# HG changeset patch # User artbio # Date 1633253344 0 # Node ID 8182d1625433f0ccb2f6c3baaff13f0f0f9136b6 # Parent 56c8869a231e08fc7d6b42ec8121ed3c7b8a6ee3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37" diff -r 56c8869a231e -r 8182d1625433 mutational_patterns.R --- a/mutational_patterns.R Fri Jun 04 22:35:48 2021 +0000 +++ b/mutational_patterns.R Sun Oct 03 09:29:04 2021 +0000 @@ -184,7 +184,7 @@ rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum) # Plot the 96-profile of the signatures: p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE) - new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ variable, value.var = "value") + new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq") new_sig_matrix <- format(new_sig_matrix, scientific = TRUE) write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t") grid.arrange(p5) @@ -229,6 +229,7 @@ colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v2, March 2015)" cosmic_colors <- col_vector[1:30] + names(cosmic_colors) <- colnames(cancer_signatures) } else { sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv" cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) @@ -239,6 +240,7 @@ colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v3, May 2019)" cosmic_colors <- col_vector[1:67] + names(cosmic_colors) <- colnames(cancer_signatures) } # Plot mutational profiles of the COSMIC signatures @@ -259,8 +261,9 @@ fit_res <- fit_to_signatures(pseudo_mut_mat, cancer_signatures) # Plot contribution barplots - pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute") - pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative") + pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute") + pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative") + if (is.na(opt$levels)[1]) { # if there are NO levels to display in graphs pc3_data <- pc3$data pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) + geom_bar(stat = "identity", position = "stack") + @@ -282,6 +285,7 @@ theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right", text = element_text(size = 8), axis.text.x = element_text(angle = 90, hjust = 1)) + } ##### # ggplot2 alternative if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs @@ -342,7 +346,6 @@ } worklist <- as.data.frame(melt(worklist)) worklist[, 2] <- paste0(worklist[, 4], " - ", worklist[, 2]) - head(worklist) } colnames(worklist) <- c("signature", "sample", "value", "level") @@ -356,7 +359,7 @@ coord_polar("y", start = 0) + facet_wrap(.~sample) + labs(x = "", y = "Samples", fill = cosmic_tag) + scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"), - values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) + + values = cosmic_colors[levels(worklist$signature)]) + theme(axis.text = element_blank(), axis.ticks = element_blank(), panel.grid = element_blank()) diff -r 56c8869a231e -r 8182d1625433 mutational_patterns.xml --- a/mutational_patterns.xml Fri Jun 04 22:35:48 2021 +0000 +++ b/mutational_patterns.xml Sun Oct 03 09:29:04 2021 +0000 @@ -1,13 +1,13 @@ - + from genomic variations in vcf files - bioconductor-mutationalpatterns - r-optparse - r-rjson - r-nmf - r-gridextra - bioconductor-bsgenome.hsapiens.ucsc.hg19 - bioconductor-bsgenome.hsapiens.ucsc.hg38 + bioconductor-mutationalpatterns + r-optparse + r-rjson + r-nmf + r-gridextra + bioconductor-bsgenome.hsapiens.ucsc.hg19 + bioconductor-bsgenome.hsapiens.ucsc.hg38 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -219,53 +298,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 56c8869a231e -r 8182d1625433 test-data/cosmic_output1.pdf Binary file test-data/cosmic_output1.pdf has changed diff -r 56c8869a231e -r 8182d1625433 test-data/cosmic_output2.pdf Binary file test-data/cosmic_output2.pdf has changed diff -r 56c8869a231e -r 8182d1625433 test-data/cosmic_output_v3.pdf Binary file test-data/cosmic_output_v3.pdf has changed diff -r 56c8869a231e -r 8182d1625433 test-data/denovo_1.RData Binary file test-data/denovo_1.RData has changed diff -r 56c8869a231e -r 8182d1625433 test-data/denovo_output1.pdf Binary file test-data/denovo_output1.pdf has changed diff -r 56c8869a231e -r 8182d1625433 test-data/sig_contrib_table.tsv --- a/test-data/sig_contrib_table.tsv Fri Jun 04 22:35:48 2021 +0000 +++ b/test-data/sig_contrib_table.tsv Sun Oct 03 09:29:04 2021 +0000 @@ -1,5 +1,5 @@ sample s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 -ovary-I.vcf 0.110142906240717 0.0107179228940658 0.250337884546217 0 0.123574305205091 0.00064433123164414 0 0.132427942951795 0.0645286099734586 0 0.0449394465051191 0.0482562813691387 0.0021792135773442 0 0.0208527968750023 0.113202769843279 0 0 0 0 0 0 0 0 0.0534957402074307 0 0 0.0246998485796975 0 0 -ovary-H.vcf 0.105077406305297 0.0161426031811577 0.213744671485429 0 0.267847442499011 0 0 0.0744758833337775 0.0589788373729043 0 0.0260566297995198 0.00332317088253305 0.0101947253359771 0 0 0.165596602885273 0 0 0 0 0 0 0 0 0.0157724425494898 0 0.0064649564106814 0.0363246279589487 0 0 -lung-G.vcf 0.211033078587086 0.0166966912787851 0.172186940126079 0 0.286633042356631 0 0 0.00842344130070046 0.11400762247453 0 0.0288922172140213 0.0327352792025852 0 0 0 0.034128625357202 0 0 0.0288565039877324 0 0 0 0 0 0.0631355806535697 0 0.000844012191577089 0.00242696526950036 0 0 -lung-F.vcf 0.275881644071761 0.00660164806875313 0.17426347088712 0 0.102714094410494 0 0 0.0917555941611345 0.0202950075653247 0 0.0296908924905143 0.0090315352239272 0 0 0 0.188940992761965 0 0 0 0 0 0 0 0 0.0273695319074987 0 0.00555599996394483 0.0404508145574958 0 0.0274487739300663 +ovary-I.vcf 0.11366483685008 0.0109938593266657 0.261053482791866 0 0.102195880307416 0.00220769920517984 0 0.121596331607151 0.0667024002680757 0 0.0463559883343337 0.0477514837858505 0.00153570456409855 0 0.0196723565031216 0.125168078635871 0 0 0 0 0 0 0 0 0.056462960047836 0 0.000124367513387182 0.0245145702590675 0 0 +ovary-H.vcf 0.108363933620392 0.0163896275457592 0.219669872246722 0 0.267579919199733 0 0 0.0644683944374041 0.0647530723986353 0 0.0255690291284295 0 0.0096156971999939 0 0 0.16879742588098 0 0 0 0 0 0 0 0 0.0144022954450145 0 0.00628915179499457 0.0341015811019413 0 0 +lung-G.vcf 0.216042386729494 0.0163285606624902 0.174782553623772 0 0.243519493008331 0 0 0.00859703357366864 0.122147877946073 0 0.031028717517658 0.0398485713623127 0 0 0 0.0426507272713916 0 0 0.0331593375475991 0 0 0 0 0 0.0690376730723399 0 0.00121112083973226 0.00164594684513809 0 0 +lung-F.vcf 0.277447721812717 0.00581547878718051 0.177348626019748 0 0.1009356992577 0 0 0.0920458551898083 0.0183096024827367 0 0.0300240298284301 0.00396441475927008 0 0 0 0.195845126035802 0 0 0 0 0 0 0 0 0.0270963890910293 0 0.0049085436021671 0.041321577314175 0 0.0249369358192356 diff -r 56c8869a231e -r 8182d1625433 test-data/sig_contrib_table_v3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sig_contrib_table_v3.tsv Sun Oct 03 09:29:04 2021 +0000 @@ -0,0 +1,5 @@ +sample s1 s2 s3 s4 s5 s6 s7a s7b s7c s7d s8 s9 s10a s10b s11 s12 s13 s14 s15 s16 s17a s17b s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 s31 s32 s33 s34 s35 s36 s37 s38 s39 s40 s41 s42 s43 s44 s45 s46 s47 s48 s49 s50 s51 s52 s53 s54 s55 s56 s57 s58 s59 s60 s84 s85 +ovary-I.vcf 0.0292102144556227 0 0 0.00144007322742414 0 0.0504390788292217 0.00194348408726673 0 0.0525707708741538 0 0.0914724303738797 0 0.000832163233383592 0 0 0 0.00842487825711237 0 0.0135094432679645 0.0366586044772389 0 0 0.0185740536261001 0.00229375063200434 0 0.00970266938170121 0 0 0.00599759333539559 0.0421114673613094 0.0114310779471638 0 0.0135490307866796 0 0.0296793772659665 0.0277524342410843 0.0454269664537971 0.00938724128600892 0.0136144947369238 0 0 0.0833465920869942 0 0.137690178135469 0 0 0 0.00953146514960113 0.0202102619863343 0 0 0 0 4.88486910392704e-05 0.00760389505513268 0.0232276886439185 0 0 0.013878903464201 0 0 0.058642750046278 0.129529443690174 0.000268674913454976 0 0 0 +ovary-H.vcf 0.0523809674402057 0 0 0.0073487755957751 0 0 0.00289534105048845 0 0.028141106223541 0.00357241172591758 0.0900610723552876 0 0.00471257812773401 0 0 0 0.0152354080005807 0 0 0.056026125482423 0 0.00257191790029753 0 0.0165305233542475 0 0.000141899985605957 0 0 0.00488001259024111 0.00918859610852697 0.00475106755263085 0.00663010539344573 0.017109685037444 0 0.04731550745362 0.00365691117000763 0.0328768691449399 0.0120314432988265 0.0167811048132417 0 0 0.0950039544413254 0 0.137196255594851 0 0 0 0 0.0597953621090927 0 0 0 0 4.23604750551013e-05 0.0121309998776711 0.00973226374395621 0 0.00222509583262053 0.0251951439030708 0.0118558225702647 0 0.0846395405044328 0.125310604958315 0.00203316618431609 0 0 0 +lung-G.vcf 0.0873029632099988 0 0 0 0 0.0479104551341112 0.00776867305403075 0 0.0313814579173264 0 0.0609850595672004 0.0172622613117254 0 0.00012666179996385 0 0 0.00765587561722924 0 0 0.0278690467140333 0.000454577309760022 0 0.0206812596225624 0.0359443715017539 0 0.0120875070366763 0.00187879472330278 0 0.00683351257522683 0.0494238708587332 0 0 0 0 0.0480909479022159 0.00328524460204372 0.037243337279276 0.000684746817696913 0.0170460736503824 0 0 0.120242044269861 0 0.0912990485885233 0 0 0.00198825222515588 0 0.00367924369018231 0 0 0.00127107492891469 0 0 0 0.0337265499103692 0 0.00040976068762453 0.035143574313439 0 0 0.080043690949342 0.096390826001613 0 0.00205878889713283 0.0118304473325925 0 +lung-F.vcf 0.130972951527932 0 0.0761687896979774 0 0 0 0 0 0.0340317364900266 0 0.0786848101409268 0 0.00232431375487017 0.00924283426133058 0 0 0 0 0 0.0454990529437777 0 0 0.0111440674145277 0.0156984823484767 0 0.00368064004289289 0.00101383322501298 0 0.00769126266914517 0.0114608643279846 0 0.000168984385199036 0.0236023336834282 0 0.064421387701359 0.00659674935231646 0.036711297327122 0.00568327050616103 0.00956407247236277 0 0 0.0874117950073058 0 0.0752825647107504 0 0 0 0.00313252048097358 0.0213677245928594 0 0 0.0221471177980541 0 0.000825664351643732 0 0.0132117228813227 0 0.00204298080257053 0.0390511638798427 0 0 0.0245617897055234 0.122391156939586 0.00304240662816143 0 0.0111696579485762 0 diff -r 56c8869a231e -r 8182d1625433 test-data/sigmatrix.tab --- a/test-data/sigmatrix.tab Fri Jun 04 22:35:48 2021 +0000 +++ b/test-data/sigmatrix.tab Sun Oct 03 09:29:04 2021 +0000 @@ -1,97 +1,97 @@ substitution context NewSig_1 NewSig_2 NewSig_3 NewSig_4 -C>A A.A 2.012349e-02 2.099063e-02 1.788529e-02 2.529973e-02 -C>A A.C 1.232623e-02 5.099845e-05 2.019020e-02 8.344265e-03 -C>A A.G 2.056317e-03 5.061512e-03 5.110667e-03 5.598599e-04 -C>A A.T 4.276274e-03 7.030586e-03 1.433976e-02 9.044799e-03 -C>A C.A 9.858499e-03 6.774294e-03 1.254817e-02 1.109854e-02 -C>A C.C 7.182083e-03 5.137412e-03 1.754580e-02 7.871756e-03 -C>A C.G 3.071657e-03 7.744685e-04 3.478215e-03 3.033573e-03 -C>A C.T 9.805120e-04 1.022892e-02 8.612445e-03 1.089991e-02 -C>A G.A 1.295094e-02 5.191677e-03 2.838657e-03 1.229298e-02 -C>A G.C 4.262714e-03 5.183579e-03 8.941540e-03 5.390685e-03 -C>A G.G 3.769228e-03 1.557726e-03 1.699600e-03 3.945304e-03 -C>A G.T 6.573060e-03 1.031818e-04 1.059791e-02 7.185424e-03 -C>A T.A 3.862713e-03 1.624881e-02 5.519485e-03 1.246359e-02 -C>A T.C 8.824563e-03 6.792814e-03 4.042968e-03 1.212436e-02 -C>A T.G 1.024188e-03 9.815808e-04 2.029646e-03 1.087012e-03 -C>A T.T 1.181704e-02 9.618044e-03 1.665114e-02 1.307952e-02 -C>G A.A 1.983228e-02 1.270519e-02 1.655687e-02 1.398506e-02 -C>G A.C 4.742892e-11 1.043116e-02 9.102239e-03 2.314023e-20 -C>G A.G 2.906055e-03 1.687383e-03 5.265593e-03 2.218107e-03 -C>G A.T 6.407465e-03 8.581278e-03 1.079483e-02 9.668306e-03 -C>G C.A 3.411641e-03 6.888991e-03 7.212837e-03 7.949635e-03 -C>G C.C 1.962245e-04 9.715947e-03 1.158418e-12 7.156965e-03 -C>G C.G 3.300401e-20 1.855024e-03 4.346525e-03 6.200559e-03 -C>G C.T 9.865314e-03 1.922285e-03 6.273441e-03 6.226190e-03 -C>G G.A 1.351834e-19 2.119713e-03 1.072168e-02 8.229779e-03 -C>G G.C 2.379848e-03 4.610717e-03 8.965747e-04 6.505033e-03 -C>G G.G 6.979718e-04 1.181697e-03 4.111756e-03 2.523959e-03 -C>G G.T 2.220903e-03 5.934769e-03 8.611327e-03 6.739344e-03 -C>G T.A 3.709345e-03 8.786940e-03 7.620791e-03 8.983741e-03 -C>G T.C 3.827093e-03 8.865683e-03 6.057793e-03 6.240498e-03 -C>G T.G 1.899263e-04 4.938065e-03 3.040335e-03 1.626378e-03 -C>G T.T 3.860261e-03 2.446381e-02 2.353559e-02 1.511199e-02 -C>T A.A 3.499419e-02 3.714546e-02 4.085734e-02 3.151538e-02 -C>T A.C 1.719840e-02 1.389005e-02 5.154001e-03 1.603745e-02 -C>T A.G 7.482535e-02 1.348050e-02 3.052063e-02 1.592390e-02 -C>T A.T 1.607143e-02 1.438585e-02 1.967215e-02 1.741898e-02 -C>T C.A 1.606874e-02 1.435234e-02 1.105389e-02 1.125796e-02 -C>T C.C 1.700219e-02 9.214402e-03 1.282668e-02 1.377429e-02 -C>T C.G 4.356691e-02 1.624586e-02 1.169686e-02 1.963077e-02 -C>T C.T 2.301602e-02 3.266347e-02 1.574218e-02 2.039183e-02 -C>T G.A 1.970589e-02 7.742080e-03 1.178227e-02 1.297792e-02 -C>T G.C 1.466426e-02 1.914382e-02 6.909098e-03 1.355502e-02 -C>T G.G 3.701827e-02 2.542796e-02 1.262381e-02 3.190790e-02 -C>T G.T 1.382222e-02 2.392818e-02 6.174897e-03 1.508942e-02 -C>T T.A 1.143013e-02 1.914536e-02 1.002998e-02 7.458921e-03 -C>T T.C 1.879514e-02 2.009898e-02 1.421423e-02 1.556176e-02 -C>T T.G 3.061491e-02 4.743450e-03 1.167740e-02 7.144683e-03 -C>T T.T 3.133938e-02 2.219653e-02 3.807693e-02 3.192865e-02 -T>A A.A 1.841481e-02 8.914346e-03 1.741295e-02 1.361688e-02 -T>A A.C 3.425691e-03 8.698638e-03 3.992626e-03 5.443164e-03 -T>A A.G 9.072656e-03 1.149533e-02 1.354019e-03 8.223373e-03 -T>A A.T 9.659453e-03 1.830189e-02 1.174139e-02 1.710128e-02 -T>A C.A 2.727069e-03 7.915424e-03 5.772823e-03 4.530720e-03 -T>A C.C 1.215316e-02 3.470147e-03 7.886743e-03 1.369393e-02 -T>A C.G 3.791221e-03 6.605963e-03 3.294232e-03 8.818173e-03 -T>A C.T 6.289729e-03 1.435186e-02 3.597548e-03 1.211551e-02 -T>A G.A 6.615841e-04 4.146662e-03 4.933783e-03 4.863214e-03 -T>A G.C 1.515807e-03 4.210462e-03 3.382936e-03 9.183128e-04 -T>A G.G 1.070023e-02 1.089710e-02 5.492536e-03 8.802992e-03 -T>A G.T 8.128051e-03 4.233917e-03 9.103699e-03 1.259684e-02 -T>A T.A 1.476324e-02 6.549494e-03 1.579044e-02 7.620545e-03 -T>A T.C 6.738527e-03 8.767946e-04 7.353978e-03 5.436410e-03 -T>A T.G 2.186518e-03 5.445354e-03 2.568144e-03 7.932364e-03 -T>A T.T 1.942541e-02 1.590353e-02 2.306069e-02 3.009347e-02 -T>C A.A 3.011297e-02 3.375076e-02 4.906885e-02 3.383597e-02 -T>C A.C 9.041893e-03 8.933211e-03 8.243474e-03 6.303632e-03 -T>C A.G 2.247578e-02 9.001629e-03 1.950973e-02 8.972544e-03 -T>C A.T 1.210116e-02 1.578255e-02 1.360358e-02 9.528566e-03 -T>C C.A 6.835997e-03 6.652934e-03 1.036887e-02 7.994706e-03 -T>C C.C 9.462334e-03 6.392714e-03 8.437885e-03 1.653238e-02 -T>C C.G 7.156018e-03 1.612832e-02 1.225799e-02 9.579249e-03 -T>C C.T 1.040136e-02 2.530647e-02 1.208573e-02 1.371705e-02 -T>C G.A 8.743261e-03 1.074754e-02 5.087249e-03 1.090594e-02 -T>C G.C 6.111817e-03 6.456267e-03 3.668932e-20 6.346677e-03 -T>C G.G 1.768834e-02 1.377477e-02 1.512171e-02 1.240640e-02 -T>C G.T 3.605052e-03 1.397132e-02 1.282818e-02 1.036663e-02 -T>C T.A 5.577357e-03 1.122841e-02 7.516272e-03 9.852123e-03 -T>C T.C 2.142753e-02 1.003311e-02 1.311934e-02 1.883301e-02 -T>C T.G 3.231084e-03 7.639140e-03 1.374439e-02 6.010940e-03 -T>C T.T 1.771125e-02 5.247659e-02 2.430165e-02 3.016747e-02 -T>G A.A 1.331124e-02 1.426333e-02 7.805243e-05 7.473665e-03 -T>G A.C 3.887921e-03 1.684454e-03 1.435130e-04 6.445063e-04 -T>G A.G 2.394241e-03 5.040173e-03 6.853239e-03 6.994037e-03 -T>G A.T 6.066623e-03 7.374853e-03 2.079215e-10 5.136694e-03 -T>G C.A 5.000218e-10 8.218020e-03 3.668932e-20 2.314023e-20 -T>G C.C 3.300401e-20 1.904378e-03 4.043369e-03 4.672135e-03 -T>G C.G 4.310666e-03 2.256883e-03 8.181657e-03 1.928646e-03 -T>G C.T 2.128603e-03 9.425709e-04 8.787753e-03 6.815812e-04 -T>G G.A 2.012235e-03 4.628783e-04 4.459546e-03 1.814827e-03 -T>G G.C 3.997247e-03 1.335924e-03 1.270853e-03 3.568581e-03 -T>G G.G 7.790802e-03 1.175435e-02 8.700500e-03 8.985015e-03 -T>G G.T 6.538479e-03 1.329525e-02 4.903674e-03 1.074729e-02 -T>G T.A 2.781217e-03 4.774228e-03 2.965653e-03 7.301491e-03 -T>G T.C 5.182071e-03 5.200467e-03 5.617300e-03 2.629881e-03 -T>G T.G 5.245736e-03 1.345072e-02 1.698469e-02 9.832179e-03 -T>G T.T 2.041928e-02 1.752970e-02 3.978473e-02 1.976735e-02 +C>A A.A 1.856821e-02 2.482023e-02 1.879304e-02 2.144868e-02 +C>A A.C 1.985096e-02 8.856811e-03 4.176376e-03 7.275623e-03 +C>A A.G 4.613707e-03 1.032560e-03 7.399596e-03 1.283205e-03 +C>A A.T 1.077097e-02 1.152945e-02 1.110411e-02 3.506614e-03 +C>A C.A 1.234686e-02 1.058479e-02 7.778853e-03 8.511073e-03 +C>A C.C 1.527507e-02 9.706857e-03 1.091358e-02 3.977471e-03 +C>A C.G 3.595068e-03 3.053798e-03 1.065706e-03 2.488491e-03 +C>A C.T 4.654944e-03 1.331055e-02 1.146678e-02 3.015206e-03 +C>A G.A 5.984606e-03 9.241989e-03 1.639336e-13 1.380331e-02 +C>A G.C 7.683094e-03 6.339795e-03 8.137271e-03 3.391593e-03 +C>A G.G 2.406023e-03 3.640987e-03 1.456895e-04 3.942915e-03 +C>A G.T 1.020608e-02 7.739365e-03 2.399885e-03 4.235560e-03 +C>A T.A 3.961933e-03 1.275900e-02 1.466472e-02 6.814391e-03 +C>A T.C 5.337093e-03 1.162648e-02 9.105310e-04 1.013653e-02 +C>A T.G 1.877937e-03 6.162730e-04 1.878461e-03 6.682628e-04 +C>A T.T 1.560352e-02 1.326934e-02 1.247051e-02 9.445224e-03 +C>G A.A 1.972775e-02 1.228149e-02 1.195633e-02 1.727448e-02 +C>G A.C 5.836059e-03 1.655810e-03 1.694621e-02 9.062109e-07 +C>G A.G 5.200216e-03 2.559643e-03 3.166565e-03 1.532897e-03 +C>G A.T 9.324164e-03 1.095739e-02 1.081958e-02 6.258396e-03 +C>G C.A 5.617809e-03 9.345902e-03 8.284139e-03 3.880938e-03 +C>G C.C 3.534086e-20 8.210895e-03 7.727184e-03 2.254830e-03 +C>G C.G 2.262327e-03 7.340603e-03 3.022013e-03 9.156563e-05 +C>G C.T 8.224646e-03 5.017294e-03 7.003901e-04 8.665738e-03 +C>G G.A 6.954941e-03 1.139806e-02 4.622361e-03 3.514270e-20 +C>G G.C 7.064656e-04 6.998058e-03 2.537477e-03 3.965493e-03 +C>G G.G 3.080436e-03 3.328074e-03 2.929015e-03 1.461945e-04 +C>G G.T 6.360999e-03 8.512373e-03 9.008932e-03 2.005772e-03 +C>G T.A 5.553775e-03 1.062558e-02 9.424149e-03 4.924035e-03 +C>G T.C 5.248185e-03 7.233109e-03 9.634964e-03 4.359934e-03 +C>G T.G 1.845306e-03 2.417185e-03 6.595859e-03 6.782687e-04 +C>G T.T 1.587889e-02 2.049222e-02 3.439640e-02 5.050564e-03 +C>T A.A 3.911250e-02 3.225079e-02 4.206848e-02 3.385188e-02 +C>T A.C 8.757053e-03 1.352629e-02 6.991724e-03 1.974727e-02 +C>T A.G 5.231138e-02 1.925044e-07 3.026394e-03 6.399169e-02 +C>T A.T 1.874677e-02 1.836710e-02 1.620182e-02 1.541248e-02 +C>T C.A 1.408680e-02 9.572305e-03 1.224985e-02 1.529038e-02 +C>T C.C 1.412526e-02 1.293054e-02 7.720717e-03 1.618405e-02 +C>T C.G 2.458679e-02 1.097265e-02 2.704009e-03 4.320455e-02 +C>T C.T 1.682814e-02 1.962601e-02 2.870932e-02 2.757164e-02 +C>T G.A 1.501424e-02 1.146890e-02 4.373561e-03 1.710170e-02 +C>T G.C 8.581633e-03 1.197143e-02 1.469853e-02 1.798870e-02 +C>T G.G 2.050911e-02 2.694316e-02 1.193358e-02 4.080066e-02 +C>T G.T 6.725450e-03 1.485333e-02 2.022066e-02 1.821305e-02 +C>T T.A 9.790349e-03 7.433059e-03 1.994759e-02 1.263779e-02 +C>T T.C 1.594645e-02 1.460332e-02 1.802766e-02 1.886875e-02 +C>T T.G 2.019449e-02 4.552012e-04 8.162605e-12 2.690217e-02 +C>T T.T 3.604766e-02 3.365274e-02 2.789390e-02 2.769743e-02 +T>A A.A 1.765667e-02 1.321109e-02 1.065894e-02 1.583119e-02 +T>A A.C 1.820098e-03 5.510611e-03 8.183147e-03 4.599082e-03 +T>A A.G 4.665541e-03 6.215514e-03 6.135328e-03 1.001896e-02 +T>A A.T 9.785657e-03 1.833578e-02 1.768249e-02 1.248205e-02 +T>A C.A 4.242335e-03 5.517088e-03 9.041105e-03 3.634763e-03 +T>A C.C 8.948010e-03 1.166917e-02 2.179799e-05 1.148913e-02 +T>A C.G 2.492456e-03 9.694116e-03 4.293775e-03 5.700343e-03 +T>A C.T 2.882218e-03 1.297743e-02 1.071267e-02 1.009712e-02 +T>A G.A 3.223737e-03 6.245735e-03 5.842451e-03 9.200857e-04 +T>A G.C 2.805377e-03 1.213230e-03 5.828460e-03 1.503090e-03 +T>A G.G 6.898206e-03 7.300718e-03 8.003532e-03 1.222177e-02 +T>A G.T 9.120314e-03 1.347850e-02 3.249901e-03 7.453304e-03 +T>A T.A 1.622536e-02 6.931133e-03 9.627554e-03 1.174564e-02 +T>A T.C 6.760912e-03 5.595476e-03 9.698282e-04 5.499357e-03 +T>A T.G 1.866485e-03 8.652201e-03 2.256983e-03 3.519494e-03 +T>A T.T 2.145214e-02 3.177788e-02 1.505847e-02 1.981508e-02 +T>C A.A 4.427759e-02 3.786828e-02 4.544423e-02 2.650778e-02 +T>C A.C 8.998306e-03 4.599474e-03 1.004905e-02 8.722935e-03 +T>C A.G 2.243087e-02 6.118842e-03 1.134205e-02 1.802892e-02 +T>C A.T 1.373384e-02 9.886587e-03 1.685322e-02 1.176445e-02 +T>C C.A 8.656233e-03 9.072748e-03 8.862799e-03 6.112781e-03 +T>C C.C 8.714585e-03 1.690442e-02 3.565029e-03 9.871972e-03 +T>C C.G 1.071206e-02 1.004291e-02 1.850434e-02 7.540034e-03 +T>C C.T 1.017263e-02 1.448259e-02 2.608108e-02 1.403170e-02 +T>C G.A 5.126616e-03 1.108508e-02 8.768450e-03 1.036693e-02 +T>C G.C 5.204634e-12 5.747845e-03 3.143501e-03 8.849255e-03 +T>C G.G 1.669831e-02 1.133208e-02 1.267705e-02 1.603702e-02 +T>C G.T 8.671437e-03 1.325475e-02 1.721725e-02 5.039773e-03 +T>C T.A 6.260030e-03 1.102551e-02 1.167533e-02 7.016389e-03 +T>C T.C 1.517718e-02 1.699912e-02 6.470473e-03 2.077129e-02 +T>C T.G 9.336917e-03 8.764205e-03 1.160437e-02 2.331889e-03 +T>C T.T 1.903513e-02 3.432098e-02 5.540849e-02 2.562376e-02 +T>G A.A 3.993541e-03 4.978625e-03 8.356632e-03 1.578506e-02 +T>G A.C 1.728186e-03 3.099935e-20 6.777648e-15 3.511484e-03 +T>G A.G 5.502959e-03 8.711266e-03 5.367147e-03 2.059172e-03 +T>G A.T 1.499753e-03 4.210842e-03 3.978567e-03 7.977656e-03 +T>G C.A 3.534086e-20 4.234149e-16 8.909125e-03 1.246735e-03 +T>G C.C 1.909719e-03 6.194908e-03 2.037866e-03 5.448839e-04 +T>G C.G 7.443573e-03 2.206694e-03 4.942085e-03 2.758675e-03 +T>G C.T 7.417469e-03 1.454301e-03 5.521245e-03 5.632697e-19 +T>G G.A 4.032749e-03 2.126988e-03 2.146375e-03 9.845592e-04 +T>G G.C 2.308308e-03 3.091434e-03 3.322218e-20 3.632777e-03 +T>G G.G 8.852942e-03 9.064804e-03 1.199615e-02 7.843944e-03 +T>G G.T 4.276432e-03 1.084606e-02 1.101937e-02 9.425060e-03 +T>G T.A 2.351390e-03 8.100255e-03 3.683601e-03 3.923489e-03 +T>G T.C 5.580464e-03 2.444033e-03 5.806015e-03 5.018502e-03 +T>G T.G 1.287955e-02 1.265933e-02 1.969184e-02 4.871262e-03 +T>G T.T 3.545360e-02 2.295036e-02 2.946636e-02 1.477102e-02 diff -r 56c8869a231e -r 8182d1625433 test-data/spectrum_output1.pdf Binary file test-data/spectrum_output1.pdf has changed