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mdbarnesUCSDmdbarnesUCSD
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Merge pull request #65 from AlexandrovLab/id_decomp
v0.0.23: Fix ID decomp plots and add ID tests
2 parents 5b1b3cd + 1f103a0 commit 104c68f

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‎SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py‎

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@@ -94,6 +94,13 @@ def install_cosmic_plots(context_type="96", genome_build="GRCh37", cosmic_versio
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context_type_str + "_" + genome_build + \
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exome_str + ".json"
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# ID signatures exome=False, genome_build=GRCh37
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if context_type in ID_CONTEXTS:
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cosmic_file_name = "COSMIC_v" + str(cosmic_version) + "_ID_GRCh37.txt"
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json_file_name = "COSMIC_v" + str(cosmic_version) + "_ID_GRCh37.json"
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genome_build = "GRCh37"
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exome_str = ""
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# Load cosmic plots if they exist
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filename= os.path.join(TEMPLATE_PATH, json_file_name)
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if os.path.exists(filename):

‎SigProfilerAssignment/data/tests/txt_input/ID83_S3_Signatures.txt‎

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MutationType ID83A ID83B ID83C
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1:Del:C:0 0.01552089974284172 0.01836557388305664 0.018322814255952835
3+
1:Del:C:1 0.0069086004979908465 0.01619331929832697 0.01834214646369219
4+
1:Del:C:2 0.02053752578794956 0.01598518341779709 0.014462384022772312
5+
1:Del:C:3 0.013614081405103206 0.008683239761739969 0.015987554937601088
6+
1:Del:C:4 0.009314348921179771 0.00024371793940929364 0.0016800787299871445
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1:Del:C:5 0.007787916157394647 0.009530944097787142 0.011807155795395374
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1:Del:T:0 0.005638626217842102 0.01655332501977682 0.006385881453752518
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1:Del:T:1 0.01800905857235193 0.02155500538647175 0.008246992900967597
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1:Del:T:2 0.015447193384170532 0.012928047403693198 0.01533989068120718
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1:Del:T:3 0.005341296549886465 0.010106318350881337 0.013877170532941819
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1:Del:T:4 0.005170127144083381 0.025064129009842874 0.006535247899591923
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1:Del:T:5 0.007137195859104395 0.01438701841980219 0.013611399568617344
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1:Ins:C:0 0.0014045221265405416 0.01781204529106617 0.009489483293145895
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1:Ins:C:1 0.009524904191493988 0.011274121049791575 0.012582640256732702
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1:Ins:C:2 0.021233538538217543 0.004457215126603842 0.00664978725835681
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1:Ins:C:3 0.011413085833191871 0.0008190260734409094 0.00831654602661729
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1:Ins:C:4 0.014042909257113934 0.01582697741687298 0.006201695557683707
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1:Ins:C:5 0.008941171783953905 0.021361579559743403 0.012530934251844882
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1:Ins:T:0 0.011115472018718719 0.0016707785893231631 0.01976347081363201
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1:Ins:T:1 0.008047780767083169 0.0168801074847579 0.006528178229928017
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1:Ins:T:2 0.011846481263637543 0.016916079632937907 0.009012485109269618
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1:Ins:T:3 0.007855050265789032 0.02464706413447857 0.02271738722920418
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1:Ins:T:4 0.005759815848432481 0.02599736787378788 0.0066769055789336566
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1:Ins:T:5 0.01869687680155039 4.007601361877278e-09 0.00720283966511488
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2:Del:R:0 0.011604203842580318 0.016068467311561106 0.01693541631102562
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2:Del:R:1 0.018628297373652458 0.00015456903493031858 0.013641474023461341
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2:Del:R:2 0.005884661339223385 0.005785112036392093 0.015316670387983322
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2:Del:R:3 0.008226432837545872 0.01475061196833849 0.010230568796396255
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2:Del:R:4 0.015759820863604546 0.006919342186301946 0.001082157902419567
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2:Del:R:5 0.01748779695481062 0.007296297606080771 0.001445105066522956
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3:Del:R:0 0.0061534404754638675 0.01389029175043106 0.018324674852192403
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3:Del:R:1 0.006274043768644333 0.011804968118667603 0.01756908167153597
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3:Del:R:2 0.01337041724473238 0.01059441026300192 0.002079418860375881
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3:Del:R:3 0.0051048532593995334 0.017660107091069223 0.013663888722658158
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3:Del:R:4 0.004250402795150876 0.027172407880425454 0.019252810813486575
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3:Del:R:5 0.015725806914269926 0.005580935161560774 0.0029790374799631538
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4:Del:R:0 0.00493397624231875 0.004780510882847011 0.012742848135530949
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4:Del:R:1 0.0054566740524023775 0.016508652456104757 0.007305806316435337
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4:Del:R:2 0.013096509873867035 0.019357234984636307 0.001680528372526169
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4:Del:R:3 0.0 0.019024350680410862 0.015442132204771041
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4:Del:R:4 0.021610872447490694 0.01587334629148245 0.010876196715980769
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4:Del:R:5 0.01570777576416731 0.012889952771365643 0.014674902521073818
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5:Del:R:0 0.009537634160369634 2.1404877870168093e-08 0.020937998406589033
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5:Del:R:1 0.017395626939833164 0.009418613836169243 0.008547488693147897
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5:Del:R:2 0.0034063507919199765 0.027714962512254714 0.010107571445405483
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5:Del:R:3 0.02084033377468586 0.0025198620482115076 0.02146480083465576
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5:Del:R:4 0.006279857503250242 0.016275193355977536 0.00941754151135683
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5:Del:R:5 0.0253225103020668 0.004656673641875386 0.015013317205011844
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2:Ins:R:0 0.00994875431060791 0.021561840921640395 0.018046821979805828
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2:Ins:R:1 0.014260496571660041 0.005878760013729334 0.00894643682986498
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2:Ins:R:2 0.007946436386555433 0.012972877733409405 0.011792520992457867
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2:Ins:R:3 0.0016391240758821368 0.018773137032985686 0.004629821004346013
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2:Ins:R:4 0.02031779158860445 0.012426098808646202 0.004098545981105417
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2:Ins:R:5 0.008801651187241077 0.015211208164691925 0.019095016829669475
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3:Ins:R:0 0.01544196754693985 0.0 0.021384117752313615
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3:Ins:R:1 0.003524290444329381 0.01905301045626402 0.02385335639119148
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3:Ins:R:2 0.015133536979556083 0.00721076475456357 0.015423193201422691
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3:Ins:R:3 0.004433090658858418 0.019106461480259896 0.02041440773755312
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3:Ins:R:4 0.01730408500880003 0.020471487194299698 0.003551992541179061
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3:Ins:R:5 0.006318332441151142 0.012590283900499344 0.01807646844536066
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4:Ins:R:0 0.012217667885124683 0.005157841183245182 0.009851658716797829
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4:Ins:R:1 0.019230526685714722 0.009122257772833108 0.017684606090188026
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4:Ins:R:2 0.02386026121675968 0.005232751928269863 0.01833217404782772
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4:Ins:R:3 0.018376968801021576 0.01653488986194134 0.00767759196460247
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4:Ins:R:4 0.0005885282182134688 0.015822342596948147 0.018708418216556312
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4:Ins:R:5 0.02422640472650528 0.01673214230686426 0.010051818657666444
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5:Ins:R:0 0.006062797410413623 0.017241557128727436 0.0020400073379278185
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5:Ins:R:1 0.03078121803700924 0.00977607686072588 0.00658940514549613
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5:Ins:R:2 0.01957440488040447 0.016687506064772605 0.00872995015233755
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5:Ins:R:3 0.01950443536043167 0.0017270417651161552 0.015995433181524278
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5:Ins:R:4 0.008595254458487033 0.007981004193425179 0.007817897386848927
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5:Ins:R:5 0.023834212869405746 0.00567436758428812 0.01069606002420187
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2:Del:M:1 0.025606596469879152 0.008685900736600161 0.025054383277893066
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3:Del:M:1 0.00022195814235601575 0.02496328130364418 0.023307540267705918
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3:Del:M:2 0.009213168639689684 0.010691352188587189 0.005652932077646255
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4:Del:M:1 0.01948954053223133 0.007824970874935389 0.014851748198270797
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4:Del:M:2 0.013516583014279604 2.552704714275933e-09 0.023032572492957114
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4:Del:M:3 0.005355971911922097 0.007257822155952454 0.005215172888711095
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5:Del:M:1 0.023358191177248955 0.014727579802274704 0.008158179000020027
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5:Del:M:2 0.014967231638729572 0.001884639821946621 0.019077837094664575
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5:Del:M:3 0.010301465913653374 0.002377575292484835 0.010195160284638405
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5:Del:M:4 0.00431287670508027 0.013421394862234592 0.0028720614849589766
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5:Del:M:5 0.009367346297949553 0.0012647423078306018 0.006092122569680214

‎SigProfilerAssignment/data/tests/txt_input/sample_matrix.txt‎

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This file was deleted.

‎SigProfilerAssignment/data/tests/txt_input/sample_matrix_ID.txt‎

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MutationType Sample1 Sample2 Sample3 Sample4 Sample5
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1:Del:C:0 61 53 89 79 73
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1:Del:C:1 26 64 20 67 87
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1:Del:C:2 88 27 96 77 56
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1:Del:C:3 66 52 4 47 95
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1:Del:C:4 34 32 9 1 6
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1:Del:C:5 29 33 37 36 53
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1:Del:T:0 31 41 14 76 23
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1:Del:T:1 61 71 79 96 23
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1:Del:T:2 63 64 56 54 55
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1:Del:T:3 23 32 40 47 57
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1:Del:T:4 26 97 1 83 32
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1:Del:T:5 35 23 33 70 59
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1:Ins:C:0 7 39 12 78 50
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1:Ins:C:1 20 46 78 42 31
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1:Ins:C:2 79 58 59 18 19
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1:Ins:C:3 42 28 44 3 32
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1:Ins:C:4 82 19 27 92 35
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1:Ins:C:5 34 87 27 80 54
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1:Ins:T:0 42 55 3 5 97
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1:Ins:T:1 41 26 32 90 25
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1:Ins:T:2 67 50 14 85 41
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1:Ins:T:3 30 55 86 97 82
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1:Ins:T:4 6 89 85 67 5
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1:Ins:T:5 63 54 50 0 21
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2:Del:R:0 45 73 39 67 60
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2:Del:R:1 94 11 40 1 81
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2:Del:R:2 13 3 77 23 46
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2:Del:R:3 48 8 32 86 52
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2:Del:R:4 68 45 33 31 0
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2:Del:R:5 69 66 22 20 3
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3:Del:R:0 25 42 38 61 78
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3:Del:R:1 19 1 97 52 54
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3:Del:R:2 69 19 33 65 0
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3:Del:R:3 22 63 31 70 57
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3:Del:R:4 18 90 45 98 77
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3:Del:R:5 82 14 39 31 2
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4:Del:R:0 13 27 42 17 43
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4:Del:R:1 20 15 59 77 18
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4:Del:R:2 59 59 40 81 0
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4:Del:R:3 0 20 92 63 37
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4:Del:R:4 99 46 67 84 36
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4:Del:R:5 46 85 63 45 45
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5:Del:R:0 15 71 37 0 74
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5:Del:R:1 47 96 51 28 23
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5:Del:R:2 5 88 90 74 15
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5:Del:R:3 87 12 96 16 91
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5:Del:R:4 15 20 87 68 18
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5:Del:R:5 78 75 94 16 40
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2:Ins:R:0 52 70 12 93 95
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2:Ins:R:1 88 33 3 27 46
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2:Ins:R:2 22 34 85 43 33
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2:Ins:R:3 9 21 7 99 19
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2:Ins:R:4 88 25 76 57 5
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2:Ins:R:5 33 47 55 63 84
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3:Ins:R:0 38 35 73 0 80
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3:Ins:R:1 12 57 70 69 91
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3:Ins:R:2 59 57 55 29 63
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3:Ins:R:3 22 55 47 70 89
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3:Ins:R:4 89 35 54 98 5
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3:Ins:R:5 26 47 40 49 68
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4:Ins:R:0 69 6 22 29 53
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4:Ins:R:1 84 43 63 41 82
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4:Ins:R:2 79 68 97 21 59
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4:Ins:R:3 91 69 23 76 31
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4:Ins:R:4 4 79 23 45 62
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4:Ins:R:5 99 95 66 59 28
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5:Ins:R:0 23 40 41 62 0
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5:Ins:R:1 94 98 90 33 7
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5:Ins:R:2 99 37 31 88 42
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5:Ins:R:3 86 46 36 6 77
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5:Ins:R:4 22 44 53 26 18
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5:Ins:R:5 80 82 61 18 34
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2:Del:M:1 90 95 97 31 94
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3:Del:M:1 2 91 42 84 93
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3:Del:M:2 40 58 15 37 23
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4:Del:M:1 96 12 82 42 53
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4:Del:M:2 31 26 86 1 90
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4:Del:M:3 25 1 50 43 16
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5:Del:M:1 77 98 69 50 26
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5:Del:M:2 56 47 43 8 88
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5:Del:M:3 41 6 50 13 40
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5:Del:M:4 10 35 44 53 3
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5:Del:M:5 30 3 55 7 14

‎setup.py‎

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if os.path.exists("dist"):
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shutil.rmtree("dist")
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VERSION = '0.0.22'
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VERSION = '0.0.23'
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def write_version_py(filename='SigProfilerAssignment/version.py'):
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# THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
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short_version = '%(version)s'
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version = '%(version)s'
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Update = 'Resolve issue with ID decomposition plots, JOBMETADATA upgrade, add DBS tests.'
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Update = 'v0.0.23: ID Decomposition Plots exome fix and ID tests'
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2020
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"""

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