SigProfilerAssignment 1.1.3__tar.gz → 1.1.4__tar.gz

sigprofilerassignment-1.1.4/PKG-INFO

@@ -0,0 +1,86 @@
+Metadata-Version: 2.4
+Name: SigProfilerAssignment
+Version: 1.1.4
+Summary: Mutational signatures attribution and decomposition tool
+Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
+Author: Raviteja Vangara
+Author-email: rvangara@health.ucsd.edu
+License: UCSD
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: scipy>=1.13
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
+Requires-Dist: sigProfilerPlotting>=1.4.0
+Requires-Dist: reportlab>=3.5.42
+Requires-Dist: pypdf>=6.0.0
+Requires-Dist: alive_progress>=2.4.1
+Requires-Dist: pdf2image>=1.16.0
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://sigprofilersuite.github.io/SigProfilerAssignment/)
+[![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
+[![CI](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml/badge.svg)](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml)
+
+<img src="docs/assets/images/SigProfilerAssignment.png" alt="SigProfilerAssignment" width="1000"/>
+
+# SigProfilerAssignment
+SigProfilerAssignment enables assignment of previously known mutational signatures to individual samples and individual somatic mutations. The tool refits different types of reference mutational signatures, including [COSMIC signatures](https://cancer.sanger.ac.uk/signatures/), as well as custom signature databases. SigProfilerAssignment makes use of [SigProfilerMatrixGenerator](https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator) and [SigProfilerPlotting](https://github.com/SigProfilerSuite/SigProfilerPlotting), seamlessly integrating with other in [SigProfilerSuite](https://github.com/SigProfilerSuite).
+
+## Documentation
+Detailed documentation can be found at https://sigprofilersuite.github.io/SigProfilerAssignment.
+
+## Quick Start Guide
+###  Installation
+
+Install the current stable PyPi version of SigProfilerAssignment:
+```
+$ pip install SigProfilerAssignment
+```
+
+If mutation calling files (MAF, VCF, or simple text files) are used as input, please install your desired reference genome as follows (available reference genomes are: GRCh37, GRCh38, mm9, mm10, rn6, and rn7):
+```python
+$ python
+from SigProfilerMatrixGenerator import install as genInstall
+genInstall.install('GRCh37')
+```
+
+
+### Running
+
+Assignment of known mutational signatures to individual samples is performed using the `cosmic_fit` function. Input samples are provided using the `samples` parameter in the form of mutation calling files (VCFs, MAFs, or simple text files), segmentation files, or mutational matrices. COSMIC mutational signatures v3.5 are used as the default reference signatures, although previous COSMIC versions and custom signature databases are also supported using the `cosmic_version` and `signature_database` parameters. Results will be found in the folder specified in the `output` parameter.
+
+```python
+from SigProfilerAssignment import Analyzer as Analyze
+Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96")
+```
+
+You can also run SigProfilerAssignment `cosmic_fit` function from command line: 
+
+``` bash
+$ SigProfilerAssignment cosmic_fit samples output --input_type "matrix" --context_type "96"
+
+```
+
+## Reference
+
+Díaz-Gay M, Vangara R, Barnes M, *et al.*, Alexandrov LB. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment. *Bioinformatics*. 2023;39(12):btad756. [https://doi.org/10.1093/bioinformatics/btad756](https://doi.org/10.1093/bioinformatics/btad756)
+
+## Contact
+
+For questions, support requests, or bug reports, please contact the SigProfilerSuite team via GitHub [issues](https://github.com/SigProfilerSuite/SigProfilerAssignment/issues) or by email at [contact@sigprofilersuite.org](mailto:contact@sigprofilersuite.org).
+

sigprofilerassignment-1.1.4/README.md

@@ -0,0 +1,52 @@
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://sigprofilersuite.github.io/SigProfilerAssignment/)
+[![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
+[![CI](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml/badge.svg)](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml)
+
+<img src="docs/assets/images/SigProfilerAssignment.png" alt="SigProfilerAssignment" width="1000"/>
+
+# SigProfilerAssignment
+SigProfilerAssignment enables assignment of previously known mutational signatures to individual samples and individual somatic mutations. The tool refits different types of reference mutational signatures, including [COSMIC signatures](https://cancer.sanger.ac.uk/signatures/), as well as custom signature databases. SigProfilerAssignment makes use of [SigProfilerMatrixGenerator](https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator) and [SigProfilerPlotting](https://github.com/SigProfilerSuite/SigProfilerPlotting), seamlessly integrating with other in [SigProfilerSuite](https://github.com/SigProfilerSuite).
+
+## Documentation
+Detailed documentation can be found at https://sigprofilersuite.github.io/SigProfilerAssignment.
+
+## Quick Start Guide
+###  Installation
+
+Install the current stable PyPi version of SigProfilerAssignment:
+```
+$ pip install SigProfilerAssignment
+```
+
+If mutation calling files (MAF, VCF, or simple text files) are used as input, please install your desired reference genome as follows (available reference genomes are: GRCh37, GRCh38, mm9, mm10, rn6, and rn7):
+```python
+$ python
+from SigProfilerMatrixGenerator import install as genInstall
+genInstall.install('GRCh37')
+```
+
+
+### Running
+
+Assignment of known mutational signatures to individual samples is performed using the `cosmic_fit` function. Input samples are provided using the `samples` parameter in the form of mutation calling files (VCFs, MAFs, or simple text files), segmentation files, or mutational matrices. COSMIC mutational signatures v3.5 are used as the default reference signatures, although previous COSMIC versions and custom signature databases are also supported using the `cosmic_version` and `signature_database` parameters. Results will be found in the folder specified in the `output` parameter.
+
+```python
+from SigProfilerAssignment import Analyzer as Analyze
+Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96")
+```
+
+You can also run SigProfilerAssignment `cosmic_fit` function from command line: 
+
+``` bash
+$ SigProfilerAssignment cosmic_fit samples output --input_type "matrix" --context_type "96"
+
+```
+
+## Reference
+
+Díaz-Gay M, Vangara R, Barnes M, *et al.*, Alexandrov LB. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment. *Bioinformatics*. 2023;39(12):btad756. [https://doi.org/10.1093/bioinformatics/btad756](https://doi.org/10.1093/bioinformatics/btad756)
+
+## Contact
+
+For questions, support requests, or bug reports, please contact the SigProfilerSuite team via GitHub [issues](https://github.com/SigProfilerSuite/SigProfilerAssignment/issues) or by email at [contact@sigprofilersuite.org](mailto:contact@sigprofilersuite.org).
+

{sigprofilerassignment-1.1.3 → sigprofilerassignment-1.1.4}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py

@@ -1046,6 +1046,7 @@ def run_PlotSSDecomposition(
     custom_text=None,
     exome=False,
     volume=None,
+    use_custom_basis=False,
 ):
     """
     Generates a reconstruction of a sample given a set of signatures.
@@ -1084,30 +1085,45 @@ def run_PlotSSDecomposition(
 
     exome: Boolean. True if using exome COSMIC signatures, and False if not.
 
+    use_custom_basis: Boolean. True if basis_mtx comes from a custom signature_database
+    (renders basis plots directly from basis_mtx instead of the cached COSMIC plots).
+
     Returns:
     -------
     None.
     """
 
-    # Create the denovo plots
-    denovo_plots_dict = gen_sub_plots(
-        denovo_mtx,
-        None,
-        output_path,
-        project,
-        context_type,
-        ss_decomp=True,
-        volume=volume,
-    )
-    denovo_plots_dict = denovo_plots_dict[0]
-    # Load in the COSMIC plots
-    basis_plots_dict = install_cosmic_plots(
-        context_type=context_type,
-        genome_build=genome_build,
-        cosmic_version=cosmic_version,
-        exome=exome,
-        volume=volume,
-    )
+    if use_custom_basis:
+        # Custom signature database: render basis (signature) plots directly
+        # from the provided matrix instead of the cached COSMIC reference plots.
+        denovo_plots_dict, basis_plots_dict = gen_sub_plots(
+            denovo_mtx,
+            basis_mtx,
+            output_path,
+            project,
+            context_type,
+            ss_decomp=True,
+            volume=volume,
+        )
+    else:
+        # Create the denovo plots
+        denovo_plots_dict, _ = gen_sub_plots(
+            denovo_mtx,
+            None,
+            output_path,
+            project,
+            context_type,
+            ss_decomp=True,
+            volume=volume,
+        )
+        # Load in the COSMIC plots
+        basis_plots_dict = install_cosmic_plots(
+            context_type=context_type,
+            genome_build=genome_build,
+            cosmic_version=cosmic_version,
+            exome=exome,
+            volume=volume,
+        )
 
     # Create reconstructed matrix and plot
     reconstructed_mtx, reconstruction_plot_dict = gen_reconstructed_png_numerical(

{sigprofilerassignment-1.1.3 → sigprofilerassignment-1.1.4}/SigProfilerAssignment/controllers/cli_controller.py

@@ -13,6 +13,8 @@ def str2bool(v):
     else:
         raise argparse.ArgumentTypeError("Boolean value expected.")
 
+def str2list(arg):
+    return arg.split(",")
 
 def parse_arguments_common(args: List[str], description: str) -> argparse.Namespace:
     parser = argparse.ArgumentParser(description=description)
@@ -99,6 +101,7 @@ def parse_arguments_common(args: List[str], description: str) -> argparse.Namesp
     )
     parser.add_argument(
         "--exclude_signature_subgroups",
+        type=str2list,
         default=None,
         help="Remove specific signature subgroups.",
     )

{sigprofilerassignment-1.1.3 → sigprofilerassignment-1.1.4}/SigProfilerAssignment/decomposition.py

@@ -103,6 +103,10 @@ def generate_sample_reconstruction(
     #       png     = pdf generation + png conversion + pdf removal
     project = "test_run"
     mtype = "96"
+    is_custom_database = execution_parameters.get("signature_database") is not None
+    cosmic_version_label = (
+        "Custom" if is_custom_database else str(execution_parameters["cosmic_version"])
+    )
 
     final_pdf = PdfWriter()
     samples = samples_input.copy(deep=True)
@@ -140,9 +144,10 @@ def generate_sample_reconstruction(
             project,
             mtype,
             genome_build=execution_parameters["reference_genome"],
-            cosmic_version=str(execution_parameters["cosmic_version"]),
+            cosmic_version=cosmic_version_label,
             exome=execution_parameters["exome"],
             volume=get_storage_dir(execution_parameters["volume"]),
+            use_custom_basis=is_custom_database,
         )
 
         result.seek(0)
@@ -1015,9 +1020,6 @@ def spa_analyze(
                 cosmic_version=cosmic_version,
                 exome=exome,
             )[0]
-            # for sample reconstruction plots
-            cosmic_sig_ref = processAvg.copy(deep=True)
-            cosmic_sig_ref.reset_index(inplace=True)
         else:
 
             try:
@@ -1055,6 +1057,12 @@ def spa_analyze(
         # #
         processAvg.drop(sig_exclusion_list, axis=1, inplace=True, errors="ignore")
 
+        # for sample reconstruction plots; built after collapsing/exclusion so it
+        # matches the signatures actually used, whether from COSMIC or a custom
+        # signature_database.
+        cosmic_sig_ref = processAvg.copy(deep=True)
+        cosmic_sig_ref.reset_index(inplace=True)
+
         # processAvg= originalProcessAvg
         # index = genomes.index
         # colnames = genomes.columns
@@ -1138,7 +1146,6 @@ def spa_analyze(
         isinstance(sample_reconstruction_plots, str)
         and sample_reconstruction_plots.lower() in recon_output_types
         and mutation_type == "96"
-        and signature_database is None
     ):
         ss_recon_odir = os.path.join(
             layer_directory3, "Activities", "SampleReconstruction"

{sigprofilerassignment-1.1.3 → sigprofilerassignment-1.1.4}/SigProfilerAssignment/version.py

@@ -1,7 +1,7 @@
 
 # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
-short_version = '1.1.3'
-version = '1.1.3'
+short_version = '1.1.4'
+version = '1.1.4'
 Update = 'v1.1.3: Fixed set_index() calls for Python 3.12 StringArray compatibility'
 
     

sigprofilerassignment-1.1.4/SigProfilerAssignment.egg-info/PKG-INFO

@@ -0,0 +1,86 @@
+Metadata-Version: 2.4
+Name: SigProfilerAssignment
+Version: 1.1.4
+Summary: Mutational signatures attribution and decomposition tool
+Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
+Author: Raviteja Vangara
+Author-email: rvangara@health.ucsd.edu
+License: UCSD
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: scipy>=1.13
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: SigProfilerMatrixGenerator>=1.3.0
+Requires-Dist: sigProfilerPlotting>=1.4.0
+Requires-Dist: reportlab>=3.5.42
+Requires-Dist: pypdf>=6.0.0
+Requires-Dist: alive_progress>=2.4.1
+Requires-Dist: pdf2image>=1.16.0
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://sigprofilersuite.github.io/SigProfilerAssignment/)
+[![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
+[![CI](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml/badge.svg)](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml)
+
+<img src="docs/assets/images/SigProfilerAssignment.png" alt="SigProfilerAssignment" width="1000"/>
+
+# SigProfilerAssignment
+SigProfilerAssignment enables assignment of previously known mutational signatures to individual samples and individual somatic mutations. The tool refits different types of reference mutational signatures, including [COSMIC signatures](https://cancer.sanger.ac.uk/signatures/), as well as custom signature databases. SigProfilerAssignment makes use of [SigProfilerMatrixGenerator](https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator) and [SigProfilerPlotting](https://github.com/SigProfilerSuite/SigProfilerPlotting), seamlessly integrating with other in [SigProfilerSuite](https://github.com/SigProfilerSuite).
+
+## Documentation
+Detailed documentation can be found at https://sigprofilersuite.github.io/SigProfilerAssignment.
+
+## Quick Start Guide
+###  Installation
+
+Install the current stable PyPi version of SigProfilerAssignment:
+```
+$ pip install SigProfilerAssignment
+```
+
+If mutation calling files (MAF, VCF, or simple text files) are used as input, please install your desired reference genome as follows (available reference genomes are: GRCh37, GRCh38, mm9, mm10, rn6, and rn7):
+```python
+$ python
+from SigProfilerMatrixGenerator import install as genInstall
+genInstall.install('GRCh37')
+```
+
+
+### Running
+
+Assignment of known mutational signatures to individual samples is performed using the `cosmic_fit` function. Input samples are provided using the `samples` parameter in the form of mutation calling files (VCFs, MAFs, or simple text files), segmentation files, or mutational matrices. COSMIC mutational signatures v3.5 are used as the default reference signatures, although previous COSMIC versions and custom signature databases are also supported using the `cosmic_version` and `signature_database` parameters. Results will be found in the folder specified in the `output` parameter.
+
+```python
+from SigProfilerAssignment import Analyzer as Analyze
+Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96")
+```
+
+You can also run SigProfilerAssignment `cosmic_fit` function from command line: 
+
+``` bash
+$ SigProfilerAssignment cosmic_fit samples output --input_type "matrix" --context_type "96"
+
+```
+
+## Reference
+
+Díaz-Gay M, Vangara R, Barnes M, *et al.*, Alexandrov LB. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment. *Bioinformatics*. 2023;39(12):btad756. [https://doi.org/10.1093/bioinformatics/btad756](https://doi.org/10.1093/bioinformatics/btad756)
+
+## Contact
+
+For questions, support requests, or bug reports, please contact the SigProfilerSuite team via GitHub [issues](https://github.com/SigProfilerSuite/SigProfilerAssignment/issues) or by email at [contact@sigprofilersuite.org](mailto:contact@sigprofilersuite.org).
+

{sigprofilerassignment-1.1.3 → sigprofilerassignment-1.1.4}/SigProfilerAssignment.egg-info/SOURCES.txt

@@ -26,20 +26,6 @@ SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py
 SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py
 SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SV32.py
 SigProfilerAssignment/DecompositionPlots/SigProfilerPlottingMatrix.py
-SigProfilerAssignment/DecompositionPlots/ExampleSample/CNV48_De-Novo_Signatures.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_CNV48_Signatures.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_DBS78_Signatures.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_ID83_Signatures.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_SBS288_Signatures.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_SV32_Signatures.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_DINUC.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_INDEL.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS1536.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS288.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/De_Novo_Solution_Signatures_SBS96.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/Decomposed_Solution_Signatures_SBS1536.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/Decomposed_Solution_Signatures_SBS96.txt
-SigProfilerAssignment/DecompositionPlots/ExampleSample/SV32_De-Novo_Signatures.txt
 SigProfilerAssignment/DecompositionPlots/ReferenceFiles/Accolade_fermante.png
 SigProfilerAssignment/DecompositionPlots/ReferenceFiles/CREDIT.md
 SigProfilerAssignment/DecompositionPlots/ReferenceFiles/Fonts/Arial Bold.ttf

{sigprofilerassignment-1.1.3 → sigprofilerassignment-1.1.4}/setup.py

@@ -6,7 +6,7 @@ import os
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.1.3"
+VERSION = "1.1.4"
 
 
 def write_version_py(filename="SigProfilerAssignment/version.py"):

{sigprofilerassignment-1.1.3 → sigprofilerassignment-1.1.4}/tests/test_cli.py

@@ -3,6 +3,7 @@ import argparse
 from SigProfilerAssignment.controllers.cli_controller import (
     parse_arguments_common,
     str2bool,
+    str2list
 )
 
 
@@ -44,6 +45,8 @@ def test_argument_parsing():
             "True",
             "--sample_reconstruction_plots",
             "png",
+            "--exclude_signature_subgroups",
+            "MMR_deficiency_signatures,POL_deficiency_signatures,HR_deficiency_signatures,BER_deficiency_signatures,Chemotherapy_signatures,Immunosuppressants_signatures,Treatment_signatures,APOBEC_signatures,Tobacco_signatures,UV_signatures,AA_signatures,Colibactin_signatures,Artifact_signatures,Lymphoid_signatures"
         ],
         "Test argument parsing",
     )
@@ -59,6 +62,7 @@ def test_argument_parsing():
     assert args.export_probabilities_per_mutation == True
     assert args.exome == True
     assert args.sample_reconstruction_plots == "png"
+    assert args.exclude_signature_subgroups == ['MMR_deficiency_signatures', 'POL_deficiency_signatures', 'HR_deficiency_signatures' , 'BER_deficiency_signatures', 'Chemotherapy_signatures', 'Immunosuppressants_signatures', 'Treatment_signatures', 'APOBEC_signatures', 'Tobacco_signatures', 'UV_signatures', 'AA_signatures', 'Colibactin_signatures', 'Artifact_signatures', 'Lymphoid_signatures']
 
 
 def test_boolean_conversion():
@@ -75,6 +79,10 @@ def test_boolean_conversion():
     with pytest.raises(argparse.ArgumentTypeError):
         str2bool("maybe")
 
+def test_str2list():
+    assert str2list("arg1,arg2,arg3") == ["arg1", "arg2","arg3"]
+    assert str2list("arg_unique") == ["arg_unique"]
+    assert str2list("wrong.sepparator") == ["wrong.sepparator"]
 
 if __name__ == "__main__":
     pytest.main()