From 2c2412c2f0294a9ee5fabc3f4eef444d5c773980 Mon Sep 17 00:00:00 2001 From: Nate Guerin Date: Sun, 20 Nov 2022 20:21:22 -0500 Subject: [PATCH] Add mutational signatures for cancer types colorectal cancer, lung adenmocarcinoma, melanoma, and stomach cancer. Also update the version to Osprey 3.3 --- build.gradle.kts | 5 +- .../colorectal_cancer.json | 322 ++++++++++++++++++ .../lung_adenocarcinoma.json | 322 ++++++++++++++++++ .../mutational-signatures/melanoma.json | 322 ++++++++++++++++++ .../mutational-signatures/stomach_cancer.json | 322 ++++++++++++++++++ 5 files changed, 1291 insertions(+), 2 deletions(-) create mode 100755 src/main/julia/resistor/mutational-signatures/colorectal_cancer.json create mode 100755 src/main/julia/resistor/mutational-signatures/lung_adenocarcinoma.json create mode 100755 src/main/julia/resistor/mutational-signatures/melanoma.json create mode 100755 src/main/julia/resistor/mutational-signatures/stomach_cancer.json diff --git a/build.gradle.kts b/build.gradle.kts index 999f90755..5c3718d78 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -59,7 +59,7 @@ group = "edu.duke.cs" * This version number is largely cosmetic, compared to the versioning scheme for the Osprey Service * But it does help users provide some information to developers when reporting issues. */ -version = "4.0.2" +version = "3.3" repositories { mavenCentral() @@ -224,7 +224,8 @@ tasks.withType { maxHeapSize = "2g" useJUnit() failFast = true - Jvm.addModuleArgs(jvmArgs) + // method call appends additional arguments for the JVM + jvmArgs(Jvm.moduleArgs) testLogging { setExceptionFormat("full") diff --git a/src/main/julia/resistor/mutational-signatures/colorectal_cancer.json b/src/main/julia/resistor/mutational-signatures/colorectal_cancer.json new file mode 100755 index 000000000..c7f0bcc03 --- /dev/null +++ b/src/main/julia/resistor/mutational-signatures/colorectal_cancer.json @@ -0,0 +1,322 @@ +{ + "AAA" : { + "ACA" : 0.002251402, + "AGA" : 0.003883608, + "ATA" : 0.000961065 + }, + "AAC" : { + "ACC" : 0.000601336, + "AGC" : 0.005198815, + "ATC" : 0.000504114 + }, + "AAG" : { + "ACG" : 0.001820715, + "AGG" : 0.006886609, + "ATG" : 0.001049023 + }, + "AAT" : { + "ACT" : 0.000835687, + "AGT" : 0.005694241, + "ATT" : 0.001679238 + }, + "ACA" : { + "AAA" : 0.001708509, + "AGA" : 0.000828116, + "ATA" : 0.006498599 + }, + "ACC" : { + "AAC" : 0.001661245, + "AGC" : 0.000727878, + "ATC" : 0.003818251 + }, + "ACG" : { + "AAG" : 0.000264205, + "AGG" : 0.000158004, + "ATG" : 0.015854537 + }, + "ACT" : { + "AAT" : 0.001263405, + "AGT" : 0.000949, + "ATT" : 0.003958479 + }, + "AGA" : { + "AAA" : 0.004413345, + "ACA" : 0.00114861, + "ATA" : 0.005792534 + }, + "AGC" : { + "AAC" : 0.007210625, + "ACC" : 0.0006307, + "ATC" : 0.001896027 + }, + "AGG" : { + "AAG" : 0.003954967, + "ACG" : 0.000572839, + "ATG" : 0.006014902 + }, + "AGT" : { + "AAT" : 0.003958479, + "ACT" : 0.000949, + "ATT" : 0.001263405 + }, + "ATA" : { + "AAA" : 0.000777486, + "ACA" : 0.005692943, + "AGA" : 0.000136402 + }, + "ATC" : { + "AAC" : 0.001909194, + "ACC" : 0.004232849, + "AGC" : 0.000316299 + }, + "ATG" : { + "AAG" : 0.00107702, + "ACG" : 0.005555689, + "AGG" : 0.000627456 + }, + "ATT" : { + "AAT" : 0.001679238, + "ACT" : 0.005694241, + "AGT" : 0.000835687 + }, + "CAA" : { + "CCA" : 0.000524509, + "CGA" : 0.002944184, + "CTA" : 0.000326501 + }, + "CAC" : { + "CCC" : 0.000756944, + "CGC" : 0.003891829, + "CTC" : 0.000420948 + }, + "CAG" : { + "CCG" : 0.000896579, + "CGG" : 0.005946786, + "CTG" : 0.000633509 + }, + "CAT" : { + "CCT" : 0.000627456, + "CGT" : 0.005555689, + "CTT" : 0.00107702 + }, + "CCA" : { + "CAA" : 0.002691811, + "CGA" : 0.000300167, + "CTA" : 0.005243752 + }, + "CCC" : { + "CAC" : 0.002736404, + "CGC" : 0.000422373, + "CTC" : 0.003786673 + }, + "CCG" : { + "CAG" : 0.001058204, + "CGG" : 0.000162736, + "CTG" : 0.012987556 + }, + "CCT" : { + "CAT" : 0.006014902, + "CGT" : 0.000572839, + "CTT" : 0.003954967 + }, + "CGA" : { + "CAA" : 0.009956757, + "CCA" : 0.000110068, + "CTA" : 0.000673967 + }, + "CGC" : { + "CAC" : 0.0165884, + "CCC" : 2.6334e-05, + "CTC" : 0.000372331 + }, + "CGG" : { + "CAG" : 0.012987556, + "CCG" : 0.000162736, + "CTG" : 0.001058204 + }, + "CGT" : { + "CAT" : 0.015854537, + "CCT" : 0.000158004, + "CTT" : 0.000264205 + }, + "CTA" : { + "CAA" : 0.000390422, + "CCA" : 0.002568071, + "CGA" : 0.000145181 + }, + "CTC" : { + "CAC" : 0.000927223, + "CCC" : 0.005547155, + "CGC" : 0.000697439 + }, + "CTG" : { + "CAG" : 0.000633509, + "CCG" : 0.005946786, + "CGG" : 0.000896579 + }, + "CTT" : { + "CAT" : 0.001049023, + "CCT" : 0.006886609, + "CGT" : 0.001820715 + }, + "GAA" : { + "GCA" : 0.000728493, + "GGA" : 0.004281007, + "GTA" : 0.000993413 + }, + "GAC" : { + "GCC" : 0.000258255, + "GGC" : 0.004551004, + "GTC" : 0.000648729 + }, + "GAG" : { + "GCG" : 0.000697439, + "GGG" : 0.005547155, + "GTG" : 0.000927223 + }, + "GAT" : { + "GCT" : 0.000316299, + "GGT" : 0.004232849, + "GTT" : 0.001909194 + }, + "GCA" : { + "GAA" : 0.002754393, + "GGA" : 0.000307573, + "GTA" : 0.008430829 + }, + "GCC" : { + "GAC" : 0.001469207, + "GGC" : 0.000641657, + "GTC" : 0.009348964 + }, + "GCG" : { + "GAG" : 0.000372331, + "GGG" : 2.6334e-05, + "GTG" : 0.0165884 + }, + "GCT" : { + "GAT" : 0.001896027, + "GGT" : 0.0006307, + "GTT" : 0.007210625 + }, + "GGA" : { + "GAA" : 0.004354559, + "GCA" : 0.00060226, + "GTA" : 0.002206242 + }, + "GGC" : { + "GAC" : 0.009348964, + "GCC" : 0.000641657, + "GTC" : 0.001469207 + }, + "GGG" : { + "GAG" : 0.003786673, + "GCG" : 0.000422373, + "GTG" : 0.002736404 + }, + "GGT" : { + "GAT" : 0.003818251, + "GCT" : 0.000727878, + "GTT" : 0.001661245 + }, + "GTA" : { + "GAA" : 0.000512491, + "GCA" : 0.00352488, + "GGA" : 6.5835e-05 + }, + "GTC" : { + "GAC" : 0.000648729, + "GCC" : 0.004551004, + "GGC" : 0.000258255 + }, + "GTG" : { + "GAG" : 0.000420948, + "GCG" : 0.003891829, + "GGG" : 0.000756944 + }, + "GTT" : { + "GAT" : 0.000504114, + "GCT" : 0.005198815, + "GGT" : 0.000601336 + }, + "TAA" : { + "TCA" : 0.000261637, + "TGA" : 0.002018701, + "TTA" : 0.000806968 + }, + "TAC" : { + "TCC" : 6.5835e-05, + "TGC" : 0.00352488, + "TTC" : 0.000512491 + }, + "TAG" : { + "TCG" : 0.000145181, + "TGG" : 0.002568071, + "TTG" : 0.000390422 + }, + "TAT" : { + "TCT" : 0.000136402, + "TGT" : 0.005692943, + "TTT" : 0.000777486 + }, + "TCA" : { + "TAA" : 0.00279994, + "TGA" : 0.000395836, + "TTA" : 0.004466346 + }, + "TCC" : { + "TAC" : 0.002206242, + "TGC" : 0.00060226, + "TTC" : 0.004354559 + }, + "TCG" : { + "TAG" : 0.000673967, + "TGG" : 0.000110068, + "TTG" : 0.009956757 + }, + "TCT" : { + "TAT" : 0.005792534, + "TGT" : 0.00114861, + "TTT" : 0.004413345 + }, + "TGA" : { + "TAA" : 0.004466346, + "TCA" : 0.000395836, + "TTA" : 0.00279994 + }, + "TGC" : { + "TAC" : 0.008430829, + "TCC" : 0.000307573, + "TTC" : 0.002754393 + }, + "TGG" : { + "TAG" : 0.005243752, + "TCG" : 0.000300167, + "TTG" : 0.002691811 + }, + "TGT" : { + "TAT" : 0.006498599, + "TCT" : 0.000828116, + "TTT" : 0.001708509 + }, + "TTA" : { + "TAA" : 0.000806968, + "TCA" : 0.002018701, + "TGA" : 0.000261637 + }, + "TTC" : { + "TAC" : 0.000993413, + "TCC" : 0.004281007, + "TGC" : 0.000728493 + }, + "TTG" : { + "TAG" : 0.000326501, + "TCG" : 0.002944184, + "TGG" : 0.000524509 + }, + "TTT" : { + "TAT" : 0.000961065, + "TCT" : 0.003883608, + "TGT" : 0.002251402 + } +} diff --git a/src/main/julia/resistor/mutational-signatures/lung_adenocarcinoma.json b/src/main/julia/resistor/mutational-signatures/lung_adenocarcinoma.json new file mode 100755 index 000000000..d1256c1ac --- /dev/null +++ b/src/main/julia/resistor/mutational-signatures/lung_adenocarcinoma.json @@ -0,0 +1,322 @@ +{ + "AAA" : { + "ACA" : 0.001296555, + "AGA" : 0.002178105, + "ATA" : 0.002376093 + }, + "AAC" : { + "ACC" : 0.000299724, + "AGC" : 0.002230074, + "ATC" : 0.002032707 + }, + "AAG" : { + "ACG" : 0.001186914, + "AGG" : 0.0035988, + "ATG" : 0.00508743 + }, + "AAT" : { + "ACT" : 0.000402204, + "AGT" : 0.004131507, + "ATT" : 0.002030235 + }, + "ACA" : { + "AAA" : 0.015347823, + "AGA" : 0.004439358, + "ATA" : 0.007001988 + }, + "ACC" : { + "AAC" : 0.012852828, + "AGC" : 0.002596398, + "ATC" : 0.004323732 + }, + "ACG" : { + "AAG" : 0.007230498, + "AGG" : 0.001321383, + "ATG" : 0.005956437 + }, + "ACT" : { + "AAT" : 0.010086003, + "AGT" : 0.002847507, + "ATT" : 0.003973962 + }, + "AGA" : { + "AAA" : 0.00814365, + "ACA" : 0.007072317, + "ATA" : 0.016337817 + }, + "AGC" : { + "AAC" : 0.005172219, + "ACC" : 0.002779725, + "ATC" : 0.010743126 + }, + "AGG" : { + "AAG" : 0.009921048, + "ACG" : 0.004182762, + "ATG" : 0.017835018 + }, + "AGT" : { + "AAT" : 0.003973962, + "ACT" : 0.002847507, + "ATT" : 0.010086003 + }, + "ATA" : { + "AAA" : 0.002378709, + "ACA" : 0.006174201, + "AGA" : 0.000131952 + }, + "ATC" : { + "AAC" : 0.002500698, + "ACC" : 0.001844361, + "AGC" : 0.000193428 + }, + "ATG" : { + "AAG" : 0.004681878, + "ACG" : 0.004929042, + "AGG" : 0.000979173 + }, + "ATT" : { + "AAT" : 0.002030235, + "ACT" : 0.004131507, + "AGT" : 0.000402204 + }, + "CAA" : { + "CCA" : 0.001534311, + "CGA" : 0.002144751, + "CTA" : 0.003455211 + }, + "CAC" : { + "CCC" : 0.001168908, + "CGC" : 0.002583672, + "CTC" : 0.005420073 + }, + "CAG" : { + "CCG" : 0.002162517, + "CGG" : 0.005024985, + "CTG" : 0.01364442 + }, + "CAT" : { + "CCT" : 0.000979173, + "CGT" : 0.004929042, + "CTT" : 0.004681878 + }, + "CCA" : { + "CAA" : 0.019380867, + "CGA" : 0.004455786, + "CTA" : 0.010564593 + }, + "CCC" : { + "CAC" : 0.024369153, + "CGC" : 0.004138908, + "CTC" : 0.007259598 + }, + "CCG" : { + "CAG" : 0.003696483, + "CGG" : 0.002562078, + "CTG" : 0.006257307 + }, + "CCT" : { + "CAT" : 0.017835018, + "CGT" : 0.004182762, + "CTT" : 0.009921048 + }, + "CGA" : { + "CAA" : 0.003887301, + "CCA" : 0.001438341, + "CTA" : 0.004512234 + }, + "CGC" : { + "CAC" : 0.00441477, + "CCC" : 0.002424006, + "CTC" : 0.008922042 + }, + "CGG" : { + "CAG" : 0.006257307, + "CCG" : 0.002562078, + "CTG" : 0.003696483 + }, + "CGT" : { + "CAT" : 0.005956437, + "CCT" : 0.001321383, + "CTT" : 0.007230498 + }, + "CTA" : { + "CAA" : 0.003080319, + "CCA" : 0.002850429, + "CGA" : 0.00010044 + }, + "CTC" : { + "CAC" : 0.00472626, + "CCC" : 0.001945389, + "CGC" : 0.00075615 + }, + "CTG" : { + "CAG" : 0.01364442, + "CCG" : 0.005024985, + "CGG" : 0.002162517 + }, + "CTT" : { + "CAT" : 0.00508743, + "CCT" : 0.0035988, + "CGT" : 0.001186914 + }, + "GAA" : { + "GCA" : 0.000485538, + "GGA" : 0.001616808, + "GTA" : 0.002332653 + }, + "GAC" : { + "GCC" : 8.0088e-05, + "GGC" : 0.001475124, + "GTC" : 0.002311734 + }, + "GAG" : { + "GCG" : 0.00075615, + "GGG" : 0.001945389, + "GTG" : 0.00472626 + }, + "GAT" : { + "GCT" : 0.000193428, + "GGT" : 0.001844361, + "GTT" : 0.002500698 + }, + "GCA" : { + "GAA" : 0.016081719, + "GGA" : 0.003027816, + "GTA" : 0.005417547 + }, + "GCC" : { + "GAC" : 0.016100535, + "GGC" : 0.003865299, + "GTC" : 0.005181186 + }, + "GCG" : { + "GAG" : 0.008922042, + "GGG" : 0.002424006, + "GTG" : 0.00441477 + }, + "GCT" : { + "GAT" : 0.010743126, + "GGT" : 0.002779725, + "GTT" : 0.005172219 + }, + "GGA" : { + "GAA" : 0.006204717, + "GCA" : 0.00547503, + "GTA" : 0.022164159 + }, + "GGC" : { + "GAC" : 0.005181186, + "GCC" : 0.003865299, + "GTC" : 0.016100535 + }, + "GGG" : { + "GAG" : 0.007259598, + "GCG" : 0.004138908, + "GTG" : 0.024369153 + }, + "GGT" : { + "GAT" : 0.004323732, + "GCT" : 0.002596398, + "GTT" : 0.012852828 + }, + "GTA" : { + "GAA" : 0.002904207, + "GCA" : 0.003460653, + "GGA" : 6.348e-05 + }, + "GTC" : { + "GAC" : 0.002311734, + "GCC" : 0.001475124, + "GGC" : 8.0088e-05 + }, + "GTG" : { + "GAG" : 0.005420073, + "GCG" : 0.002583672, + "GGG" : 0.001168908 + }, + "GTT" : { + "GAT" : 0.002032707, + "GCT" : 0.002230074, + "GGT" : 0.000299724 + }, + "TAA" : { + "TCA" : 0.000169176, + "TGA" : 0.002035563, + "TTA" : 0.002248938 + }, + "TAC" : { + "TCC" : 6.348e-05, + "TGC" : 0.003460653, + "TTC" : 0.002904207 + }, + "TAG" : { + "TCG" : 0.00010044, + "TGG" : 0.002850429, + "TTG" : 0.003080319 + }, + "TAT" : { + "TCT" : 0.000131952, + "TGT" : 0.006174201, + "TTT" : 0.002378709 + }, + "TCA" : { + "TAA" : 0.014662212, + "TGA" : 0.005351697, + "TTA" : 0.00956343 + }, + "TCC" : { + "TAC" : 0.022164159, + "TGC" : 0.00547503, + "TTC" : 0.006204717 + }, + "TCG" : { + "TAG" : 0.004512234, + "TGG" : 0.001438341, + "TTG" : 0.003887301 + }, + "TCT" : { + "TAT" : 0.016337817, + "TGT" : 0.007072317, + "TTT" : 0.00814365 + }, + "TGA" : { + "TAA" : 0.00956343, + "TCA" : 0.005351697, + "TTA" : 0.014662212 + }, + "TGC" : { + "TAC" : 0.005417547, + "TCC" : 0.003027816, + "TTC" : 0.016081719 + }, + "TGG" : { + "TAG" : 0.010564593, + "TCG" : 0.004455786, + "TTG" : 0.019380867 + }, + "TGT" : { + "TAT" : 0.007001988, + "TCT" : 0.004439358, + "TTT" : 0.015347823 + }, + "TTA" : { + "TAA" : 0.002248938, + "TCA" : 0.002035563, + "TGA" : 0.000169176 + }, + "TTC" : { + "TAC" : 0.002332653, + "TCC" : 0.001616808, + "TGC" : 0.000485538 + }, + "TTG" : { + "TAG" : 0.003455211, + "TCG" : 0.002144751, + "TGG" : 0.001534311 + }, + "TTT" : { + "TAT" : 0.002376093, + "TCT" : 0.002178105, + "TGT" : 0.001296555 + } +} diff --git a/src/main/julia/resistor/mutational-signatures/melanoma.json b/src/main/julia/resistor/mutational-signatures/melanoma.json new file mode 100755 index 000000000..44dab15c1 --- /dev/null +++ b/src/main/julia/resistor/mutational-signatures/melanoma.json @@ -0,0 +1,322 @@ +{ + "AAA" : { + "ACA" : 0.001531141, + "AGA" : 0.002598117, + "ATA" : 0.004063999 + }, + "AAC" : { + "ACC" : 0.000799114, + "AGC" : 0.00690382, + "ATC" : 0.000874693 + }, + "AAG" : { + "ACG" : 0.00138002, + "AGG" : 0.004276518, + "ATG" : 0.0016908 + }, + "AAT" : { + "ACT" : 0.000203184, + "AGT" : 0.002559217, + "ATT" : 0.003134217 + }, + "ACA" : { + "AAA" : 0.000889121, + "AGA" : 0.000291336, + "ATA" : 0.001601212 + }, + "ACC" : { + "AAC" : 0.000904956, + "AGC" : 0.000244258, + "ATC" : 0.016219572 + }, + "ACG" : { + "AAG" : 9.0736e-05, + "AGG" : 6.7773e-05, + "ATG" : 0.003907291 + }, + "ACT" : { + "AAT" : 0.000679789, + "AGT" : 0.000384117, + "ATT" : 0.004596298 + }, + "AGA" : { + "AAA" : 0.065248536, + "ACA" : 0.000918219, + "ATA" : 0.002057003 + }, + "AGC" : { + "AAC" : 0.013622301, + "ACC" : 0.000203229, + "ATC" : 0.00053556 + }, + "AGG" : { + "AAG" : 0.060752938, + "ACG" : 0.00043516, + "ATG" : 0.001548356 + }, + "AGT" : { + "AAT" : 0.004596298, + "ACT" : 0.000384117, + "ATT" : 0.000679789 + }, + "ATA" : { + "AAA" : 0.001010545, + "ACA" : 0.002195299, + "AGA" : 5.644e-05 + }, + "ATC" : { + "AAC" : 0.001277772, + "ACC" : 0.000731155, + "AGC" : 5.0796e-05 + }, + "ATG" : { + "AAG" : 0.001130012, + "ACG" : 0.001550518, + "AGG" : 0.000884341 + }, + "ATT" : { + "AAT" : 0.003134217, + "ACT" : 0.002559217, + "AGT" : 0.000203184 + }, + "CAA" : { + "CCA" : 0.000915119, + "CGA" : 0.001851597, + "CTA" : 0.000879815 + }, + "CAC" : { + "CCC" : 0.001544918, + "CGC" : 0.000804098, + "CTC" : 0.000564887 + }, + "CAG" : { + "CCG" : 0.000860855, + "CGG" : 0.001422269, + "CTG" : 0.000686518 + }, + "CAT" : { + "CCT" : 0.000884341, + "CGT" : 0.001550518, + "CTT" : 0.001130012 + }, + "CCA" : { + "CAA" : 0.001439217, + "CGA" : 0.000193842, + "CTA" : 0.058090745 + }, + "CCC" : { + "CAC" : 0.000736481, + "CGC" : 0.000476074, + "CTC" : 0.077262288 + }, + "CCG" : { + "CAG" : 8.4343e-05, + "CGG" : 0.000521688, + "CTG" : 0.018185187 + }, + "CCT" : { + "CAT" : 0.001548356, + "CGT" : 0.00043516, + "CTT" : 0.060752938 + }, + "CGA" : { + "CAA" : 0.076587595, + "CCA" : 0.000271565, + "CTA" : 0.000347626 + }, + "CGC" : { + "CAC" : 0.002957812, + "CCC" : 1.145e-05, + "CTC" : 8.5164e-05 + }, + "CGG" : { + "CAG" : 0.018185187, + "CCG" : 0.000521688, + "CTG" : 8.4343e-05 + }, + "CGT" : { + "CAT" : 0.003907291, + "CCT" : 6.7773e-05, + "CTT" : 9.0736e-05 + }, + "CTA" : { + "CAA" : 8.0933e-05, + "CCA" : 0.001201973, + "CGA" : 5.0796e-05 + }, + "CTC" : { + "CAC" : 0.001303562, + "CCC" : 0.001155089, + "CGC" : 0.000730304 + }, + "CTG" : { + "CAG" : 0.000686518, + "CCG" : 0.001422269, + "CGG" : 0.000860855 + }, + "CTT" : { + "CAT" : 0.0016908, + "CCT" : 0.004276518, + "CGT" : 0.00138002 + }, + "GAA" : { + "GCA" : 0.00094748, + "GGA" : 0.001941152, + "GTA" : 0.001435339 + }, + 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