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Merge pull request #59 from AlexandrovLab/development
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@mdbarnesUCSD
mdbarnesUCSD authored Nov 30, 2022
2 parents 653e1af + 7c05d22 commit 07119f9
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4 changes: 2 additions & 2 deletions .gitignore
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Expand Up @@ -54,8 +54,8 @@ cover/
SigProfilerAssignment/data/tests/vcf_input/input/
SigProfilerAssignment/data/tests/vcf_input/logs/
SigProfilerAssignment/data/tests/vcf_input/output/
output_vcf_example/
output_txt_example/
SigProfilerAssignment/DecompositionPlots/CosmicTemplates/
TestOutput/



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3 changes: 3 additions & 0 deletions .travis.yml
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@@ -1,6 +1,9 @@
dist: xenial
language: python

vm:
size: large

python:
- '3.8'

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5 changes: 2 additions & 3 deletions MANIFEST.in
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@@ -1,13 +1,12 @@
include README.md
include SigProfilerAssignment/data/*
include SigProfilerAssignment/data/vcftest/*
include SigProfilerAssignment/data/Reference_Signatures/GRCh37/*
include SigProfilerAssignment/data/Reference_Signatures/GRCh38/*
include SigProfilerAssignment/data/Reference_Signatures/mm9/*
include SigProfilerAssignment/data/Reference_Signatures/mm10/*
include SigProfilerAssignment/data/Reference_Signatures/rn6/*
include SigProfilerAssignment/DecompositionPlots/reference_files/Fonts/*
include SigProfilerAssignment/DecompositionPlots/reference_files/*
include SigProfilerAssignment/DecompositionPlots/ReferenceFiles/Fonts/*
include SigProfilerAssignment/DecompositionPlots/ReferenceFiles/*
include SigProfilerAssignment/DecompositionPlots/*
include SigProfilerAssignment/data/tests/vcf_input/*
include SigProfilerAssignment/data/tests/txt_input/*
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4 changes: 2 additions & 2 deletions SigProfilerAssignment/Analyzer.py
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Expand Up @@ -7,5 +7,5 @@ def decompose_fit(samples, output, signatures=None, signature_database=None,nnls
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=3.3, 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=3.3, 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):
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)
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=3.3, 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)
49 changes: 49 additions & 0 deletions SigProfilerAssignment/DecompositionPlots/ExampleSample/CNV48_De-Novo_Signatures.txt
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MutationType CNV48A CNV48B CNV48C CNV48D CNV48E
0:homdel:0-100kb 0.00000083 0.00000295 0.00227050 0.00000075 0.00096858
0:homdel:100kb-1Mb 0.00410855 0.00039561 0.00207384 0.02703219 0.00559786
0:homdel:>1Mb 0.00000554 0.00122668 0.00000000 0.02703635 0.00696978
1:LOH:0-100kb 0.00112830 0.00000063 0.01226193 0.00000000 0.00708714
1:LOH:100kb-1Mb 0.00000391 0.01552501 0.00613728 0.03899750 0.03144637
1:LOH:1Mb-10Mb 0.00401818 0.00000253 0.00000093 0.14062679 0.07397784
1:LOH:10Mb-40Mb 0.00005266 0.00000012 0.00000048 0.10997624 0.04210990
1:LOH:>40Mb 0.00000102 0.00000124 0.00000247 0.00002991 0.13316480
2:LOH:0-100kb 0.00455813 0.00000060 0.00401138 0.01406873 0.00522486
2:LOH:100kb-1Mb 0.00000259 0.01066978 0.04899240 0.00456627 0.00313024
2:LOH:1Mb-10Mb 0.00019789 0.08507254 0.02222360 0.09357127 0.00935381
2:LOH:10Mb-40Mb 0.00000000 0.08543525 0.04039981 0.08964456 0.00120907
2:LOH:>40Mb 0.04000652 0.03252400 0.00482349 0.07308834 0.00000109
3-4:LOH:0-100kb 0.00000000 0.00062965 0.00486737 0.00402011 0.00000348
3-4:LOH:100kb-1Mb 0.00000000 0.02211930 0.00352244 0.01443590 0.00000289
3-4:LOH:1Mb-10Mb 0.01154405 0.04058766 0.00000179 0.04505698 0.00000080
3-4:LOH:10Mb-40Mb 0.00000431 0.01798391 0.03246762 0.01713715 0.00000000
3-4:LOH:>40Mb 0.00010679 0.03244896 0.00503232 0.00000456 0.00000196
5-8:LOH:0-100kb 0.00412411 0.00000286 0.00000075 0.00540728 0.00213831
5-8:LOH:100kb-1Mb 0.00000000 0.01173257 0.00575306 0.00000030 0.00000283
5-8:LOH:1Mb-10Mb 0.00831646 0.01147780 0.01165105 0.00003824 0.00000276
5-8:LOH:10Mb-40Mb 0.00000041 0.00521012 0.00000159 0.00843632 0.00000427
5-8:LOH:>40Mb 0.00082246 0.00295490 0.00000154 0.00000174 0.00000358
9+:LOH:0-100kb 0.00000189 0.01177812 0.00000083 0.01804860 0.00002121
9+:LOH:100kb-1Mb 0.00000000 0.00492384 0.00080071 0.00000000 0.00486780
9+:LOH:1Mb-10Mb 0.00000000 0.01272578 0.00000243 0.00001046 0.00213166
9+:LOH:10Mb-40Mb 0.00000168 0.00000432 0.00000648 0.00000194 0.00000654
9+:LOH:>40Mb 0.00000168 0.00000432 0.00000648 0.00000194 0.00000654
2:het:0-100kb 0.00424056 0.00000053 0.00183007 0.00000000 0.00545910
2:het:100kb-1Mb 0.00000025 0.00000105 0.00494850 0.03848499 0.04887068
2:het:1Mb-10Mb 0.02097226 0.00756213 0.00000000 0.00000012 0.12582459
2:het:10Mb-40Mb 0.01623286 0.00846561 0.00877833 0.00000000 0.14361308
2:het:>40Mb 0.00000046 0.00000128 0.00000645 0.00000556 0.32189335
3-4:het:0-100kb 0.00000335 0.00000000 0.03500289 0.00305884 0.00017426
3-4:het:100kb-1Mb 0.03277032 0.00000000 0.14771851 0.04636413 0.02342268
3-4:het:1Mb-10Mb 0.47610782 0.00000132 0.00000610 0.07745060 0.00000115
3-4:het:10Mb-40Mb 0.05013614 0.30243415 0.06416661 0.00749927 0.00000000
3-4:het:>40Mb 0.00000735 0.00000731 0.46907268 0.00000069 0.00000308
5-8:het:0-100kb 0.01322548 0.00000000 0.00611310 0.00000070 0.00000266
5-8:het:100kb-1Mb 0.03631060 0.00000958 0.01778273 0.07310104 0.00000113
5-8:het:1Mb-10Mb 0.20339816 0.09416172 0.00008219 0.00000176 0.00000000
5-8:het:10Mb-40Mb 0.00006818 0.16540860 0.00001318 0.00000155 0.00000200
5-8:het:>40Mb 0.01074217 0.00131701 0.01877488 0.00000803 0.00000051
9+:het:0-100kb 0.00534523 0.00000160 0.00239221 0.00000048 0.00127719
9+:het:100kb-1Mb 0.04305627 0.00000063 0.00095669 0.00312988 0.00000363
9+:het:1Mb-10Mb 0.00000000 0.01518129 0.01502529 0.01964883 0.00000520
9+:het:10Mb-40Mb 0.00837288 0.00000088 0.00000859 0.00000119 0.00000306
9+:het:>40Mb 0.00000168 0.00000432 0.00000648 0.00000194 0.00000654
49 changes: 49 additions & 0 deletions SigProfilerAssignment/DecompositionPlots/ExampleSample/COSMIC_CNV48_Signatures.txt
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MutationType CN1 CN2 CN9 CN20 CNV48B CNV48D
0:homdel:0-100kb 0.00179505 0.00223767 0.00818184 0.00004078 0.00000295 0.00000075
0:homdel:100kb-1Mb 0.00380710 0.00719579 0.02099919 0.00017845 0.00039561 0.02703219
0:homdel:>1Mb 0.00243675 0.00383711 0.00900922 0.00011722 0.00122668 0.02703635
1:LOH:0-100kb 0.00284045 0.00282654 0.01858365 0.00050182 0.00000063 0.00000000
1:LOH:100kb-1Mb 0.01226306 0.00632391 0.13080787 0.00081924 0.01552501 0.03899750
1:LOH:1Mb-10Mb 0.01916342 0.00102376 0.15994920 0.00624116 0.00000253 0.14062679
1:LOH:10Mb-40Mb 0.04729776 0.00048336 0.07622936 0.00283775 0.00000012 0.10997624
1:LOH:>40Mb 0.07364600 0.00012432 0.02700069 0.00001202 0.00000124 0.00002991
2:LOH:0-100kb 0.00118798 0.00248892 0.00411906 0.00060974 0.00000060 0.01406873
2:LOH:100kb-1Mb 0.00430310 0.01946487 0.01377423 0.00134094 0.01066978 0.00456627
2:LOH:1Mb-10Mb 0.00443801 0.03355154 0.01159439 0.01443458 0.08507254 0.09357127
2:LOH:10Mb-40Mb 0.00431859 0.05229117 0.00494515 0.00966270 0.08543525 0.08964456
2:LOH:>40Mb 0.01221565 0.06737476 0.00240730 0.00049936 0.03252400 0.07308834
3-4:LOH:0-100kb 0.00137995 0.00271740 0.00183353 0.00256100 0.00062965 0.00402011
3-4:LOH:100kb-1Mb 0.00166785 0.01381945 0.00284860 0.02182453 0.02211930 0.01443590
3-4:LOH:1Mb-10Mb 0.00151428 0.01247139 0.00344351 0.02055562 0.04058766 0.04505698
3-4:LOH:10Mb-40Mb 0.00010220 0.01063124 0.00139001 0.00224340 0.01798391 0.01713715
3-4:LOH:>40Mb 0.00736761 0.01742692 0.00119860 0.00094554 0.03244896 0.00000456
5-8:LOH:0-100kb 0.00035130 0.00168941 0.00037594 0.00091844 0.00000286 0.00540728
5-8:LOH:100kb-1Mb 0.00021211 0.00341625 0.00083617 0.00241053 0.01173257 0.00000030
5-8:LOH:1Mb-10Mb 0.00020778 0.00449531 0.00066162 0.00524955 0.01147780 0.00003824
5-8:LOH:10Mb-40Mb 0.00009972 0.00275604 0.00037649 0.00029923 0.00521012 0.00843632
5-8:LOH:>40Mb 0.00033194 0.01008962 0.00038263 0.00012116 0.00295490 0.00000174
9+:LOH:0-100kb 0.00013399 0.00052020 0.00075942 0.00014531 0.01177812 0.01804860
9+:LOH:100kb-1Mb 0.00041199 0.00066864 0.00123437 0.00085741 0.00492384 0.00000000
9+:LOH:1Mb-10Mb 0.00020077 0.00082900 0.00057456 0.00046208 0.01272578 0.00001046
9+:LOH:10Mb-40Mb 0.00000651 0.00035090 0.00001019 0.00010940 0.00000432 0.00000194
9+:LOH:>40Mb 0.00000276 0.00071277 0.00000455 0.00001071 0.00000432 0.00000194
2:het:0-100kb 0.00012686 0.00107728 0.00281376 0.00053199 0.00000053 0.00000000
2:het:100kb-1Mb 0.00239269 0.00144857 0.05745673 0.00464189 0.00000105 0.03848499
2:het:1Mb-10Mb 0.01722643 0.00057147 0.15992032 0.00278654 0.00756213 0.00000012
2:het:10Mb-40Mb 0.11204389 0.00040127 0.12954364 0.00139670 0.00846561 0.00000000
2:het:>40Mb 0.64754824 0.00000162 0.00676787 0.00000815 0.00000128 0.00000556
3-4:het:0-100kb 0.00098644 0.00130161 0.00668678 0.00077956 0.00000000 0.00305884
3-4:het:100kb-1Mb 0.00362315 0.01521748 0.06747132 0.08651517 0.00000000 0.04636413
3-4:het:1Mb-10Mb 0.00173459 0.05815643 0.04351086 0.33498798 0.00000132 0.07745060
3-4:het:10Mb-40Mb 0.00300954 0.13520088 0.00753038 0.16201175 0.30243415 0.00749927
3-4:het:>40Mb 0.00537392 0.39028478 0.00287618 0.00119273 0.00000731 0.00000069
5-8:het:0-100kb 0.00074121 0.00171720 0.00171967 0.01515300 0.00000000 0.00000070
5-8:het:100kb-1Mb 0.00011638 0.01163041 0.00135021 0.14454268 0.00000958 0.07310104
5-8:het:1Mb-10Mb 0.00020400 0.01933555 0.00113611 0.10976846 0.09416172 0.00000176
5-8:het:10Mb-40Mb 0.00001935 0.02564167 0.00046809 0.01800115 0.16540860 0.00000155
5-8:het:>40Mb 0.00052566 0.04417481 0.00041355 0.00182344 0.00131701 0.00000803
9+:het:0-100kb 0.00010526 0.00099145 0.00168183 0.00357070 0.00000160 0.00000048
9+:het:100kb-1Mb 0.00031818 0.00324101 0.00425206 0.00971177 0.00000063 0.00312988
9+:het:1Mb-10Mb 0.00018704 0.00377986 0.00080882 0.00568101 0.01518129 0.01964883
9+:het:10Mb-40Mb 0.00000174 0.00190840 0.00003117 0.00085042 0.00000088 0.00000119
9+:het:>40Mb 0.00001176 0.00209996 0.00002929 0.00003526 0.00000432 0.00000194
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