SigProfilerExtractor 1.2.1__tar.gz → 1.2.3__tar.gz

{sigprofilerextractor-1.2.1/SigProfilerExtractor.egg-info → sigprofilerextractor-1.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.1
+Version: 1.2.3
 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
@@ -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** |  |  |  | 

{sigprofilerextractor-1.2.1 → sigprofilerextractor-1.2.3}/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** |  |  |  | 

{sigprofilerextractor-1.2.1 → sigprofilerextractor-1.2.3}/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-1.2.1 → sigprofilerextractor-1.2.3}/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,
 ):
     """
@@ -1093,45 +1094,39 @@ 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"
-
-        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-1.2.1 → sigprofilerextractor-1.2.3}/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-1.2.3/SigProfilerExtractor/version.py

@@ -0,0 +1,7 @@
+
+# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
+short_version = '1.2.3'
+version = '1.2.3'
+Update = 'v1.2.3: Add support for rn7 and mm39 genomes'
+    
+    

{sigprofilerextractor-1.2.1 → sigprofilerextractor-1.2.3/SigProfilerExtractor.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerExtractor
-Version: 1.2.1
+Version: 1.2.3
 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
@@ -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** |  |  |  | 

{sigprofilerextractor-1.2.1 → sigprofilerextractor-1.2.3}/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-1.2.1 → sigprofilerextractor-1.2.3}/setup.py

@@ -8,7 +8,7 @@ import subprocess
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.2.1"
+VERSION = "1.2.3"
 
 
 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 = 'v1.2.1: Fix CLI non-zero exit code issue'
+Update = 'v1.2.3: Add support for rn7 and mm39 genomes'
     
     """
     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-1.2.1/SigProfilerExtractor/version.py

@@ -1,7 +0,0 @@
-
-# THIS FILE IS GENERATED FROM SIGPROFILEREXTRACTOR SETUP.PY
-short_version = '1.2.1'
-version = '1.2.1'
-Update = 'v1.2.1: Fix CLI non-zero exit code issue'
-    
-