diff --git a/.gitignore b/.gitignore index 524d0baa..47b47dbe 100755 --- a/.gitignore +++ b/.gitignore @@ -82,6 +82,7 @@ target/ # exclude data from source control by default /data/ data +data/ # Mac OS-specific storage files .DS_Store diff --git a/parameters/simulation/simple.yaml b/Analysis/simulations/binomial_growth/parameters/simple_v01.yaml similarity index 92% rename from parameters/simulation/simple.yaml rename to Analysis/simulations/binomial_growth/parameters/simple_v01.yaml index 321916fd..e6f2215e 100644 --- a/parameters/simulation/simple.yaml +++ b/Analysis/simulations/binomial_growth/parameters/simple_v01.yaml @@ -1,10 +1,13 @@ # One set of parameters for simulating cells and their lineages -local_outdir: 'simulation' -prefix: 'simple' +#local_outdir: 'simulation' +prefix: 'sweep_v01' + num_iterations: 100 num_cells: 10000 num_mt_positions: 10 +cpus: 36 + initialize: coverage: type: 'constant' # {'poisson', 'constant', 'growth'} diff --git a/Analysis/simulations/binomial_growth/parameters/sweep_v01.yaml b/Analysis/simulations/binomial_growth/parameters/sweep_v01.yaml new file mode 100644 index 00000000..c0b2c7a2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/parameters/sweep_v01.yaml @@ -0,0 +1,15 @@ +# One set of parameters for simulating cells and their lineages +outdir: 'results' +prefix: 'sweep_v01' +data_outdir: 'data/out' +#num_iterations: 100 +#num_cells: 10000 +#num_mt_positions: 10 +cpus: 36 + +grid: + cov_constant: [5, 10, 50, 100] + dominant_clone_sizes: [0.02,0.1,0.2, 0.4] + dominant_het: [0.02, 0.2, 0.5, 0.8] + dominant_growth: [0.1, 0.5, 0.8] + het_err_rate: [0.05, 0.15] diff --git a/Analysis/simulations/binomial_growth/results/0.before_after.tsv b/Analysis/simulations/binomial_growth/results/0.before_after.tsv new file mode 100644 index 00000000..357f7c33 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/0.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 198 224 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a/Analysis/simulations/binomial_growth/results/0.metrics.tsv b/Analysis/simulations/binomial_growth/results/0.metrics.tsv new file mode 100644 index 00000000..825887b4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/0.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.018527408003428943 0.01653002515769531 0.019094637170015902 0.018199307888534185 0.01819155530200554 0.01896134500562538 0.017619657318190676 0.01833408311151479 0.016065456790086752 0.017383118115291585 0.017740581437120186 0.01575176811990491 0.017152158307344394 0.01991669563336525 0.019344142722199933 0.017210686357407155 0.01675838332924371 0.01590293593178758 0.018547567113683886 0.01863077681137966 0.019667387503894768 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b/Analysis/simulations/binomial_growth/results/1.metrics.tsv new file mode 100644 index 00000000..a1674664 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/1.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.017774874620052016 0.014439277044265243 0.016285105329129374 0.018680593315441734 0.014181174601065728 0.014784356044203808 0.016713407620360846 0.01559607945672057 0.01785893123423735 0.016574756116380075 0.01611045181131616 0.015893128501414392 0.01696836864712912 0.014923884035382654 0.01659015452750959 0.015857547883730328 0.01651226672756088 0.015450618518383035 0.015296715468619888 0.0152906919664126 0.014700156805128197 0.014287955149275184 0.016855043238467166 0.014150818467953295 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a/Analysis/simulations/binomial_growth/results/106.metrics.tsv b/Analysis/simulations/binomial_growth/results/106.metrics.tsv new file mode 100644 index 00000000..53c0f687 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/106.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.6474972521239981 0.642435226472165 0.6529353365780456 0.6280184959701905 0.6490334134232144 0.6216481630231255 0.6080031665823289 0.6755089969333296 0.6155149390391214 0.6282560403742612 0.6612125939044 0.6765834702648523 0.665505995124219 0.6616147433638108 0.6343135846852309 0.6563108369115316 0.6624296760282957 0.6022070714862559 0.6942330093000879 0.6577248404276492 0.6334262383402416 0.6013849447810804 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0.9985912638139424 0.9989657763879549 0.9985340719029665 0.9991416761072357 0.9991129708452264 0.9988659037044287 0.9986363635701427 0.998657960967787 0.9985515093701758 0.9987111081618794 0.9986304236994511 0.9977975338246526 0.9988792913961698 0.999155351250757 0.9985404015907026 0.998921888650617 0.9991190045437766 0.9991656912480239 0.998260730153697 0.9990490963545293 0.9991214457807627 0.9985719974951336 0.9984734203067279 0.9989755288939248 0.9988854182132573 0.9986969722493589 0.9985712788031966 0.9986128053543382 0.9989252636314179 0.9985263309002864 0.9989183362864018 0.9990383572279703 0.9987971422783852 0.9983794955145799 0.9988429719795784 0.999154914779526 0.9989579946931433 0.9986975526538001 0.9991315185508399 0.998620632708427 0.9987185707696553 0.9984272509596973 0.9990332218600302 0.9990725786407672 0.9988799583148765 0.9987221325225482 0.9989056399592088 0.9989854367040445 +Dropout 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 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2351 1.129745314752523 +4 1994 2068 1.037111334002006 +5 2035 2193 1.0776412776412776 +6 2029 2131 1.0502710694923607 +7 1897 2088 1.1006852925672115 +8 1970 2005 1.017766497461929 +9 1963 2086 1.0626591951095263 +10 1989 2067 1.0392156862745099 +11 1980 2107 1.064141414141414 +12 2034 2206 1.0845624385447394 +13 2007 2088 1.0403587443946187 +14 2001 2153 1.0759620189905048 +15 1939 2058 1.0613718411552346 +16 2032 2186 1.0757874015748032 +17 1979 2132 1.077311773623042 +18 1900 2060 1.0842105263157895 +19 1982 2126 1.072653884964682 +20 2017 2159 1.0704015865146257 +21 2022 2132 1.0544015825914936 +22 2026 2159 1.0656465942744324 +23 2037 2177 1.0687285223367697 +24 1967 2075 1.0549059481443823 +25 2008 2197 1.0941235059760956 +26 2065 2166 1.048910411622276 +27 1959 1982 1.0117406840224605 +28 1998 2099 1.0505505505505506 +29 2009 2120 1.055251368840219 +30 1996 2119 1.061623246492986 +31 1971 2078 1.054287163876205 +32 2019 2134 1.0569588905398712 +33 2050 2171 1.0590243902439025 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1.0606494746895894 +65 1981 2175 1.0979303382130237 +66 2001 2224 1.1114442778610694 +67 2016 2146 1.064484126984127 +68 2009 2126 1.0582379293180686 +69 1940 2102 1.0835051546391752 +70 2026 2143 1.0577492596248765 +71 2021 2186 1.0816427511133102 +72 2024 2176 1.075098814229249 +73 1993 2101 1.0541896638233819 +74 2035 2148 1.0555282555282555 +75 2068 2154 1.0415860735009672 +76 2014 2197 1.0908639523336643 +77 1986 2101 1.0579053373615308 +78 2076 2203 1.061175337186898 +79 1963 2151 1.0957717778909832 +80 1954 2142 1.0962128966223132 +81 2054 2271 1.105647517039922 +82 2008 2159 1.075199203187251 +83 2033 2094 1.030004918839154 +84 2088 2270 1.0871647509578544 +85 2046 2149 1.0503421309872922 +86 2012 2124 1.0556660039761432 +87 1978 2111 1.0672396359959555 +88 2022 2146 1.0613254203758655 +89 2007 2046 1.0194319880418534 +90 2031 2118 1.0428360413589366 +91 1975 2094 1.060253164556962 +92 2071 2218 1.0709802028005795 +93 1983 2026 1.021684316691881 +94 1998 2169 1.0855855855855856 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b/Analysis/simulations/binomial_growth/results/145.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 1953 2102 1.0762928827444957 +1 2025 2135 1.054320987654321 +2 2017 2091 1.0366881507188894 +3 2033 2164 1.0644367929168717 +4 2016 2087 1.035218253968254 +5 2037 2183 1.071674030436917 +6 2040 2194 1.0754901960784313 +7 2000 2105 1.0525 +8 2057 2211 1.0748663101604279 +9 2050 2192 1.069268292682927 +10 1939 2112 1.0892212480660135 +11 1956 2079 1.062883435582822 +12 2037 2206 1.0829651448208149 +13 1974 2103 1.0653495440729484 +14 2062 2151 1.0431619786614936 +15 1917 2036 1.06207616066771 +16 1944 2118 1.0895061728395061 +17 2029 2198 1.0832922621981271 +18 1963 2183 1.1120733571064696 +19 1982 2134 1.0766902119071644 +20 2024 2068 1.0217391304347827 +21 2021 2178 1.0776843146956951 +22 1996 2033 1.0185370741482966 +23 2044 2173 1.0631115459882583 +24 2019 2160 1.0698365527488856 +25 1970 2024 1.0274111675126905 +26 2032 2219 1.092027559055118 +27 2034 2100 1.0324483775811208 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1991 1.048446550816219 +90 2004 2197 1.0963073852295409 +91 1950 2108 1.081025641025641 +92 1975 2025 1.0253164556962024 +93 1992 2083 1.0456827309236947 +94 2017 2158 1.0699058006941002 +95 2008 2074 1.0328685258964143 +96 2071 2160 1.04297440849831 +97 1995 2136 1.0706766917293233 +98 2001 2150 1.0744627686156922 +99 2008 2147 1.0692231075697212 diff --git a/Analysis/simulations/binomial_growth/results/145.metrics.tsv b/Analysis/simulations/binomial_growth/results/145.metrics.tsv new file mode 100644 index 00000000..c5542d07 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/145.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.14816092549425103 0.15095430460683706 0.14981446619241115 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a/Analysis/simulations/binomial_growth/results/146.before_after.tsv b/Analysis/simulations/binomial_growth/results/146.before_after.tsv new file mode 100644 index 00000000..9789ac51 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/146.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 2060 2124 1.0310679611650486 +1 2038 2171 1.0652600588812562 +2 2041 2137 1.0470357667809898 +3 2062 2251 1.091658583899127 +4 2020 2196 1.0871287128712872 +5 1956 2063 1.0547034764826175 +6 2018 2131 1.05599603567889 +7 2005 2143 1.0688279301745636 +8 2059 2251 1.093249150072851 +9 1991 2241 1.1255650426921144 +10 1973 2028 1.0278763304612266 +11 2002 2196 1.0969030969030968 +12 1960 2025 1.0331632653061225 +13 2029 2174 1.0714637752587481 +14 1976 2110 1.0678137651821862 +15 1975 2055 1.040506329113924 +16 2020 2215 1.0965346534653466 +17 2017 2144 1.0629647992067426 +18 1952 2066 1.0584016393442623 +19 2018 2154 1.0673934588701686 +20 2007 2088 1.0403587443946187 +21 1978 2117 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2025 2120 1.0469135802469136 +53 1991 2091 1.0502260170768458 +54 1954 2101 1.0752302968270215 +55 1997 2109 1.056084126189284 +56 2017 2082 1.0322260783341597 +57 1996 2112 1.0581162324649298 +58 1957 2015 1.0296371997956055 +59 1996 2099 1.0516032064128256 +60 1984 2120 1.0685483870967742 +61 2042 2193 1.073947110675808 +62 2032 2187 1.076279527559055 +63 1993 2046 1.0265930757651782 +64 2000 2090 1.045 +65 1903 2040 1.071991592222806 +66 1987 2051 1.0322093608454956 +67 1931 2033 1.0528223718280683 +68 1932 2011 1.0408902691511388 +69 2011 2093 1.0407757334659373 +70 1990 2046 1.028140703517588 +71 1958 2016 1.0296220633299284 +72 1909 2035 1.0660031430068098 +73 2005 2136 1.0653366583541146 +74 2017 2160 1.0708973723351511 +75 1963 2086 1.0626591951095263 +76 1980 2064 1.0424242424242425 +77 2035 2088 1.026044226044226 +78 1949 2017 1.034889687018984 +79 1979 2108 1.0651844365841334 +80 1946 2032 1.0441932168550874 +81 1996 2093 1.0485971943887775 +82 2116 2242 1.059546313799622 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/dev/null and b/Analysis/simulations/binomial_growth/results/146.rocs.p differ diff --git a/Analysis/simulations/binomial_growth/results/147.before_after.tsv b/Analysis/simulations/binomial_growth/results/147.before_after.tsv new file mode 100644 index 00000000..dabbfc94 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/147.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 1990 2087 1.048743718592965 +1 1987 2135 1.0744841469552089 +2 1981 2169 1.0949015648662292 +3 2039 2111 1.0353114271701815 +4 1982 2071 1.044904137235116 +5 2031 2262 1.1137370753323486 +6 2012 2161 1.0740556660039762 +7 2014 2127 1.0561072492552135 +8 2066 2196 1.0629235237173282 +9 2059 2173 1.0553666828557553 +10 1952 2127 1.0896516393442623 +11 1947 2094 1.0755007704160247 +12 2051 2152 1.0492442710872745 +13 1993 2058 1.0326141495233316 +14 2021 2169 1.0732310737258783 +15 2023 2160 1.0677212061295107 +16 1989 2064 1.0377073906485672 +17 2033 2179 1.071815051647811 +18 1957 2032 1.0383239652529381 +19 1925 2095 1.0883116883116883 +20 2004 2156 1.0758483033932136 +21 1964 2090 1.0641547861507128 +22 1997 2093 1.0480721081622433 +23 1977 2080 1.0520991401112798 +24 1998 2094 1.048048048048048 +25 2084 2182 1.0470249520153552 +26 1982 2166 1.0928355196770938 +27 2045 2156 1.054278728606357 +28 2007 2119 1.0558046836073742 +29 2061 2192 1.0635613779718582 +30 2061 2194 1.064531780688986 +31 1923 1982 1.03068122724909 +32 1992 2110 1.0592369477911647 +33 2081 2233 1.0730418068236425 +34 1971 2034 1.0319634703196348 +35 2084 2235 1.0724568138195778 +36 2019 2073 1.026745913818722 +37 1920 2059 1.0723958333333334 +38 2023 2136 1.0558576371725161 +39 1920 2140 1.1145833333333333 +40 1910 2014 1.0544502617801048 +41 2012 2119 1.0531809145129225 +42 2040 2160 1.0588235294117647 +43 2014 2157 1.071002979145978 +44 2002 2129 1.0634365634365635 +45 1995 2089 1.0471177944862156 +46 2033 2115 1.0403344810624693 +47 2020 2153 1.065841584158416 +48 2002 2149 1.0734265734265733 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1.0229591836734695 +80 1971 1983 1.0060882800608828 +81 1991 2121 1.0652938221998995 +82 2022 2209 1.0924826904055391 +83 2000 2071 1.0355 +84 1993 2119 1.0632212744606122 +85 2015 2154 1.0689826302729528 +86 1995 2121 1.063157894736842 +87 2048 2068 1.009765625 +88 1972 2108 1.0689655172413792 +89 2007 2219 1.1056302939711011 +90 2010 2072 1.0308457711442787 +91 2012 2163 1.0750497017892644 +92 2014 2198 1.0913604766633564 +93 1999 2089 1.0450225112556277 +94 1923 2092 1.0878835153406137 +95 1964 1976 1.0061099796334012 +96 2001 2060 1.0294852573713142 +97 1980 2093 1.057070707070707 +98 1977 2063 1.0435002529084472 +99 2025 2151 1.0622222222222222 diff --git a/Analysis/simulations/binomial_growth/results/147.metrics.tsv b/Analysis/simulations/binomial_growth/results/147.metrics.tsv new file mode 100644 index 00000000..d94deaa0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/147.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.2878657116732418 0.2747082925897535 0.2770627577286471 0.268997554266197 0.2921010318467838 0.29725660435662116 0.26542757661947425 0.27742334516008665 0.2842751102616815 0.2833815040156288 0.28316743674080264 0.28560046060065547 0.28875338645750237 0.2759337015204518 0.28955220867134235 0.28601131489295883 0.27408472780048937 0.2975201555776445 0.27105974429596913 0.26344402416471874 0.281093142202729 0.28136228252116857 0.28046628322306083 0.27930864428837326 0.2957109020395392 0.2909920739356988 0.2853913691886337 0.29280028121108054 0.2687007540976817 0.2916451032469328 0.2913949373205056 0.2574827893283581 0.2834033643870877 0.3040681277581543 0.2748857687896413 0.3150667385141492 0.2850006585861874 0.28079865788082736 0.2854198066534389 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a/Analysis/simulations/binomial_growth/results/147.rocs.p b/Analysis/simulations/binomial_growth/results/147.rocs.p new file mode 100644 index 00000000..17f4013e Binary files /dev/null and b/Analysis/simulations/binomial_growth/results/147.rocs.p differ diff --git a/Analysis/simulations/binomial_growth/results/148.before_after.tsv b/Analysis/simulations/binomial_growth/results/148.before_after.tsv new file mode 100644 index 00000000..0cf3e6f1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/148.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 2001 2117 1.0579710144927537 +1 2046 2098 1.0254154447702835 +2 1989 2107 1.0593262946204123 +3 1962 2130 1.0856269113149848 +4 1978 2105 1.064206268958544 +5 1964 2056 1.0468431771894093 +6 1992 2061 1.0346385542168675 +7 1988 2090 1.051307847082495 +8 2048 2165 1.05712890625 +9 2030 2180 1.0738916256157636 +10 2028 2127 1.0488165680473374 +11 1975 2053 1.039493670886076 +12 2024 2114 1.0444664031620554 +13 1924 2082 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1.0775733465937345 +53 1997 2103 1.0530796194291436 +54 2007 2059 1.025909317389138 +55 2001 2140 1.0694652673663168 +56 1923 2101 1.0925637025481019 +57 2026 2139 1.0557749259624876 +58 1982 2102 1.060544904137235 +59 1897 2055 1.0832894043226147 +60 1996 2093 1.0485971943887775 +61 1948 2070 1.0626283367556468 +62 2020 2212 1.0950495049504951 +63 2006 2172 1.082751744765703 +64 2005 2134 1.0643391521197008 +65 1980 2115 1.0681818181818181 +66 2021 2128 1.0529440870856013 +67 1967 2094 1.0645653279105236 +68 2003 2074 1.035446829755367 +69 2030 2104 1.0364532019704433 +70 2010 2117 1.0532338308457712 +71 1948 2017 1.0354209445585216 +72 1921 2063 1.0739198334200937 +73 1983 2062 1.0398386283408976 +74 2009 2087 1.0388252862120457 +75 2080 2210 1.0625 +76 2059 2149 1.0437105390966488 +77 2001 2233 1.1159420289855073 +78 2012 2162 1.0745526838966202 +79 1980 2109 1.0651515151515152 +80 2003 2092 1.0444333499750373 +81 2023 2198 1.0865051903114187 +82 1985 2122 1.0690176322418137 +83 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2974 17.49411764705882 +89 213 3395 15.938967136150234 +90 211 3234 15.327014218009479 +91 202 3389 16.777227722772277 +92 222 3383 15.23873873873874 +93 192 3158 16.447916666666668 +94 232 3684 15.879310344827585 +95 189 3072 16.253968253968253 +96 187 3020 16.149732620320854 +97 200 3219 16.095 +98 222 3468 15.621621621621621 +99 187 3193 17.074866310160427 diff --git a/Analysis/simulations/binomial_growth/results/200.metrics.tsv b/Analysis/simulations/binomial_growth/results/200.metrics.tsv new file mode 100644 index 00000000..6b5ee7d5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/200.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.1547570630535513 0.1912848303981219 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0.21067997265649163 0.22061676968688299 0.1671813602141761 0.19245907949476804 0.18398278461821405 0.19960723871171668 0.19761679652523662 0.17740149777973313 0.1974901121384612 0.18649518000375606 0.19156562157356588 0.20433917993687123 0.18396110123032444 0.20044784911637048 0.18785757499202443 0.22321773853187707 0.23906514640284213 0.19737682923730696 0.18850720156727657 0.20761534446611807 0.22737611517374795 0.18225864679139758 0.1919498780668423 0.21990054714855445 0.20053832147610495 0.2023640209354334 0.1677332235756291 0.18255019191387828 0.17532229902141355 0.21066577915920798 0.17241180160191083 0.1971704608524471 0.18364727571531372 0.20070297763339034 0.1903849871554742 0.2013590904214147 0.2096866844752061 0.2062658484427244 0.18341590196344665 0.2142328296074611 0.18120301023147792 0.17667955269528912 0.21226821957823197 0.19692403416215618 0.1674062748439184 0.1923559167821916 0.2085202099509694 0.20037206743707162 +Dropout 0.00335 0.0038 0.00475 0.00475 0.00445 0.0055 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a/Analysis/simulations/binomial_growth/results/201.before_after.tsv b/Analysis/simulations/binomial_growth/results/201.before_after.tsv new file mode 100644 index 00000000..b75070cb --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/201.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 199 3241 16.28643216080402 +1 183 3000 16.39344262295082 +2 208 3342 16.067307692307693 +3 221 3526 15.95475113122172 +4 201 3191 15.875621890547263 +5 187 3266 17.46524064171123 +6 198 3285 16.59090909090909 +7 196 3206 16.357142857142858 +8 210 3421 16.29047619047619 +9 235 3680 15.659574468085106 +10 205 3263 15.917073170731708 +11 191 3032 15.87434554973822 +12 188 3136 16.680851063829788 +13 188 3084 16.404255319148938 +14 189 3203 16.947089947089946 +15 200 3266 16.33 +16 193 3230 16.735751295336787 +17 188 3192 16.97872340425532 +18 199 3111 15.633165829145728 +19 192 3142 16.364583333333332 +20 209 3460 16.555023923444978 +21 216 3308 15.314814814814815 +22 204 3251 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17.791907514450866 +88 210 3194 15.209523809523809 +89 210 3315 15.785714285714286 +90 203 3300 16.25615763546798 +91 214 3230 15.093457943925234 +92 205 3474 16.946341463414633 +93 213 3280 15.39906103286385 +94 157 2665 16.97452229299363 +95 223 3393 15.215246636771301 +96 175 2965 16.942857142857143 +97 206 3223 15.645631067961165 +98 193 3219 16.678756476683937 +99 206 3219 15.62621359223301 diff --git a/Analysis/simulations/binomial_growth/results/201.metrics.tsv b/Analysis/simulations/binomial_growth/results/201.metrics.tsv new file mode 100644 index 00000000..95e78a7f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/201.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 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4.283492222779729 +60 2011 8552 4.252610641471905 +61 1998 8634 4.321321321321322 +62 2055 8574 4.172262773722628 +63 1914 8501 4.441483803552769 +64 2005 8562 4.2703241895261845 +65 2006 8582 4.278165503489531 +66 2016 8543 4.2375992063492065 +67 1991 8608 4.323455549974887 +68 2022 8567 4.236894164193868 +69 1982 8592 4.335015136226034 +70 2006 8541 4.257726819541376 +71 2037 8625 4.2341678939617085 +72 1996 8519 4.268036072144288 +73 1929 8512 4.412649040953862 +74 1980 8585 4.335858585858586 +75 1989 8484 4.2654600301659125 +76 1990 8517 4.279899497487437 +77 1996 8599 4.30811623246493 +78 1970 8557 4.343654822335026 +79 2088 8618 4.1273946360153255 +80 2008 8541 4.253486055776892 +81 1979 8586 4.33855482566953 +82 2039 8566 4.201078960274645 +83 1990 8588 4.315577889447236 +84 1910 8513 4.457068062827225 +85 1903 8574 4.5055176037835 +86 1990 8590 4.316582914572864 +87 2020 8534 4.2247524752475245 +88 2014 8573 4.256703078450844 +89 2006 8599 4.286640079760718 +90 2013 8633 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b/Analysis/simulations/binomial_growth/results/25.rocs.p differ diff --git a/Analysis/simulations/binomial_growth/results/250.before_after.tsv b/Analysis/simulations/binomial_growth/results/250.before_after.tsv new file mode 100644 index 00000000..d10e01e1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/250.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 2056 8526 4.146887159533074 +1 2016 8561 4.246527777777778 +2 1991 8492 4.265193370165746 +3 2044 8580 4.197651663405088 +4 1986 8575 4.317724068479356 +5 2024 8606 4.2519762845849804 +6 1992 8542 4.288152610441767 +7 1985 8571 4.3178841309823675 +8 2010 8624 4.290547263681592 +9 1978 8589 4.342264914054601 +10 1981 8576 4.329126703685008 +11 2023 8576 4.239248640632724 +12 2015 8593 4.264516129032258 +13 2001 8517 4.256371814092954 +14 1993 8504 4.266934269944807 +15 1975 8571 4.339746835443038 +16 1885 8457 4.486472148541114 +17 1985 8610 4.337531486146096 +18 2061 8677 4.210092188258127 +19 2045 8682 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4.2964646464646465 +51 1975 8571 4.339746835443038 +52 1994 8565 4.295386158475426 +53 2071 8623 4.16368903911154 +54 1997 8594 4.303455182774162 +55 2013 8522 4.233482364629905 +56 1981 8555 4.318525996971227 +57 1940 8557 4.4108247422680416 +58 1912 8475 4.432531380753138 +59 2082 8660 4.159462055715658 +60 1980 8495 4.290404040404041 +61 2012 8707 4.327534791252485 +62 1983 8581 4.327281896116994 +63 1942 8521 4.387744593202884 +64 1973 8526 4.321338063862139 +65 1959 8522 4.350178662582951 +66 2001 8555 4.27536231884058 +67 2021 8632 4.27115289460663 +68 2022 8644 4.274975272007913 +69 1932 8562 4.431677018633541 +70 1984 8556 4.3125 +71 2026 8625 4.25715695952616 +72 2007 8562 4.266068759342302 +73 1959 8530 4.354262378764676 +74 2022 8525 4.216122650840751 +75 2037 8531 4.188021600392735 +76 1904 8500 4.464285714285714 +77 2008 8598 4.281872509960159 +78 2006 8570 4.272183449651047 +79 2042 8598 4.210577864838394 +80 1932 8478 4.388198757763975 +81 2028 8628 4.254437869822485 +82 2006 8615 4.294616151545364 +83 1979 8575 4.33299646286003 +84 2008 8599 4.282370517928287 +85 1979 8596 4.343607882769075 +86 2017 8532 4.230044620723847 +87 1937 8522 4.399586990191017 +88 1982 8556 4.316851664984863 +89 1952 8548 4.379098360655738 +90 1950 8564 4.391794871794872 +91 2005 8519 4.248877805486284 +92 2044 8597 4.2059686888454015 +93 1979 8512 4.301162203132895 +94 2014 8641 4.290466732869911 +95 2022 8625 4.265578635014837 +96 2009 8569 4.26530612244898 +97 1955 8504 4.349872122762148 +98 2024 8547 4.2228260869565215 +99 1975 8557 4.332658227848102 diff --git a/Analysis/simulations/binomial_growth/results/250.metrics.tsv b/Analysis/simulations/binomial_growth/results/250.metrics.tsv new file mode 100644 index 00000000..34b42b4c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/250.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.9506742806855281 0.9518380472209607 0.9498722722263617 0.9533459073310082 0.9566898092227646 0.9551582164274001 0.9493594428013111 0.9531768541837198 0.955398738476772 0.9538117267768518 0.9540944704860482 0.9513452861889099 0.9489284992661184 0.9502780011561449 0.9514103788972402 0.9529404240634854 0.9484676173978204 0.9526958954315141 0.9557520732401206 0.95544956428235 0.9522991918760175 0.9491239129884844 0.9539994863738566 0.9506070175473044 0.9531146747470368 0.9470566034945607 0.9536443139019851 0.9529704383604349 0.9554086009874375 0.9522027622378029 0.9553835013227419 0.9547907804000957 0.9525244206211331 0.9522048977643579 0.9528572728950273 0.9557206503889549 0.953747541754464 0.9503138305416499 0.9523933865992531 0.9455804824334717 0.9502838783664553 0.9492464463023955 0.9476640721723548 0.9490631963455417 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b/Analysis/simulations/binomial_growth/results/253.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 2028 8611 4.246055226824458 +1 2010 8579 4.268159203980099 +2 2023 8616 4.259021255561048 +3 1995 8587 4.304260651629073 +4 1988 8577 4.314386317907445 +5 2018 8666 4.294350842418236 +6 2003 8556 4.271592611083375 +7 2013 8539 4.241927471435668 +8 1971 8476 4.300355149670218 +9 1974 8545 4.328774062816616 +10 1984 8565 4.317036290322581 +11 1969 8478 4.305738953783647 +12 1951 8550 4.382368016401845 +13 1943 8596 4.424086464230571 +14 2005 8562 4.2703241895261845 +15 2013 8543 4.243914555389965 +16 1937 8524 4.400619514713474 +17 1952 8436 4.32172131147541 +18 2040 8551 4.191666666666666 +19 2063 8626 4.181289384391663 +20 2023 8576 4.239248640632724 +21 1953 8566 4.386072708653354 +22 1995 8542 4.281704260651629 +23 1977 8488 4.293373798684876 +24 1895 8509 4.49023746701847 +25 1981 8559 4.320545179202423 +26 1994 8583 4.304413239719158 +27 2005 8579 4.278802992518703 +28 1993 8556 4.293025589563472 +29 1984 8568 4.318548387096774 +30 2020 8621 4.267821782178218 +31 2005 8524 4.251371571072319 +32 2034 8527 4.192232055063913 +33 2034 8609 4.2325467059980335 +34 2046 8689 4.246823069403715 +35 1999 8531 4.267633816908455 +36 2051 8575 4.180887372013652 +37 2007 8581 4.27553562531141 +38 1987 8539 4.297433316557624 +39 1971 8552 4.338914256722476 +40 1971 8564 4.345002536783359 +41 2063 8651 4.193407658749394 +42 2021 8566 4.238495794161306 +43 1997 8555 4.28392588883325 +44 2026 8621 4.255182625863771 +45 2019 8582 4.250619118375433 +46 2009 8629 4.295171727227476 +47 1986 8566 4.313192346424975 +48 1963 8554 4.357615894039735 +49 2050 8616 4.202926829268293 +50 1984 8555 4.311995967741935 +51 1999 8629 4.316658329164582 +52 2076 8577 4.131502890173411 +53 1982 8560 4.318869828456105 +54 1965 8559 4.355725190839695 +55 2066 8603 4.164085188770571 +56 1952 8507 4.358094262295082 +57 2013 8605 4.27471435668157 +58 1972 8513 4.3169371196754565 +59 2014 8607 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4.180887372013652 +37 2007 8581 4.27553562531141 +38 1987 8539 4.297433316557624 +39 1971 8552 4.338914256722476 +40 1971 8564 4.345002536783359 +41 2063 8651 4.193407658749394 +42 2021 8566 4.238495794161306 +43 1997 8555 4.28392588883325 +44 2026 8621 4.255182625863771 +45 2019 8582 4.250619118375433 +46 2009 8629 4.295171727227476 +47 1986 8566 4.313192346424975 +48 1963 8554 4.357615894039735 +49 2050 8616 4.202926829268293 +50 1984 8555 4.311995967741935 +51 1999 8629 4.316658329164582 +52 2076 8577 4.131502890173411 +53 1982 8560 4.318869828456105 +54 1965 8559 4.355725190839695 +55 2066 8603 4.164085188770571 +56 1952 8507 4.358094262295082 +57 2013 8605 4.27471435668157 +58 1972 8513 4.3169371196754565 +59 2014 8607 4.273584905660377 +60 2002 8631 4.311188811188811 +61 2001 8585 4.290354822588705 +62 1981 8600 4.341241797072186 +63 2061 8656 4.199902959728287 +64 1953 8512 4.358422939068101 +65 2010 8572 4.264676616915423 +66 1972 8558 4.3397565922920895 +67 2049 8642 4.2176671547096145 +68 1938 8507 4.389576883384933 +69 1968 8526 4.3323170731707314 +70 1983 8559 4.316187594553707 +71 2027 8558 4.222002960039467 +72 2026 8596 4.24284304047384 +73 2041 8648 4.237138657520823 +74 1993 8558 4.2940291018564976 +75 2045 8609 4.209779951100244 +76 2035 8603 4.227518427518428 +77 1995 8580 4.3007518796992485 +78 2001 8582 4.288855572213893 +79 1977 8554 4.326757713707638 +80 2036 8584 4.216110019646365 +81 1913 8578 4.484056455828542 +82 1983 8592 4.332829046898638 +83 1952 8518 4.363729508196721 +84 1976 8554 4.328947368421052 +85 2080 8637 4.152403846153846 +86 1998 8592 4.3003003003003 +87 1974 8499 4.305471124620061 +88 1980 8576 4.331313131313132 +89 1980 8561 4.323737373737374 +90 2048 8630 4.2138671875 +91 1961 8567 4.368689444161142 +92 1950 8515 4.366666666666666 +93 1998 8582 4.295295295295295 +94 1983 8614 4.343923348461926 +95 1992 8576 4.305220883534137 +96 1966 8508 4.327568667344862 +97 2063 8598 4.167716917111004 +98 2018 8544 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0.0138 0.0146 0.0132 0.01385 0.0148 0.0118 0.01295 0.0142 0.01455 0.01315 0.01335 0.014 0.0144 0.0141 0.0159 0.0141 0.0128 0.01365 0.01305 0.01475 0.01365 0.01305 0.01295 0.0147 0.01545 0.01535 0.01295 0.01365 0.0138 0.01445 0.0142 0.0143 0.01385 0.0144 0.01435 0.01535 0.01675 0.0148 0.01365 diff --git a/Analysis/simulations/binomial_growth/results/344.rocs.p b/Analysis/simulations/binomial_growth/results/344.rocs.p new file mode 100644 index 00000000..be9ed4e0 Binary files /dev/null and b/Analysis/simulations/binomial_growth/results/344.rocs.p differ diff --git a/Analysis/simulations/binomial_growth/results/345.before_after.tsv b/Analysis/simulations/binomial_growth/results/345.before_after.tsv new file mode 100644 index 00000000..5eb202e2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/345.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 1968 8570 4.354674796747967 +1 1946 8529 4.382836587872559 +2 2030 8538 4.205911330049261 +3 2024 8629 4.263339920948616 +4 2064 8527 4.1312984496124034 +5 1991 8476 4.25715720743345 +6 1897 8459 4.459146020031629 +7 2027 8562 4.223976319684263 +8 2002 8564 4.277722277722278 +9 2013 8629 4.286636860407352 +10 2029 8553 4.215377033021193 +11 1956 8509 4.350204498977505 +12 1964 8603 4.380346232179226 +13 1989 8544 4.295625942684766 +14 1964 8594 4.375763747454175 +15 1963 8562 4.361691288843606 +16 2040 8623 4.226960784313725 +17 2019 8581 4.250123823675087 +18 2018 8584 4.253716551040634 +19 2034 8583 4.21976401179941 +20 1956 8521 4.356339468302658 +21 2000 8559 4.2795 +22 2038 8593 4.216388616290481 +23 2003 8547 4.26709935097354 +24 1973 8564 4.3405980739989865 +25 2057 8644 4.20223626640739 +26 1959 8561 4.3700867789688616 +27 1965 8526 4.338931297709924 +28 2035 8577 4.214742014742015 +29 1979 8560 4.325416877210713 +30 2035 8580 4.216216216216216 +31 2012 8581 4.264910536779324 +32 2091 8683 4.152558584409373 +33 2044 8594 4.204500978473582 +34 2025 8527 4.2108641975308645 +35 2043 8625 4.221732745961821 +36 2051 8509 4.14870794734276 +37 2026 8562 4.226061204343534 +38 2041 8581 4.204311611954924 +39 2021 8501 4.206333498268184 +40 1935 8539 4.412919896640827 +41 2069 8618 4.165297245045916 +42 1997 8570 4.2914371557336 +43 2010 8590 4.27363184079602 +44 2018 8580 4.2517343904856295 +45 1994 8515 4.270310932798395 +46 1939 8498 4.382671480144404 +47 1955 8530 4.3631713554987215 +48 1935 8535 4.410852713178294 +49 1947 8531 4.381612737544941 +50 1895 8412 4.4390501319261215 +51 1964 8618 4.387983706720978 +52 1997 8576 4.294441662493741 +53 1962 8503 4.333843017329256 +54 2026 8632 4.260612043435341 +55 1953 8543 4.3742959549411164 +56 2015 8551 4.243672456575682 +57 1995 8590 4.305764411027569 +58 2006 8561 4.267696909272184 +59 2030 8536 4.2049261083743845 +60 2039 8653 4.243746934771947 +61 1910 8479 4.439267015706807 +62 2032 8644 4.253937007874016 +63 1954 8490 4.344933469805527 +64 2023 8659 4.280276816608996 +65 1987 8639 4.3477604428787116 +66 2001 8590 4.292853573213393 +67 2013 8585 4.264778936910084 +68 1916 8474 4.422755741127348 +69 1947 8504 4.367745249101182 +70 1982 8613 4.34561049445005 +71 2036 8559 4.203831041257367 +72 1982 8596 4.337033299697276 +73 2039 8650 4.242275625306523 +74 1957 8628 4.408788962698007 +75 2027 8564 4.22496299950666 +76 2060 8650 4.199029126213592 +77 2009 8512 4.2369337979094075 +78 1999 8538 4.271135567783892 +79 2066 8642 4.182962245885769 +80 2093 8598 4.107978977544195 +81 1972 8518 4.31947261663286 +82 1999 8503 4.2536268134067035 +83 1944 8612 4.4300411522633745 +84 1995 8576 4.29874686716792 +85 2010 8587 4.272139303482587 +86 2014 8595 4.2676266137040715 +87 2001 8593 4.294352823588206 +88 2030 8665 4.268472906403941 +89 2012 8604 4.276341948310139 +90 2011 8537 4.245151665837891 +91 1977 8610 4.355083459787557 +92 1956 8533 4.362474437627812 +93 2003 8582 4.284573140289566 +94 2028 8563 4.2223865877712035 +95 2012 8587 4.2678926441351885 +96 2095 8576 4.093556085918855 +97 1980 8563 4.324747474747475 +98 1911 8374 4.381998953427525 +99 2013 8579 4.261798310978639 diff --git a/Analysis/simulations/binomial_growth/results/345.metrics.tsv b/Analysis/simulations/binomial_growth/results/345.metrics.tsv new file mode 100644 index 00000000..9cfffb86 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/345.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.34685538482444717 0.3427544028642336 0.3486387344447782 0.35177119591781825 0.34809100781365465 0.34446652266896105 0.33843929176836973 0.3485233181365544 0.34583353146702844 0.35157643721198567 0.35063159941513583 0.34164427606478875 0.350363052662245 0.3477310676280163 0.3460564067927565 0.3464025661503927 0.3496648251319216 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4.152575315840622 +2 1974 8575 4.343971631205674 +3 1938 8581 4.427760577915377 +4 2021 8587 4.248886689757546 +5 2001 8555 4.27536231884058 +6 1941 8543 4.401339515713549 +7 2079 8636 4.153920153920154 +8 1996 8614 4.31563126252505 +9 2054 8636 4.204479065238559 +10 2035 8598 4.225061425061425 +11 2012 8622 4.285288270377734 +12 2047 8552 4.177821201758671 +13 2024 8684 4.290513833992095 +14 2085 8673 4.159712230215828 +15 1989 8528 4.287581699346405 +16 1991 8564 4.3013561024610745 +17 1917 8516 4.442357850808555 +18 1995 8627 4.324310776942356 +19 2032 8599 4.231791338582677 +20 1986 8504 4.281973816717019 +21 2042 8549 4.186581782566112 +22 1970 8523 4.326395939086295 +23 1996 8523 4.270040080160321 +24 1949 8593 4.4089276552077985 +25 1999 8504 4.254127063531766 +26 2005 8588 4.283291770573566 +27 1969 8583 4.359065515490096 +28 2034 8607 4.231563421828908 +29 1992 8541 4.287650602409639 +30 1994 8621 4.323470411233701 +31 2034 8585 4.220747295968535 +32 1967 8470 4.306049822064057 +33 1941 8499 4.378670788253477 +34 1982 8581 4.329465186680121 +35 1983 8487 4.279878971255673 +36 2003 8578 4.2825761357963055 +37 2006 8570 4.272183449651047 +38 1964 8536 4.346232179226069 +39 2029 8548 4.212912764908822 +40 2045 8531 4.171638141809291 +41 1968 8571 4.3551829268292686 +42 1969 8565 4.349923819197563 +43 2002 8599 4.295204795204795 +44 1994 8589 4.307422266800401 +45 2014 8515 4.2279046673286995 +46 1943 8552 4.401441070509521 +47 1952 8507 4.358094262295082 +48 2028 8593 4.237179487179487 +49 1987 8522 4.288877705083039 +50 2038 8563 4.201668302257115 +51 1867 8479 4.541510444563471 +52 1993 8587 4.308580030105369 +53 1993 8516 4.27295534370296 +54 1985 8483 4.273551637279597 +55 2000 8600 4.3 +56 1965 8523 4.337404580152672 +57 2018 8503 4.213577799801784 +58 2031 8583 4.225997045790251 +59 2056 8625 4.195038910505836 +60 2004 8568 4.275449101796407 +61 2011 8598 4.275484833416211 +62 1920 8515 4.434895833333333 +63 1978 8571 4.333164812942366 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b/Analysis/simulations/binomial_growth/results/57.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 2027 8564 4.22496299950666 +1 2076 8612 4.148362235067437 +2 1990 8605 4.324120603015075 +3 2012 8576 4.262425447316104 +4 1964 8561 4.358961303462322 +5 2042 8635 4.22869735553379 +6 2002 8574 4.282717282717282 +7 2001 8674 4.334832583708146 +8 2003 8578 4.2825761357963055 +9 2042 8561 4.192458374142997 +10 1970 8552 4.341116751269036 +11 1963 8590 4.375955170657157 +12 1978 8560 4.3276036400404445 +13 1960 8545 4.35969387755102 +14 2063 8600 4.168686379059622 +15 2001 8573 4.284357821089455 +16 1999 8592 4.298149074537268 +17 2062 8640 4.190106692531523 +18 2040 8547 4.189705882352941 +19 1927 8489 4.405293201868189 +20 2003 8557 4.27209186220669 +21 1978 8577 4.336198179979777 +22 1965 8526 4.338931297709924 +23 2049 8660 4.226451927769643 +24 1979 8601 4.346134411318848 +25 2017 8555 4.2414476945959345 +26 1927 8522 4.422418266735859 +27 2033 8561 4.21101819970487 +28 2016 8556 4.244047619047619 +29 1959 8512 4.345074017355794 +30 2011 8547 4.250124316260567 +31 1960 8544 4.359183673469388 +32 1982 8507 4.292129162462159 +33 2031 8576 4.222550467749877 +34 2029 8579 4.22819122720552 +35 1988 8575 4.313380281690141 +36 2052 8608 4.1949317738791425 +37 2000 8561 4.2805 +38 2003 8515 4.251123315027459 +39 2107 8669 4.11438063597532 +40 2031 8545 4.207287050713934 +41 1987 8577 4.316557624559637 +42 1967 8495 4.318759532282664 +43 2011 8556 4.2545997016409745 +44 1994 8549 4.287362086258776 +45 1957 8542 4.364844149207971 +46 2071 8613 4.158860453887011 +47 2004 8566 4.274451097804391 +48 1956 8508 4.3496932515337425 +49 2028 8598 4.239644970414201 +50 2001 8593 4.294352823588206 +51 1988 8638 4.345070422535211 +52 1958 8473 4.327374872318693 +53 2012 8633 4.290755467196819 +54 1948 8516 4.371663244353183 +55 2052 8595 4.18859649122807 +56 1973 8466 4.290927521540801 +57 1999 8572 4.288144072036018 +58 2012 8632 4.290258449304175 +59 1958 8564 4.373850868232891 +60 2011 8533 4.243162605668822 +61 2039 8660 4.24717999019127 +62 1891 8380 4.431517715494447 +63 2033 8616 4.238071815051648 +64 1964 8506 4.330957230142566 +65 1992 8509 4.271586345381526 +66 1990 8565 4.3040201005025125 +67 2069 8651 4.181246979217013 +68 1991 8607 4.3229532898041185 +69 2069 8626 4.169163847269212 +70 1971 8443 4.283612379502791 +71 2098 8705 4.149189704480458 +72 1961 8522 4.345741968383478 +73 2041 8575 4.2013718765311125 +74 1960 8567 4.370918367346939 +75 1935 8504 4.394832041343669 +76 2024 8548 4.223320158102767 +77 2010 8564 4.260696517412935 +78 1989 8522 4.28456510809452 +79 1948 8540 4.383983572895278 +80 2017 8664 4.295488349033218 +81 2062 8653 4.196411251212415 +82 1991 8554 4.2963335007533905 +83 1925 8545 4.438961038961039 +84 1971 8586 4.3561643835616435 +85 2029 8631 4.253819615574175 +86 2027 8596 4.2407498766650225 +87 2013 8592 4.268256333830104 +88 1995 8608 4.314786967418546 +89 2039 8617 4.226091221186857 +90 2013 8632 4.288127173373075 +91 2029 8649 4.262690980778709 +92 2023 8612 4.257043994068216 +93 2018 8529 4.226461843409316 +94 1946 8499 4.367420349434738 +95 1995 8570 4.295739348370927 +96 2000 8645 4.3225 +97 2032 8646 4.2549212598425195 +98 1915 8483 4.429765013054831 +99 2048 8562 4.1806640625 diff --git a/Analysis/simulations/binomial_growth/results/57.metrics.tsv b/Analysis/simulations/binomial_growth/results/57.metrics.tsv new file mode 100644 index 00000000..46a9972e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/57.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.38361798423344945 0.39225655150026906 0.3880549125740282 0.39007091192291066 0.38414225503224564 0.3928539392009523 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100644 index 00000000..c65ea9d2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/58.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 2029 8665 4.270576638738294 +1 2038 8600 4.2198233562316 +2 2047 8585 4.193942354665364 +3 2043 8638 4.228095937347039 +4 1944 8484 4.364197530864198 +5 2015 8584 4.260049627791563 +6 1980 8576 4.331313131313132 +7 2065 8640 4.184019370460049 +8 2033 8590 4.225282833251352 +9 2009 8562 4.261821801891489 +10 2084 8657 4.154030710172744 +11 1979 8561 4.325922182920667 +12 1985 8554 4.309319899244333 +13 2130 8674 4.072300469483568 +14 2029 8586 4.231641202562839 +15 2024 8607 4.252470355731226 +16 1982 8625 4.351664984863774 +17 2048 8632 4.21484375 +18 2088 8590 4.113984674329502 +19 1960 8442 4.307142857142857 +20 2035 8609 4.23046683046683 +21 2014 8535 4.237835153922542 +22 2037 8572 4.208149239077074 +23 2031 8588 4.228458887247661 +24 1994 8651 4.33851554663992 +25 1999 8620 4.31215607803902 +26 2024 8592 4.24505928853755 +27 1912 8429 4.40847280334728 +28 1990 8564 4.303517587939698 +29 2058 8647 4.201652089407191 +30 1967 8482 4.312150482968988 +31 2017 8567 4.247397124442241 +32 2028 8572 4.226824457593688 +33 2031 8645 4.2565238798621365 +34 1923 8535 4.438377535101404 +35 2008 8649 4.307270916334661 +36 2021 8609 4.259772389905987 +37 1975 8607 4.357974683544303 +38 2014 8480 4.2105263157894735 +39 1990 8519 4.280904522613065 +40 2031 8515 4.192516001969473 +41 1958 8554 4.368743615934627 +42 1986 8585 4.322759315206445 +43 2037 8556 4.200294550810015 +44 1988 8543 4.29728370221328 +45 2063 8575 4.156568104701891 +46 2020 8564 4.23960396039604 +47 1980 8597 4.3419191919191915 +48 1949 8579 4.4017444843509494 +49 2015 8521 4.2287841191067 +50 1995 8583 4.302255639097744 +51 2051 8635 4.210141394441735 +52 2011 8607 4.279960218796619 +53 1989 8613 4.330316742081448 +54 2048 8627 4.21240234375 +55 1906 8491 4.454879328436516 +56 2008 8520 4.243027888446215 +57 2015 8550 4.2431761786600495 +58 1984 8601 4.335181451612903 +59 2002 8562 4.276723276723277 +60 2029 8600 4.238541153277477 +61 1931 8498 4.400828586224754 +62 1965 8509 4.330279898218829 +63 1976 8544 4.323886639676114 +64 2039 8567 4.201569396763119 +65 2033 8587 4.2238071815051645 +66 1945 8588 4.415424164524421 +67 1999 8617 4.310655327663832 +68 2015 8627 4.281389578163772 +69 2048 8638 4.2177734375 +70 2013 8551 4.247888723298559 +71 2047 8604 4.2032242305813385 +72 1986 8561 4.31067472306143 +73 2034 8643 4.2492625368731565 +74 2006 8555 4.264705882352941 +75 2023 8603 4.252595155709343 +76 1972 8484 4.302231237322515 +77 1962 8489 4.326707441386341 +78 2035 8579 4.2157248157248155 +79 1987 8547 4.301459486663312 +80 2015 8600 4.267990074441688 +81 1964 8547 4.35183299389002 +82 2054 8597 4.185491723466407 +83 2067 8628 4.174165457184325 +84 1953 8577 4.391705069124424 +85 2037 8535 4.1899852724594995 +86 2024 8638 4.267786561264822 +87 2016 8633 4.282242063492063 +88 2047 8633 4.217391304347826 +89 1986 8585 4.322759315206445 +90 2067 8641 4.180454765360426 +91 2019 8590 4.254581475978207 +92 1973 8529 4.322858590978206 +93 2002 8566 4.278721278721279 +94 2024 8638 4.267786561264822 +95 2029 8538 4.207984228684081 +96 1948 8505 4.366016427104722 +97 2048 8624 4.2109375 +98 2005 8531 4.254862842892768 +99 1961 8595 4.382967873533912 diff --git a/Analysis/simulations/binomial_growth/results/58.metrics.tsv b/Analysis/simulations/binomial_growth/results/58.metrics.tsv new file mode 100644 index 00000000..9709bba0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/58.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.7830250332644436 0.787164944109265 0.7865745717406223 0.7808403878926043 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4.281156530408774 +90 2011 8630 4.291397314768772 +91 1973 8513 4.314749113025849 +92 2003 8552 4.269595606590115 +93 1938 8508 4.390092879256966 +94 2077 8642 4.1608088589311505 +95 1957 8559 4.373530914665304 +96 2012 8596 4.272365805168986 +97 2015 8524 4.230272952853598 +98 2024 8655 4.276185770750988 +99 1958 8485 4.333503575076609 diff --git a/Analysis/simulations/binomial_growth/results/59.metrics.tsv b/Analysis/simulations/binomial_growth/results/59.metrics.tsv new file mode 100644 index 00000000..6f26b28e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/59.metrics.tsv @@ -0,0 +1,3 @@ + 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.6059388806530726 0.6152794033354653 0.6121232132305031 0.6154419285302127 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0.0 0.0 0.0 0.0 0.0 diff --git a/Analysis/simulations/binomial_growth/results/6.rocs.p b/Analysis/simulations/binomial_growth/results/6.rocs.p new file mode 100644 index 00000000..85df67c8 Binary files /dev/null and b/Analysis/simulations/binomial_growth/results/6.rocs.p differ diff --git a/Analysis/simulations/binomial_growth/results/60.before_after.tsv b/Analysis/simulations/binomial_growth/results/60.before_after.tsv new file mode 100644 index 00000000..d31111fd --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/60.before_after.tsv @@ -0,0 +1,101 @@ + Before After A/B +0 1998 8530 4.2692692692692695 +1 2042 8517 4.170910871694417 +2 1886 8424 4.466595970307529 +3 2017 8647 4.287059990084283 +4 1952 8545 4.377561475409836 +5 1991 8542 4.290306378704169 +6 2032 8578 4.221456692913386 +7 1989 8519 4.283056812468577 +8 1983 8560 4.316691880988402 +9 1954 8545 4.373080859774821 +10 1967 8544 4.343670564311133 +11 2035 8690 4.27027027027027 +12 2034 8588 4.222222222222222 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1982 8500 4.288597376387488 +44 1987 8543 4.299446401610468 +45 1974 8513 4.312563323201621 +46 2069 8678 4.194296761720638 +47 1995 8534 4.277694235588973 +48 2020 8597 4.255940594059406 +49 1960 8523 4.348469387755102 +50 2022 8616 4.261127596439169 +51 2024 8524 4.211462450592886 +52 1979 8548 4.3193532086912585 +53 1986 8563 4.311681772406848 +54 2012 8577 4.262922465208748 +55 1974 8417 4.263931104356637 +56 2051 8594 4.190151145782545 +57 2033 8546 4.20363994097393 +58 2020 8570 4.242574257425742 +59 1940 8534 4.398969072164949 +60 2006 8522 4.248255234297108 +61 1989 8616 4.33182503770739 +62 2013 8609 4.2767014406358665 +63 2006 8535 4.254735792622133 +64 1994 8528 4.276830491474423 +65 2049 8595 4.194729136163982 +66 1977 8567 4.333333333333333 +67 1900 8543 4.496315789473684 +68 1970 8505 4.317258883248731 +69 2007 8532 4.251121076233184 +70 2013 8653 4.298559364133134 +71 2014 8534 4.23733862959285 +72 1998 8584 4.296296296296297 +73 1987 8610 4.333165576245596 +74 1996 8510 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72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 +Precision 0.8525566339025563 0.8646674582750176 0.851935249192989 0.8531685138881617 0.8570605490407722 0.8590919738774522 0.8571898352210846 0.8539007264149324 0.852406448504205 0.8465038560214712 0.8523784725363192 0.848610823652626 0.8543970937502298 0.8527463638182937 0.8511459871465209 0.8574588308452995 0.8508680216596024 0.8524580432751876 0.854419013623664 0.8573237894757098 0.8554391886008348 0.8465802593725268 0.8507693801508952 0.8545598721100695 0.8540183656351316 0.8548749917963718 0.8555972443804778 0.8491340612185728 0.8489480981437223 0.8507540660907478 0.8460244653627765 0.8531415355726817 0.8492554213440868 0.8544332803768896 0.8512173144696793 0.8522071887063261 0.8526669049504937 0.8541465886902818 0.8544072177649854 0.8550309345144557 0.8511911128021364 0.8554720009850447 0.8552953887689853 0.8474689693962689 0.8574981370369523 0.8523752998650935 0.8576407213773114 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0.00175 0.0013 0.00195 0.0013 0.0018 0.0013 diff --git a/Analysis/simulations/binomial_growth/results/99.rocs.p b/Analysis/simulations/binomial_growth/results/99.rocs.p new file mode 100644 index 00000000..afb7bd8b Binary files /dev/null and b/Analysis/simulations/binomial_growth/results/99.rocs.p differ diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/0.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/0.yaml new file mode 100644 index 00000000..c375af34 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/0.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '0' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/1.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/1.yaml new file mode 100644 index 00000000..a328a05d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/1.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '1' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/10.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/10.yaml new file mode 100644 index 00000000..83d7f209 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/10.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '10' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/100.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/100.yaml new file mode 100644 index 00000000..eb515d45 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/100.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '100' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/101.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/101.yaml new file mode 100644 index 00000000..66b9929e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/101.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '101' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/102.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/102.yaml new file mode 100644 index 00000000..ab90e92c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/102.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '102' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/103.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/103.yaml new file mode 100644 index 00000000..31b20ec0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/103.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '103' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/104.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/104.yaml new file mode 100644 index 00000000..7498def6 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/104.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '104' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/105.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/105.yaml new file mode 100644 index 00000000..3677ffa0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/105.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '105' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/106.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/106.yaml new file mode 100644 index 00000000..bbc13eab --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/106.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '106' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/107.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/107.yaml new file mode 100644 index 00000000..ad362fb2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/107.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '107' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/108.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/108.yaml new file mode 100644 index 00000000..078ef572 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/108.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '108' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/109.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/109.yaml new file mode 100644 index 00000000..bdf929e8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/109.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '109' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/11.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/11.yaml new file mode 100644 index 00000000..d5672939 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/11.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '11' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/110.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/110.yaml new file mode 100644 index 00000000..cb5ba944 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/110.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '110' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/111.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/111.yaml new file mode 100644 index 00000000..d410ebd5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/111.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '111' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/112.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/112.yaml new file mode 100644 index 00000000..d32ec9ad --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/112.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '112' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/113.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/113.yaml new file mode 100644 index 00000000..e2863a7e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/113.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '113' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/114.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/114.yaml new file mode 100644 index 00000000..525a5712 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/114.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '114' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/115.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/115.yaml new file mode 100644 index 00000000..cae5e190 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/115.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '115' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/116.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/116.yaml new file mode 100644 index 00000000..7fbd38f5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/116.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '116' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/117.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/117.yaml new file mode 100644 index 00000000..e5d3c34b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/117.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '117' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/118.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/118.yaml new file mode 100644 index 00000000..1eb8845f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/118.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '118' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/119.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/119.yaml new file mode 100644 index 00000000..11680684 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/119.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '119' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/12.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/12.yaml new file mode 100644 index 00000000..c2b538ae --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/12.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '12' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/120.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/120.yaml new file mode 100644 index 00000000..a015de0f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/120.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '120' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/121.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/121.yaml new file mode 100644 index 00000000..16d5f7ae --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/121.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '121' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/122.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/122.yaml new file mode 100644 index 00000000..24a92039 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/122.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '122' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/123.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/123.yaml new file mode 100644 index 00000000..51eb3c71 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/123.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '123' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/124.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/124.yaml new file mode 100644 index 00000000..0824a5cc --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/124.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '124' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/125.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/125.yaml new file mode 100644 index 00000000..2c82b34c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/125.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '125' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/126.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/126.yaml new file mode 100644 index 00000000..d00def68 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/126.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '126' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/127.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/127.yaml new file mode 100644 index 00000000..571210cb --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/127.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '127' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/128.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/128.yaml new file mode 100644 index 00000000..16df0425 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/128.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '128' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/129.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/129.yaml new file mode 100644 index 00000000..45fcb83d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/129.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '129' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/13.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/13.yaml new file mode 100644 index 00000000..e9f7a8b7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/13.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '13' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/130.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/130.yaml new file mode 100644 index 00000000..d4381a03 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/130.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '130' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/131.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/131.yaml new file mode 100644 index 00000000..be12b88b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/131.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '131' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/132.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/132.yaml new file mode 100644 index 00000000..0c08f954 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/132.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '132' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/133.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/133.yaml new file mode 100644 index 00000000..ccb1e593 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/133.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '133' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/134.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/134.yaml new file mode 100644 index 00000000..0cc5cbbc --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/134.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '134' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/135.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/135.yaml new file mode 100644 index 00000000..f178aed3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/135.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '135' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/136.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/136.yaml new file mode 100644 index 00000000..efb61283 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/136.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '136' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/137.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/137.yaml new file mode 100644 index 00000000..64e6ffe4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/137.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '137' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/138.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/138.yaml new file mode 100644 index 00000000..80b5b101 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/138.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '138' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/139.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/139.yaml new file mode 100644 index 00000000..ffaaaa32 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/139.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '139' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/14.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/14.yaml new file mode 100644 index 00000000..229cf97f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/14.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '14' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/140.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/140.yaml new file mode 100644 index 00000000..587dbb07 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/140.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '140' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/141.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/141.yaml new file mode 100644 index 00000000..e6424414 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/141.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '141' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/142.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/142.yaml new file mode 100644 index 00000000..fe335200 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/142.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '142' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/143.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/143.yaml new file mode 100644 index 00000000..980ebe32 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/143.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '143' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/144.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/144.yaml new file mode 100644 index 00000000..1b051738 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/144.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '144' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/145.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/145.yaml new file mode 100644 index 00000000..c30d4a03 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/145.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '145' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/146.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/146.yaml new file mode 100644 index 00000000..83af3fd7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/146.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '146' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/147.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/147.yaml new file mode 100644 index 00000000..764d8819 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/147.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '147' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/148.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/148.yaml new file mode 100644 index 00000000..eb520b93 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/148.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '148' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/149.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/149.yaml new file mode 100644 index 00000000..8f8e411e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/149.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '149' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/15.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/15.yaml new file mode 100644 index 00000000..baadf2d0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/15.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '15' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/150.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/150.yaml new file mode 100644 index 00000000..4d02c7ff --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/150.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '150' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/151.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/151.yaml new file mode 100644 index 00000000..2bf18cc4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/151.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '151' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/152.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/152.yaml new file mode 100644 index 00000000..afb6308b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/152.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '152' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/153.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/153.yaml new file mode 100644 index 00000000..131c5cf4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/153.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '153' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/154.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/154.yaml new file mode 100644 index 00000000..10ef2f42 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/154.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '154' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/155.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/155.yaml new file mode 100644 index 00000000..ac9de608 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/155.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '155' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/156.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/156.yaml new file mode 100644 index 00000000..49b4a033 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/156.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '156' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/157.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/157.yaml new file mode 100644 index 00000000..c36aee1f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/157.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '157' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/158.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/158.yaml new file mode 100644 index 00000000..d8011cab --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/158.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '158' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/159.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/159.yaml new file mode 100644 index 00000000..56220950 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/159.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '159' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/16.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/16.yaml new file mode 100644 index 00000000..5eb5bdb5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/16.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '16' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/160.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/160.yaml new file mode 100644 index 00000000..4e34fd03 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/160.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '160' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/161.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/161.yaml new file mode 100644 index 00000000..e3de0b84 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/161.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '161' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/162.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/162.yaml new file mode 100644 index 00000000..74b44e88 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/162.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '162' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/163.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/163.yaml new file mode 100644 index 00000000..555b588b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/163.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '163' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/164.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/164.yaml new file mode 100644 index 00000000..b7e1b661 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/164.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '164' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/165.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/165.yaml new file mode 100644 index 00000000..55601bb0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/165.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '165' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/166.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/166.yaml new file mode 100644 index 00000000..ba3f4830 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/166.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '166' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/167.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/167.yaml new file mode 100644 index 00000000..46dfcb8c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/167.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '167' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/168.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/168.yaml new file mode 100644 index 00000000..3eb5890c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/168.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '168' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/169.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/169.yaml new file mode 100644 index 00000000..808ef705 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/169.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '169' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/17.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/17.yaml new file mode 100644 index 00000000..99878e62 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/17.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '17' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/170.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/170.yaml new file mode 100644 index 00000000..87cd9e8b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/170.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '170' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/171.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/171.yaml new file mode 100644 index 00000000..d451a31c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/171.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '171' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/172.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/172.yaml new file mode 100644 index 00000000..f6f9a934 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/172.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '172' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/173.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/173.yaml new file mode 100644 index 00000000..c71dfa71 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/173.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '173' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/174.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/174.yaml new file mode 100644 index 00000000..15068ed1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/174.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '174' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/175.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/175.yaml new file mode 100644 index 00000000..9ee3a00e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/175.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '175' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/176.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/176.yaml new file mode 100644 index 00000000..d522fcf3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/176.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '176' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/177.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/177.yaml new file mode 100644 index 00000000..46634e4d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/177.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '177' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/178.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/178.yaml new file mode 100644 index 00000000..7060266d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/178.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '178' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/179.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/179.yaml new file mode 100644 index 00000000..cea74524 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/179.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '179' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/18.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/18.yaml new file mode 100644 index 00000000..de19a071 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/18.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '18' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/180.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/180.yaml new file mode 100644 index 00000000..5943d289 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/180.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '180' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/181.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/181.yaml new file mode 100644 index 00000000..8c01a2ee --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/181.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '181' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/182.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/182.yaml new file mode 100644 index 00000000..74a140b8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/182.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '182' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/183.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/183.yaml new file mode 100644 index 00000000..8405ac8d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/183.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '183' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/184.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/184.yaml new file mode 100644 index 00000000..b385876a --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/184.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '184' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/185.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/185.yaml new file mode 100644 index 00000000..fe2d993b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/185.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '185' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/186.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/186.yaml new file mode 100644 index 00000000..e25c18a7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/186.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '186' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/187.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/187.yaml new file mode 100644 index 00000000..ba94a9e3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/187.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '187' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/188.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/188.yaml new file mode 100644 index 00000000..ba598865 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/188.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '188' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/189.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/189.yaml new file mode 100644 index 00000000..443df494 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/189.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '189' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/19.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/19.yaml new file mode 100644 index 00000000..9250565d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/19.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '19' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/190.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/190.yaml new file mode 100644 index 00000000..1b4eb327 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/190.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '190' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/191.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/191.yaml new file mode 100644 index 00000000..56f361f4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/191.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '191' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/192.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/192.yaml new file mode 100644 index 00000000..6e28c505 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/192.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '192' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/193.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/193.yaml new file mode 100644 index 00000000..b95c11bb --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/193.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '193' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/194.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/194.yaml new file mode 100644 index 00000000..17eac4f0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/194.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '194' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/195.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/195.yaml new file mode 100644 index 00000000..d90c4be3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/195.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '195' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/196.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/196.yaml new file mode 100644 index 00000000..cf0d9390 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/196.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '196' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/197.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/197.yaml new file mode 100644 index 00000000..9718d4e7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/197.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '197' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/198.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/198.yaml new file mode 100644 index 00000000..e83bc1ce --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/198.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '198' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/199.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/199.yaml new file mode 100644 index 00000000..6088ec41 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/199.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '199' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/2.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/2.yaml new file mode 100644 index 00000000..ce0e10c3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/2.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '2' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/20.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/20.yaml new file mode 100644 index 00000000..3cacc2bf --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/20.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '20' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/200.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/200.yaml new file mode 100644 index 00000000..8adf1314 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/200.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '200' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/201.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/201.yaml new file mode 100644 index 00000000..2770f30d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/201.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '201' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/202.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/202.yaml new file mode 100644 index 00000000..ed3af130 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/202.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '202' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/203.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/203.yaml new file mode 100644 index 00000000..f71ccce7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/203.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '203' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/204.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/204.yaml new file mode 100644 index 00000000..37c5a418 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/204.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '204' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/205.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/205.yaml new file mode 100644 index 00000000..8331ec3e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/205.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '205' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/206.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/206.yaml new file mode 100644 index 00000000..ee112199 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/206.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '206' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/207.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/207.yaml new file mode 100644 index 00000000..ac7d09ca --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/207.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '207' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/208.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/208.yaml new file mode 100644 index 00000000..79181ade --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/208.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '208' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/209.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/209.yaml new file mode 100644 index 00000000..a69a89b0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/209.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '209' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/21.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/21.yaml new file mode 100644 index 00000000..c5b9d74c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/21.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '21' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/210.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/210.yaml new file mode 100644 index 00000000..0164184e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/210.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '210' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/211.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/211.yaml new file mode 100644 index 00000000..156b8005 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/211.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '211' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/212.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/212.yaml new file mode 100644 index 00000000..d9c176c3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/212.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '212' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/213.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/213.yaml new file mode 100644 index 00000000..304ec932 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/213.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '213' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/214.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/214.yaml new file mode 100644 index 00000000..bb9297c0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/214.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '214' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/215.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/215.yaml new file mode 100644 index 00000000..4895f20b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/215.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '215' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/216.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/216.yaml new file mode 100644 index 00000000..0fe9d535 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/216.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '216' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/217.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/217.yaml new file mode 100644 index 00000000..0bce3dfd --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/217.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '217' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/218.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/218.yaml new file mode 100644 index 00000000..af57999d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/218.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '218' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/219.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/219.yaml new file mode 100644 index 00000000..e722bce9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/219.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '219' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/22.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/22.yaml new file mode 100644 index 00000000..2c4eda39 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/22.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '22' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/220.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/220.yaml new file mode 100644 index 00000000..4c15c21c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/220.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '220' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/221.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/221.yaml new file mode 100644 index 00000000..986d24b9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/221.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '221' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/222.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/222.yaml new file mode 100644 index 00000000..22f2211c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/222.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '222' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/223.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/223.yaml new file mode 100644 index 00000000..89acba32 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/223.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '223' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/224.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/224.yaml new file mode 100644 index 00000000..6e744ef3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/224.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '224' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/225.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/225.yaml new file mode 100644 index 00000000..392247d7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/225.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '225' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/226.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/226.yaml new file mode 100644 index 00000000..606eb277 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/226.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '226' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/227.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/227.yaml new file mode 100644 index 00000000..0228684c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/227.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '227' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/228.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/228.yaml new file mode 100644 index 00000000..4e9a1ce0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/228.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '228' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/229.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/229.yaml new file mode 100644 index 00000000..9414ccd5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/229.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '229' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/23.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/23.yaml new file mode 100644 index 00000000..5b322b2f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/23.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '23' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/230.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/230.yaml new file mode 100644 index 00000000..9e970a99 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/230.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '230' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/231.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/231.yaml new file mode 100644 index 00000000..f0e12f06 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/231.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '231' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/232.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/232.yaml new file mode 100644 index 00000000..fafc146b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/232.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '232' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/233.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/233.yaml new file mode 100644 index 00000000..96e91d15 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/233.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '233' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/234.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/234.yaml new file mode 100644 index 00000000..05e8ff11 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/234.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '234' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/235.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/235.yaml new file mode 100644 index 00000000..de3a2d48 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/235.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '235' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/236.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/236.yaml new file mode 100644 index 00000000..88b37ff2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/236.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '236' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/237.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/237.yaml new file mode 100644 index 00000000..977e5d50 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/237.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '237' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/238.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/238.yaml new file mode 100644 index 00000000..4b9319f8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/238.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '238' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/239.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/239.yaml new file mode 100644 index 00000000..1f5a570c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/239.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '239' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/24.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/24.yaml new file mode 100644 index 00000000..d1412742 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/24.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '24' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/240.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/240.yaml new file mode 100644 index 00000000..3fcbcf04 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/240.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '240' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/241.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/241.yaml new file mode 100644 index 00000000..2c2f5e0d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/241.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '241' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/242.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/242.yaml new file mode 100644 index 00000000..acac6d7c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/242.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '242' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/243.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/243.yaml new file mode 100644 index 00000000..a1b95242 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/243.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '243' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/244.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/244.yaml new file mode 100644 index 00000000..52c00c3a --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/244.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '244' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/245.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/245.yaml new file mode 100644 index 00000000..24a2eca8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/245.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '245' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/246.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/246.yaml new file mode 100644 index 00000000..b43b8556 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/246.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '246' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/247.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/247.yaml new file mode 100644 index 00000000..cb9a688c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/247.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '247' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/248.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/248.yaml new file mode 100644 index 00000000..e244d868 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/248.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '248' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/249.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/249.yaml new file mode 100644 index 00000000..de2450b9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/249.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '249' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/25.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/25.yaml new file mode 100644 index 00000000..7b7b59d0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/25.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '25' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/250.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/250.yaml new file mode 100644 index 00000000..dae3c6be --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/250.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '250' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/251.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/251.yaml new file mode 100644 index 00000000..ebead49c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/251.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '251' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/252.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/252.yaml new file mode 100644 index 00000000..735e6fbc --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/252.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '252' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/253.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/253.yaml new file mode 100644 index 00000000..6046b207 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/253.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '253' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/254.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/254.yaml new file mode 100644 index 00000000..8e729fa7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/254.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '254' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/255.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/255.yaml new file mode 100644 index 00000000..86914f06 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/255.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '255' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/256.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/256.yaml new file mode 100644 index 00000000..779935e8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/256.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '256' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/257.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/257.yaml new file mode 100644 index 00000000..55fd1146 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/257.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '257' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/258.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/258.yaml new file mode 100644 index 00000000..9e145d30 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/258.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '258' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/259.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/259.yaml new file mode 100644 index 00000000..7cb40e6a --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/259.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '259' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/26.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/26.yaml new file mode 100644 index 00000000..5d985446 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/26.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '26' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/260.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/260.yaml new file mode 100644 index 00000000..d643e5db --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/260.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '260' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/261.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/261.yaml new file mode 100644 index 00000000..488e9684 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/261.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '261' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/262.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/262.yaml new file mode 100644 index 00000000..08d265f0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/262.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '262' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/263.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/263.yaml new file mode 100644 index 00000000..dfaf58b4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/263.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '263' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/264.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/264.yaml new file mode 100644 index 00000000..7a78871d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/264.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '264' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/265.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/265.yaml new file mode 100644 index 00000000..9eb9d8c5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/265.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '265' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/266.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/266.yaml new file mode 100644 index 00000000..2c6d0801 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/266.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '266' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/267.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/267.yaml new file mode 100644 index 00000000..1caa76c2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/267.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '267' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/268.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/268.yaml new file mode 100644 index 00000000..43803fba --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/268.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '268' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/269.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/269.yaml new file mode 100644 index 00000000..89bb7434 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/269.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '269' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/27.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/27.yaml new file mode 100644 index 00000000..a9a7594a --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/27.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '27' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/270.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/270.yaml new file mode 100644 index 00000000..914d653c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/270.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '270' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/271.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/271.yaml new file mode 100644 index 00000000..01b68722 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/271.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '271' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/272.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/272.yaml new file mode 100644 index 00000000..3ffa744a --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/272.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '272' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/273.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/273.yaml new file mode 100644 index 00000000..a7667f82 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/273.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '273' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/274.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/274.yaml new file mode 100644 index 00000000..7639abaf --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/274.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '274' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/275.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/275.yaml new file mode 100644 index 00000000..6a1f3d27 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/275.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '275' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/276.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/276.yaml new file mode 100644 index 00000000..a3ab3dc7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/276.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '276' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/277.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/277.yaml new file mode 100644 index 00000000..f4a72f97 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/277.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '277' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/278.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/278.yaml new file mode 100644 index 00000000..abbfb6bf --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/278.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '278' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/279.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/279.yaml new file mode 100644 index 00000000..b1d664d7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/279.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '279' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/28.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/28.yaml new file mode 100644 index 00000000..9e37e3eb --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/28.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '28' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/280.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/280.yaml new file mode 100644 index 00000000..c5f73233 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/280.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '280' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/281.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/281.yaml new file mode 100644 index 00000000..386f87a2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/281.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '281' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/282.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/282.yaml new file mode 100644 index 00000000..9026e39d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/282.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '282' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/283.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/283.yaml new file mode 100644 index 00000000..34dc9fe1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/283.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '283' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/284.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/284.yaml new file mode 100644 index 00000000..36281b20 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/284.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '284' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/285.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/285.yaml new file mode 100644 index 00000000..5e4d7bfc --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/285.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '285' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/286.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/286.yaml new file mode 100644 index 00000000..55606be0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/286.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '286' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/287.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/287.yaml new file mode 100644 index 00000000..00c99060 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/287.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 50.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '287' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/288.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/288.yaml new file mode 100644 index 00000000..ecba5786 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/288.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '288' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/289.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/289.yaml new file mode 100644 index 00000000..7bd8acaa --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/289.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '289' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/29.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/29.yaml new file mode 100644 index 00000000..78e71970 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/29.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '29' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/290.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/290.yaml new file mode 100644 index 00000000..9f549657 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/290.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '290' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/291.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/291.yaml new file mode 100644 index 00000000..bbdb5d53 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/291.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '291' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/292.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/292.yaml new file mode 100644 index 00000000..aee90427 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/292.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '292' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/293.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/293.yaml new file mode 100644 index 00000000..b3d667d1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/293.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '293' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/294.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/294.yaml new file mode 100644 index 00000000..99e0e5f1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/294.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '294' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/295.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/295.yaml new file mode 100644 index 00000000..d4b012f7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/295.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '295' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/296.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/296.yaml new file mode 100644 index 00000000..a22f9d47 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/296.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '296' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/297.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/297.yaml new file mode 100644 index 00000000..b4b96346 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/297.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '297' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/298.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/298.yaml new file mode 100644 index 00000000..b6660f62 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/298.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '298' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/299.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/299.yaml new file mode 100644 index 00000000..5a99e063 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/299.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '299' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/3.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/3.yaml new file mode 100644 index 00000000..c221c388 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/3.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '3' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/30.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/30.yaml new file mode 100644 index 00000000..f0b4f364 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/30.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '30' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/300.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/300.yaml new file mode 100644 index 00000000..52b024e7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/300.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '300' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/301.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/301.yaml new file mode 100644 index 00000000..15c6f533 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/301.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '301' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/302.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/302.yaml new file mode 100644 index 00000000..0f6bc0ce --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/302.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '302' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/303.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/303.yaml new file mode 100644 index 00000000..72034efd --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/303.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '303' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/304.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/304.yaml new file mode 100644 index 00000000..2b08b912 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/304.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '304' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/305.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/305.yaml new file mode 100644 index 00000000..aacf4db9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/305.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '305' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/306.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/306.yaml new file mode 100644 index 00000000..4559003d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/306.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '306' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/307.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/307.yaml new file mode 100644 index 00000000..2c9626e7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/307.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '307' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/308.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/308.yaml new file mode 100644 index 00000000..f82605c2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/308.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '308' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/309.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/309.yaml new file mode 100644 index 00000000..9dcc9f3d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/309.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '309' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/31.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/31.yaml new file mode 100644 index 00000000..6118aa97 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/31.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '31' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/310.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/310.yaml new file mode 100644 index 00000000..316a95a1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/310.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '310' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/311.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/311.yaml new file mode 100644 index 00000000..458ea285 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/311.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '311' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/312.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/312.yaml new file mode 100644 index 00000000..4831b547 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/312.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '312' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/313.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/313.yaml new file mode 100644 index 00000000..2d90045e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/313.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '313' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/314.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/314.yaml new file mode 100644 index 00000000..4731f299 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/314.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '314' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/315.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/315.yaml new file mode 100644 index 00000000..9d7da1af --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/315.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '315' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/316.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/316.yaml new file mode 100644 index 00000000..086f588d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/316.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '316' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/317.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/317.yaml new file mode 100644 index 00000000..b2c6881a --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/317.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '317' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/318.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/318.yaml new file mode 100644 index 00000000..fe1e8570 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/318.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '318' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/319.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/319.yaml new file mode 100644 index 00000000..d76916cd --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/319.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '319' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/32.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/32.yaml new file mode 100644 index 00000000..01b39feb --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/32.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '32' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/320.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/320.yaml new file mode 100644 index 00000000..69bf0ad5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/320.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '320' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/321.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/321.yaml new file mode 100644 index 00000000..543ae3ef --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/321.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '321' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/322.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/322.yaml new file mode 100644 index 00000000..fbf71251 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/322.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '322' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/323.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/323.yaml new file mode 100644 index 00000000..b4716007 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/323.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '323' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/324.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/324.yaml new file mode 100644 index 00000000..dc1239df --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/324.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '324' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/325.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/325.yaml new file mode 100644 index 00000000..dc366820 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/325.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '325' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/326.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/326.yaml new file mode 100644 index 00000000..7497115b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/326.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '326' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/327.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/327.yaml new file mode 100644 index 00000000..af4778c0 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/327.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '327' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/328.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/328.yaml new file mode 100644 index 00000000..5c62ec03 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/328.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '328' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/329.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/329.yaml new file mode 100644 index 00000000..7eb26206 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/329.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '329' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/33.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/33.yaml new file mode 100644 index 00000000..dffcfb81 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/33.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '33' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/330.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/330.yaml new file mode 100644 index 00000000..6c6fbfd8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/330.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '330' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/331.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/331.yaml new file mode 100644 index 00000000..e920914d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/331.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '331' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/332.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/332.yaml new file mode 100644 index 00000000..a12b650f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/332.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '332' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/333.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/333.yaml new file mode 100644 index 00000000..c87a1af6 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/333.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '333' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/334.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/334.yaml new file mode 100644 index 00000000..f3f0caae --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/334.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '334' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/335.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/335.yaml new file mode 100644 index 00000000..4d34f7ba --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/335.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '335' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/336.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/336.yaml new file mode 100644 index 00000000..16caf37b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/336.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '336' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/337.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/337.yaml new file mode 100644 index 00000000..74076afe --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/337.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '337' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/338.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/338.yaml new file mode 100644 index 00000000..1db3dfb1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/338.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '338' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/339.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/339.yaml new file mode 100644 index 00000000..af51fa04 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/339.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '339' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/34.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/34.yaml new file mode 100644 index 00000000..0832ece3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/34.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '34' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/340.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/340.yaml new file mode 100644 index 00000000..e7c2d23d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/340.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '340' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/341.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/341.yaml new file mode 100644 index 00000000..b7385e78 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/341.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '341' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/342.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/342.yaml new file mode 100644 index 00000000..417e4df7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/342.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '342' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/343.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/343.yaml new file mode 100644 index 00000000..3bf8db76 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/343.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '343' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/344.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/344.yaml new file mode 100644 index 00000000..4c335fd6 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/344.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '344' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/345.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/345.yaml new file mode 100644 index 00000000..41b3f8d8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/345.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '345' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/346.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/346.yaml new file mode 100644 index 00000000..6dc93268 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/346.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '346' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/347.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/347.yaml new file mode 100644 index 00000000..65a1304d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/347.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '347' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/348.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/348.yaml new file mode 100644 index 00000000..fa612ac6 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/348.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '348' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/349.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/349.yaml new file mode 100644 index 00000000..6f39782a --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/349.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '349' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/35.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/35.yaml new file mode 100644 index 00000000..a0de5c96 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/35.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '35' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/350.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/350.yaml new file mode 100644 index 00000000..f35c54a1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/350.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '350' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/351.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/351.yaml new file mode 100644 index 00000000..49be2b39 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/351.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '351' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/352.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/352.yaml new file mode 100644 index 00000000..734984a1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/352.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '352' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/353.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/353.yaml new file mode 100644 index 00000000..e2443669 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/353.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '353' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/354.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/354.yaml new file mode 100644 index 00000000..8aab9602 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/354.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '354' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/355.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/355.yaml new file mode 100644 index 00000000..39cdd644 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/355.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '355' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/356.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/356.yaml new file mode 100644 index 00000000..20502d9c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/356.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '356' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/357.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/357.yaml new file mode 100644 index 00000000..a323c496 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/357.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '357' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/358.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/358.yaml new file mode 100644 index 00000000..a4235cb8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/358.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '358' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/359.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/359.yaml new file mode 100644 index 00000000..e425492b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/359.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '359' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/36.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/36.yaml new file mode 100644 index 00000000..69c8ad34 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/36.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '36' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/360.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/360.yaml new file mode 100644 index 00000000..b90c6827 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/360.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '360' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/361.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/361.yaml new file mode 100644 index 00000000..1c81fbed --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/361.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '361' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/362.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/362.yaml new file mode 100644 index 00000000..421d7d67 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/362.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '362' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/363.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/363.yaml new file mode 100644 index 00000000..7cd4ce19 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/363.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '363' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/364.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/364.yaml new file mode 100644 index 00000000..c353c3d3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/364.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '364' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/365.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/365.yaml new file mode 100644 index 00000000..8496218b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/365.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '365' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/366.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/366.yaml new file mode 100644 index 00000000..9eccff27 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/366.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '366' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/367.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/367.yaml new file mode 100644 index 00000000..03147472 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/367.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '367' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/368.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/368.yaml new file mode 100644 index 00000000..224830fa --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/368.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '368' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/369.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/369.yaml new file mode 100644 index 00000000..bbe45947 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/369.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '369' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/37.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/37.yaml new file mode 100644 index 00000000..67fa81ad --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/37.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '37' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/370.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/370.yaml new file mode 100644 index 00000000..59863184 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/370.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '370' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/371.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/371.yaml new file mode 100644 index 00000000..91cf628d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/371.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '371' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/372.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/372.yaml new file mode 100644 index 00000000..c9ca26da --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/372.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '372' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/373.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/373.yaml new file mode 100644 index 00000000..15c5104f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/373.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '373' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/374.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/374.yaml new file mode 100644 index 00000000..db2fd184 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/374.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '374' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/375.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/375.yaml new file mode 100644 index 00000000..6f74aceb --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/375.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '375' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/376.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/376.yaml new file mode 100644 index 00000000..00878bf1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/376.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '376' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/377.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/377.yaml new file mode 100644 index 00000000..aeb12111 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/377.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '377' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/378.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/378.yaml new file mode 100644 index 00000000..7819ddff --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/378.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '378' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/379.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/379.yaml new file mode 100644 index 00000000..9a8f197f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/379.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '379' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/38.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/38.yaml new file mode 100644 index 00000000..3269ec46 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/38.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '38' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/380.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/380.yaml new file mode 100644 index 00000000..5d2821d2 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/380.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '380' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/381.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/381.yaml new file mode 100644 index 00000000..93b85d15 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/381.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '381' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/382.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/382.yaml new file mode 100644 index 00000000..9631f7cc --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/382.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '382' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/383.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/383.yaml new file mode 100644 index 00000000..5edc87db --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/383.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 100.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '383' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/39.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/39.yaml new file mode 100644 index 00000000..99c93547 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/39.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '39' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/4.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/4.yaml new file mode 100644 index 00000000..db8b92a7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/4.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '4' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/40.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/40.yaml new file mode 100644 index 00000000..4c5d2478 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/40.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '40' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/41.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/41.yaml new file mode 100644 index 00000000..18710a46 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/41.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '41' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/42.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/42.yaml new file mode 100644 index 00000000..7eb7796b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/42.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '42' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/43.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/43.yaml new file mode 100644 index 00000000..96ded543 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/43.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '43' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/44.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/44.yaml new file mode 100644 index 00000000..9ff1c3bd --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/44.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '44' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/45.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/45.yaml new file mode 100644 index 00000000..a1973de9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/45.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '45' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/46.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/46.yaml new file mode 100644 index 00000000..6e4701b3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/46.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '46' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/47.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/47.yaml new file mode 100644 index 00000000..e4ac67c5 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/47.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.8 + - 0.1 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '47' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/48.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/48.yaml new file mode 100644 index 00000000..4046ddda --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/48.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '48' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/49.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/49.yaml new file mode 100644 index 00000000..259c4611 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/49.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '49' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/5.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/5.yaml new file mode 100644 index 00000000..9bd4a3ab --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/5.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '5' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/50.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/50.yaml new file mode 100644 index 00000000..b2352218 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/50.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '50' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/51.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/51.yaml new file mode 100644 index 00000000..4fb2b47d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/51.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '51' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/52.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/52.yaml new file mode 100644 index 00000000..0d63579f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/52.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '52' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/53.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/53.yaml new file mode 100644 index 00000000..2bdc322b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/53.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '53' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/54.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/54.yaml new file mode 100644 index 00000000..d7515152 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/54.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '54' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/55.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/55.yaml new file mode 100644 index 00000000..42f37287 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/55.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '55' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/56.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/56.yaml new file mode 100644 index 00000000..5da03481 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/56.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '56' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/57.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/57.yaml new file mode 100644 index 00000000..c8c5ccdd --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/57.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '57' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/58.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/58.yaml new file mode 100644 index 00000000..0b32ed8f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/58.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '58' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/59.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/59.yaml new file mode 100644 index 00000000..c4a8f2c3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/59.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '59' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/6.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/6.yaml new file mode 100644 index 00000000..9f1446b3 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/6.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '6' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/60.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/60.yaml new file mode 100644 index 00000000..0389f34d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/60.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '60' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/61.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/61.yaml new file mode 100644 index 00000000..02baf86f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/61.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '61' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/62.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/62.yaml new file mode 100644 index 00000000..27959bf9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/62.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '62' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/63.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/63.yaml new file mode 100644 index 00000000..2ea1bec7 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/63.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '63' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/64.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/64.yaml new file mode 100644 index 00000000..be37fbf4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/64.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '64' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/65.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/65.yaml new file mode 100644 index 00000000..591af70e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/65.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '65' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/66.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/66.yaml new file mode 100644 index 00000000..6b4a62d6 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/66.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '66' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/67.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/67.yaml new file mode 100644 index 00000000..86c569fa --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/67.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '67' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/68.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/68.yaml new file mode 100644 index 00000000..60b74fd8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/68.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '68' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/69.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/69.yaml new file mode 100644 index 00000000..09c63955 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/69.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '69' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/7.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/7.yaml new file mode 100644 index 00000000..04cd2261 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/7.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '7' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/70.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/70.yaml new file mode 100644 index 00000000..0d904972 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/70.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '70' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/71.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/71.yaml new file mode 100644 index 00000000..a074aad6 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/71.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.7 + - 0.2 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '71' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/72.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/72.yaml new file mode 100644 index 00000000..8280f59c --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/72.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '72' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/73.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/73.yaml new file mode 100644 index 00000000..99bab7ee --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/73.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '73' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/74.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/74.yaml new file mode 100644 index 00000000..bb49b94d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/74.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '74' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/75.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/75.yaml new file mode 100644 index 00000000..5b1d0860 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/75.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '75' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/76.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/76.yaml new file mode 100644 index 00000000..a7d3ffa6 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/76.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '76' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/77.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/77.yaml new file mode 100644 index 00000000..5e42ccbd --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/77.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '77' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/78.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/78.yaml new file mode 100644 index 00000000..00a5cf6d --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/78.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '78' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/79.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/79.yaml new file mode 100644 index 00000000..d32c3727 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/79.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '79' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/8.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/8.yaml new file mode 100644 index 00000000..247683b4 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/8.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '8' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/80.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/80.yaml new file mode 100644 index 00000000..c690426f --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/80.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '80' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/81.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/81.yaml new file mode 100644 index 00000000..ad04f821 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/81.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '81' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/82.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/82.yaml new file mode 100644 index 00000000..21c673f8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/82.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '82' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/83.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/83.yaml new file mode 100644 index 00000000..754a9cf1 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/83.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '83' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/84.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/84.yaml new file mode 100644 index 00000000..ed3cde7e --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/84.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '84' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/85.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/85.yaml new file mode 100644 index 00000000..b4775887 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/85.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '85' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/86.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/86.yaml new file mode 100644 index 00000000..90f41897 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/86.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '86' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/87.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/87.yaml new file mode 100644 index 00000000..ef972307 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/87.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '87' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/88.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/88.yaml new file mode 100644 index 00000000..45dc980b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/88.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '88' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/89.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/89.yaml new file mode 100644 index 00000000..b67a3b57 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/89.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '89' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/9.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/9.yaml new file mode 100644 index 00000000..2e723d37 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/9.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.5 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '9' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/90.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/90.yaml new file mode 100644 index 00000000..66eda869 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/90.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '90' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/91.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/91.yaml new file mode 100644 index 00000000..2560c187 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/91.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '91' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/92.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/92.yaml new file mode 100644 index 00000000..ff99a9a9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/92.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '92' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/93.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/93.yaml new file mode 100644 index 00000000..45cf839b --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/93.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.5 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '93' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/94.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/94.yaml new file mode 100644 index 00000000..4435bd92 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/94.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '94' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/95.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/95.yaml new file mode 100644 index 00000000..c8f1f387 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/95.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.8 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.8 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.5 + - 0.4 + - 0.1 + coverage: + cov_constant: 5.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '95' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/96.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/96.yaml new file mode 100644 index 00000000..00ab41c8 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/96.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '96' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/97.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/97.yaml new file mode 100644 index 00000000..6c342ff9 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/97.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.02 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '97' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/98.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/98.yaml new file mode 100644 index 00000000..f3755d60 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/98.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.05 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '98' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/results/sweep_v01/99.yaml b/Analysis/simulations/binomial_growth/results/sweep_v01/99.yaml new file mode 100644 index 00000000..a4bbc581 --- /dev/null +++ b/Analysis/simulations/binomial_growth/results/sweep_v01/99.yaml @@ -0,0 +1,39 @@ +cpus: 36 +data_outdir: data/out/sweep_v01 +growth: + binomial: + rates: + - 0.1 + - 0.1 + - 0.01 + time_steps: 10 + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: false + poisson: + rates: + - 0.05 + - 1 + - 0.9 + type: binomial +het: +- 0.2 +- 0.2 +het_err_rate: 0.15 +initialize: + clone_sizes: + - 0.88 + - 0.02 + - 0.1 + coverage: + cov_constant: 10.0 + poisson_mu_per_cell: 50 + type: constant + mt_clone_map: null +local_outdir: results +name: '99' +num_cells: 10000 +num_iterations: 100 +num_mt_positions: 10 +prefix: sweep_v01 +sequence_subsample: null diff --git a/Analysis/simulations/binomial_growth/wrapper_v01.py b/Analysis/simulations/binomial_growth/wrapper_v01.py new file mode 100644 index 00000000..55c4e48a --- /dev/null +++ b/Analysis/simulations/binomial_growth/wrapper_v01.py @@ -0,0 +1,23 @@ +""" +Running the first version of the lineage tracing simulation. +Files are simple_v01.yaml and wrapper_v01.yaml. +1000 iterations, 10000 num_cells +""" + +from src.simulations import Simulation, ParameterSweep, FullSimulation +from src.simulations.utils.config import read_config_file +from src.config import RESULTS, ROOT_DIR +import time +from os.path import join +import os + +#os.chdir(RESULTS) + +default_params_f = 'parameters/simple_v01.yaml' +sweep_params_f = 'parameters/sweep_v01.yaml' +sweep = ParameterSweep(default_params_f, sweep_params_f) + +sweep.run_sweep() # Runs the simulation +sweep.save() +sweep.plot_before_after_all_clones() +sweep.plot_sensitivity_and_dropout() # plots results \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..a233e023 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or 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The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/docs/commands.html b/docs/commands.html new file mode 100644 index 00000000..4ce0b908 --- /dev/null +++ b/docs/commands.html @@ -0,0 +1,385 @@ + + + + + + +Commands + + + +
+

Commands

+ +

The Makefile contains the central entry points for common tasks related to this project.

+
+

System Message: ERROR/3 (/data2/mito_lineage/docs/commands.rst, line 7)

+

Unknown directive type "autoclass".

+
+.. autoclass:: src.simulations.parametersweep.ParameterSweep
+   :members:
+
+
+
+
+

System Message: ERROR/3 (/data2/mito_lineage/docs/commands.rst, line 10)

+

Unknown directive type "autoclass".

+
+.. autoclass:: src.simulations.simulation.Simulation
+
+
+
+ + diff --git a/docs/commands.rst b/docs/commands.rst new file mode 100644 index 00000000..304cf72a --- /dev/null +++ b/docs/commands.rst @@ -0,0 +1,10 @@ +Commands +======== + +The Makefile contains the central entry points for common tasks related to this project. + + +.. autoclass:: src.simulations.parametersweep.ParameterSweep + :members: + +.. autoclass:: src.simulations.simulation.Simulation diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 00000000..038b16a9 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,249 @@ +# -*- coding: utf-8 -*- +# +# src documentation build configuration file, created by +# sphinx-quickstart. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import os +import sys + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +print('here', os.path.abspath('../')) +print('and here', os.path.abspath('./')) + +sys.path.insert(0, os.path.abspath('../')) +sys.path.insert(0, os.path.abspath('./')) + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +#extensions = [] +extensions = ['sphinx.ext.autodoc'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'src' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '0.1' +# The full version, including alpha/beta/rc tags. +release = '0.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +# modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'srcdoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # 'papersize': 'letterpaper', + + # The font size ('10pt', '11pt' or '12pt'). + # 'pointsize': '10pt', + + # Additional stuff for the LaTeX preamble. + # 'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', + 'src.tex', + u'src Documentation', + u"Isaac Shamie", 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'src', u'src Documentation', + [u"Isaac Shamie"], 1) +] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'src', u'src Documentation', + u"Isaac Shamie", 'src', + 'Lineaege Tracing with MTs', 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' diff --git a/docs/getting-started.html b/docs/getting-started.html new file mode 100644 index 00000000..9dc5024b --- /dev/null +++ b/docs/getting-started.html @@ -0,0 +1,371 @@ + + + + + + +Getting started + + + +
+

Getting started

+ +

This is where you describe how to get set up on a clean install, including the +commands necessary to get the raw data (using the sync_data_from_s3 command, +for example), and then how to make the cleaned, final data sets.

+
+ + diff --git a/docs/getting-started.rst b/docs/getting-started.rst new file mode 100644 index 00000000..b4f71c3a --- /dev/null +++ b/docs/getting-started.rst @@ -0,0 +1,6 @@ +Getting started +=============== + +This is where you describe how to get set up on a clean install, including the +commands necessary to get the raw data (using the `sync_data_from_s3` command, +for example), and then how to make the cleaned, final data sets. diff --git a/docs/getting_started_simuations.md b/docs/getting_started_simuations.md new file mode 100644 index 00000000..86934e41 --- /dev/null +++ b/docs/getting_started_simuations.md @@ -0,0 +1,22 @@ +## Introduction: +This will give information on how to run lineage simulations with the +src.simulations module. + +## Installation: +With conda: +`conda install src` + + +## Modes: + + +## Input: + + +## Output: + + +## Pacakge Dependencies: + + +## Future Directions: \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 00000000..5c73c771 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,24 @@ +.. src documentation master file, created by + sphinx-quickstart. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +src documentation! +============================================== + +Contents: + +.. toctree:: + :maxdepth: 2 + + getting-started + commands + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/make.bat b/docs/make.bat new file mode 100755 index 00000000..cc46f3aa --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,190 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ is one of + echo. html to make standalone HTML files + echo. dirhtml to make HTML files named index.html in directories + echo. singlehtml to make a single large HTML file + echo. pickle to make pickle files + echo. json to make JSON files + echo. htmlhelp to make HTML files and a HTML help project + echo. qthelp to make HTML files and a qthelp project + echo. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over all changed/added/deprecated items + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\src.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\src.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +:end diff --git a/docs/simuations.md b/docs/simuations.md new file mode 100644 index 00000000..cbd624c8 --- /dev/null +++ b/docs/simuations.md @@ -0,0 +1,10 @@ +## Introduction + + +## Methods + + +## Results + + +## Future Directions \ No newline at end of file diff --git a/docs/simulations/simple_v01.md b/docs/simulations/simple_v01.md new file mode 100644 index 00000000..6e4688af --- /dev/null +++ b/docs/simulations/simple_v01.md @@ -0,0 +1,48 @@ +One set of parameters for simulating cells and their lineages +:: + + local_outdir: 'simulation' + prefix: 'sweep_v01' + num_iterations: 100 + num_cells: 10000 + num_mt_positions: 10 + + cpus: 36 + """ Number of cpus + + :type int + """ + + initialize: + coverage: + type: 'constant' # {'poisson', 'constant', 'growth'} + cov_constant: 50 + poisson_mu_per_cell: 50 + + clone_sizes: #distribution of clone sizes. The first one is the non-clone population. Length should be len(het)+1, and it should sum to 1 + [0.5, 0.4, 0.1] + + mt_clone_map: + # [(10), (16500)] + # [(10), (16500), (16500, 7)] + + het: # Heterozygous values + [0.2, 0.2] + het_err_rate: 0.05 + + + sequence_subsample: #10000 + + growth: + type: binomial + binomial: + rates: [0.1, 0.8, 0.01] + time_steps: 10 + #type: poisson + poisson: + rates: [0.05, 1, 0.9] + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: False + + diff --git a/docs/simulations/sweep.cwl b/docs/simulations/sweep.cwl new file mode 100644 index 00000000..77bd07eb --- /dev/null +++ b/docs/simulations/sweep.cwl @@ -0,0 +1,31 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: CommandLineTool +baseCommand: echo +inputs: + example_flag: + type: boolean + inputBinding: + position: 1 + prefix: -f + example_string: + type: string + inputBinding: + position: 3 + prefix: --example-string + example_int: + type: int + inputBinding: + position: 2 + prefix: -i + separate: false + example_file: + type: File? + inputBinding: + prefix: --file= + separate: false + position: 4 + +outputs: + cell_af: [] \ No newline at end of file diff --git a/figures/simulation/extfig3/._extFig3_ij.png b/figures/simulation/extfig3/._extFig3_ij.png index 167810cb..eb8bf2fd 100644 Binary files a/figures/simulation/extfig3/._extFig3_ij.png and b/figures/simulation/extfig3/._extFig3_ij.png differ diff --git a/notebooks/mgatk_test/parameters/2020_09_07_v01.yaml b/notebooks/mgatk_test/parameters/2020_09_07_v01.yaml new file mode 100644 index 00000000..67e1a76d --- /dev/null +++ b/notebooks/mgatk_test/parameters/2020_09_07_v01.yaml @@ -0,0 +1,4 @@ +bam_f: /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/possorted_genome_bam.bam +bam_dir: /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/ +outdir: results/ +feature_barcodes: /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/filtered_feature_bc_matrix/barcodes.tsv diff --git a/notebooks/mgatk_test/results/mgatk_out/final/MT_refAllele.txt b/notebooks/mgatk_test/results/mgatk_out/final/MT_refAllele.txt new file mode 100644 index 00000000..078c3b92 --- /dev/null +++ b/notebooks/mgatk_test/results/mgatk_out/final/MT_refAllele.txt @@ -0,0 +1,16569 @@ +1 G +2 A +3 T +4 C +5 A +6 C +7 A +8 G +9 G +10 T +11 C +12 T +13 A +14 T +15 C +16 A +17 C +18 C +19 C +20 T +21 A +22 T +23 T +24 A +25 A +26 C +27 C +28 A +29 C +30 T +31 C +32 A +33 C +34 G +35 G +36 G +37 A +38 G +39 C +40 T +41 C +42 T +43 C +44 C +45 A +46 T +47 G +48 C +49 A +50 T +51 T +52 T +53 G +54 G +55 T +56 A +57 T +58 T +59 T +60 T +61 C +62 G +63 T +64 C +65 T +66 G +67 G +68 G +69 G +70 G +71 G +72 T +73 A +74 T +75 G +76 C +77 A +78 C +79 G +80 C +81 G +82 A +83 T +84 A +85 G +86 C +87 A +88 T +89 T +90 G +91 C +92 G +93 A +94 G +95 A +96 C +97 G +98 C 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"ExecuteTime": { + "end_time": "2020-10-26T23:24:41.852419Z", + "start_time": "2020-10-26T23:24:41.849877Z" + } + }, + "outputs": [], + "source": [ + "params_f = 'parameters/2020_09_07_v01.yaml'" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T23:24:41.903945Z", + "start_time": "2020-10-26T23:24:41.854630Z" + } + }, + "outputs": [], + "source": [ + "p = read_config_file(params_f)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T23:24:42.624784Z", + "start_time": "2020-10-26T23:24:41.907005Z" + }, + "scrolled": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "mgatk tenx -i /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/possorted_genome_bam.bam -o results//mgatk_out -g GRCh38 -b /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/filtered_feature_bc_matrix/barcodes.tsv \n", + "Mon Oct 26 23:24:42 UTC 2020: mgatk v0.5.9\n", + "ERROR: in `tenx` mode, must specify a valid read tag ID (generally two letters).\n" + ] + } + ], + "source": [ + "cmd = f\"mgatk tenx -i {p['bam_f']} -o {p['outdir']}/mgatk_out -g GRCh38 -b {p['feature_barcodes']} \"\n", + "print(cmd)\n", + "!{cmd}" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T23:25:24.916668Z", + "start_time": "2020-10-26T23:24:42.627010Z" + }, + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "mgatk tenx -i /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/possorted_genome_bam.bam -o results/mgatk_out -g GRCh38 -b /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/filtered_feature_bc_matrix/barcodes.tsv -bt CB\n", + "Mon Oct 26 23:24:42 UTC 2020: mgatk v0.5.9\n", + "Mon Oct 26 23:24:43 UTC 2020: Found bam file: /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/possorted_genome_bam.bam for genotyping.\n", + "Mon Oct 26 23:24:43 UTC 2020: Found file of barcodes to be parsed: /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/filtered_feature_bc_matrix/barcodes.tsv\n", + "Mon Oct 26 23:24:43 UTC 2020: User specified mitochondrial genome matches .bam file\n", + "Mon Oct 26 23:25:13 UTC 2020: Finished determining/splitting barcodes for genotyping.\n", + "Mon Oct 26 23:25:14 UTC 2020: Genotyping samples with 64 threads\n", + "\u001b[33mBuilding DAG of jobs...\u001b[0m\n", + "\u001b[33mUsing shell: /bin/bash\u001b[0m\n", + "\u001b[33mProvided cores: 64\u001b[0m\n", + "\u001b[33mRules claiming more threads will be scaled down.\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tall\n", + "\t1\tmake_depth_table\n", + "\t1\tmake_final_sparse_matrices\n", + "\t64\tprocess_one_slice\n", + "\t67\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:19 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.62.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.62.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.62.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.62.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.62.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.62.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.62.coverage.txt\n", + " jobid: 8\n", + " wildcards: sample=barcodes.62\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:19 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.55.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.55.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.55.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.55.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.55.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.55.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.55.coverage.txt\n", + " jobid: 16\n", + " wildcards: sample=barcodes.55\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:19 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.11.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.11.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.coverage.txt\n", + " jobid: 4\n", + " wildcards: sample=barcodes.11\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:19 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.21.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.21.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.21.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.21.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.21.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.21.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.21.coverage.txt\n", + " jobid: 44\n", + " wildcards: sample=barcodes.21\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tprocess_one_slice\n", + "\t1\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:19 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.23.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.23.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.23.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.23.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.23.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.23.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.23.coverage.txt\n", + " jobid: 49\n", + " wildcards: sample=barcodes.23\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tprocess_one_slice\n", + "\t1\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:19 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.29.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.29.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.29.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.29.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.29.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.29.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.29.coverage.txt\n", + " jobid: 51\n", + " wildcards: sample=barcodes.29\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tprocess_one_slice\n", + "\t1\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:20 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.61.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.61.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.coverage.txt\n", + " jobid: 42\n", + " wildcards: sample=barcodes.61\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tprocess_one_slice\n", + "\t1\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tprocess_one_slice\n", + "\t1\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:20 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.26.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.26.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.26.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.26.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.26.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.26.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.26.coverage.txt\n", + " jobid: 50\n", + " wildcards: sample=barcodes.26\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tprocess_one_slice\n", + "\t1\u001b[0m\n", + "Error in checkGrep(grep(\".A.txt\", files)) : \n", + " Improper folder specification; file missing / extra file present. See documentation\n", + "Calls: importMito -> checkGrep\n", + "Execution halted\n", + "\u001b[31mWorkflowError in line 8 of /home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx:\n", + "Config file results/mgatk_out/.internal/parseltongue/snake.scatter.yaml not found.\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx\", line 8, in \u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:21 2020]\u001b[0m\n", + "\u001b[31mError in rule process_one_slice:\u001b[0m\n", + "\u001b[31m jobid: 0\u001b[0m\n", + "\u001b[31m output: results/mgatk_out/qc/depth/barcodes.11.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.11.coverage.txt\u001b[0m\n", + "\u001b[31m\u001b[0m\n", + "\u001b[31mRuleException:\n", + "FileNotFoundError in line 73 of /home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx:\n", + "[Errno 2] No such file or directory: 'results/mgatk_out/.internal/samples/barcodes.11.bam.txt'\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx\", line 73, in __rule_process_one_slice\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/concurrent/futures/thread.py\", line 57, in run\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:22 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.50.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.50.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.50.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.50.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.50.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.50.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.50.coverage.txt\n", + " jobid: 30\n", + " wildcards: sample=barcodes.50\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[33mJob counts:\n", + "\tcount\tjobs\n", + "\t1\tprocess_one_slice\n", + "\t1\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:22 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.32.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.32.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.32.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.32.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.32.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.32.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.32.coverage.txt\n", + " jobid: 25\n", + " wildcards: sample=barcodes.32\u001b[0m\n", + "\u001b[32m\u001b[0m\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[31mExiting because a job execution failed. Look above for error message\u001b[0m\n", + "\u001b[31mWorkflowError in line 8 of /home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx:\n", + "Config file results/mgatk_out/.internal/parseltongue/snake.scatter.yaml not found.\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx\", line 8, in \u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:23 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.19.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.19.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.19.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.19.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.19.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.19.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.19.coverage.txt\n", + " jobid: 10\n", + " wildcards: sample=barcodes.19\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[31mWorkflowError in line 8 of /home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx:\n", + "Config file results/mgatk_out/.internal/parseltongue/snake.scatter.yaml not found.\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx\", line 8, in \u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:24 2020]\u001b[0m\n", + "\u001b[31mError in rule process_one_slice:\u001b[0m\n", + "\u001b[31m jobid: 0\u001b[0m\n", + "\u001b[31m output: results/mgatk_out/qc/depth/barcodes.61.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.61.coverage.txt\u001b[0m\n", + "\u001b[31m\u001b[0m\n", + "\u001b[31mRuleException:\n", + "FileNotFoundError in line 73 of /home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx:\n", + "[Errno 2] No such file or directory: 'results/mgatk_out/.internal/samples/barcodes.61.bam.txt'\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx\", line 73, in __rule_process_one_slice\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/concurrent/futures/thread.py\", line 57, in run\u001b[0m\n", + "\u001b[31mWorkflowError in line 8 of /home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx:\n", + "Config file results/mgatk_out/.internal/parseltongue/snake.scatter.yaml not found.\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx\", line 8, in \u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:24 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.7.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.7.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.7.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.7.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.7.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.7.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.7.coverage.txt\n", + " jobid: 36\n", + " wildcards: sample=barcodes.7\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[31mExiting because a job execution failed. Look above for error message\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:24 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.30.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.30.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.30.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.30.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.30.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.30.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.30.coverage.txt\n", + " jobid: 47\n", + " wildcards: sample=barcodes.30\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:24 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.34.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.34.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.34.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.34.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.34.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.34.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.34.coverage.txt\n", + " jobid: 45\n", + " wildcards: sample=barcodes.34\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[32m[Mon Oct 26 23:25:24 2020]\u001b[0m\n", + "\u001b[32mrule process_one_slice:\n", + " input: results/mgatk_out/.internal/samples/barcodes.57.bam.txt\n", + " output: results/mgatk_out/qc/depth/barcodes.57.depth.txt, results/mgatk_out/temp/sparse_matrices/barcodes.57.A.txt, results/mgatk_out/temp/sparse_matrices/barcodes.57.C.txt, results/mgatk_out/temp/sparse_matrices/barcodes.57.G.txt, results/mgatk_out/temp/sparse_matrices/barcodes.57.T.txt, results/mgatk_out/temp/sparse_matrices/barcodes.57.coverage.txt\n", + " jobid: 34\n", + " wildcards: sample=barcodes.57\u001b[0m\n", + "\u001b[32m\u001b[0m\n", + "\u001b[31mWorkflowError in line 8 of /home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx:\n", + "Config file results/mgatk_out/.internal/parseltongue/snake.scatter.yaml not found.\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/bin/snake/Snakefile.tenx\", line 8, in \u001b[0m\n", + "Traceback (most recent call last):\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/bin/mgatk\", line 8, in \n", + " sys.exit(main())\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/click/core.py\", line 829, in __call__\n", + " return self.main(*args, **kwargs)\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/click/core.py\", line 782, in main\n", + " rv = self.invoke(ctx)\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/click/core.py\", line 1066, in invoke\n", + " return ctx.invoke(self.callback, **ctx.params)\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/click/core.py\", line 610, in invoke\n", + " return callback(*args, **kwargs)\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/site-packages/mgatk/cli.py\", line 430, in main\n", + " shutil.rmtree(of + \"/temp\")\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/shutil.py\", line 491, in rmtree\n", + " _rmtree_safe_fd(fd, path, onerror)\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/shutil.py\", line 433, in _rmtree_safe_fd\n", + " onerror(os.rmdir, fullname, sys.exc_info())\n", + " File \"/home/isshamie/software/anaconda2/envs/mito_trace/lib/python3.7/shutil.py\", line 431, in _rmtree_safe_fd\n", + " os.rmdir(entry.name, dir_fd=topfd)\n", + "OSError: [Errno 39] Directory not empty: 'temp_bam'\n" + ] + } + ], + "source": [ + "cmd = f\"mgatk tenx -i {p['bam_f']} -o {p['outdir']}mgatk_out -g GRCh38 -b {p['feature_barcodes']} -bt CB\"\n", + "print(cmd)\n", + "!{cmd}" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T23:25:24.925009Z", + "start_time": "2020-10-26T23:25:24.921218Z" + }, + "scrolled": true + }, + "outputs": [], + "source": [ + "# cmd = f\"mgatk tenx -i {p['bam_f']} -o {p['outdir']}mgatk_out -g GRCh38 -b {p['feature_barcodes']} -bt CB --ncores 32\"\n", + "# print(cmd)\n", + "# !{cmd}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T23:25:24.934666Z", + "start_time": "2020-10-26T23:25:24.927142Z" + }, + "scrolled": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "mgatk bcall -i /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/possorted_genome_bam.bam -o results//mgatk_out -g GRCh38 -bt CB -b /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/filtered_feature_bc_matrix/barcodes.tsv --ncores 32\n" + ] + } + ], + "source": [ + "cmd = f\"mgatk bcall -i {p['bam_f']} -o {p['outdir']}/mgatk_out -g GRCh38 -bt CB -b {p['feature_barcodes']} --ncores 32\"\n", + "print(cmd)\n", + "#!{cmd}" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.3" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/mgatk_test/run_mgatk_check.ipynb b/notebooks/mgatk_test/run_mgatk_check.ipynb new file mode 100644 index 00000000..d5875785 --- /dev/null +++ b/notebooks/mgatk_test/run_mgatk_check.ipynb @@ -0,0 +1,101 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T21:31:18.198984Z", + "start_time": "2020-10-26T21:31:18.156958Z" + } + }, + "outputs": [], + "source": [ + "from src.utils.config import read_config_file" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T21:31:18.204307Z", + "start_time": "2020-10-26T21:31:18.201344Z" + }, + "tags": [ + "parameters" + ] + }, + "outputs": [], + "source": [ + "params_f = 'parameters/2020_09_07_v01.yaml'" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T21:31:18.216896Z", + "start_time": "2020-10-26T21:31:18.207684Z" + } + }, + "outputs": [], + "source": [ + "p = read_config_file(params_f)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "ExecuteTime": { + "end_time": "2020-10-26T21:31:18.912455Z", + "start_time": "2020-10-26T21:31:18.219123Z" + }, + "slideshow": { + "slide_type": "-" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "mgatk check -i /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/ -b /data2/isshamie/mito_lineage/data/processed/2020_09_07_Croker_mito/CD34_PolydT_fiveprime/outs/filtered_feature_bc_matrix/barcodes.tsv.gz -o results//mgatk_out -g GRCh38\n", + "Mon Oct 26 21:31:18 UTC 2020: mgatk v0.5.9\n", + "Mon Oct 26 21:31:18 UTC 2020: checking dependencies...\n", + "Mon Oct 26 21:31:18 UTC 2020: mgatk check passed! mgatk will process 1 samples if same parameters are run in `call` mode\n" + ] + } + ], + "source": [ + "cmd = f\"mgatk check -i {p['bam_dir']} -b {p['feature_barcodes']} -o {p['outdir']}/mgatk_out -g GRCh38\"\n", + "print(cmd)\n", + "!{cmd}" + ] + } + ], + "metadata": { + "celltoolbar": "Tags", + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.3" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/01 - preprocess - preliminary data.ipynb b/notebooks/optimization_experiments/01 - preprocess - preliminary data.ipynb similarity index 100% rename from notebooks/01 - preprocess - preliminary data.ipynb rename to notebooks/optimization_experiments/01 - preprocess - preliminary data.ipynb diff --git a/notebooks/Check mapq.ipynb b/notebooks/optimization_experiments/Check mapq.ipynb similarity index 100% rename from notebooks/Check mapq.ipynb rename to notebooks/optimization_experiments/Check mapq.ipynb diff --git a/notebooks/Compare barcodes from bam vs barcode text file from GSM3271867 Human2_002.ipynb b/notebooks/optimization_experiments/Compare barcodes from bam vs barcode text file from GSM3271867 Human2_002.ipynb similarity index 100% rename from notebooks/Compare barcodes from bam vs barcode text file from GSM3271867 Human2_002.ipynb rename to notebooks/optimization_experiments/Compare barcodes from bam vs barcode text file from GSM3271867 Human2_002.ipynb diff --git a/notebooks/Create reverse complement for R2.ipynb b/notebooks/optimization_experiments/Create reverse complement for R2.ipynb similarity index 100% rename from notebooks/Create reverse complement for R2.ipynb rename to notebooks/optimization_experiments/Create reverse complement for R2.ipynb diff --git a/notebooks/STAR QC.ipynb b/notebooks/optimization_experiments/STAR QC.ipynb similarity index 100% rename from notebooks/STAR QC.ipynb rename to notebooks/optimization_experiments/STAR QC.ipynb diff --git a/notebooks/prelim_get_mt_barcode.ipynb b/notebooks/optimization_experiments/prelim_get_mt_barcode.ipynb similarity index 100% rename from notebooks/prelim_get_mt_barcode.ipynb rename to notebooks/optimization_experiments/prelim_get_mt_barcode.ipynb diff --git a/notebooks/run STAR after trim.ipynb b/notebooks/optimization_experiments/run STAR after trim.ipynb similarity index 100% rename from notebooks/run STAR after trim.ipynb rename to notebooks/optimization_experiments/run STAR after trim.ipynb diff --git "a/parameters/simulation/Icon\r" "b/parameters/simulations/Icon\r" similarity index 100% rename from "parameters/simulation/Icon\r" rename to "parameters/simulations/Icon\r" diff --git a/parameters/simulation/clones.yaml b/parameters/simulations/clones.yaml similarity index 100% rename from parameters/simulation/clones.yaml rename to parameters/simulations/clones.yaml diff --git a/parameters/simulation/mt_rates.yaml b/parameters/simulations/mt_rates.yaml similarity index 100% rename from parameters/simulation/mt_rates.yaml rename to parameters/simulations/mt_rates.yaml diff --git a/parameters/simulations/simple_v01.yaml b/parameters/simulations/simple_v01.yaml new file mode 100644 index 00000000..e6f2215e --- /dev/null +++ b/parameters/simulations/simple_v01.yaml @@ -0,0 +1,43 @@ +# One set of parameters for simulating cells and their lineages +#local_outdir: 'simulation' +prefix: 'sweep_v01' + +num_iterations: 100 +num_cells: 10000 +num_mt_positions: 10 + +cpus: 36 + +initialize: + coverage: + type: 'constant' # {'poisson', 'constant', 'growth'} + cov_constant: 50 + poisson_mu_per_cell: 50 + + clone_sizes: #distribution of clone sizes. The first one is the non-clone population. Length should be len(het)+1, and it should sum to 1 + [0.5, 0.4, 0.1] + + mt_clone_map: + # [(10), (16500)] + # [(10), (16500), (16500, 7)] + +het: # Heterozygous values + [0.2, 0.2] +het_err_rate: 0.05 + + +sequence_subsample: #10000 + +growth: + type: binomial + binomial: + rates: [0.1, 0.8, 0.01] + time_steps: 10 + #type: poisson + poisson: + rates: [0.05, 1, 0.9] + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: False + + diff --git a/parameters/simulations/sweep_v01.yaml b/parameters/simulations/sweep_v01.yaml new file mode 100644 index 00000000..c0b2c7a2 --- /dev/null +++ b/parameters/simulations/sweep_v01.yaml @@ -0,0 +1,15 @@ +# One set of parameters for simulating cells and their lineages +outdir: 'results' +prefix: 'sweep_v01' +data_outdir: 'data/out' +#num_iterations: 100 +#num_cells: 10000 +#num_mt_positions: 10 +cpus: 36 + +grid: + cov_constant: [5, 10, 50, 100] + dominant_clone_sizes: [0.02,0.1,0.2, 0.4] + dominant_het: [0.02, 0.2, 0.5, 0.8] + dominant_growth: [0.1, 0.5, 0.8] + het_err_rate: [0.05, 0.15] diff --git a/parameters/simulations/test_simple.yaml b/parameters/simulations/test_simple.yaml new file mode 100644 index 00000000..6830c9d1 --- /dev/null +++ b/parameters/simulations/test_simple.yaml @@ -0,0 +1,46 @@ +# One set of parameters for simulating cells and their lineages +local_outdir: 'simulation' +prefix: 'test_simple' +num_iterations: 10 +num_cells: 10000 +num_mt_positions: 10 + +cpus: 36 +#""" Number of cpus +# +#:type int +#""" + +initialize: + coverage: + type: 'constant' # {'poisson', 'constant', 'growth'} + cov_constant: 50 + poisson_mu_per_cell: 50 + + clone_sizes: #distribution of clone sizes. The first one is the non-clone population. Length should be len(het)+1, and it should sum to 1 + [0.5, 0.4, 0.1] + + mt_clone_map: + # [(10), (16500)] + # [(10), (16500), (16500, 7)] + +het: # Heterozygous values + [0.2, 0.2] +het_err_rate: 0.05 + + +sequence_subsample: #10000 + +growth: + type: binomial + binomial: + rates: [0.1, 0.8, 0.01] + time_steps: 10 + #type: poisson + poisson: + rates: [0.05, 1, 0.9] + mutant_af_sigma_noise: 0.05 + non_mutants: + to_mutate: False + + diff --git a/parameters/simulations/test_sweep.yaml b/parameters/simulations/test_sweep.yaml new file mode 100644 index 00000000..a3f3ee77 --- /dev/null +++ b/parameters/simulations/test_sweep.yaml @@ -0,0 +1,15 @@ +# One set of parameters for simulating cells and their lineages +outdir: 'simulation' +prefix: 'test_sweep' +#num_iterations: 100 +#num_cells: 10000 +#num_mt_positions: 10 +cpus: 24 + + +grid: + cov_constant: [5, 100] + dominant_clone_sizes: [0.02,0.2] + dominant_het: [0.02, 0.2] + dominant_growth: [0.1, 0.5] + het_err_rate: [0.05, 0.15] \ No 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b/reports/references/Ludwig_2019/AF_distance.png similarity index 100% rename from docs/references/Ludwig_2019/AF_distance.png rename to reports/references/Ludwig_2019/AF_distance.png diff --git a/docs/references/Ludwig_2019/Leif2019_Fig3.png b/reports/references/Ludwig_2019/Leif2019_Fig3.png similarity index 100% rename from docs/references/Ludwig_2019/Leif2019_Fig3.png rename to reports/references/Ludwig_2019/Leif2019_Fig3.png diff --git a/docs/references/papers/dataset_list.txt b/reports/references/papers/dataset_list.txt similarity index 100% rename from docs/references/papers/dataset_list.txt rename to reports/references/papers/dataset_list.txt diff --git a/src/simulations/__init__.py b/src/simulations/__init__.py index e69de29b..5c64c58d 100644 --- a/src/simulations/__init__.py +++ b/src/simulations/__init__.py @@ -0,0 +1,3 @@ +from src.simulations.fullsimulation import FullSimulation +from src.simulations.simulation import Simulation +from src.simulations.parametersweep import ParameterSweep \ No newline at end of file diff --git a/src/simulations/dominant_clone.py b/src/simulations/dominant_clone.py index ad2f42e4..6443d0c0 100644 --- a/src/simulations/dominant_clone.py +++ b/src/simulations/dominant_clone.py @@ -11,132 +11,4 @@ from mplh.fig_utils import legend_from_color -""" Run the simulation similar to in Extended Data Fig 3 from - Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling""" - - -def simulate(n_sim, n_cells, n_dom_cells, coverage, het, err_het): - dropout = np.zeros([n_sim, ]) - cell_af = np.zeros([n_sim, n_cells]) - rocs = [] - prec_scores = [] - y_true = np.append(np.ones(n_dom_cells),np.zeros(n_cells-n_dom_cells) ) - - for sim in tqdm(range(n_sim)): - af_i = random.binomial(coverage,het, n_dom_cells)/coverage - af_j = random.binomial(coverage, err_het, n_cells-n_dom_cells)/coverage - - dropout[sim] = (af_i == 0).sum() - cell_af[sim, :n_dom_cells] = af_i - cell_af[sim, n_dom_cells:] = af_j - - rocs.append(roc_curve(y_true, cell_af[sim])) - prec_scores.append(average_precision_score(y_true, cell_af[sim])) - - # Construct sensitivity-specificity - #cell_af[sim, y_true] - - return cell_af, y_true, rocs, prec_scores, dropout - - -def expand_cell_af(cell_af, growth, sigma): - return random.normal(cell_af, sigma, size=growth) - - -def simulate_expand_cells_af(af, growth, sigma): - """ - Given a cell-by-af vector, expand the AF - :param af: - :param growth: - :param sigma: - :return: - """ - new_af = [] - for ind, cell in enumerate(af): - new_af.append(expand_cell_af(cell, growth[ind], sigma )) - - new_af = np.append(af, np.concatenate(new_af)) - return new_af - - -def grow_poisson(af, clone_meta, clone_growth, non_clone_growth, num_cells, sigma=0.05): - # First group by clones, then simulate growth, then sample number of cells - - ## ToDO for multiple clones - #new_af = dict() # Dictonary for each clone - # clones = set(clone_meta) - #for c in clones: - # curr = af[np.where(clone_meta==c)] - clones_af = af[clone_meta==1] - nonclones_af = af[clone_meta==0] - - # Sample from poisson the growth - grow_clones = random.poisson(lam=clone_growth, size=(clone_meta == 1)) - grow_nonclones = random.poisson(lam=non_clone_growth, size=(clone_meta == 0)) - - - # Expand the cells by adding and changing vary their AFs by normal distribution - new_c = simulate_expand_cells_af(clones_af, grow_clones, sigma=sigma) - new_nonc = simulate_expand_cells_af(nonclones_af, grow_nonclones, sigma=sigma) - - # Subsample from the new cells - new_meta = np.append(np.ones(shape=[len(new_c),]), - np.zeros(shape=[len(new_nonc),])) - - # Subsample num_cells by sampling from the clone IDs. - # Then just take the first indices for the clone and nonclones, since - # the ordering is random anyway. - new_meta = random.choice(new_meta, size=num_cells , replace=False) - new_af = np.append(new_c[:(new_meta==1).sum()], - new_nonc[:(new_meta==0).sum()]) - - #new_af[c] - return new_af, new_meta - - -def simulate_growth(cell_af, clone_meta, clone_growth, non_clone_growth=0.5, num_cells=None): - """ - - :param cell_af: iteration-by-cells AF - :param clone_meta: |cells| np array indicating if it is the clone or not - :param clone_growth: Poisson parameter for the clone cells - :param non_clone_growth: poisson parameter for non-clone cells - :param num_cells: Number of cells to sample from after growth. If None, defaults to the current number of cells - :return: - """ - n_sim = cell_af.shape[0] - n_cells_orig = cell_af.shape[1] - - # For each clone, see how they grow with lambda - if num_cells is None: - num_cells = n_cells_orig - - cell_af_growth = np.zeros(n_sim, num_cells) - cell_af_meta = -1*np.ones(n_sim, num_cells) - - for sim in tqdm(range(n_sim)): - new_af, new_meta = grow_poisson(cell_af[sim], clone_meta, clone_growth, non_clone_growth, num_cells) - cell_af_growth[sim] = new_af - cell_af_meta[sim] = new_meta - - return cell_af_growth, cell_af_meta - - -def generate_coverage(num_cells, num_pos=None, cov_constant=None, mu_cov_per_cell=None, mu_dist_reads=None, type='constant'): - """ - There are different modes to the coverage, either a constant or through a distribution. - :return: - """ - c = np.zeros([num_cells, num_pos]) - if type == 'constant': - c[:, :] = cov_constant - return c - elif type=="poisson": - # Get the number of coverage per cell based on poisson (should be reads) - num_reads_per_cell = random.poisson(lam=mu_cov_per_cell, size=num_cells) - - # Number of reads at each position, based on the average for each cell - for i in num_cells: - c[i,:] = random.poisson(num_reads_per_cell[i], size=num_pos) - return c diff --git a/src/simulations/dominant_clone_extfig3.py b/src/simulations/dominant_clone_extfig3.py index b1e3fcd7..be121651 100644 --- a/src/simulations/dominant_clone_extfig3.py +++ b/src/simulations/dominant_clone_extfig3.py @@ -33,6 +33,135 @@ err_het=0.1 + +""" Run the simulation similar to in Extended Data Fig 3 from + Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling""" +def simulate(n_sim, n_cells, n_dom_cells, coverage, het, err_het): + dropout = np.zeros([n_sim, ]) + cell_af = np.zeros([n_sim, n_cells]) + rocs = [] + prec_scores = [] + y_true = np.append(np.ones(n_dom_cells),np.zeros(n_cells-n_dom_cells) ) + + for sim in tqdm(range(n_sim)): + af_i = random.binomial(coverage,het, n_dom_cells)/coverage + af_j = random.binomial(coverage, err_het, n_cells-n_dom_cells)/coverage + + dropout[sim] = (af_i == 0).sum() + cell_af[sim, :n_dom_cells] = af_i + cell_af[sim, n_dom_cells:] = af_j + + rocs.append(roc_curve(y_true, cell_af[sim])) + prec_scores.append(average_precision_score(y_true, cell_af[sim])) + + # Construct sensitivity-specificity + #cell_af[sim, y_true] + + return cell_af, y_true, rocs, prec_scores, dropout + + +def expand_cell_af(cell_af, growth, sigma): + return random.normal(cell_af, sigma, size=growth) + + +def simulate_expand_cells_af(af, growth, sigma): + """ + Given a cell-by-af vector, expand the AF + :param af: + :param growth: + :param sigma: + :return: + """ + new_af = [] + for ind, cell in enumerate(af): + new_af.append(expand_cell_af(cell, growth[ind], sigma )) + + new_af = np.append(af, np.concatenate(new_af)) + return new_af + + +def grow_poisson(af, clone_meta, clone_growth, non_clone_growth, num_cells, sigma=0.05): + # First group by clones, then simulate growth, then sample number of cells + + ## ToDO for multiple clones + #new_af = dict() # Dictonary for each clone + # clones = set(clone_meta) + #for c in clones: + # curr = af[np.where(clone_meta==c)] + clones_af = af[clone_meta==1] + nonclones_af = af[clone_meta==0] + + # Sample from poisson the growth + grow_clones = random.poisson(lam=clone_growth, size=(clone_meta == 1)) + grow_nonclones = random.poisson(lam=non_clone_growth, size=(clone_meta == 0)) + + + # Expand the cells by adding and changing vary their AFs by normal distribution + new_c = simulate_expand_cells_af(clones_af, grow_clones, sigma=sigma) + new_nonc = simulate_expand_cells_af(nonclones_af, grow_nonclones, sigma=sigma) + + # Subsample from the new cells + new_meta = np.append(np.ones(shape=[len(new_c),]), + np.zeros(shape=[len(new_nonc),])) + + # Subsample num_cells by sampling from the clone IDs. + # Then just take the first indices for the clone and nonclones, since + # the ordering is random anyway. + new_meta = random.choice(new_meta, size=num_cells , replace=False) + new_af = np.append(new_c[:(new_meta==1).sum()], + new_nonc[:(new_meta==0).sum()]) + + #new_af[c] + return new_af, new_meta + + +def simulate_growth(cell_af, clone_meta, clone_growth, non_clone_growth=0.5, num_cells=None): + """ + + :param cell_af: iteration-by-cells AF + :param clone_meta: |cells| np array indicating if it is the clone or not + :param clone_growth: Poisson parameter for the clone cells + :param non_clone_growth: poisson parameter for non-clone cells + :param num_cells: Number of cells to sample from after growth. If None, defaults to the current number of cells + :return: + """ + n_sim = cell_af.shape[0] + n_cells_orig = cell_af.shape[1] + + # For each clone, see how they grow with lambda + if num_cells is None: + num_cells = n_cells_orig + + cell_af_growth = np.zeros(n_sim, num_cells) + cell_af_meta = -1*np.ones(n_sim, num_cells) + + for sim in tqdm(range(n_sim)): + new_af, new_meta = grow_poisson(cell_af[sim], clone_meta, clone_growth, non_clone_growth, num_cells) + cell_af_growth[sim] = new_af + cell_af_meta[sim] = new_meta + + return cell_af_growth, cell_af_meta + + +def generate_coverage(num_cells, num_pos=None, cov_constant=None, mu_cov_per_cell=None, mu_dist_reads=None, type='constant'): + """ + There are different modes to the coverage, either a constant or through a distribution. + :return: + """ + c = np.zeros([num_cells, num_pos]) + if type == 'constant': + c[:, :] = cov_constant + return c + elif type=="poisson": + # Get the number of coverage per cell based on poisson (should be reads) + num_reads_per_cell = random.poisson(lam=mu_cov_per_cell, size=num_cells) + + # Number of reads at each position, based on the average for each cell + for i in num_cells: + c[i,:] = random.poisson(num_reads_per_cell[i], size=num_pos) + return c + + def plot_multiple_rocs(rocs): ## Needed for putting all curves in same space base_fpr = np.linspace(0, 1, 101) diff --git a/src/simulations/fullsimulation.py b/src/simulations/fullsimulation.py new file mode 100644 index 00000000..7d27ba3f --- /dev/null +++ b/src/simulations/fullsimulation.py @@ -0,0 +1,268 @@ +#import pymc3 as pm +import numpy as np +from numpy import random +import os +import pandas as pd +from tqdm import tqdm +#from src.config import ROOT_DIR +from sklearn.metrics import roc_curve, average_precision_score, confusion_matrix +import matplotlib.pyplot as plt +import pickle +import seaborn as sns +import glob +from sklearn.cluster import KMeans +from sklearn import metrics +from scipy.spatial.distance import cdist +from pandarallel import pandarallel + +from mplh.color_utils import get_colors +from mplh.fig_utils import legend_from_color +from mplh import cluster_help as ch +from src.simulations.utils.config import read_config_file, write_config_file + +from dynamicTreeCut import cutreeHybrid +from scipy.spatial.distance import pdist +from scipy.cluster.hierarchy import linkage +from sklearn.model_selection import ParameterGrid +from src.simulations.utils.config import check_required + +from .simulation import Simulation + + +# Does this ruin running the MCMC? I don't think so, b/c that format is going to be put in after anyway +class FullSimulation: + """ + Class that simulates cell growth for lineage tracing. Reads in a + parameter file and runs a certain number of iterations based on + the num_iterations parameter. + + :ivar n_iter: Number of iterations + :type n_iter: int + :ivar num_cells: Number of cells to sequence + :type num_cells: int + + :ivar sim: Each index is a different iteration of the simulation. + :type sim: pandas Series + + """ + def __init__(self, params_f): + params = read_config_file(params_f) + self.n_iter = params['num_iterations'] + self.num_cells = params['num_cells'] + self.params = params + + # Store the metrics with this + self.metrics = dict() + + # Files to save + self.outdir = os.path.join(self.params['local_outdir']) + self.data_outdir = os.path.join(self.params['data_outdir']) + self.f_save_data = os.path.join(self.data_outdir, + self.params['name'] + '.p') + self.f_save = os.path.join(self.outdir, self.params['name'] + '.p') + self.f_save_metrics = self.f_save.replace('.p', '.metrics.tsv') + self.f_save_cluster = self.f_save.replace('.p', '.cluster.tsv') + self.f_save_befaft = self.f_save.replace('.p', '.before_after.tsv') + self.f_save_rocs = self.f_save.replace('.p', '.rocs.p') + + + return + #for i in self.n_iter: + + def run(self): + """ + Runs the simulation and stores it in sim attr. Will also pickle + the objects and save. + + This uses Pandaralel to parallelize the runs. + :return: + """ + # Parallelize df + df = pd.Series(index=range(self.n_iter)) + df = df.apply(self.run_sim, args=(self.params,)) + + #pandarallel.initialize(nb_workers=self.params['cpus']) + #df = df.parallel_apply(self.run_sim, args=(self.params,)) + + self.sim = df + return + + @staticmethod + def run_sim(x, params): + """Run iteration of simulation. + + For a single iteration, it will initialize, grow, subsample, + and merge the before stimulus and after stimulus variables. + It willl also run + :param x: Placeholder variable + :param params: The parameter dictionary to use + :type params: dict + :return: + """ + s = Simulation(params) + s.initialize() + s.grow() + s.subsample_new(to_delete=True) + s.combine_init_growth() + return s + + def run_metrics(self): + """ + Get metrics performances and save. + :return: + """ + self.sim_performance_dominant(group='both') + self.stats_before_after() + # self.cluster_before_after() + + + def flatten_sim(self): + ## TODO + # This will extract out the classes of df + return + + def sim_performance_dominant(self, group='both'): + """ + Will colect metrics that are averaged over the simulations. + These are specifically for looking at the main, dominant clone, + and what the allele-frequency of that clone variant + is for each cell. + + :param group: {'init', 'growth', 'both'} This will indicate to group by + :ivar dropout: Number of dominant clone cells that have 0 reads + at the lineage variant position. + :type dropout: list + :ivar prec_scores: sklearn average precision score based on + the allele frequencies seen in the dominant clone cells versus + the non-clone cells. + :type prec_scores: list + :ivar rocs: ROC curves for each iteration based on allele + frequencies. + + :return: + """ + dropout = [] + rocs = [] + prec_scores = [] + + + for iter, s in enumerate(self.sim.values): + # First get the dominant clone , which is indexed as 1 + mt_pos = s.clone_mt_dict[1] + # TODO account for mt_pos being a list not an int + if group == 'init': + clones = s.clone_cell + cell_af = s.cell_af.loc[:,mt_pos] + elif group == 'growth': + clones = s.new_clone_cell + cell_af = s.new_cell_af.loc[:,mt_pos] + elif group == 'both': + #clones = pd.concat((s.clone_cell, s.subsample_new_clone_cell)).reset_index(drop=True) + #cell_af = pd.concat((s.cell_af.loc[:,mt_pos], s.subsample_new_cell_af.loc[:,mt_pos])).reset_index(drop=True) + clones = s.combined_clones + cell_af = s.combined_cell_af.loc[:,mt_pos] + else: + raise ValueError('group variable not properly set.') + + y_true = clones.values.copy() + y_true[y_true != 1] = 0 # Set nondominant clones to 0 + rocs.append(roc_curve(y_true, cell_af)) + prec_scores.append(average_precision_score(y_true, cell_af)) + dropout.append((cell_af[clones==1]==0).sum()/cell_af.shape[0]) + + self.dropout = dropout + self.prec_scores = prec_scores + self.rocs = rocs + pd.DataFrame([prec_scores, dropout], index=['Precision', 'Dropout']).to_csv(self.f_save_metrics, sep='\t') + self.metrics['prec_scores'] = prec_scores + self.metrics['dropout'] = dropout + self.metrics['rocs'] = rocs + pickle.dump(rocs, open(self.f_save_rocs, 'wb')) + + return + + + def reduce_cells(self, cell_af): + #self.sim + return + + + def stats_before_after(self, clone_id=1): + b_a_df = pd.DataFrame(index=np.arange(0,len(self.sim)), columns=["Before", "After", "A/B"], dtype=str) + for iter, s in enumerate(self.sim.values): + b_clones = s.clone_cell + a_clones = s.subsample_new_clone_cell + b_a_df.at[iter, "Before"] = (b_clones == clone_id).sum() + b_a_df.at[iter, "After"] = (a_clones==clone_id).sum() + b_a_df.at[iter,"A/B"] = (b_a_df.at[iter, "After"]/b_a_df.at[iter, "Before"]) + self.b_a_df = b_a_df + b_a_df.to_csv(self.f_save_befaft, sep='\t') + self.metrics['b_a_df'] = b_a_df + return + + + def cluster_before_after(self): + """ + Loops through the simulations and for each, + it clusters the cells. + + :ivar cluster_results: Cluster labels for each cell in each + iteration. + :type List of tuples, which is a list of + a tuple, where the tuple is indexed by the cell and the value + is the cell's cluster label + """ + cluster_results = [] + print('clustering') + for s in tqdm(self.sim.values): + cluster_results.append(s.cluster(s.combined_cell_af)) + print(len(cluster_results[-1])) + self.cluster_results = cluster_results + + + def stats_cluster_before_after(self, clone_id=1): + """ + Confusion matrix for clustering the proper clone cells together. + :param clone_id: Which clone to get metrics for + :return: + """ + + + b_a_df = pd.DataFrame(index=len(self.sim), + columns=["TN", "FP", "FN", "TP"], dtype=int) + for ind, s in enumerate(self.sim.values): + y_true = s.combined_clones + y_true[y_true!=1] = 0 + y_pred = self.cluster_results[ind] + + # y_true, y_pred + tn, fp, fn, tp = confusion_matrix(y_true, y_pred).ravel() + b_a_df.loc[ind] = [tn, fp, fn, tp] + self.b_a_df = b_a_df + return + + + def save(self, f_save=None): + if f_save is None: + f_save = self.f_save_data + f = open(f_save, 'wb') + pickle.dump(self.__dict__, f, 2) + f.close() + + + def load(self, f_save=None): + #filename = self.params['filename'] + if f_save is None: + f_save = self.f_save + f = open(f_save, 'rb') + tmp_dict = pickle.load(f) + f.close() + self.__dict__.update(tmp_dict) + + +def main(): + return + + +if "__name__" == "__main__": + main() \ No newline at end of file diff --git a/src/simulations/parametersweep.py b/src/simulations/parametersweep.py new file mode 100644 index 00000000..d2fefc82 --- /dev/null +++ b/src/simulations/parametersweep.py @@ -0,0 +1,295 @@ +#import pymc3 as pm +import numpy as np +import os +import pandas as pd +import pickle +import seaborn as sns +from pandarallel import pandarallel +pandarallel.initialize(nb_workers=32) +import matplotlib.pyplot as plt + +from mplh.color_utils import get_colors +from mplh.fig_utils import legend_from_color +from mplh import cluster_help as ch +from src.simulations.utils.config import read_config_file, write_config_file + +from dynamicTreeCut import cutreeHybrid +from scipy.spatial.distance import pdist +from scipy.cluster.hierarchy import linkage +from sklearn.model_selection import ParameterGrid +from src.simulations.utils.config import check_required + + +from .fullsimulation import FullSimulation + +""" Run the simulation similar to in Extended Data Fig 3 from + Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling""" + + +def replace_item(obj, key, replace_value): + # https: // stackoverflow.com / a / 45335542 + for k, v in obj.items(): + if isinstance(v, dict): + obj[k] = replace_item(v, key, replace_value) + if key in obj: + obj[key] = replace_value + return obj + + +class ParameterSweep: + """ + A class for running a lineage simulation with varying parameters. + + :ivar outdir: Directory to save all output to + :ivar sweep_params: The hyperparameters dictionary used + :ivar default_params: The baseline parameters used. + :ivar metrics: pd DataFrame that contains output metrics + """ + def __init__(self, default_params_f, sweep_params_f): + """ + + Initialize ParameterSweep creates the pipeline yaml files to be + run with run_sweep. + :param default_params_f: File that contains the baseline + parameters for the simulation that all runs will use. + Grid is the key in the parameter file that contains the + hyperparameters. + :type default_params_f: str + :param sweep_params_f: File that contains the hyperparameters to + do a grid of all parameters to run the pipeline on. + :type str + + """ + params = read_config_file(default_params_f) + sweep_params = read_config_file(sweep_params_f) + self.sweep_params_f = sweep_params_f + self.default_params_f = default_params_f + self.sweep_params = sweep_params + self.default_params = params + + # Create the yaml files in the directory indicated by local_outdir and prefix in sweep_params_f + self.outdir = os.path.join(sweep_params["outdir"], sweep_params["prefix"]) + if not os.path.exists(self.outdir): + os.makedirs(self.outdir) + self.f_save = \ + os.path.join(self.outdir,self.sweep_params['prefix'] + '.p') + self.tmp_f_save = self.f_save.replace('.p', '') + '_tmp.p' + + self.data_outdir = os.path.join(sweep_params['data_outdir'], sweep_params["prefix"]) + if not os.path.exists(self.data_outdir): + os.makedirs(self.data_outdir) + + # Create a grid. + # Loop through and set each parameter in the the params grid parameter. + self.params_df = pd.DataFrame(list(ParameterGrid(sweep_params['grid']))) + params_dict = dict() + + for ind, val in self.params_df.iterrows(): + f_name = os.path.join(self.outdir, str(ind)+'.yaml' ) + # Create the name + params['name'] = str(ind) + params['data_outdir'] = self.data_outdir + params['local_outdir'] = self.sweep_params["outdir"] + params['prefix'] = self.sweep_params["prefix"] + for name, v in val.iteritems(): + # Set the specific variables that need to be updated + if name == 'dominant_clone_sizes': + params["initialize"]["clone_sizes"][1] = v + # Set the non-clone such that all clones sum to 1 + params["initialize"]["clone_sizes"][0] = 1-sum(params["initialize"]["clone_sizes"][1:]) + assert(np.abs(sum(params["initialize"]["clone_sizes"]) - 1)<0.0001) + elif name == 'dominant_het': + params["het"][0] = v + elif name == 'dominant_growth': + params["growth"]["binomial"]["rates"][1] = v + else: # These parameters assumed to have the same name + # In both files + params = replace_item(params, name, v) + write_config_file(f_name, params) + params_dict[f_name] = params + return + + + @staticmethod + def run_single_sweep(f, outdir): + print(f'Running file {f}') + params_f = os.path.join(outdir, str(f) + '.yaml') + sim = FullSimulation(params_f) + sim.run() + sim.run_metrics() + sim.save() + return sim.metrics + + def run_sweep(self, subset=None): + """ Loops through params_df and runs the simulation on that parameter. + + Each run will be saved, and not stored. However, the metrics + will be stored here. + :param subset: Which files to run the simulation. If list, + list of files to run on, if int, number of files to randomly + choose. If None, run on all. + :type subset: int or None or list (default=None) + """ + params_df = self.params_df + if isinstance(subset, int): + params_df = params_df.sample(n=subset) + + sweep_results_df = pd.Series(index=params_df.index, data=params_df.index) + ### + #sweep_results_df = sweep_results_df.apply(self.run_single_sweep, args=(self.outdir,)) + pandarallel.initialize(nb_workers=self.sweep_params['cpus']) + sweep_results_df = sweep_results_df.parallel_apply(self.run_single_sweep, args=(self.outdir,)) + ### + + self.sweep_results = sweep_results_df + + # sweep_results = dict() + # + # for f, val in params_df.iterrows(): + # params_f = os.path.join(self.outdir, str(f) +'.yaml') + # print(f"Running with file: {f}") + # sim = FullSimulation(params_f) + # sim.run() + # sim.run_metrics() + # sim.save() + # + # # Only store the current metrics, not the entire simulation. + # sweep_results[f] = sim.metrics + # #self.save(f_save=self.tmp_f_save) + # self.sweep_results = sweep_results + return + + + def plot_sensitivity_and_dropout(self): + """ + Scatterplots of the average precision score and dropout + against variant heteroplasmy. + + Additional simulation parameters used for groupings are + coverage (color), and error rate (column). + Uses sklearn's average_precision_score to get precision. + For dropout, estimates how many times the counts are 0 in the + clone mitochondrial variant. + """ + + metrics = self.params_df.copy() + metrics['Avg. Precision'] = -1.0 + metrics['% dropout'] = -1.0 + + # Add these results to self.results, which has the meta information too + for ind, val in self.params_df.iterrows(): + curr_results = self.sweep_results[ind] + dropout = curr_results['dropout'] + prec_scores = curr_results['prec_scores'] + rocs = curr_results['rocs'] + + metrics.at[ind, 'Avg. Precision'] = np.mean(prec_scores) + metrics.at[ind, '% dropout'] = np.mean(dropout) + + self.metrics = metrics + """df that contains simulation performance metric. + """ + # Seaborn Factorplot + g = sns.FacetGrid(data=metrics, col="het_err_rate", hue="cov_constant") + g.map(sns.scatterplot, "dominant_het", "Avg. Precision") + g.add_legend() + g.savefig(os.path.join(self.outdir,'precision.png')) + + g = sns.FacetGrid(data=metrics, col="het_err_rate", hue="cov_constant") + g.map(sns.scatterplot, "dominant_het", "% dropout") + g.add_legend() + g.savefig(os.path.join(self.outdir, 'dropout.png')) + return None + + def plot_ppv(self): + return + + + def cluster_before_after(self): + for f in self.sweep_results: + self.sweep_results[f].cluster_before_after() + return + + + def plot_before_after_all_clones(self): + """ + Plot the growth of each clone. Boxplots with x-axis being + the growth rate for the dominant clone, the y-axis the + after/before ratio, the color the dominant clone cell size. + + # Expand params_df to include each iteration, which will + # allow for violinplots. This will lead to + params_df.shape[0]*num_iterations rows. + :return: + """ + df_full = [] + for ind, val in self.params_df.iterrows(): + curr_results = self.sweep_results[ind] + b_a_df = curr_results['b_a_df'] + # Each element will be a list of the values. + s = self.params_df.loc[ind].copy() + curr = pd.DataFrame([s.copy()] * len(b_a_df)) + curr["A/B"] = b_a_df["A/B"].values + df_full.append(curr) + + df_full = pd.concat(df_full) + df_full = df_full.astype( + {'dominant_growth': str, 'dominant_clone_sizes': str, + 'A/B': float}) + + sns.violinplot(data=df_full, y="A/B", hue="dominant_growth", + x="dominant_clone_sizes") + plt.savefig(os.path.join(self.outdir, 'growth_before_after.png')) + #g.savefig(os.path.join(self.outdir, 'precision.png')) + return None + + def plot_before_after_true_growth(self): + """ + Plot the growth of cells in each clone before and after. + Dotplot/heatmap, where each row is a het value, each column + is growth rate, and the value is dominant clone cells + growth (after/before). Can make multiple where each column is + coverage, each row is error rate. + + :return: + """ + return + + def plot_before_after_cluster_growth(self): + """ + Plot the growth of cells in each clone before and after. + Dotplot/heatmap, where each row is a het value, each column + is growth rate, and the value is dominant clone cell cluster + growth (after/before). Can make multiple where each column is + coverage, each row is error rate. + :return: + """ + return + + + def plot_error_cluster_growth(self): + """ + Plot the deviation of the growth rates for each pipeline run. + If A=true growth rate, B=predicted, (C = A-B) + :return: + """ + + def delete_tmp(self): + if os.path.exists(self.tmp_f_save): + os.remove(self.tmp_f_save) + + def save(self, f_save=None): + if f_save is None: + f_save = self.f_save + f = open(f_save, 'wb') + pickle.dump(self.__dict__, f, 2) + f.close() + + def load(self, f_save=None): + if f_save is None: + f_save = self.f_save + #filename = self.params['filename'] + f = open(f_save, 'rb') + tmp_dict = pickle.load(f) + f.close() + self.__dict__.update(tmp_dict) \ No newline at end of file diff --git a/src/simulations/pipeline.py b/src/simulations/pipeline.py index eae4add4..4cd5b82a 100644 --- a/src/simulations/pipeline.py +++ b/src/simulations/pipeline.py @@ -8,57 +8,185 @@ from sklearn.metrics import roc_curve, average_precision_score from scipy import interp import matplotlib.pyplot as plt -from mplh.color_utils import get_colors -from mplh.fig_utils import legend_from_color import pickle -from pandarallel import pandarallel -pandarallel.initialize(nb_workers=24) -from src.simulations.utils.config import read_config_file +import seaborn as sns import glob +from sklearn.cluster import KMeans +from sklearn import metrics +from scipy.spatial.distance import cdist +from pandarallel import pandarallel +pandarallel.initialize(nb_workers=32) +from mplh.color_utils import get_colors +from mplh.fig_utils import legend_from_color +from mplh import cluster_help as ch +from src.simulations.utils.config import read_config_file, write_config_file +from dynamicTreeCut import cutreeHybrid +from scipy.spatial.distance import pdist +from scipy.cluster.hierarchy import linkage +from sklearn.model_selection import ParameterGrid from src.simulations.utils.config import check_required """ Run the simulation similar to in Extended Data Fig 3 from Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling""" +def replace_item(obj, key, replace_value): + # https: // stackoverflow.com / a / 45335542 + for k, v in obj.items(): + if isinstance(v, dict): + obj[k] = replace_item(v, key, replace_value) + if key in obj: + obj[key] = replace_value + return obj + class ParameterSweep: - # TODO Sweep across het, growth rate, coverage, error, cluster size, - def __init__(self, params_dir): - self.params_dir = params_dir - self.files = glob.glob(params_dir+'/*.yaml') - sweep_params = dict() - # Create a dictionary for each parameter across files - for f in self.files: - sweep_params[f] = read_config_file(f) + """ + A class for running a lineage simulation with varying parameters. + + :ivar outdir: Directory to save all output to + :ivar sweep_params: The hyperparameters dictionary used + :ivar default_params: The baseline parameters used. + :ivar metrics: pd DataFrame that contains output metrics + """ + def __init__(self, default_params_f, sweep_params_f): + """ + + Initialize ParameterSweep creates the pipeline yaml files to be + run with run_sweep. + :param default_params_f: File that contains the baseline + parameters for the simulation that all runs will use. + Grid is the key in the parameter file that contains the + hyperparameters. + :type default_params_f: str + :param sweep_params_f: File that contains the hyperparameters to + do a grid of all parameters to run the pipeline on. + :type str + + :attributes: + + + """ + self.sweep_params_f = sweep_params_f + self.default_params_f = default_params_f + params = read_config_file(default_params_f) + sweep_params = read_config_file(sweep_params_f) self.sweep_params = sweep_params + self.default_params = params + + # Create the yaml files in the directory indicated by local_outdir and prefix in sweep_params_f + self.outdir = os.path.join(sweep_params["local_outdir"], sweep_params["prefix"]) + if not os.path.exists(self.outdir): + os.makedirs(self.outdir) + + # Create a grid. + # Loop through and set each parameter in the the params grid parameter. + self.params_df = pd.DataFrame(list(ParameterGrid(sweep_params['grid']))) + params_dict = dict() + + for ind, val in self.params_df.iterrows(): + f_name = os.path.join(self.outdir, str(ind)+'.yaml' ) + for name, v in val.iteritems(): + # Set the specific variables that need to be updated + if name == 'dominant_clone_sizes': + params["initialize"]["clone_sizes"][1] = v + # Set the non-clone such that all clones sum to 1 + params["initialize"]["clone_sizes"][0] = 1-sum(params["initialize"]["clone_sizes"][1:]) + assert(np.abs(sum(params["initialize"]["clone_sizes"]) - 1)<0.0001) + elif name == 'dominant_het': + params["het"][0] = v + elif name == 'dominant_growth': + params["growth"]["binomial"]["rates"][1] = v + else: # These parameters assumed to have the same name + # In both files + params = replace_item(params, name, v) + write_config_file(f_name, params) + params_dict[f_name] = params return - def run_sweep(self): + def run_sweep(self, subset=None): + """ + Loops through self.params_df and runs the simulation on that + parameter. + + :param subset: Which files to run the simulation. If list, + list of files to run on, if int, number of files to randomly + choose. If None, run on all. + :type subset: int or None or list (default=None) + + """ + + params_df = self.params_df + if isinstance(subset, int): + params_df = params_df.sample(n=subset) + sweep_results = dict() - for f in self.sweep_params: - params = self.sweep_params[f] + for f, val in params_df.iterrows(): + params_f = os.path.join(self.outdir, str(f) +'.yaml') print(f"Running with file: {f}") - sim = FullSimulation(params) + sim = FullSimulation(params_f) sim.run() sweep_results[f] = sim + self.sweep_results = sweep_results return - def plot_sensitivity(self, vars=None): + def plot_sensitivity_and_dropout(self): + """ + Scatterplots of the average precision score and dropout + against variant heteroplasmy. + + + Additional simulation parameters used for groupings are + coverage (color), and error rate (column). + Uses sklearn's average_precision_score to get precision. + For dropout, estimates how many times the counts are 0 in the + clone mitochondrial variant. + """ + + metrics = self.params_df.copy() + metrics['Avg. Precision'] = -1 + metrics['% dropout'] = -1 + + # Add these results to self.results, which has the meta information too + for ind, val in self.params_df.iterrows(): + full_sim = self.sweep_results[ind] + dropout = full_sim.dropout + prec_scores = full_sim.prec_scores + rocs = full_sim.rocs + metrics.at[ind, 'Avg. Precision'] = np.mean(prec_scores) + metrics.at[ind, '% dropout'] = np.mean(dropout) + + self.metrics = metrics + # colors, _ = get_colors("categorical", names=coverages, + # n_colors=len(coverages)) + # Seaborn Factorplot + g = sns.FacetGrid(data=metrics, col="het_err_rate", hue="cov_constant") + g.map_dataframe(sns.scatterplot, x="dominant_het", y="Avg. Precision") + g.add_legend() + g.savefig(os.path.join(self.outdir,'precision.png')) + + + g = sns.FacetGrid(data=metrics, col="het_err_rate", hue="cov_constant") + g.map_dataframe(sns.scatterplot, x="dominant_het", y="% dropout") + g.add_legend() + g.savefig(os.path.join(self.outdir, 'dropout.png')) return + def plot_ppv(self): return def cluster_before_after(self): + for f in self.sweep_results: + self.sweep_results[f].cluster() return - def save(self, f_save=None): - if f_save is None: - f_save = os.path.join(self.params['local_outdir'], self.params['prefix']+'.p') + + def save(self): + f_save = os.path.join(self.outdir, self.sweep_params['prefix']+'.p') f = open(f_save, 'wb') pickle.dump(self.__dict__, f, 2) f.close() @@ -76,9 +204,9 @@ def load(self, filename): # Does this ruin running the MCMC? I don't think so, b/c that format is going to be put in after anyway class FullSimulation: def __init__(self, params_f): - # TODO parallel_apply over simulations params = read_config_file(params_f) self.n_iter = params['num_iterations'] + self.num_cells = params['num_cells'] self.params = params return #for i in self.n_iter: @@ -86,8 +214,12 @@ def __init__(self, params_f): def run(self): # Parallelize df df = pd.Series(index=range(self.n_iter)) - df = df.parallel_apply(self.run_sim, args=(self.params,)) + df = df.apply(self.run_sim, args=(self.params,)) + #df = df.parallel_apply(self.run_sim, args=(self.params,)) + self.sim = df + #self.cluster_before_after() + self.sim_performance_dominant(group='both') return @staticmethod @@ -96,6 +228,7 @@ def run_sim(x, params): s.initialize() s.grow() s.subsample_new(to_delete=True) + s.combine_init_growth() return s def flatten_sim(self): @@ -103,6 +236,65 @@ def flatten_sim(self): # This will extract out the classes of df return + def sim_performance_dominant(self, group='both'): + """ + Will average metrics over simulations. + :param group: {'init', 'growth', 'both'} This will indicate to group by + :return: + """ + dropout = [] + rocs = [] + prec_scores = [] + + for iter, s in enumerate(self.sim.values): + # First get the dominant clone , which is indexed as 1 + mt_pos = s.clone_mt_dict[1] + # TODO account for mt_pos being a list not an int + if group == 'init': + clones = s.clone_cell + cell_af = s.cell_af.loc[:,mt_pos] + elif group == 'growth': + clones = s.new_clone_cell + cell_af = s.new_cell_af.loc[:,mt_pos] + elif group == 'both': + #clones = pd.concat((s.clone_cell, s.subsample_new_clone_cell)).reset_index(drop=True) + #cell_af = pd.concat((s.cell_af.loc[:,mt_pos], s.subsample_new_cell_af.loc[:,mt_pos])).reset_index(drop=True) + clones = s.combined_clones + cell_af = s.combined_cell_af.loc[:,mt_pos] + else: + raise ValueError('group variable not properly set.') + + y_true = clones.values.copy() + y_true[y_true != 1] = 0 # Set nondominant clones to 0 + rocs.append(roc_curve(y_true, cell_af)) + prec_scores.append(average_precision_score(y_true, cell_af)) + dropout.append((cell_af[clones==1]==0).sum()/cell_af.shape[0]) + + + + self.dropout = dropout + self.prec_scores = prec_scores + self.rocs = rocs + return + + + def reduce_cells(self, cell_af): + #self.sim + return + + + def cluster_before_after(self): + cluster_results = [] + print('clustering') + for s in tqdm(self.sim.values): + cluster_results.append(s.cluster(s.combined_cell_af)) + print(len(cluster_results[-1])) + self.cluster_results = cluster_results + return + + + + def save(self, f_save=None): if f_save is None: f_save = os.path.join(self.params['local_outdir'], self.params['prefix']+'.p') @@ -120,7 +312,11 @@ def load(self, filename): class Simulation: def __init__(self, params_f): - params = read_config_file(params_f) + if isinstance(params_f, str): + params = read_config_file(params_f) + else: + params = params_f + self.params = params check_required(params, ['initialize', 'num_cells', 'num_mt_positions', 'prefix']) self.prefix = params['prefix'] @@ -150,18 +346,18 @@ def grow(self): def clone_counts_to_cell_series(clone_counts): clone_counts = np.array(clone_counts) num_cells = clone_counts.sum() - clone_cell_df = -1 * np.ones(shape=[num_cells, ]) + clone_cell = -1 * np.ones(shape=[num_cells, ]) - clone_cell_df[:clone_counts[0]] = 0 + clone_cell[:clone_counts[0]] = 0 for ind, val in enumerate(clone_counts[1:]): start = clone_counts[:ind + 1].sum() end = clone_counts[:ind + 1].sum() + val # starts at sum(clone_counts[i-1]) ends at clone_counts[i].sum() - clone_cell_df[start:end] = ind + 1 + clone_cell[start:end] = ind + 1 - clone_cell_df = pd.Series(clone_cell_df, dtype=int) - return clone_cell_df + clone_cell = pd.Series(clone_cell, dtype=int) + return clone_cell def init_clone_dict(self): ### Add in potential to overwrite the values @@ -172,23 +368,22 @@ def init_clone_dict(self): # Option 1: List of fraction of size of each clone. 0s are nonclone size, listed first if type(clones) == list: - #clone_cell_df = pd.Series(index=range(num_cells)) + #clone_cell = pd.Series(index=range(num_cells)) clone_counts = np.random.multinomial(num_cells, clones) - clone_cell_df = self.clone_counts_to_cell_series(clone_counts) - self.clone_cell_df = clone_cell_df + clone_cell = self.clone_counts_to_cell_series(clone_counts) + self.clone_cell = clone_cell # Option 2: 1 clone. ID'd as 1 elif type(clones) == int: #One number for dominant clone. the others are not. - clone_cell_df = np.zeros(shape=[num_cells,]) - clone_cell_df[:num_cells] = 1 - clone_cell_df = clone_cell_df[::-1] - clone_cell_df = pd.Series(clone_cell_df, dtype=int) - self.clone_cell_df = clone_cell_df + clone_cell = np.zeros(shape=[num_cells,]) + clone_cell[:num_cells] = 1 + clone_cell = clone_cell[::-1] + clone_cell = pd.Series(clone_cell, dtype=int) + self.clone_cell = clone_cell # Option 3 To ADD, beta binomial and more complex distributions - self.num_clones = len(set(clone_cell_df.values))-1 # Remove the non-clone - - return clone_cell_df + self.num_clones = len(set(clone_cell.values))-1 # Remove the non-clone + return clone_cell def init_cell_coverage(self): @@ -229,7 +424,7 @@ def init_cell_af(self): hets = self.params['het'] q = self.params['het_err_rate'] - clone_df = self.clone_cell_df + clone_df = self.clone_cell num_clones = self.num_clones n_cells = self.num_cells n_mt = self.num_mt_positions @@ -251,6 +446,8 @@ def init_cell_af(self): # If there is a heteroplasmy table in params, it is list of mutant heteroplasmy AFs. # If not, will randomly draw based on number of clones if type(hets) == list: + if (len(hets) != num_clones): + print('here') assert(len(hets) == num_clones) ## Loop through each clone, @@ -314,7 +511,7 @@ def average_clone_mt(self): return def extract_clone_cells(self, clone_id): - ids = np.flatnonzero(self.clone_cell_df == clone_id) + ids = np.flatnonzero(self.clone_cell == clone_id) return ids def simulate_expand_cells_af(self, af, growth_inds, sigma): @@ -353,7 +550,6 @@ def grow_binomial(self, p): #new_ids = new_cells = self.simulate_expand_cells_af(new_cells, growth_inds, sigma) - new_dict[curr_clone] = new_cells # Create list of cells @@ -365,7 +561,7 @@ def grow_binomial(self, p): ## Add death + stimulation rate as well as growth # Save the new cell clones df and cell af clone_counts = [i.shape[0] for i in new_dict.values()] - self.new_cell_clone = self.clone_counts_to_cell_series(clone_counts) + self.new_clone_cell = self.clone_counts_to_cell_series(clone_counts) self.new_cell_af = pd.DataFrame(new_dict[0]) for clone in range(1, self.num_clones+1): @@ -386,13 +582,31 @@ def subsample_new(self, to_delete=False): else: self.subsample_new_cell_af = new_cell_af.sample(n=self.num_cells) - self.subsample_new_cell_clone = self.new_cell_clone.loc[ + self.subsample_new_clone_cell = self.new_clone_cell.loc[ self.subsample_new_cell_af.index] if to_delete: self.new_cell_af = None - self.new_cell_clone = None - + self.new_clone_cell = None + + + def combine_init_growth(self): + clones = pd.concat( + (self.clone_cell, self.subsample_new_clone_cell)).reset_index( + drop=True) + combined_cell_af = self.cell_af.append(self.subsample_new_cell_af).reset_index(drop=True) + + combined_meta = np.concatenate((np.ones(shape=[self.cell_af.shape[0],]), np.zeros(shape=[self.subsample_new_cell_af.shape[0]]))) + combined_meta = pd.Series(combined_meta, name='After Growth', dtype=int) + assert(combined_meta.shape[0] == self.cell_af.shape[0]+self.subsample_new_cell_af.shape[0]) + assert (combined_cell_af.shape[0] == self.cell_af.shape[0] + + self.subsample_new_cell_af.shape[0]) + assert(combined_meta.shape[0] == clones.shape[0]) + assert (combined_cell_af.shape[0] == clones.shape[0]) + self.combined_meta = combined_meta + self.combined_clones = clones + self.combined_cell_af = combined_cell_af + return def save(self, f_save=None): if f_save is None: @@ -417,12 +631,46 @@ def load(self): def compare_before_after(self): return + @staticmethod + def plot_cluster(cell_af, cell_meta=None, mt_meta=None, f_save=None): + ch.plot_cluster(cell_af, row_meta=cell_meta, col_meta=mt_meta, + fsave=f_save, to_col_clust=False, to_z=True) + + @staticmethod + def cluster(cell_af): + """ + Dynamic tree clustering of the rows of cell_af + :param cell_af: + :return: + """ + distances = pdist(cell_af, "euclidean") + link = linkage(distances, "average") + clusters = cutreeHybrid(link, distances)['labels'] + return clusters + + @staticmethod + def cluster_kmeans(cell_af): + distortions = [] + inertias = [] + mapping1 = {} + mapping2 = {} + K = range(1, 10) + + for k in K: + # Building and fitting the model + kmeanModel = KMeans(n_clusters=k).fit(cell_af) + kmeanModel.fit(cell_af) + + distortions.append(sum( + np.min(cdist(cell_af, kmeanModel.cluster_centers_, 'euclidean'), + axis=1)) / cell_af.shape[0]) + inertias.append(kmeanModel.inertia_) + + mapping1[k] = sum( + np.min(cdist(cell_af, kmeanModel.cluster_centers_, 'euclidean'), + axis=1)) / cell_af.shape[0] + mapping2[k] = kmeanModel.inertia_ -# s = Simulation(params) -# s.grow() -# s.compare_before_after() -# s.cluster() -# s.get_variants() def main(): return diff --git a/src/simulations/plots.py b/src/simulations/plots.py index 73dfc9c3..87837467 100644 --- a/src/simulations/plots.py +++ b/src/simulations/plots.py @@ -2,9 +2,22 @@ class plots: def __init__(self): return +class plot_rocs(rocs): + def __init__(self): + return + def plot_multiple_rocs(self): + ## Needed for putting all curves in same space + base_fpr = np.linspace(0, 1, 101) + tprs = [] + for roc in rocs: + fpr, tpr = roc[0], roc[1] + tpr = interp(base_fpr, fpr, tpr) + tpr[0] = 0.0 + tprs.append(tpr) - -class plot_ppc(plots): - def __init__(self): - return \ No newline at end of file + tprs = np.array(tprs) + print(tprs) + print(len(tprs)) + mean_tprs = tprs.mean(axis=0) + std = tprs.std(axis=0) \ No newline at end of file diff --git a/src/simulations/simulation.py b/src/simulations/simulation.py new file mode 100644 index 00000000..f6c81d73 --- /dev/null +++ b/src/simulations/simulation.py @@ -0,0 +1,458 @@ +#import pymc3 as pm +import numpy as np +from numpy import random +import os +import pandas as pd +from tqdm import tqdm +#from src.config import ROOT_DIR +import matplotlib.pyplot as plt +import pickle +import seaborn as sns +import glob +from sklearn.cluster import KMeans +from sklearn import metrics +from scipy.spatial.distance import cdist +from pandarallel import pandarallel +pandarallel.initialize(nb_workers=32) + +from mplh.color_utils import get_colors +from mplh.fig_utils import legend_from_color +from mplh import cluster_help as ch +from src.simulations.utils.config import read_config_file, write_config_file + +from dynamicTreeCut import cutreeHybrid +from scipy.spatial.distance import pdist +from scipy.cluster.hierarchy import linkage +from sklearn.model_selection import ParameterGrid +from src.simulations.utils.config import check_required + + +class Simulation: + """Lineage tracing simulation of one sample + + Will initialize cells based on their parameters and grow as well. This + should be a flexible framework, to add different ways to initialize, grow, + and metrics to have. Additionally can cluster these results. + + :ivar params + :type params: dict + """ + + def __init__(self, params_f): + """ + :param params_f: Parameter yaml file for the specifications + :type params_f: yaml file or dict + """ + if isinstance(params_f, str): + params = read_config_file(params_f) + else: + params = params_f + + self.params = params + check_required(params, ['initialize', 'num_cells', 'num_mt_positions', 'prefix']) + self.prefix = params['prefix'] + self.num_mt_positions = params['num_mt_positions'] + self.num_cells = params['num_cells'] + if not os.path.exists(params['local_outdir']): + os.mkdir(params['local_outdir']) + + + def initialize(self): + self.init_clone_dict() + self.init_cell_coverage() + self.init_cell_af() + #self.init_clone_mt() + + #should be external method + def grow(self): + p = self.params + type = p["growth"]["type"] + if type == "poisson": + self.grow_poisson(p['growth']['poisson']) + elif type == "binomial": + self.grow_binomial(p['growth']['binomial']) + return + + # Static Method + @staticmethod + def clone_counts_to_cell_series(clone_counts): + """ + Args: + clone_counts: + """ + clone_counts = np.array(clone_counts) + num_cells = clone_counts.sum() + clone_cell = -1 * np.ones(shape=[num_cells, ]) + + + clone_cell[:clone_counts[0]] = 0 + for ind, val in enumerate(clone_counts[1:]): + start = clone_counts[:ind + 1].sum() + end = clone_counts[:ind + 1].sum() + val + # starts at sum(clone_counts[i-1]) ends at clone_counts[i].sum() + clone_cell[start:end] = ind + 1 + + clone_cell = pd.Series(clone_cell, dtype=int) + return clone_cell + + def init_clone_dict(self): + ### Add in potential to overwrite the values + + # Gets the clone dictionary. Should also have clone to mt dict. + clones = self.params['initialize']['clone_sizes'] + num_cells = self.num_cells + + # Option 1: List of fraction of size of each clone. 0s are nonclone size, listed first + if type(clones) == list: + #clone_cell = pd.Series(index=range(num_cells)) + clone_counts = np.random.multinomial(num_cells, clones) + clone_cell = self.clone_counts_to_cell_series(clone_counts) + self.clone_cell = clone_cell + # Option 2: 1 clone. ID'd as 1 + elif type(clones) == int: #One number for dominant clone. the others are not. + clone_cell = np.zeros(shape=[num_cells,]) + clone_cell[:num_cells] = 1 + clone_cell = clone_cell[::-1] + clone_cell = pd.Series(clone_cell, dtype=int) + self.clone_cell = clone_cell + + # Option 3 To ADD, beta binomial and more complex distributions + + self.num_clones = len(set(clone_cell.values))-1 # Remove the non-clone + return clone_cell + + + def init_cell_coverage(self): + """There are different modes to the coverage, either a constant or + through a distribution. :return: + """ + p = self.params['initialize']['coverage'] + type = p['type'] + + num_cells = self.num_cells + num_pos = self.num_mt_positions + c = np.zeros([num_cells, num_pos]) + + if type == 'constant': + c[:, :] = p['cov_constant'] + elif type == "poisson": + # Get the number of coverage per cell based on poisson (should be reads) + mu_cov_per_cell = p['mu_cov_per_cell'] + num_reads_per_cell = random.poisson(lam=mu_cov_per_cell, + size=num_cells) + + # Number of reads at each position, based on the average for each cell + for i in num_cells: + c[i, :] = random.poisson(num_reads_per_cell[i], + size=num_pos) + self.cells_mt_coverage = c + return c + + + def init_cell_af(self): + """Initialize the cell-by-mtPos af dataframe. Unless a clone:mt dict was + provided, the first N MT positions will be the clone AFs. Creates + self.clone_mt_dict and self.cell_af + """ + + p = self.params['initialize'] + + hets = self.params['het'] + q = self.params['het_err_rate'] + clone_df = self.clone_cell + num_clones = self.num_clones + n_cells = self.num_cells + n_mt = self.num_mt_positions + + # Output + cell_af = pd.DataFrame(np.zeros(shape=[n_cells, n_mt])) + + + if 'mt_clone_map' in p and p['mt_clone_map'] is not None: + self.clone_mt_dict = p['mt_clone_map'] + else: + # Each clone points to a mt position + self.clone_mt_dict = dict() + for i in range(1,num_clones+1): + self.clone_mt_dict[i] = i + + # TODO Add the MT clone map so it can contain multiple mutants in lineages + + # If there is a heteroplasmy table in params, it is list of mutant heteroplasmy AFs. + # If not, will randomly draw based on number of clones + if type(hets) == list: + if (len(hets) != num_clones): + print('here') + assert(len(hets) == num_clones) + + ## Loop through each clone, + ## Generate the AF for the clone and non-clones using coverage for each cell + ## Fill in cell_by_af for that position. + for ind in range(1, num_clones+1): + # Generate AF: (clone_df == ind).sum() + n_dom_cells = (clone_df==ind).sum() + het = hets[ind-1] + + curr_mt = self.clone_mt_dict[ind] + + + if p['coverage']['type'] == 'constant': + c = p['coverage']['cov_constant'] + + af_i = random.binomial(c, het, + n_dom_cells) / c + af_j = random.binomial(c, q, + n_cells - n_dom_cells) / c + + # Update the dom_cells and non_dom for the current MT + cell_af.loc[np.flatnonzero(clone_df == ind), curr_mt] = af_i + cell_af.loc[np.flatnonzero(clone_df != ind), curr_mt] = af_j + + # Each cell and position has it's own coverage value, so need to update each + else: + c = self.cells_mt_coverage + #Get the cells coverage for the mt position + curr_mt_cov= c[:, curr_mt] + + # Get cell indicies for the clones and nonclones + curr_clone_inds = np.flatnonzero(clone_df==ind) + curr_nonclone_inds = np.flatnonzero(clone_df!=ind) + for cell in curr_clone_inds: + # Get one value for curr_mt and cell based on coverage + cell_af.loc[cell, curr_mt] = random.binomial(curr_mt_cov[cell], het) + for cell in curr_nonclone_inds: + cell_af.loc[cell, curr_mt] = random.binomial(curr_mt_cov[cell], q) + # Loop through each coverage + #for c in n_dom_cells: + + ##### + # TODO + # Add noise to the other non-lineage positions + ##### + self.cell_af = cell_af + return + + + def init_clone_mt(self): + p = self.params + if p["initialize"]['type'] == 'growth': + ## TODO + # Create a phylogeny and then get the averages of the mutants + self.average_clone_mt() + # If not growth, should aready be there. + return + + def average_clone_mt(self): + return + + def extract_clone_cells(self, clone_id): + """ + Args: + clone_id: + """ + ids = np.flatnonzero(self.clone_cell == clone_id) + return ids + + def simulate_expand_cells_af(self, af, growth_inds, sigma): + """Given a cell-by-af vector, expand the AF. + + Expanded AF occurs by duplicating cells that grew based on the + growth_inds vector. It will add standard error to each af based on sigma + :param af: :param growth: Indices of AF to copy :param sigma: Variance + to add to AF of child. :return: + + Args: + af: + growth_inds: + sigma: + """ + + new_af = af.iloc[growth_inds].copy() + random.normal(0, sigma, size=af.iloc[growth_inds].shape) + new_af.index = np.arange(af.index[-1]+1, af.index[-1]+1+new_af.shape[0]) + new_af = pd.concat((af,new_af), axis=0) + #new_af = np.append(af, np.concatenate(new_af)) + return new_af + + def grow_binomial(self, p): + """ + Args: + p: + """ + timesteps = p["time_steps"] + rates = p["rates"] + + sigma = self.params['growth']["mutant_af_sigma_noise"] + cell_af = self.cell_af + clone_mt_dict = self.clone_mt_dict + + num_clones = self.num_clones+1 + new_dict = {} + for curr_clone in range(num_clones): + curr_rate = rates[curr_clone] + ids = self.extract_clone_cells(curr_clone) + new_cells = cell_af.loc[ids].copy() + for i in range(timesteps): + # Simulate growth for each clone separately. + growth_inds = np.flatnonzero(random.binomial(1, curr_rate, size=new_cells.shape[0])) + #new_ids = + new_cells = self.simulate_expand_cells_af(new_cells, growth_inds, sigma) + + new_dict[curr_clone] = new_cells + # Create list of cells + + ####TODO + ## new_lineage_mutants chances. This will see if a mutation will change + + + ####TODO + ## Add death + stimulation rate as well as growth + # Save the new cell clones df and cell af + clone_counts = [i.shape[0] for i in new_dict.values()] + self.new_clone_cell = self.clone_counts_to_cell_series(clone_counts) + + self.new_cell_af = pd.DataFrame(new_dict[0]) + for clone in range(1, self.num_clones+1): + self.new_cell_af = pd.concat((self.new_cell_af, new_dict[clone]),axis=0).reset_index(drop=True) + return + + + def grow_poisson(self): + # TODO growth of poisson refactor + return + + + def subsample_new(self, to_delete=False): + """ + Args: + to_delete: + """ + new_cell_af = self.new_cell_af + p = self.params + if 'sequence_subsample' in p and p['sequence_subsample'] is not None: + self.subsample_new_cell_af = new_cell_af.sample(n=self.params['sequence_subsample']) + else: + self.subsample_new_cell_af = new_cell_af.sample(n=self.num_cells) + + self.subsample_new_clone_cell = self.new_clone_cell.loc[ + self.subsample_new_cell_af.index] + + if to_delete: + self.new_cell_af = None + self.new_clone_cell = None + + + def combine_init_growth(self): + clones = pd.concat( + (self.clone_cell, self.subsample_new_clone_cell)).reset_index( + drop=True) + combined_cell_af = self.cell_af.append(self.subsample_new_cell_af).reset_index(drop=True) + + combined_meta = np.concatenate((np.ones(shape=[self.cell_af.shape[0],]), np.zeros(shape=[self.subsample_new_cell_af.shape[0]]))) + combined_meta = pd.Series(combined_meta, name='After Growth', dtype=int) + assert(combined_meta.shape[0] == self.cell_af.shape[0]+self.subsample_new_cell_af.shape[0]) + assert (combined_cell_af.shape[0] == self.cell_af.shape[0] + + self.subsample_new_cell_af.shape[0]) + assert(combined_meta.shape[0] == clones.shape[0]) + assert(combined_cell_af.shape[0] == clones.shape[0]) + self.combined_meta = combined_meta + self.combined_clones = clones + self.combined_cell_af = combined_cell_af + return + + def save(self, f_save=None): + """ + Args: + f_save: + """ + if f_save is None: + f_save = os.path.join(self.params['local_outdir'], self.params['prefix']+'.p') + f = open(f_save, 'wb') + pickle.dump(self.__dict__, f, 2) + f.close() + + def save_to_mgatk_format(self): + """Converts into the proper files needed for mgatk. (i.e variant and + coverage files) :return: + """ + + def load(self): + filename = self.params['filename'] + f = open(filename, 'rb') + tmp_dict = pickle.load(f) + f.close() + self.__dict__.update(tmp_dict) + + def compare_before_after(self): + """Creates a df that contains information on the number of cells from + each clone before as well as after. :return: df.at[ind, "Dominant + Before"] = (full_sim.clone_cell == 1).sum() df.at[ind, "Dominant After"] + = (full_sim.subsample_new_clone_cell == 1).sum() + """ + + return + + def cluster_compare_before_after(self): + """Compares the performance of clustering on grouping the same clones + together. :return: + """ + return + + @staticmethod + def plot_cluster(cell_af, cell_meta=None, mt_meta=None, f_save=None): + """ + Args: + cell_af: + cell_meta: + mt_meta: + f_save: + """ + ch.plot_cluster(cell_af, row_meta=cell_meta, col_meta=mt_meta, + fsave=f_save, to_col_clust=False, to_z=True) + + @staticmethod + def cluster(cell_af): + """Dynamic tree clustering of the rows of cell_af :param cell_af: + :return: + + Args: + cell_af: + """ + distances = pdist(cell_af, "euclidean") + link = linkage(distances, "average") + clusters = cutreeHybrid(link, distances)['labels'] + return clusters + + @staticmethod + def cluster_kmeans(cell_af): + """ + Args: + cell_af: + """ + distortions = [] + inertias = [] + mapping1 = {} + mapping2 = {} + K = range(1, 10) + for k in K: + # Building and fitting the model + kmeanModel = KMeans(n_clusters=k).fit(cell_af) + kmeanModel.fit(cell_af) + + distortions.append(sum( + np.min(cdist(cell_af, kmeanModel.cluster_centers_, 'euclidean'), + axis=1)) / cell_af.shape[0]) + inertias.append(kmeanModel.inertia_) + + mapping1[k] = sum( + np.min(cdist(cell_af, kmeanModel.cluster_centers_, 'euclidean'), + axis=1)) / cell_af.shape[0] + mapping2[k] = kmeanModel.inertia_ + + + +def main(): + return + + +if "__name__" == "__main__": + main() \ No newline at end of file diff --git a/src/simulations/test_pipeline.py b/src/simulations/test_pipeline.py deleted file mode 100644 index e67049d5..00000000 --- a/src/simulations/test_pipeline.py +++ /dev/null @@ -1,33 +0,0 @@ -from src.simulations.pipeline import Simulation, FullSimulation -from src.simulations.utils.config import read_config_file -from src.config import RESULTS, ROOT_DIR -import time -import os - -os.chdir(RESULTS) -params = os.path.join(ROOT_DIR, 'parameters/simulation/simple.yaml') -#params = read_config_file(params) - - -def test_oneIter(): - s = Simulation(params) - s.initialize() - s.grow() - s.subsample_new(to_delete=False) - s.save(f_save='simulation/simple_oneIter.p') - return - - -def testIter(): - t = time.time() - sim = FullSimulation(params) - sim.run() - print("time", time.time()-t) - sim.save() - - return sim - - - -sim = testIter() - diff --git a/src/simulations/wrap_dominant_clone.py b/src/simulations/wrap_dominant_clone.py deleted file mode 100644 index 3dc2ce38..00000000 --- a/src/simulations/wrap_dominant_clone.py +++ /dev/null @@ -1,9 +0,0 @@ -from src.config import ROOT_DIR, DATA_DIR -import os - -os.chdir(ROOT_DIR) -params_f = "parameters/simulation/clones.yaml" - - -from .dominant_clone import simulate_growth - diff --git a/src/simulations/wrapper_v01.py b/src/simulations/wrapper_v01.py new file mode 100644 index 00000000..160673d2 --- /dev/null +++ b/src/simulations/wrapper_v01.py @@ -0,0 +1,24 @@ +""" +Running the first version of the lineage tracing simulation. +Files are simple_v01.yaml and wrapper_v01.yaml. +1000 iterations, 10000 num_cells +""" + +from src.simulations import Simulation, ParameterSweep, FullSimulation +from src.simulations.utils.config import read_config_file +from src.config import RESULTS, ROOT_DIR +import time +from os.path import join +import os + + +#os.chdir(RESULTS) + +default_params_f = join(ROOT_DIR, 'parameters/simulations/simple_v01.yaml') +sweep_params_f = join(ROOT_DIR, 'parameters/simulations/sweep_v01.yaml') +sweep = ParameterSweep(default_params_f, sweep_params_f) + +sweep.run_sweep() # Runs the simulation +sweep.save() +sweep.plot_before_after_all_clones() +sweep.plot_sensitivity_and_dropout() # plots results \ No newline at end of file diff --git "a/src/test/Icon\r" "b/src/tests/Icon\r" similarity index 100% rename from "src/test/Icon\r" rename to "src/tests/Icon\r" diff --git a/src/test/__init__.py b/src/tests/__init__.py similarity index 100% rename from src/test/__init__.py rename to src/tests/__init__.py diff --git a/src/tests/simulations/__init__.py b/src/tests/simulations/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/src/tests/simulations/test_fullsimulation.py b/src/tests/simulations/test_fullsimulation.py new file mode 100644 index 00000000..6e7320c7 --- /dev/null +++ b/src/tests/simulations/test_fullsimulation.py @@ -0,0 +1,25 @@ +from src.simulations import Simulation, ParameterSweep, FullSimulation +from src.simulations.utils.config import read_config_file +from src.config import RESULTS, ROOT_DIR +import time +from os.path import join +import os +import unittest + + +os.chdir(RESULTS) +params = os.path.join(ROOT_DIR, 'parameters/simulations/test_simple.yaml') +#params = read_config_file(params) + +class TestSum(unittest.TestCase): + def test_iter(self): + t = time.time() + sim = FullSimulation(params) + sim.run() + print("time", time.time()-t) + sim.save() + return sim + +if __name__ == '__main__': + unittest.main() + diff --git a/src/tests/simulations/test_parametersweep.py b/src/tests/simulations/test_parametersweep.py new file mode 100644 index 00000000..d64fce78 --- /dev/null +++ b/src/tests/simulations/test_parametersweep.py @@ -0,0 +1,46 @@ +from src.simulations import Simulation, ParameterSweep, FullSimulation +from src.simulations.utils.config import read_config_file +from src.config import RESULTS, ROOT_DIR +import time +from os.path import join +import os +import unittest + + +os.chdir(RESULTS) +params = os.path.join(ROOT_DIR, 'parameters/simulations/test_simple.yaml') +#params = read_config_file(params) + + +class TestSum(unittest.TestCase): + def test_sweepparams(self): + default_params_f = join(ROOT_DIR, + 'parameters/simulations/test_simple.yaml') + sweep_params_f = join(ROOT_DIR, + 'parameters/simulations/test_sweep.yaml') + sweep = ParameterSweep(default_params_f, sweep_params_f) + + sweep.run_sweep() # Runs the simulation + sweep.save() + x = sweep.plot_before_after_all_clones() + self.assertTrue(x is None) + + x = sweep.plot_sensitivity_and_dropout() # plots results + self.assertTrue(x is None) + # def test_plotsweepparams(self): + # default_params_f = join(ROOT_DIR, + # 'parameters/simulations/test_simple.yaml') + # sweep_params_f = join(ROOT_DIR, + # 'parameters/simulations/test_sweep.yaml') + # sweep = ParameterSweep(default_params_f, sweep_params_f) + # sweep.load() + # x = sweep.plot_before_after_all_clones() + # self.assertTrue(x is None) + # + # x = sweep.plot_sensitivity_and_dropout() # plots results + # self.assertTrue(x is None) + +if __name__ == '__main__': + unittest.main() + + diff --git a/src/tests/simulations/test_simulation.py b/src/tests/simulations/test_simulation.py new file mode 100644 index 00000000..dbc8a3da --- /dev/null +++ b/src/tests/simulations/test_simulation.py @@ -0,0 +1,25 @@ +from src.simulations import Simulation +from src.simulations.utils.config import read_config_file +from src.config import RESULTS, ROOT_DIR +import time +from os.path import join +import os +import unittest + + +os.chdir(RESULTS) +params = os.path.join(ROOT_DIR, 'parameters/simulations/test_simple.yaml') +#params = read_config_file(params) + +class TestSum(unittest.TestCase): + def test_oneIter(self): + s = Simulation(params) + s.initialize() + s.grow() + s.subsample_new(to_delete=False) + s.save(f_save='simulation/simple_oneIter.p') + return + +if __name__ == '__main__': + unittest.main() + diff --git a/src/test_af_filters.py b/src/tests/test_af_filters.py similarity index 78% rename from src/test_af_filters.py rename to src/tests/test_af_filters.py index 078a2203..5dc018da 100644 --- a/src/test_af_filters.py +++ b/src/tests/test_af_filters.py @@ -2,13 +2,16 @@ import numpy as np def test_create_barcode_filter(coverage_tensor, cells_d,bq_tensor,barcode_f): - """ - Use the cells dictionary and the barcode names in barcodes_f to filter for the indicies of the tensors - :param coverage_tensor: - :param cells_d: {cell:index} dictionary for the tensors - :param bq_tensor: - :param barcode_f: + """Use the cells dictionary and the barcode names in barcodes_f to filter + for the indicies of the tensors :param coverage_tensor: :param cells_d: + {cell:index} dictionary for the tensors :param bq_tensor: :param barcode_f: :return: + + Args: + coverage_tensor: + cells_d: + bq_tensor: + barcode_f: """ CB_read_number = pickle.load(open(barcode_f, "rb")) cb_keys = list(CB_read_number.keys()) @@ -32,6 +35,14 @@ def test_create_barcode_filter(coverage_tensor, cells_d,bq_tensor,barcode_f): def test_create_position_counts_filter(coverage_tensor, bq_tensor, pos_d, min_cells=100, min_reads=100): #pos_filter = (coverage_tensor.sum(axis=2) >= min_reads).sum(axis=0) >= min_cells + """ + Args: + coverage_tensor: + bq_tensor: + pos_d: + min_cells: + min_reads: + """ pos_filter = np.where((coverage_tensor.sum(axis=2) >= min_reads).sum( axis=0) >= min_cells)[0] coverage_tensor = coverage_tensor[:, pos_filter,:] @@ -46,6 +57,13 @@ def test_create_position_counts_filter(coverage_tensor, bq_tensor, pos_d, min_ce def test_create_top_positions_filter(coverage_tensor,bq_tensor, pos_dict, topPositions=-1): + """ + Args: + coverage_tensor: + bq_tensor: + pos_dict: + topPositions: + """ coverage_pos = coverage_tensor.sum(axis=2).sum(axis=0) pos_inds = coverage_pos.argsort()[::-1] if topPositions > 0: @@ -65,6 +83,14 @@ def test_create_top_positions_filter(coverage_tensor,bq_tensor, pos_dict, topPos def test_create_top_cells_filter(coverage_tensor, bq_tensor, cell_dict, topCells=-1, by='coverage'): #| cell | - | pos | - | nucs | + """ + Args: + coverage_tensor: + bq_tensor: + cell_dict: + topCells: + by: + """ coverage_cells = coverage_tensor.sum(axis=1).sum(axis=1) cell_inds = coverage_cells.argsort()[::-1] if topCells > 0: @@ -83,6 +109,13 @@ def test_create_top_cells_filter(coverage_tensor, bq_tensor, cell_dict, topCells def bq_filter(coverage_tensor, bq_tensor, pos_d, type='Gaussian'): + """ + Args: + coverage_tensor: + bq_tensor: + pos_d: + type: + """ bq_vals = bq_tensor.flatten() gm = GaussianMixture(n_components=3) gm.fit(bq_vals) diff --git a/src/test_calculate_AF.py b/src/tests/test_calculate_AF.py similarity index 100% rename from src/test_calculate_AF.py rename to src/tests/test_calculate_AF.py diff --git a/src/test_calculate_AF_by_cell.py b/src/tests/test_calculate_AF_by_cell.py similarity index 100% rename from src/test_calculate_AF_by_cell.py rename to src/tests/test_calculate_AF_by_cell.py diff --git "a/src/utils/Icon\r" "b/src/utils/Icon\r" new file mode 100644 index 00000000..e69de29b diff --git a/src/utils/__init__.py b/src/utils/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/src/utils/config.py b/src/utils/config.py new file mode 100644 index 00000000..569f4c03 --- /dev/null +++ b/src/utils/config.py @@ -0,0 +1,149 @@ +""" +Configuration handling +.. todo:: + switch ruamel.yaml to round trip loading + to preserver order and comments? +Authors: + Thomas A. Hopf +""" + +import ruamel.yaml as yaml + + +class MissingParameterError(Exception): + """ + Exception for missing parameters + """ + + +class InvalidParameterError(Exception): + """ + Exception for invalid parameter settings + """ + + +def parse_config(config_str, preserve_order=False): + """ + Parse a configuration string + Parameters + ---------- + config_str : str + Configuration to be parsed + preserve_order : bool, optional (default: True) + Preserve formatting of input configuration + string + Returns + ------- + dict + Configuration dictionary + """ + try: + if preserve_order: + return yaml.load(config_str, Loader=yaml.RoundTripLoader) + else: + return yaml.safe_load(config_str) + except yaml.parser.ParserError as e: + raise InvalidParameterError( + "Could not parse input configuration. " + "Formatting mistake in config file? " + "See ParserError above for details." + ) from e + + +def read_config_file(filename, preserve_order=False): + """ + Read and parse a configuration file. + Parameters + ---------- + filename : str + Path of configuration file + Returns + ------- + dict + Configuration dictionary + """ + with open(filename) as f: + return parse_config(f, preserve_order) + + +def write_config_file(out_filename, config): + """ + Save configuration data structure in YAML file. + Parameters + ---------- + out_filename : str + Filename of output file + config : dict + Config data that will be written to file + """ + if isinstance(config, yaml.comments.CommentedBase): + dumper = yaml.RoundTripDumper + else: + dumper = yaml.Dumper + + with open(out_filename, "w") as f: + f.write( + yaml.dump(config, Dumper=dumper, default_flow_style=False) + ) + + +def check_required(params, keys): + """ + Verify if required set of parameters is present in configuration + Parameters + ---------- + params : dict + Dictionary with parameters + keys : list-like + Set of parameters that has to be present in params + Raises + ------ + MissingParameterError + """ + missing = [k for k in keys if k not in params] + + if len(missing) > 0: + raise MissingParameterError( + "Missing required parameters: {} \nGiven: {}".format( + ", ".join(missing), params + ) + ) + + +def iterate_files(outcfg, subset=None): + """ + Generator function to iterate a list of file + items in an outconfig + Parameters + ---------- + outcfg : dict(str) + Configuration to extract file items for iteration from + subset : list(str) + List of keys in outcfg to restrict iteration to + Returns + ------- + tuple(str, str, int) + Generator over tuples (file path, entry key, index). + index will be None if this is a single file entry + (i.e. ending with _file rather than _files). + """ + for k, v in outcfg.items(): + # skip items if there is a subset filter and it matches + if subset is not None and k not in subset: + continue + + # also skip in case file has a null value + if v is None: + continue + + # only look at file entries, so skip everything else + # if not (k.endswith("_file") or k.endswith("_files")): + # continue + if k.endswith("_file"): + yield (v, k, None) + elif k.endswith("_files"): + for i, f in enumerate(v): + yield (f, k, i) + else: + # skip any other entries + pass \ No newline at end of file diff --git a/Snakefile b/workflows/Snakefile similarity index 100% rename from Snakefile rename to workflows/Snakefile diff --git a/lineage.snakefile b/workflows/lineage.snakefile similarity index 100% rename from lineage.snakefile rename to workflows/lineage.snakefile diff --git a/simulation.snakefile b/workflows/simulation.snakefile similarity index 100% rename from simulation.snakefile rename to workflows/simulation.snakefile diff --git a/trim.snakefile b/workflows/trim.snakefile similarity index 100% rename from trim.snakefile rename to workflows/trim.snakefile