SigProfilerAssignment 1.0.4__tar.gz → 1.1.1__tar.gz

{sigprofilerassignment-1.0.4/SigProfilerAssignment.egg-info → sigprofilerassignment-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SigProfilerAssignment
-Version: 1.0.4
+Version: 1.1.1
 Summary: Mutational signatures attribution and decomposition tool
 Home-page: https://github.com/AlexandrovLab/SigProfilerAssignment.git
 Author: Raviteja Vangara
@@ -76,12 +76,12 @@ If you plan to use `sample_reconstruction_plots='png'` or `'both'`, the external
 
 ## <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 v3.4 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.
+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",
-                   collapse_to_SBS96=True, cosmic_version=3.4, exome=False,
+                   collapse_to_SBS96=True, cosmic_version=3.5, exome=False,
                    genome_build="GRCh37", signature_database=None,
                    exclude_signature_subgroups=None, export_probabilities=False,
                    export_probabilities_per_mutation=False, make_plots=False,
@@ -98,7 +98,7 @@ 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, 3.3, and 3.4. The default value is 3.4. |
+| 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, 3.4, and 3.5. The default value is 3.5. |
 | 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. |
@@ -147,7 +147,7 @@ The full list of signature subgroups is included in the following table:
 |Immunosuppressants_signatures| 32|                             -|      -|
 |Treatment_signatures|          11, 25, 31, 32, 35, 86, 87, 90, 99| 5|      -|
 |APOBEC_signatures|             2, 13|                          -|      -|
-|Tobacco_signatures |           4, 29, 92|                      2|      3|
+|Tobacco_signatures |           4, 29, 92, 100, 109|                      2|      3|
 |UV_signatures|                 7a, 7b, 7c, 7d, 38|             1|      13|
 |AA_signatures|                 22a, 22b|                             20|      23|
 |Colibactin_signatures|         88|                             -|      18|
@@ -169,7 +169,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/vcf_input",
                    input_type="vcf",
                    context_type="96",
                    genome_build="GRCh37",
-                   cosmic_version=3.4)
+                   cosmic_version=3.5)
 ```
 
 
@@ -182,7 +182,7 @@ 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=3.4,
+                   cosmic_version=3.5,
                    collapse_to_SBS96=False)
 ```
 
@@ -196,7 +196,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/txt_input/sample_matrix_
                    output="example_mm",
                    input_type="matrix",
                    genome_build="GRCh37",
-                   cosmic_version=3.4)
+                   cosmic_version=3.5)
 ```
 
 ## <a name="denovo"></a> _De novo_ extraction of mutational signatures downstream analysis

{sigprofilerassignment-1.0.4 → sigprofilerassignment-1.1.1}/README.md

@@ -42,12 +42,12 @@ If you plan to use `sample_reconstruction_plots='png'` or `'both'`, the external
 
 ## <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 v3.4 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.
+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",
-                   collapse_to_SBS96=True, cosmic_version=3.4, exome=False,
+                   collapse_to_SBS96=True, cosmic_version=3.5, exome=False,
                    genome_build="GRCh37", signature_database=None,
                    exclude_signature_subgroups=None, export_probabilities=False,
                    export_probabilities_per_mutation=False, make_plots=False,
@@ -64,7 +64,7 @@ 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, 3.3, and 3.4. The default value is 3.4. |
+| 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, 3.4, and 3.5. The default value is 3.5. |
 | 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. |
@@ -113,7 +113,7 @@ The full list of signature subgroups is included in the following table:
 |Immunosuppressants_signatures| 32|                             -|      -|
 |Treatment_signatures|          11, 25, 31, 32, 35, 86, 87, 90, 99| 5|      -|
 |APOBEC_signatures|             2, 13|                          -|      -|
-|Tobacco_signatures |           4, 29, 92|                      2|      3|
+|Tobacco_signatures |           4, 29, 92, 100, 109|                      2|      3|
 |UV_signatures|                 7a, 7b, 7c, 7d, 38|             1|      13|
 |AA_signatures|                 22a, 22b|                             20|      23|
 |Colibactin_signatures|         88|                             -|      18|
@@ -135,7 +135,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/vcf_input",
                    input_type="vcf",
                    context_type="96",
                    genome_build="GRCh37",
-                   cosmic_version=3.4)
+                   cosmic_version=3.5)
 ```
 
 
@@ -148,7 +148,7 @@ 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=3.4,
+                   cosmic_version=3.5,
                    collapse_to_SBS96=False)
 ```
 
@@ -162,7 +162,7 @@ Analyze.cosmic_fit(samples=spa.__path__[0]+"/data/tests/txt_input/sample_matrix_
                    output="example_mm",
                    input_type="matrix",
                    genome_build="GRCh37",
-                   cosmic_version=3.4)
+                   cosmic_version=3.5)
 ```
 
 ## <a name="denovo"></a> _De novo_ extraction of mutational signatures downstream analysis

{sigprofilerassignment-1.0.4 → sigprofilerassignment-1.1.1}/SigProfilerAssignment/Analyzer.py

@@ -10,7 +10,7 @@ def decompose_fit(
     nnls_remove_penalty=0.01,
     initial_remove_penalty=0.05,
     genome_build="GRCh37",
-    cosmic_version=3.4,
+    cosmic_version=3.5,
     make_plots=True,
     collapse_to_SBS96=True,
     connected_sigs=True,
@@ -67,7 +67,7 @@ def denovo_fit(
     nnls_remove_penalty=0.01,
     initial_remove_penalty=0.05,
     genome_build="GRCh37",
-    cosmic_version=3.4,
+    cosmic_version=3.5,
     make_plots=True,
     collapse_to_SBS96=True,
     connected_sigs=True,
@@ -122,7 +122,7 @@ def cosmic_fit(
     nnls_remove_penalty=0.01,
     initial_remove_penalty=0.05,
     genome_build="GRCh37",
-    cosmic_version=3.4,
+    cosmic_version=3.5,
     make_plots=True,
     collapse_to_SBS96=True,
     connected_sigs=True,

{sigprofilerassignment-1.0.4 → sigprofilerassignment-1.1.1}/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py

@@ -77,7 +77,7 @@ cosmic_template_path = os.path.join(DECOMPOSITION_PATH, "CosmicTemplates")
 def install_cosmic_plots(
     context_type="96",
     genome_build="GRCh37",
-    cosmic_version="3.4",
+    cosmic_version="3.5",
     exome=False,
     volume=None,
 ):
@@ -898,7 +898,7 @@ def run_PlotDecomposition(
     output_path,
     project,
     mtype,
-    cosmic_version="3.4",
+    cosmic_version="3.5",
     genome_build="GRCh37",
     exome=False,
     custom_text=None,
@@ -1042,7 +1042,7 @@ def run_PlotSSDecomposition(
     project,
     context_type,
     genome_build="GRCh37",
-    cosmic_version="3.4",
+    cosmic_version="3.5",
     custom_text=None,
     exome=False,
     volume=None,

{sigprofilerassignment-1.0.4 → sigprofilerassignment-1.1.1}/SigProfilerAssignment/controllers/cli_controller.py

@@ -50,8 +50,8 @@ def parse_arguments_common(args: List[str], description: str) -> argparse.Namesp
     parser.add_argument(
         "--cosmic_version",
         type=float,
-        default=3.4,
-        help="COSMIC version (default: 3.4). Valid options: {1, 2, 3, 3.1, 3.2, 3.3, 3.4}.",
+        default=3.5,
+        help="COSMIC version (default: 3.5). Valid options: {1, 2, 3, 3.1, 3.2, 3.3, 3.4, 3.5}.",
     )
     parser.add_argument(
         "--make_plots",

sigprofilerassignment-1.1.1/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.5_CN_GRCh37.txt

@@ -0,0 +1,49 @@
+Type	CN1	CN2	CN3	CN4	CN5	CN6	CN7	CN8	CN9	CN10	CN11	CN12	CN13	CN14	CN15	CN16	CN17	CN18	CN19	CN20	CN21	CN22	CN23	CN24	CN25	CN26
+0:homdel:0-100kb	0.001795054	0.002237674	0.064044243	0.00096628	0.02582249	0.0034925	0.0	0.00021626	0.008181842	0.00779524	0.00161374	0.02309338	0.00224368	0.0121477	0.0067438	0.0036673	0.00136668	0.00110894	0.00591472	4.08e-05	5.5e-07	0.266866171	0.24410253	0.000371716	0.006074244	0.00922234
+0:homdel:100kb-1Mb	0.003807104	0.007195788	0.00640384	0.00021955	0.02499357	0.007550309	0.0	0.000720975	0.020999189	0.03122532	0.0059027	0.052724771	0.03467842	0.03389276	0.02652628	0.00109281	0.00143123	0.00303045	0.00677398	0.00017845	0.00022928	0.02038467	0.02413956	0.000760546	0.009107288	0.01269433
+0:homdel:>1Mb	0.002436746	0.003837108	0.013033431	6.12e-05	0.0038887	0.00133617	0.0	0.00026934	0.009009219	0.00455881	0.00313081	0.0068661	0.01814564	4.4e-07	0.00524487	0.04053983	0.0014533	0.0007584	0.0041105	0.00011722	0.00135207	0.001282235	0.00355824	0.000575594	0.004061581	0.00522882
+1:LOH:0-100kb	0.002840449	0.002826536	0.062213582	0.056150771	0.015829115	0.00595583	0.00011082	0.000950405	0.018583652	0.00879753	0.0027543	0.02182354	0.00284705	0.00129939	0.00763888	0.00142666	0.00211427	0.0015556	0.01041569	0.00050182	0.0002482	0.02147356	0.13028998	0.000635022	0.142313643	0.00718471
+1:LOH:100kb-1Mb	0.012263057	0.006323915	0.012614821	0.247798925	0.02654494	0.010520759	0.0050408	0.00728363	0.130807872	0.03974523	0.0062317	0.065977011	0.02886982	0.01293743	0.00252662	0.00580905	0.00507205	0.00141876	0.064293751	0.00081924	0.0123588	0.034899515	0.0768859	0.004601138	0.310351003	0.02106504
+1:LOH:1Mb-10Mb	0.019163418	0.001023764	0.019283461	0.083369342	0.00135803	0.00099151	7.44e-05	0.002204905	0.159949199	0.01091525	0.01775071	0.00423455	0.12860718	2.02e-05	1e-07	0.00343106	0.0186884	0.00028103	0.03777062	0.00624116	0.05642821	0.024426895	0.03485188	0.004307654	0.026957401	0.01530544
+1:LOH:10Mb-40Mb	0.047297757	0.000483364	0.0087199	0.00010096	0.000573685	0.00040994	2e-08	0.00366415	0.076229355	0.00290428	0.00184154	4.03e-05	0.1541978	1.4e-07	4.4e-07	0.00204512	0.00550295	8e-08	0.02105378	0.00283775	0.04607252	0.003555775	0.02090447	0.002622552	0.002556706	0.01289555
+1:LOH:>40Mb	0.073645999	0.000124322	0.00409212	0.00230378	8.1e-05	0.00017917	0.0	0.006089315	0.027000693	0.00148398	5.75e-05	4.64e-06	0.21568204	1.87e-06	0.0003073	0.00064424	1.34e-06	1.65e-06	0.00174097	1.2e-05	0.01887089	0.002450425	0.00226301	0.00227007	0.000974623	0.00805582
+2:LOH:0-100kb	0.001187984	0.002488917	0.00138849	0.0141463	0.0133515	0.019251449	0.00277607	0.01111584	0.004119057	0.00635726	0.00148901	0.00590696	5.69e-05	0.00762253	0.00228469	0.00067984	0.00055893	0.00273632	0.00566334	0.00060974	0.00070358	0.00299482	4e-08	0.003253376	0.010419214	0.0204730999999999
+2:LOH:100kb-1Mb	0.004303102	0.019464869	0.033835141	0.040089381	0.255496412	0.177292158	0.0045434	0.0222829	0.013774233	0.087823539	0.01694496	0.080936481	0.02909678	0.00707926	0.0215107	0.01758306	0.00062269	0.0065518	0.054896441	0.00134094	0.06234918	0.073916265	0.00033402	0.270457816	9.09e-05	0.06078213
+2:LOH:1Mb-10Mb	0.004438013	0.033551543	0.018990581	0.00618009	0.264575824	0.116382852	0.00457336	0.00829832	0.011594393	0.131910499	0.0439202	0.132671041	0.03957572	0.02585003	0.0088679	0.01162738	0.084442329	0.00018517	0.117067141	0.01443458	0.03913487	0.079960515	0.00178993	0.2022044	0.000384815	0.17442198
+2:LOH:10Mb-40Mb	0.00431859	0.052291175	0.00267497	0.00024516	0.067065891	0.00632481	4.11e-05	0.00115938	0.004945152	0.087069829	0.02467614	0.176727892	0.01185966	0.09336807	0.00201416	0.00291477	0.088483279	0.00015695	0.04188772	0.0096627	0.00129894	0.01765472	0.00517329	0.011946964	0.000350439	0.11811706
+2:LOH:>40Mb	0.012215654	0.06737476	8.24e-05	0.00241502	0.01961649	0.00026093	0.0	0.00013197	0.002407305	0.01593395	0.01121149	0.136224511	8.5e-05	0.55221235	3.3e-07	0.00170498	0.0075038	7.26e-05	0.03389879	0.00049936	0.00195567	0.00590559	0.0	0.0050787	0.000750494	0.02060637
+3-4:LOH:0-100kb	0.001379947	0.002717402	0.0027191	0.01402566	0.005480255	0.00505183	0.00420447	0.00956472	0.001833529	0.00743812	0.00158209	0.00930253	0.00057156	0.00141835	0.00197133	0.00093853	0.00267395	0.00226406	0.01388264	0.002561	0.00053506	0.001204125	0.00072698	0.000685112	0.000296679	0.01506038
+3-4:LOH:100kb-1Mb	0.001667853	0.013819445	0.023811221	0.01144021	0.02685577	0.013510279	0.0023279	0.004662895	0.002848605	0.068455299	0.0482419	0.03071852	0.00817896	0.00688559	0.01163685	0.02159759	0.02375527	0.01402709	0.01258572	0.02182453	2.09e-05	0.00824588	0.00079858	0.011435602	8.69e-07	0.03445676
+3-4:LOH:1Mb-10Mb	0.001514284	0.012471389	0.034367671	0.00010785	0.029519046	0.00409704	0.00021573	0.00349215	0.00344351	0.096466639	0.156264722	0.04005227	0.01705423	0.00687404	0.04837325	0.043701	0.094627309	0.05963823	0.00110793	0.02055562	0.00277049	0.010814625	0.00034028	0.005760546	2.04e-05	0.09684851
+3-4:LOH:10Mb-40Mb	0.000102203	0.010631239	0.021891551	1e-07	0.00455209	5.61e-05	7.9e-07	0.002194095	0.001390007	0.04754809	0.055274161	0.02606018	0.00759605	0.00128688	0.16721937	0.0329184	0.051836149	0.07185141	0.00278047	0.0022434	0.00027444	0.00356193	0.0007486	0.00075315	1.85e-05	0.06548568
+3-4:LOH:>40Mb	0.007367609	0.017426922	0.025294791	1.3e-07	0.00073589	0.00032855	6.74e-06	0.003399115	0.001198601	0.01319828	0.03509218	0.01659015	0.00381337	7.35e-05	0.37328855	0.19071235	0.00224311	0.05059881	0.00421117	0.00094554	0.00172068	0.005440365	0.00044828	0.000533794	8.21e-05	0.02410321
+5-8:LOH:0-100kb	0.000351298	0.001689411	5.3e-07	0.025527171	0.00066453	0.00048949	0.00552275	0.010770475	0.000375937	0.00260391	0.00501223	0.00578286	0.00294361	0.00316274	0.00348453	0.0034784	0.00128554	0.00482129	2.59e-05	0.00091844	2.5e-07	0.000741885	1.4e-07	0.000227864	0.0008887	0.0070388799999999
+5-8:LOH:100kb-1Mb	0.000212107	0.003416253	0.00256956	0.00169273	0.000652505	0.00031046	0.00682636	0.009675285	0.000836165	0.02207809	0.04217432	0.00208666	0.00123595	6.47e-06	0.01942632	0.00980644	0.00726579	0.02136849	8.14e-06	0.00241053	5.46e-05	0.000521815	1.6e-06	0.000577402	0.00039106	0.00584006
+5-8:LOH:1Mb-10Mb	0.000207783	0.004495306	0.0055492	1.9e-07	0.000278185	0.00021435	6.78e-05	0.00215584	0.000661617	0.02022345	0.073571791	0.00322838	0.0061044	2.3e-07	0.02016289	0.01073875	0.01836005	0.04681185	1.58e-05	0.00524955	1.67e-05	0.001434025	1.53e-05	0.000810458	0.000206542	0.01292003
+5-8:LOH:10Mb-40Mb	9.97e-05	0.002756042	7.1e-07	1.31e-05	0.000125705	0.00011771	0.0	0.001022835	0.000376486	0.00679665	0.01532663	0.00163617	0.00077852	8.96e-06	0.01347168	0.00622641	0.00502947	0.02208834	0.00068876	0.00029923	3.6e-07	0.000605405	1.4e-07	0.00011455	1.43e-05	0.00371877
+5-8:LOH:>40Mb	0.000331938	0.010089624	0.00535955	1.4e-07	9.88e-05	0.00030406	4.93e-05	0.00145962	0.000382635	0.00017289	0.00347323	0.00110016	0.00162804	0.00572642	0.06422257	0.01067078	1.29e-06	0.00536994	0.00012041	0.00012116	3.9e-05	0.002408955	1.83e-05	8.7e-05	1.1e-07	0.00389208
+9+:LOH:0-100kb	0.000133995	0.000520196	7.1e-07	1.06e-05	0.001312595	0.00493142	0.00632901	0.022043315	0.000759424	0.00018531	0.00062013	0.00048688	4.45e-05	1.46e-06	0.00300605	0.00384194	0.00012468	0.00241473	0.00107168	0.00014531	3.6e-07	0.002498515	1.4e-07	0.00049292	0.000873954	0.0015796
+9+:LOH:100kb-1Mb	0.000411988	0.000668643	0.00216196	2.8e-07	0.00330625	0.00545954	0.02139771	0.028381515	0.001234374	0.0029966	0.01160088	0.00011188	0.00344403	8.5e-07	0.00785032	0.0047163	5.3e-05	0.01211638	0.00117826	0.00085741	3.97e-06	0.00067448	3.28e-05	0.000376804	0.001337021	0.00140594
+9+:LOH:1Mb-10Mb	0.00020077	0.000828997	0.0022066	2.8e-07	0.000649225	0.00086716	0.01464548	0.00809473	0.000574562	0.00365022	0.02224864	0.00012019	0.00163639	1.1e-05	0.00480835	2.35e-06	1.37e-05	0.01534961	1.6e-07	0.00046208	8.48e-05	0.0010781	1.4e-07	0.000121946	5.59e-05	0.00128556
+9+:LOH:10Mb-40Mb	6.51e-06	0.000350903	0.0021129	2.8e-07	1.51e-05	1.27e-05	6.1e-07	2.53e-05	1.02e-05	0.00044558	0.00252885	6.14e-05	6.1e-07	1.59e-06	0.00234481	2.35e-06	5.29e-05	0.0009794	1.6e-07	0.0001094	1.59e-05	9.02e-05	1.4e-07	5.71e-06	3.14e-05	0.00017789
+9+:LOH:>40Mb	2.76e-06	0.000712768	0.00092755	2.8e-07	1.23e-05	3.4e-05	2e-08	0.00011179	4.55e-06	9e-08	0.00148788	1.65e-05	0.00013687	1.23e-06	0.00380205	0.00333085	2.9e-07	7.7e-07	4.66e-05	1.07e-05	5.38e-05	0.00010431	1.5e-07	2.68e-06	4.97e-08	3.2e-07
+2:het:0-100kb	0.000126855	0.001077283	0.020851501	0.00018321	0.00173387	0.0035614	0.00021658	0.0010385	0.002813763	0.00213926	0.0	0.00068448	0.00242738	0.00144658	1.04e-05	0.00266672	0.00038608	0.00029759	0.0031181	0.00053199	0.00030646	0.00313745	0.00205934	0.000280432	0.059739079	0.03686276
+2:het:100kb-1Mb	0.002392692	0.001448575	0.01137198	0.0009306	0.00835966	0.00180746	0.00209292	0.0008892	0.057456734	0.00460283	1e-08	0.00313133	0.00710641	0.0003872	6.6e-05	0.00197375	0.0001888	3.02e-05	0.0312283	0.00464189	0.01868806	0.0309067	0.02112224	0.020441704	0.311415627	0.00281572
+2:het:1Mb-10Mb	0.017226427	0.000571468	0.023632351	0.00124271	0.04798882	0.008628749	0.00016457	0.002329035	0.159920321	0.0006929	0.0	0.00410482	0.06241927	0.00011283	1.17e-06	0.00185384	0.00087384	1.1e-07	0.0164266	0.00278654	0.12630567	0.161346311	0.12925873	0.196033892	0.055182533	0.00334658
+2:het:10Mb-40Mb	0.112043886	0.00040127	0.024327821	0.00653021	0.04018991	0.008931519	0.0	0.00267494	0.129543643	0.00078362	3.93e-06	0.0010782	0.06807839	1.03e-06	0.00020074	0.00136271	0.00061789	3.4e-07	0.00452687	0.0013967	0.20984675	0.108768015	0.26664244	0.179726574	0.02332703	0.00378465
+2:het:>40Mb	0.647548237	1.62e-06	0.022788761	0.047210821	6.15e-07	0.00200753	3.1e-07	0.002161405	0.006767871	6e-08	8e-08	4.3e-07	0.06958505	2.46e-06	6.46e-05	7.5e-07	0.0	3.2e-07	4.6e-07	8.15e-06	0.07227018	0.00087765	0.01902544	0.01829589	0.012052462	5.248e-05
+3-4:het:0-100kb	0.000986437	0.001301613	0.016759401	0.028397721	0.004295095	0.009499469	0.00362014	0.013551545	0.006686778	0.00557084	0.00042229	0.00495	0.00027983	0.00058958	8.1e-05	0.00179605	0.00015917	0.00117086	0.01701046	0.00077956	0.00800623	0.001840025	0.0007458	0.00050524	0.005072116	0.11355659
+3-4:het:100kb-1Mb	0.003623147	0.01521748	0.042647992	0.203288654	0.027386325	0.205503726	0.06003456	0.04139118	0.067471318	0.04177622	6.5e-06	0.00936991	0.01942203	0.00815141	5.51e-06	0.02323495	0.00188043	0.0120089	0.205701382	0.08651517	0.27819348	0.02145428	0.00157867	0.008474694	0.007390987	0.028357
+3-4:het:1Mb-10Mb	0.001734587	0.05815643	0.027620611	0.055675991	0.015401125	0.233334904	0.12143735	0.026193135	0.043510864	0.086956359	0.01763335	0.01812126	0.02082491	0.01439058	3.82e-05	0.01723295	0.185038198	0.0	0.122306121	0.33498798	0.03014244	0.044882975	0.00634558	0.015763968	0.000560018	0.00195127
+3-4:het:10Mb-40Mb	0.003009542	0.135200883	0.018505441	0.00340995	0.02038458	0.062990656	0.00493032	0.00495607	0.007530375	0.067579949	0.00761337	0.100679891	0.01275603	0.03273598	0.00189743	0.00618312	0.188270228	0.00227849	0.075935951	0.16201175	0.0061488	0.020714495	0.00077023	0.009131138	6.73e-05	0.00989549
+3-4:het:>40Mb	0.005373925	0.390284779	1.8e-07	0.00472731	0.002974155	0.00240527	0.00022509	0.02416852	0.002876185	1e-08	6.2e-05	0.00090365	0.00958487	0.16670478	0.00450937	0.00048235	0.000536	0.02652536	0.00256084	0.00119273	2.8e-07	0.00051959	2.1e-07	0.001866582	1.05e-07	0.00309533
+5-8:het:0-100kb	0.000741212	0.001717201	0.00551728	0.068606241	0.003368305	0.00362532	0.01467759	0.032617975	0.001719672	0.00596208	2.95e-05	0.00044794	0.00098094	0.0014848	0.00286475	0.01032126	0.00049621	0.00230818	0.00185133	0.015153	0.00031093	0.00058946	3.53e-05	0.002082402	0.000307891	0.02211369
+5-8:het:100kb-1Mb	0.00011638	0.011630412	0.039523742	0.056865761	0.007209015	0.00454924	0.16196039	0.127337371	0.00135021	0.04005666	0.0438027	0.00783497	0.00090333	0.00011311	0.00878768	0.04438502	0.0124036	0.02222437	0.02780896	0.14454268	0.00022234	0.00175159	0.00091931	0.004128916	0.000567382	0.00622323
+5-8:het:1Mb-10Mb	0.000204002	0.019335548	0.162603387	0.01134511	0.008309545	0.00205142	0.21136197	0.061241481	0.001136105	0.01210908	0.185368842	0.00156351	5.8e-07	3.2e-07	0.00632529	0.08961901	0.129027959	0.14409608	0.02161426	0.10976846	9.72e-06	0.004135055	0.00226165	0.005086422	7.9e-06	2.523e-05
+5-8:het:10Mb-40Mb	1.93e-05	0.025641671	0.122266015	0.00463152	0.00097313	0.00026427	0.0048432	0.008361195	0.000468092	0.00183866	0.057285501	0.00131279	0.00020304	0.00011361	0.0281915	0.08336645	0.055166629	0.18136026	0.00344696	0.01800115	0.00012714	0.001374835	0.00179573	0.002817716	2.11e-08	0.00612999
+5-8:het:>40Mb	0.000525662	0.044174807	0.076936563	1e-08	0.00127684	2.19e-05	0.00032996	0.004528565	0.000413552	0.0	0.01649539	0.00069671	6.82e-05	0.00174446	0.07821007	0.25307107	1e-08	0.09531375	2.3e-07	0.00182344	0.00247148	0.00133954	1.8e-07	0.000780186	9.32e-08	0.00164991
+9+:het:0-100kb	0.000105258	0.000991451	0.00254618	5.16e-05	0.003029025	0.016700899	0.02554054	0.094947456	0.00168183	0.00047103	1e-08	2.48e-05	0.00089424	8.2e-07	0.01505965	0.00338768	5.39e-05	0.0093412	0.00503956	0.0035707	5.99e-05	0.000483875	1.41e-05	0.000621376	0.00193162	7.706999999999999e-05
+9+:het:100kb-1Mb	0.000318177	0.00324101	0.00174383	2.15e-05	0.00738562	0.043428957	0.16018674	0.266746762	0.004252061	0.0002512	8.13e-06	0.00018166	0.00050042	0.00012566	0.00017234	0.0033166	7.49e-05	0.05049958	0.00484797	0.00971177	0.00011614	0.00014049	1.5e-07	0.001350168	0.00202686	3.57e-06
+9+:het:1Mb-10Mb	0.000187035	0.003779865	7.1e-07	2.6e-07	0.00611754	0.00489714	0.14906452	0.110528846	0.000808817	1e-08	0.052794321	0.00016027	0.0027117	9.5e-07	0.00554372	0.00998959	0.00013899	0.08409049	0.01332158	0.00568101	3.6e-07	0.00027061	1.4e-07	0.001385586	0.00173436	2.515e-05
+9+:het:10Mb-40Mb	1.74e-06	0.001908404	0.00197462	2.4e-07	6.79e-05	3.36e-05	0.00053612	0.001809925	3.12e-05	0.00012153	0.00605752	0.00013193	4.29e-05	1.06e-06	0.01155315	0.00316669	0.00012341	0.01848061	1.56e-05	0.00085042	0.00015659	0.000242765	1.4e-07	0.000133182	6.72e-06	0.00012162
+9+:het:>40Mb	1.18e-05	0.00209996	0.00203108	1.47e-05	9.3e-05	2.36e-05	2.25e-05	0.001085855	2.93e-05	0.00030777	0.0003921	3.55e-05	9.77e-05	1.27e-06	0.00768259	0.0067409	1e-08	0.00241512	2.72e-05	3.53e-05	2.31e-05	2.85e-05	1.4e-07	2.28e-05	4.97e-08	4.631e-05

sigprofilerassignment-1.1.1/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.5_DBS_GRCh37.txt

@@ -0,0 +1,79 @@
+Type	DBS1	DBS2	DBS3	DBS4	DBS5	DBS6	DBS7	DBS8	DBS9	DBS10	DBS11	DBS12	DBS13	DBS14	DBS15	DBS16	DBS17	DBS18	DBS19	DBS20	DBS21	DBS22
+AC>CA	4.97e-05	0.000374079	0.006347323	0.004141857	0.002139822	0.002660571	0.045880132	0.214923552	0.024591818	0.009630417	0.001369907	0.005055938	0.002155121	0.01993572	0.015497544	0.056543602	0.020714155	0.010322835	0.005019088	0.00503114	0.0307173617513781	0.0146332114459876
+AC>CG	2.64e-05	3.17e-05	4.65e-05	4.96e-05	0.000461962	0.000146031	0.006247295	0.000972654	0.002069312	1.77e-05	0.000193987	0.002412014	5.15e-05	0.000470977	1.23e-05	0.004274165	0.001784735	0.002708308	0.000614834	0.00190918	8.409565388888336e-05	0.0019117573810107
+AC>CT	0.004291091	0.000126027	0.003018727	8.32e-18	0.002019832	0.000240052	0.013594113	0.317886928	0.028490521	0.013500585	0.000755948	0.000465784	0.002853398	0.001475449	0.015137074	0.013859778	0.014488098	0.020157714	0.016252019	0.00237222	5.975532014842494e-08	0.0019032535142969
+AC>GA	0.000127032	0.00023705	0.005847534	0.004401974	0.000557954	0.008581841	0.009725788	0.001159588	0.025291585	0.005350232	0.00044197	0.007284703	0.002762299	0.000788733	0.016256457	0.008476822	0.019191793	0.007339722	0.003369214	0.00158594	0.0066587843046396	0.0086713197689134
+AC>GG	5.71e-05	4.17e-18	0.00044981	7.01e-18	1.11e-17	0.000104022	0.002538901	0.000809712	0.007127629	0.000590026	0.002249847	0.007540177	0.001464314	0.000265703	0.001741257	0.003519902	0.008064512	0.004986928	0.000779431	0.00263499	0.0018152869523489	0.0010654974388171
+AC>GT	0.002960753	0.000280059	0.010095742	1.12e-08	0.000821932	0.000132028	0.004498052	0.000150946	0.012095976	0.028701244	0.005709611	0.002008084	0.004439439	0.003216438	0.09285221	0.003577356	0.030542486	0.012220562	0.011904767	0.0003164	0.0241778490657548	0.0024897899418957
+AC>TA	0.001200305	0.001480313	0.001009574	0.00127057	0.001479877	0.010102168	0.005417654	0.012395591	0.041186297	0.000105005	0.000263982	0.007159833	0.002579913	0.001595998	0.002551332	0.005687769	0.008662643	0.022936838	0.006233218	0.00933111	0.0057468284861944	0.012742879001256
+AC>TG	0.000172044	6.36e-06	1.11e-17	5.31e-05	0.001119907	0.000449096	0.000997568	0.002569086	0.017894047	7.66e-06	0.000238984	0.001606502	0.004284486	7.73e-05	0.000369916	0.001091719	0.008804955	0.01387712	0.001016945	0.0001306	0.0004137358774876	0.0020984818607282
+AC>TT	0.026506737	0.002920618	1.78e-06	0.000161072	0.007469379	0.003180682	0.001179489	0.000267905	0.044385233	0.000710031	0.002819808	0.003363148	0.015739739	0.000762895	0.006943356	0.004182681	0.017468062	0.016842745	0.066818468	0.00251075	0.0050595327530672	0.0097158129574373
+AT>CA	0.000482123	3.78e-05	0.007037032	0.000916411	0.000107991	0.000114024	0.011095195	2.78e-05	0.012695776	0.003530153	0.009479354	0.001949476	0.004208115	0.002339905	0.001157098	0.007864558	0.010150171	0.004560274	0.004322273	0.0022381	0.0056221165538405	0.0051931184813781
+AT>CC	0.000297076	4.17e-18	0.009076172	7e-18	2.13e-05	6.39e-05	0.00625729	0.000142949	0.001779408	0.00116005	0.00189987	0.003491967	0.001008029	0.00037024	0.010013439	0.002090492	0.007050836	0.001818777	0.002047984	0.00123446	0.0003929255149778	0.0009965692749409
+AT>CG	3.98e-06	4.17e-18	0.014593845	9.46e-18	1.05e-17	1.82e-06	0.00110952	0.000265905	9.22e-18	0.002590112	1.74e-05	0.001357392	2.33e-06	4.37e-08	3e-07	0.003649763	0.001416492	0.000742811	0.000297899	0.00155349	3.588725020094043e-07	0.0001481920568702
+AT>GA	0.002120539	0.000168036	0.001809237	0.000324145	0.001109908	0.001620348	0.014393767	0.000161942	0.006367881	8.06e-05	0.011199236	0.006419643	0.00213368	0.0042037	0.007839901	0.004752044	0.014212182	0.002640487	0.010191431	0.00845878	0.010716311719864	0.0028069967738517
+AT>GC	0.000174044	5.85e-06	0.005247787	1.76e-05	1.05e-17	1.72e-05	0.009285979	0.00022592	0.001809398	0.004080177	0.004179715	0.004039874	0.000300299	0.000472354	0.014691143	0.001510302	0.010928285	0.000494586	0.002339553	0.00036851	0.0030102823589385	1.887867147599397e-05
+AT>TA	0.002340595	0.000458097	0.002349009	0.004532032	0.000792934	0.002200472	0.033985283	0.000314888	0.00919694	0.002930127	0.003839738	0.002697639	0.010517294	0.009285173	0.012340007	0.006543192	0.012537799	0.008000102	0.012281658	0.00293144	0.0826480680583893	0.007731031525148
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sigprofilerassignment-1.1.1/SigProfilerAssignment/data/Reference_Signatures/GRCh37/COSMIC_v3.5_DBS_GRCh37_exome.txt

@@ -0,0 +1,79 @@
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