (default: `"96,DINUC,ID"`). In the default value, `96` represents the SBS96 context, `DINUC` represents the dinucleotide context, and `ID` represents the indel context. |
 |  | **exome** | Boolean | Defines if the exomes will be extracted (default: `False`). |
 | **NMF Replicates** |  |  |  | 
@@ -149,6 +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. |
 |  | **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** |  |  |  | 

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.4}/README.md

@@ -97,7 +97,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **output** | String | The name of the output folder. The output folder will be generated in the current working directory.  |
 |  | **input_data** | String | <br>Path to input folder for input_type:<ul><li>`vcf`</li><li>`bedpe`</li></ul>Path to file for input_type:<ul><li>`matrix`</li><li>`seg:TYPE`</li></ul> |
 |  | **reference_genome** | String | The name of the reference genome (default: `"GRCh37"`). This parameter is applicable only if the `input_type` is `"vcf"`. |
-|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, and `rn6`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
+|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, `mm39`, `rn6`, and `rn7`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
 |  | **context_type** | String | Mutation context name(s), separated by commas (`,`), that define the mutational contexts for signature extraction (default: `"96,DINUC,ID"`). In the default value, `96` represents the SBS96 context, `DINUC` represents the dinucleotide context, and `ID` represents the indel context. |
 |  | **exome** | Boolean | Defines if the exomes will be extracted (default: `False`). |
 | **NMF Replicates** |  |  |  | 
@@ -116,6 +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. |
 |  | **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** |  |  |  | 

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.4}/SigProfilerExtractor/controllers/cli_controller.py

@@ -111,6 +111,12 @@ def parse_arguments_extractor(args: List[str], description: str) -> argparse.Nam
         default=-1,
         help="Number of processors to use (default: all available).",
     )
+    parser.add_argument(
+        "--assignment_cpu",
+        type=int,
+        default=-1,
+        help="Number of processors to be used by SigProfilerAssignment for the final signature assignment step (default: all available). This is independent of the 'cpu' parameter.",
+    )
     parser.add_argument(
         "--gpu",
         type=str2bool,
@@ -261,6 +267,7 @@ class CliController:
             seeds=parsed_args.seeds,
             batch_size=parsed_args.batch_size,
             cpu=parsed_args.cpu,
+            assignment_cpu=parsed_args.assignment_cpu,
             gpu=parsed_args.gpu,
             nmf_init=parsed_args.nmf_init,
             precision=parsed_args.precision,

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.4}/SigProfilerExtractor/sigpro.py

@@ -187,6 +187,7 @@ def record_parameters(sysdata, execution_parameters, start_time):
             )
         )
 
+    sysdata.write("\tassignment_cpu: {}\n".format(execution_parameters["assignment_cpu"]))
     sysdata.write("\tgpu: {}\n".format(execution_parameters["gpu"]))
     sysdata.write("Solution Estimation\n")
     sysdata.write("\tstability: {}\n".format(execution_parameters["stability"]))
@@ -248,6 +249,7 @@ def sigProfilerExtractor(
     resample=True,
     batch_size=1,
     cpu=-1,
+    assignment_cpu=-1,
     gpu=False,
     nmf_init="random",
     precision="single",
@@ -485,6 +487,7 @@ def sigProfilerExtractor(
         "maximum_signatures": maximum_signatures,
         "NMF_replicates": nmf_replicates,
         "cpu": cpu,
+        "assignment_cpu": assignment_cpu,
         "gpu": gpu,
         "batch_size": batch_size,
         "NMF_init": nmf_init,
@@ -1094,25 +1097,19 @@ def sigProfilerExtractor(
         devopts["make_decomposition_plots"] = make_decomposition_plots
 
         # Check if genome_build is available in COSMIC, if not reset to GRCh37
-        if (
-            genome_build == "GRCh37"
-            or genome_build == "GRCh38"
-            or genome_build == "mm9"
-            or genome_build == "mm10"
-            or genome_build == "rn6"
-        ):
+        if genome_build in ["GRCh37", "GRCh38", "mm9", "mm10", "mm39", "rn6", "rn7"]:
             genome_build = genome_build
         else:
             sysdata = open(out_put + "/JOB_METADATA.txt", "a")
             sysdata.write(
-                "\n[{}] The selected opportunity genome is {}. COSMIC signatures are available only for GRCh37/38, mm9/10 and rn6 genomes. So, the opportunity genome is reset to GRCh37.\n".format(
+                "\n[{}] The selected opportunity genome is {}. COSMIC signatures are available only for GRCh37/38, mm9/10/39 and rn6/7 genomes. So, the opportunity genome is reset to GRCh37.\n".format(
                     str(datetime.datetime.now()).split(".")[0], str(genome_build)
                 )
             )
             print(
                 "The selected opportunity genome is "
                 + str(genome_build)
-                + ". COSMIC signatures are available only for GRCh37/38, mm9/10 and rn6 genomes. So, the opportunity genome is reset to GRCh37."
+                + ". COSMIC signatures are available only for GRCh37/38, mm9/10/39 and rn6/7 genomes. So, the opportunity genome is reset to GRCh37."
             )
             sysdata.close()
             genome_build = "GRCh37"
@@ -1132,6 +1129,7 @@ def sigProfilerExtractor(
                 devopts=devopts,
                 make_metadata=False,
                 volume=volume,
+                cpu=assignment_cpu,
             )
 
     sysdata = open(out_put + "/JOB_METADATA.txt", "a")

sigprofilerextractor-1.2.4/SigProfilerExtractor/version.py

@@ -0,0 +1,7 @@
+
+# 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.'
+    
+    

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.4/SigProfilerExtractor.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.2
+Version: 1.2.4
 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>=0.2.4
+Requires-Dist: SigProfilerAssignment>=1.0.1
 Requires-Dist: statsmodels>=0.9.0
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: psutil>=5.6.1
@@ -130,7 +130,7 @@ sigProfilerExtractor(input_type, out_put, input_data, reference_genome="GRCh37",
 |  | **output** | String | The name of the output folder. The output folder will be generated in the current working directory.  |
 |  | **input_data** | String | <br>Path to input folder for input_type:<ul><li>`vcf`</li><li>`bedpe`</li></ul>Path to file for input_type:<ul><li>`matrix`</li><li>`seg:TYPE`</li></ul> |
 |  | **reference_genome** | String | The name of the reference genome (default: `"GRCh37"`). This parameter is applicable only if the `input_type` is `"vcf"`. |
-|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, and `rn6`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
+|  | **opportunity_genome** | String | The build or version of the reference genome for the reference signatures (default: `"GRCh37"`). When the input_type is `"vcf"`, the opportunity_genome automatically matches the input reference genome value. Only the genomes available in COSMIC are supported (`GRCh37`, `GRCh38`, `mm9`, `mm10`, `mm39`, `rn6`, and `rn7`). If a different opportunity genome is selected, the default genome `GRCh37` will be used. |
 |  | **context_type** | String | Mutation context name(s), separated by commas (`,`), that define the mutational contexts for signature extraction (default: `"96,DINUC,ID"`). In the default value, `96` represents the SBS96 context, `DINUC` represents the dinucleotide context, and `ID` represents the indel context. |
 |  | **exome** | Boolean | Defines if the exomes will be extracted (default: `False`). |
 | **NMF Replicates** |  |  |  | 
@@ -149,6 +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. |
 |  | **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** |  |  |  | 

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.4}/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>=0.2.4
+SigProfilerAssignment>=1.0.1
 statsmodels>=0.9.0
 scikit-learn>=0.24.2
 psutil>=5.6.1

{sigprofilerextractor-1.2.2 → sigprofilerextractor-1.2.4}/setup.py

@@ -8,7 +8,7 @@ import subprocess
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.2.2"
+VERSION = "1.2.4"
 
 
 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 = 'v1.2.2: Add mutation count and stability to 4608 plots in All_Solutions and a stop parameter'
+Update = 'v1.2.4: Added assignment_cpu parameter for SigProfilerAssignment v1.0.0 support.'
     
     """
     fh = open(filename, "w")
@@ -42,7 +42,7 @@ requirements = [
     "nimfa>=1.1.0",
     "sigProfilerPlotting>=1.4.1",
     "SigProfilerMatrixGenerator>=1.3.5",
-    "SigProfilerAssignment>=0.2.4",
+    "SigProfilerAssignment>=1.0.1",
     "statsmodels>=0.9.0",
     "scikit-learn>=0.24.2",
     "psutil>=5.6.1",

sigprofilerextractor-1.2.2/SigProfilerExtractor/version.py

@@ -1,7 +0,0 @@
-
-# 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'
-    
-