SigProfilerAssignment 0.0.33__tar.gz → 0.1.1__tar.gz

{SigProfilerAssignment-0.0.33 → SigProfilerAssignment-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SigProfilerAssignment
-Version: 0.0.33
+Version: 0.1.1
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
@@ -8,6 +8,19 @@ Author-email: rvangara@health.ucsd.edu
 License: UCSD
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
+Requires-Dist: scipy>=1.6.3
+Requires-Dist: numpy>=1.21.2
+Requires-Dist: pandas<2.0.0,>=1.2.4
+Requires-Dist: SigProfilerMatrixGenerator>=1.2.17
+Requires-Dist: sigProfilerPlotting>=1.3.18
+Requires-Dist: statsmodels>=0.9.0
+Requires-Dist: scikit-learn>=0.24.2
+Requires-Dist: psutil>=5.6.1
+Requires-Dist: reportlab>=3.5.42
+Requires-Dist: PyPDF2>=3.0.0
+Requires-Dist: alive_progress>=2.4.1
+Requires-Dist: pdf2image>=1.16.0
+Requires-Dist: PyMuPDF>=1.21.0
 
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/mz79v/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
@@ -47,12 +60,12 @@ genInstall.install('GRCh37')
 ```
 ## <a name="running"></a> 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 v3.3 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.
+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 v3.4 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",
-                   collapse_to_SBS96=True, cosmic_version=3.3, exome=False,
+                   collapse_to_SBS96=True, cosmic_version=3.4, exome=False,
                    genome_build="GRCh37", signature_database=None,
                    exclude_signature_subgroups=None, export_probabilities=False,
                    export_probabilities_per_mutation=False, make_plots=False,
@@ -69,7 +82,7 @@ Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96",
 | output | String | Path to the output folder. |
 | input_type | String | Three accepted input types:<ul><li> "vcf": if using mutation calling file/s (VCF, MAF, simple text file) as input</li><li>"seg:TYPE": if using a segmentation file as input. Please check the required format at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator#copy-number-matrix-generation. The accepted callers for TYPE are the following {"ASCAT", "ASCAT_NGS", "SEQUENZA", "ABSOLUTE", "BATTENBERG", "FACETS", "PURPLE", "TCGA"}. For example:"seg:BATTENBERG"</li><li>"matrix": if using a mutational matrix as input</li></ul>The default value is "matrix". |
 | context_type | String | Required context type if `input_type` is "vcf". `context_type` takes which context type of the input data is considered for assignment. Valid options include "96", "288", "1536", "DINUC", and "ID". The default value is "96". |
-| cosmic_version | Float | Defines the version of the COSMIC reference signatures. Takes a positive float among 1, 2, 3, 3.1, 3.2 and 3.3. The default value is 3.3. |
+| cosmic_version | Float | Defines the version of the COSMIC reference signatures. Takes a positive float among 1, 2, 3, 3.1, 3.2, 3.3, and 3.4. The default value is 3.4. |
 | exome | Boolean | Defines if the exome renormalized COSMIC signatures will be used. The default value is False. |
 | genome_build | String | The reference genome build, used for select the appropriate version of the COSMIC reference signatures, as well as processing the mutation calling file/s. Supported genomes include "GRCh37", "GRCh38", "mm9", "mm10" and "rn6". The default value is "GRCh37". If the selected genome is not in the supported list, the default genome will be used. |
 | signature_database | String | Path to the input set of known mutational signatures (only in case that COSMIC reference signatures are not used), a tab delimited file that contains the signature matrix where the rows are mutation types and columns are signature IDs. |
@@ -109,17 +122,17 @@ The full list of signature subgroups is included in the following table:
 | ----------- | ----------- | ----------- | ----------- |
 |MMR_deficiency_signatures|     6, 14, 15, 20, 21, 26, 44|      7, 10|  7|
 |POL_deficiency_signatures|     10a, 10b, 10c, 10d, 28|         3|      -|
-|HR_deficiency_signatures|      3|                              -|      6|
+|HR_deficiency_signatures|      3|                              13|      6|
 |BER_deficiency_signatures|     30, 36|                         -|      -|
-|Chemotherapy_signatures|       11, 25, 31, 35, 86, 87, 90|     5|      -|
+|Chemotherapy_signatures|       11, 25, 31, 35, 86, 87, 90, 99|     5|      -|
 |Immunosuppressants_signatures| 32|                             -|      -|
-|Treatment_signatures|          11, 25, 31, 32, 35, 86, 87, 90| 5|      -|
+|Treatment_signatures|          11, 25, 31, 32, 35, 86, 87, 90, 99| 5|      -|
 |APOBEC_signatures|             2, 13|                          -|      -|
 |Tobacco_signatures |           4, 29, 92|                      2|      3|
 |UV_signatures|                 7a, 7b, 7c, 7d, 38|             1|      13|
-|AA_signatures|                 22|                             -|      -|
+|AA_signatures|                 22a, 22b|                             20|      23|
 |Colibactin_signatures|         88|                             -|      18|
-|Artifact_signatures|           27, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95|-|-|
+|Artifact_signatures|           27, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95|14|-|
 |Lymphoid_signatures|           9, 84, 85|                      -|      -|
 
         
@@ -137,7 +150,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/vcf_input",
                    input_type="vcf",
                    context_type="96",
                    genome_build="GRCh37",
-                   cosmic_version=3.3)
+                   cosmic_version=3.4)
 ```
 
 
@@ -150,7 +163,7 @@ from SigProfilerAssignment import Analyzer as Analyze
 Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/cnv_input/all.breast.ascat.summary.sample.tsv", 
                    output="example_sf",
                    input_type="seg:ASCAT_NGS",
-                   cosmic_version=3.3,
+                   cosmic_version=3.4,
                    collapse_to_SBS96=False)
 ```
 
@@ -164,7 +177,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/txt_input/sample_matrix_
                    output="example_mm",
                    input_type="matrix",
                    genome_build="GRCh37",
-                   cosmic_version=3.3)
+                   cosmic_version=3.4)
 ```
 
 ## <a name="denovo"></a> _De novo_ extraction of mutational signatures downstream analysis

{SigProfilerAssignment-0.0.33 → SigProfilerAssignment-0.1.1}/README.md

@@ -36,12 +36,12 @@ genInstall.install('GRCh37')
 ```
 ## <a name="running"></a> 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 v3.3 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.
+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 v3.4 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",
-                   collapse_to_SBS96=True, cosmic_version=3.3, exome=False,
+                   collapse_to_SBS96=True, cosmic_version=3.4, exome=False,
                    genome_build="GRCh37", signature_database=None,
                    exclude_signature_subgroups=None, export_probabilities=False,
                    export_probabilities_per_mutation=False, make_plots=False,
@@ -58,7 +58,7 @@ Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96",
 | output | String | Path to the output folder. |
 | input_type | String | Three accepted input types:<ul><li> "vcf": if using mutation calling file/s (VCF, MAF, simple text file) as input</li><li>"seg:TYPE": if using a segmentation file as input. Please check the required format at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator#copy-number-matrix-generation. The accepted callers for TYPE are the following {"ASCAT", "ASCAT_NGS", "SEQUENZA", "ABSOLUTE", "BATTENBERG", "FACETS", "PURPLE", "TCGA"}. For example:"seg:BATTENBERG"</li><li>"matrix": if using a mutational matrix as input</li></ul>The default value is "matrix". |
 | context_type | String | Required context type if `input_type` is "vcf". `context_type` takes which context type of the input data is considered for assignment. Valid options include "96", "288", "1536", "DINUC", and "ID". The default value is "96". |
-| cosmic_version | Float | Defines the version of the COSMIC reference signatures. Takes a positive float among 1, 2, 3, 3.1, 3.2 and 3.3. The default value is 3.3. |
+| cosmic_version | Float | Defines the version of the COSMIC reference signatures. Takes a positive float among 1, 2, 3, 3.1, 3.2, 3.3, and 3.4. The default value is 3.4. |
 | exome | Boolean | Defines if the exome renormalized COSMIC signatures will be used. The default value is False. |
 | genome_build | String | The reference genome build, used for select the appropriate version of the COSMIC reference signatures, as well as processing the mutation calling file/s. Supported genomes include "GRCh37", "GRCh38", "mm9", "mm10" and "rn6". The default value is "GRCh37". If the selected genome is not in the supported list, the default genome will be used. |
 | signature_database | String | Path to the input set of known mutational signatures (only in case that COSMIC reference signatures are not used), a tab delimited file that contains the signature matrix where the rows are mutation types and columns are signature IDs. |
@@ -98,17 +98,17 @@ The full list of signature subgroups is included in the following table:
 | ----------- | ----------- | ----------- | ----------- |
 |MMR_deficiency_signatures|     6, 14, 15, 20, 21, 26, 44|      7, 10|  7|
 |POL_deficiency_signatures|     10a, 10b, 10c, 10d, 28|         3|      -|
-|HR_deficiency_signatures|      3|                              -|      6|
+|HR_deficiency_signatures|      3|                              13|      6|
 |BER_deficiency_signatures|     30, 36|                         -|      -|
-|Chemotherapy_signatures|       11, 25, 31, 35, 86, 87, 90|     5|      -|
+|Chemotherapy_signatures|       11, 25, 31, 35, 86, 87, 90, 99|     5|      -|
 |Immunosuppressants_signatures| 32|                             -|      -|
-|Treatment_signatures|          11, 25, 31, 32, 35, 86, 87, 90| 5|      -|
+|Treatment_signatures|          11, 25, 31, 32, 35, 86, 87, 90, 99| 5|      -|
 |APOBEC_signatures|             2, 13|                          -|      -|
 |Tobacco_signatures |           4, 29, 92|                      2|      3|
 |UV_signatures|                 7a, 7b, 7c, 7d, 38|             1|      13|
-|AA_signatures|                 22|                             -|      -|
+|AA_signatures|                 22a, 22b|                             20|      23|
 |Colibactin_signatures|         88|                             -|      18|
-|Artifact_signatures|           27, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95|-|-|
+|Artifact_signatures|           27, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 95|14|-|
 |Lymphoid_signatures|           9, 84, 85|                      -|      -|
 
         
@@ -126,7 +126,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/vcf_input",
                    input_type="vcf",
                    context_type="96",
                    genome_build="GRCh37",
-                   cosmic_version=3.3)
+                   cosmic_version=3.4)
 ```
 
 
@@ -139,7 +139,7 @@ from SigProfilerAssignment import Analyzer as Analyze
 Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/cnv_input/all.breast.ascat.summary.sample.tsv", 
                    output="example_sf",
                    input_type="seg:ASCAT_NGS",
-                   cosmic_version=3.3,
+                   cosmic_version=3.4,
                    collapse_to_SBS96=False)
 ```
 
@@ -153,7 +153,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/txt_input/sample_matrix_
                    output="example_mm",
                    input_type="matrix",
                    genome_build="GRCh37",
-                   cosmic_version=3.3)
+                   cosmic_version=3.4)
 ```
 
 ## <a name="denovo"></a> _De novo_ extraction of mutational signatures downstream analysis

SigProfilerAssignment-0.1.1/SigProfilerAssignment/Analyzer.py

@@ -0,0 +1,152 @@
+from SigProfilerAssignment import decomposition as decomp
+
+
+def decompose_fit(
+    samples,
+    output,
+    signatures=None,
+    signature_database=None,
+    nnls_add_penalty=0.05,
+    nnls_remove_penalty=0.01,
+    initial_remove_penalty=0.05,
+    genome_build="GRCh37",
+    cosmic_version=3.4,
+    make_plots=True,
+    collapse_to_SBS96=True,
+    connected_sigs=True,
+    verbose=False,
+    devopts=None,
+    new_signature_thresh_hold=0.8,
+    exclude_signature_subgroups=None,
+    exome=False,
+    input_type="matrix",
+    context_type="96",
+    export_probabilities=True,
+    export_probabilities_per_mutation=False,
+):
+    decomp.spa_analyze(
+        samples=samples,
+        output=output,
+        signatures=signatures,
+        signature_database=signature_database,
+        nnls_add_penalty=nnls_add_penalty,
+        nnls_remove_penalty=nnls_remove_penalty,
+        initial_remove_penalty=initial_remove_penalty,
+        genome_build=genome_build,
+        cosmic_version=cosmic_version,
+        make_plots=make_plots,
+        collapse_to_SBS96=collapse_to_SBS96,
+        connected_sigs=connected_sigs,
+        verbose=verbose,
+        decompose_fit_option=True,
+        denovo_refit_option=False,
+        cosmic_fit_option=False,
+        devopts=devopts,
+        new_signature_thresh_hold=new_signature_thresh_hold,
+        exclude_signature_subgroups=exclude_signature_subgroups,
+        exome=exome,
+        input_type=input_type,
+        context_type=context_type,
+        export_probabilities=export_probabilities,
+        export_probabilities_per_mutation=export_probabilities_per_mutation,
+    )
+
+
+def denovo_fit(
+    samples,
+    output,
+    signatures=None,
+    signature_database=None,
+    nnls_add_penalty=0.05,
+    nnls_remove_penalty=0.01,
+    initial_remove_penalty=0.05,
+    genome_build="GRCh37",
+    cosmic_version=3.4,
+    make_plots=True,
+    collapse_to_SBS96=True,
+    connected_sigs=True,
+    verbose=False,
+    devopts=None,
+    new_signature_thresh_hold=0.8,
+    exome=False,
+    input_type="matrix",
+    context_type="96",
+    export_probabilities=True,
+    export_probabilities_per_mutation=False,
+):
+    decomp.spa_analyze(
+        samples=samples,
+        output=output,
+        signatures=signatures,
+        signature_database=signature_database,
+        nnls_add_penalty=nnls_add_penalty,
+        nnls_remove_penalty=nnls_remove_penalty,
+        initial_remove_penalty=initial_remove_penalty,
+        genome_build=genome_build,
+        cosmic_version=cosmic_version,
+        new_signature_thresh_hold=new_signature_thresh_hold,
+        make_plots=make_plots,
+        collapse_to_SBS96=collapse_to_SBS96,
+        connected_sigs=connected_sigs,
+        verbose=verbose,
+        decompose_fit_option=False,
+        denovo_refit_option=True,
+        cosmic_fit_option=False,
+        devopts=devopts,
+        exome=exome,
+        input_type=input_type,
+        context_type=context_type,
+        export_probabilities=export_probabilities,
+        export_probabilities_per_mutation=export_probabilities_per_mutation,
+    )
+
+
+def cosmic_fit(
+    samples,
+    output,
+    signatures=None,
+    signature_database=None,
+    nnls_add_penalty=0.05,
+    nnls_remove_penalty=0.01,
+    initial_remove_penalty=0.05,
+    genome_build="GRCh37",
+    cosmic_version=3.4,
+    make_plots=True,
+    collapse_to_SBS96=True,
+    connected_sigs=True,
+    verbose=False,
+    devopts=None,
+    exclude_signature_subgroups=None,
+    exome=False,
+    input_type="matrix",
+    context_type="96",
+    export_probabilities=True,
+    export_probabilities_per_mutation=False,
+    sample_reconstruction_plots=False,
+):
+    decomp.spa_analyze(
+        samples=samples,
+        output=output,
+        signatures=signatures,
+        signature_database=signature_database,
+        nnls_add_penalty=nnls_add_penalty,
+        nnls_remove_penalty=nnls_remove_penalty,
+        initial_remove_penalty=initial_remove_penalty,
+        genome_build=genome_build,
+        cosmic_version=cosmic_version,
+        make_plots=make_plots,
+        collapse_to_SBS96=collapse_to_SBS96,
+        connected_sigs=connected_sigs,
+        verbose=verbose,
+        decompose_fit_option=False,
+        denovo_refit_option=False,
+        cosmic_fit_option=True,
+        devopts=devopts,
+        exclude_signature_subgroups=exclude_signature_subgroups,
+        exome=exome,
+        input_type=input_type,
+        context_type=context_type,
+        export_probabilities=export_probabilities,
+        export_probabilities_per_mutation=export_probabilities_per_mutation,
+        sample_reconstruction_plots=sample_reconstruction_plots,
+    )