Mercurial > repos > artbio > mutational_patterns

changeset 23:83f8c93c34b4 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
author artbio
date Wed, 27 Oct 2021 00:46:47 +0000
parents 00be8f0b2c89
children ca6c19ee7da0
files mutational_patterns.R mutational_patterns.xml test-data/cosmic_output_v3.pdf test-data/denovo_1.RData test-data/denovo_output1.pdf test-data/sig_contrib_table_user_defined.tsv test-data/sigmatrix.tab test-data/user_defined_signature.tsv test-data/user_output.pdf
diffstat 9 files changed, 141 insertions(+), 114 deletions(-) [+]
line wrap: on
line diff
--- a/mutational_patterns.R	Mon Oct 25 15:22:14 2021 +0000
+++ b/mutational_patterns.R	Wed Oct 27 00:46:47 2021 +0000
@@ -94,6 +94,12 @@
     help = "path to output dataset"
   ),
   make_option(
+    "--display_signatures",
+    default = NA,
+    type = "character",
+    help = "display input signature profiles if set to yes"
+  ),
+  make_option(
     "--sig_contrib_matrix",
     default = NA,
     type = "character",
@@ -203,6 +209,10 @@
     p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
     new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq")
     new_sig_matrix <- format(new_sig_matrix, scientific = TRUE)
+    newcol <- paste0(gsub("\\..", "", new_sig_matrix$context, perl = T),
+                     "[", new_sig_matrix$substitution, "]",
+                     gsub("^.\\.", "", new_sig_matrix$context, perl = T))
+    new_sig_matrix <- cbind(Type = newcol, new_sig_matrix[, seq_along(new_sig_matrix)[-c(1, 2)]])
     write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t")
     grid.arrange(p5)
     # Visualize the contribution of the signatures in a barplot
@@ -283,6 +293,15 @@
                                  "SBS57", "SBS58", "SBS59", "SBS60", "SBS84", "SBS85", "SBS86", "SBS87", "SBS88", "SBS89", "SBS90",
                                  "SBS91", "SBS92", "SBS93", "SBS94")
 
+    # if signature names provided are not compliant with cosmic nomenclature,
+    # we attribute these names to the active signature_colors vector, adjusted to the length
+    # of the signature names.
+
+    if (! all(colnames(sbs_signatures) %in% names(signature_colors))) { # provided signature are not all included in cosmic names
+        signature_colors <- signature_colors[seq_along(sbs_signatures)]
+        names(signature_colors) <- colnames(sbs_signatures)
+    }
+
     # This is IMPORTANT since in Galaxy we do not use the embeded function get_known_signatures()
     sbs_signatures <- as.matrix(sbs_signatures)
 
@@ -290,17 +309,19 @@
     # Plot mutational profiles of the COSMIC signatures
 
     pdf(opt$output_sigpattern, paper = "special", width = 11.69, height = 11.69)
-    for (i in head(seq(1, ncol(sbs_signatures), by = 20), -1)) {
-        p6 <- plot_96_profile(sbs_signatures[, i:(i + 19)], condensed = TRUE, ymax = 0.3)
-        grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc((i + 1) / 20) + 1, " of ",
+    if (opt$display_signatures == "yes") {
+        for (i in head(seq(1, ncol(sbs_signatures), by = 20), -1)) {
+            p6 <- plot_96_profile(sbs_signatures[, i:(i + 19)], condensed = TRUE, ymax = 0.3)
+            grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc((i + 1) / 20) + 1, " of ",
+                                                   trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
+                                            gp = gpar(fontsize = 12, font = 3)))
+        }
+        p6 <- plot_96_profile(sbs_signatures[, (trunc(ncol(sbs_signatures) / 20) * 20):(ncol(sbs_signatures))],
+                              condensed = TRUE, ymax = 0.3)
+        grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc(ncol(sbs_signatures) / 20) + 1, " of ",
                                                trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
                                         gp = gpar(fontsize = 12, font = 3)))
     }
-    p6 <- plot_96_profile(sbs_signatures[, (trunc(ncol(sbs_signatures) / 20) * 20):(ncol(sbs_signatures))],
-                          condensed = TRUE, ymax = 0.3)
-    grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc(ncol(sbs_signatures) / 20) + 1, " of ",
-                                               trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
-                                        gp = gpar(fontsize = 12, font = 3)))
 
 
     # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles
--- a/mutational_patterns.xml	Mon Oct 25 15:22:14 2021 +0000
+++ b/mutational_patterns.xml	Wed Oct 27 00:46:47 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy7">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy8">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
@@ -60,6 +60,7 @@
        
         --signum '$set_preset.signum'
         --colors '$set_preset.colors'
+        --display_signatures '$set_preset.display_signatures'
         --output_sigpattern '$sig_contrib'
 
         #if $set_preset.contrib_matrix_out == 'yes'
@@ -158,7 +159,11 @@
                 <param name="signum" type="integer" value="3" min="2" max="30"
                        label="selects the N most significant signatures in samples to express mutational patterns"
                        help="an integer between 2 and the number of elementary signatures in your signature matrix"/>
-                <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
+                <param name="display_signatures" type="select" display="radio" label="Output profiles of input signatures ?">
+                    <option value="no">No</option>
+                    <option value="yes" selected="true">Yes</option>
+                </param>
+                <param name="contrib_matrix_out" type="select" display="radio" label="Output Signature Contribution table ?"
                        help="Output the normalized signatures contributions for further visualization" >
                     <option value="no" selected="true">No</option>
                     <option value="yes">Yes</option>
@@ -195,7 +200,7 @@
 
     </outputs>
     <tests>
-         <!-- user defined (v3.2 restricted 30 minus 27) -->
+         <!-- user defined (v3.2 restricted 30 minus 27 renamed to test nomenclature effect) -->
         <test>
             <param name="vcfs">
                 <collection type="list">
@@ -249,6 +254,7 @@
                     <param name="input_signature_choices" value="cosmic" />
                     <param name="cosmic_version" value="v3.2"/>
                 </conditional>
+                <param name="display_signatures"  value="no" />
                 <param name="contrib_matrix_out"  value="yes" />
             </conditional>
             <param name="signum" value="3" />
Binary file test-data/cosmic_output_v3.pdf has changed
Binary file test-data/denovo_1.RData has changed
Binary file test-data/denovo_output1.pdf has changed
--- a/test-data/sig_contrib_table_user_defined.tsv	Mon Oct 25 15:22:14 2021 +0000
+++ b/test-data/sig_contrib_table_user_defined.tsv	Wed Oct 27 00:46:47 2021 +0000
@@ -1,5 +1,5 @@
-sample	SBS1	SBS2	SBS3	SBS4	SBS5	SBS6	SBS7a	SBS8	SBS9	SBS10a	SBS11	SBS12	SBS13	SBS14	SBS15	SBS16	SBS17a	SBS18	SBS19	SBS20	SBS21	SBS22	SBS23	SBS24	SBS25	SBS26	SBS28	SBS29	SBS30
-ovary-I.vcf	0.044741393105028	0.011069018301987	0.187803779081214	0	0.307576392721694	0.0390017684003016	0	0.133709187523867	0.0763944509288322	0	0.0336042710599181	0.00220624140261095	0.0127873005328564	0	0	0.02020342244349	0.00211060816974033	0	0.00943263947590895	0	0	0	0	0	0.0617812132959067	0.0360554090047252	0.0193480376106478	0	0.00217486694127118
-ovary-H.vcf	0.0553256363614375	0.0124754288752531	0.172657307861813	0	0.390049768714777	0	0	0.0896595811464236	0.064875377225018	0.0002310155419569	0.0154421351083386	0	0.0177741353898114	0	0	0.03211663626174	0.0016974261829219	0	0.01130045225648	0.00706360420658175	0	0	0	0	0.0511061356153333	0.0334989901908753	0.0301573738491178	0	0.014568995212121
-lung-G.vcf	0.100607683465906	0.00885784389158831	0.091705156107157	0	0.388761692211351	0.0185902394159154	0	0.0790841986452702	0.104477088095262	0	0.0248378551618795	0	0.00785386622534465	0	0	0.00158790002897007	0.00587634748109639	0	0.0340439376359571	0	0.000644451383999199	0	0	0	0.0781129677262457	0.0319243418807398	0.00678144834422734	0	0.0162529822990906
-lung-F.vcf	0.130476654237574	0.00697559248767266	0.122146706678661	0	0.427134248306192	0	0	0.106255839292615	0.0369879379068786	0	0.0223610787636894	0	0	0	0	0.0200543223993699	0	0	0.0126155822640537	0	0	0	0	0	0.0504488522544811	0.0125177073155609	0.0278975294535814	0	0.0241279486396702
+sample	SBSa	SBSb	SBSc	SBSd	SBSe	SBSf	SBS7a	SBSg	SBSh	SBS10a	SBSi	SBSj	SBSk	SBSl	SBSm	SBSn	SBS17a	SBSo	SBSp	SBSq	SBSr	SBSs	SBSt	SBSu	SBSv	SBSw	SBSx	SBSy	SBSz
+6	0.130476654237574	0.00697559248767266	0.122146706678661	0	0.427134248306192	0	0	0.106255839292615	0.0369879379068786	0	0.0223610787636894	0	0	0	0	0.0200543223993699	0	0	0.0126155822640537	0	0	0	0	0	0.0504488522544811	0.0125177073155609	0.0278975294535814	0	0.0241279486396702
+7	0.100607683465906	0.00885784389158831	0.091705156107157	0	0.388761692211351	0.0185902394159154	0	0.0790841986452702	0.104477088095262	0	0.0248378551618795	0	0.00785386622534465	0	0	0.00158790002897007	0.00587634748109639	0	0.0340439376359571	0	0.000644451383999199	0	0	0	0.0781129677262457	0.0319243418807398	0.00678144834422734	0	0.0162529822990906
+8	0.0553256363614375	0.0124754288752531	0.172657307861813	0	0.390049768714777	0	0	0.0896595811464236	0.064875377225018	0.0002310155419569	0.0154421351083386	0	0.0177741353898114	0	0	0.03211663626174	0.0016974261829219	0	0.01130045225648	0.00706360420658175	0	0	0	0	0.0511061356153333	0.0334989901908753	0.0301573738491178	0	0.014568995212121
+9	0.044741393105028	0.011069018301987	0.187803779081214	0	0.307576392721694	0.0390017684003016	0	0.133709187523867	0.0763944509288322	0	0.0336042710599181	0.00220624140261095	0.0127873005328564	0	0	0.02020342244349	0.00211060816974033	0	0.00943263947590895	0	0	0	0	0	0.0617812132959067	0.0360554090047252	0.0193480376106478	0	0.00217486694127118
--- a/test-data/sigmatrix.tab	Mon Oct 25 15:22:14 2021 +0000
+++ b/test-data/sigmatrix.tab	Wed Oct 27 00:46:47 2021 +0000
@@ -1,97 +1,97 @@
-substitution	context	NewSig_1	NewSig_2	NewSig_3	NewSig_4
-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
+Type	SBS1	SBS2	SBS3	SBS4
+A[C>A]A	2.537216e-02	2.002096e-02	1.710480e-02	2.141184e-02
+A[C>A]C	9.450873e-03	1.458332e-02	1.433290e-02	8.146530e-15
+A[C>A]G	2.154737e-06	2.245761e-03	7.951470e-03	3.165761e-03
+A[C>A]T	1.157395e-02	5.815074e-03	1.240409e-02	4.643111e-03
+C[C>A]A	1.088500e-02	1.062103e-02	1.055922e-02	6.408859e-03
+C[C>A]C	9.642499e-03	8.802069e-03	1.580375e-02	2.817272e-03
+C[C>A]G	3.260193e-03	3.291545e-03	2.316976e-03	1.206510e-03
+C[C>A]T	1.342709e-02	1.891337e-03	7.936790e-03	7.279236e-03
+G[C>A]A	1.008899e-02	1.222901e-02	3.142566e-09	9.140614e-03
+G[C>A]C	6.174019e-03	4.836613e-03	9.098106e-03	4.149261e-03
+G[C>A]G	3.986726e-03	3.691483e-03	4.513223e-04	2.546877e-03
+G[C>A]T	8.260710e-03	7.958102e-03	6.964008e-03	1.757568e-06
+T[C>A]A	1.249317e-02	3.585683e-03	8.718414e-03	1.266466e-02
+T[C>A]C	1.291698e-02	8.850082e-03	1.670388e-04	7.329271e-03
+T[C>A]G	5.004928e-04	1.156145e-03	2.337253e-03	7.830488e-04
+T[C>A]T	1.337425e-02	1.214008e-02	1.530841e-02	8.418327e-03
+A[C>G]A	1.237441e-02	1.981081e-02	1.653601e-02	1.304232e-02
+A[C>G]C	7.834505e-16	3.248220e-10	1.572297e-02	6.551608e-03
+A[C>G]G	2.523774e-03	3.253406e-03	5.114731e-03	7.858234e-04
+A[C>G]T	1.096100e-02	6.928247e-03	1.066230e-02	7.532280e-03
+C[C>G]A	9.424413e-03	3.782759e-03	7.078604e-03	5.700867e-03
+C[C>G]C	8.549212e-03	3.674810e-20	1.851021e-03	7.246756e-03
+C[C>G]G	7.748336e-03	3.487494e-04	2.371674e-03	9.595624e-04
+C[C>G]T	5.480175e-03	9.922058e-03	3.885279e-03	4.326614e-03
+G[C>G]A	1.157248e-02	1.370895e-03	7.806339e-03	3.108266e-20
+G[C>G]C	7.420157e-03	2.171773e-03	1.284785e-04	4.770442e-03
+G[C>G]G	3.372856e-03	1.135636e-03	3.554018e-03	4.457136e-04
+G[C>G]T	8.449691e-03	2.887116e-03	8.619063e-03	4.100463e-03
+T[C>G]A	1.070613e-02	4.177331e-03	7.325655e-03	7.313308e-03
+T[C>G]C	6.976389e-03	3.829361e-03	7.894157e-03	6.971152e-03
+T[C>G]G	1.997729e-03	1.042906e-04	5.183138e-03	3.550364e-03
+T[C>G]T	1.906704e-02	5.403760e-03	2.917595e-02	1.685698e-02
+A[C>T]A	3.131895e-02	3.559289e-02	4.320756e-02	3.595643e-02
+A[C>T]C	1.413245e-02	1.602975e-02	4.547827e-03	1.754285e-02
+A[C>T]G	3.979119e-05	7.124023e-02	2.719950e-02	3.367261e-02
+A[C>T]T	1.859032e-02	1.694007e-02	1.791330e-02	1.441652e-02
+C[C>T]A	9.334568e-03	1.548055e-02	1.339818e-02	1.398155e-02
+C[C>T]C	1.346106e-02	1.657747e-02	9.838139e-03	1.233688e-02
+C[C>T]G	1.184973e-02	4.118642e-02	9.104291e-03	2.848006e-02
+C[C>T]T	1.867309e-02	2.194293e-02	2.160789e-02	3.289596e-02
+G[C>T]A	1.220901e-02	1.830932e-02	8.420540e-03	1.082556e-02
+G[C>T]C	1.165663e-02	1.366817e-02	9.906539e-03	2.030184e-02
+G[C>T]G	2.837739e-02	3.492253e-02	9.763772e-03	3.371439e-02
+G[C>T]T	1.423362e-02	1.172648e-02	1.151020e-02	2.449816e-02
+T[C>T]A	6.181812e-03	1.026000e-02	1.598478e-02	1.784120e-02
+T[C>T]C	1.426343e-02	1.765650e-02	1.686071e-02	1.961689e-02
+T[C>T]G	6.697405e-04	2.981773e-02	8.807199e-03	1.357187e-02
+T[C>T]T	3.425831e-02	3.190586e-02	3.306195e-02	2.416517e-02
+A[T>A]A	1.350407e-02	1.783317e-02	1.433952e-02	1.204297e-02
+A[T>A]C	5.208908e-03	2.426998e-03	4.661406e-03	7.889899e-03
+A[T>A]G	6.203645e-03	7.899487e-03	4.210160e-03	1.020936e-02
+A[T>A]T	1.832951e-02	9.760497e-03	1.283916e-02	1.679321e-02
+C[T>A]A	5.152894e-03	2.995165e-03	7.202406e-03	6.415967e-03
+C[T>A]C	1.288517e-02	1.197751e-02	2.199823e-03	6.184057e-03
+C[T>A]G	1.017668e-02	3.858590e-03	1.797496e-03	6.521194e-03
+C[T>A]T	1.311494e-02	5.783272e-03	4.684082e-03	1.384174e-02
+G[T>A]A	6.264117e-03	1.063500e-03	4.890578e-03	2.764218e-03
+G[T>A]C	7.583102e-04	1.569458e-03	5.251988e-03	3.297294e-03
+G[T>A]G	7.218613e-03	1.024681e-02	6.403638e-03	1.217812e-02
+G[T>A]T	1.447924e-02	8.632744e-03	5.062681e-03	4.542537e-03
+T[T>A]A	6.737527e-03	1.490078e-02	1.449887e-02	8.361527e-03
+T[T>A]C	6.075934e-03	6.914890e-03	3.547468e-03	2.400262e-03
+T[T>A]G	9.247980e-03	2.446205e-03	6.669669e-04	3.742054e-03
+T[T>A]T	3.338055e-02	2.065066e-02	1.611251e-02	1.680514e-02
+A[T>C]A	3.717380e-02	3.265699e-02	4.982621e-02	2.922387e-02
+A[T>C]C	4.082749e-03	8.947616e-03	1.042822e-02	9.205745e-03
+A[T>C]G	5.725035e-03	2.233932e-02	1.897642e-02	1.192167e-02
+A[T>C]T	9.216111e-03	1.218855e-02	1.674300e-02	1.362895e-02
+C[T>C]A	9.092771e-03	6.894784e-03	9.263013e-03	6.566154e-03
+C[T>C]C	1.818673e-02	9.733987e-03	3.899203e-03	7.127605e-03
+C[T>C]G	9.199519e-03	7.413690e-03	1.642174e-02	1.224971e-02
+C[T>C]T	1.327566e-02	9.959621e-03	1.871874e-02	2.250458e-02
+G[T>C]A	1.126406e-02	7.644979e-03	5.362476e-03	1.191308e-02
+G[T>C]C	5.382469e-03	4.828479e-03	1.970185e-12	9.597621e-03
+G[T>C]G	1.123791e-02	1.724741e-02	1.516244e-02	1.372539e-02
+G[T>C]T	1.282307e-02	4.586347e-03	1.411896e-02	1.039154e-02
+T[T>C]A	1.092086e-02	5.588158e-03	8.761926e-03	1.007685e-02
+T[T>C]C	1.803799e-02	2.013810e-02	8.203282e-03	1.529979e-02
+T[T>C]G	8.490634e-03	4.340314e-03	1.235122e-02	4.467692e-03
+T[T>C]T	3.206972e-02	1.668243e-02	3.818623e-02	4.544754e-02
+A[T>G]A	4.607840e-03	1.111060e-02	4.088577e-03	1.675423e-02
+A[T>G]C	2.785895e-20	3.406825e-03	4.944014e-04	2.164564e-03
+A[T>G]G	9.026035e-03	3.004937e-03	5.635912e-03	2.524956e-03
+A[T>G]T	4.203199e-03	5.247793e-03	1.255466e-03	8.623252e-03
+C[T>G]A	2.785895e-20	3.674810e-20	3.467823e-03	6.471005e-03
+C[T>G]C	6.581920e-03	6.843904e-04	1.594754e-03	9.266438e-04
+C[T>G]G	1.978907e-03	5.066625e-03	7.694784e-03	1.800258e-03
+C[T>G]T	1.094034e-03	2.834946e-03	8.971833e-03	3.108266e-20
+G[T>G]A	2.124062e-03	2.575322e-03	3.809196e-03	5.453246e-06
+G[T>G]C	3.641890e-03	3.851018e-03	2.472880e-06	1.886510e-03
+G[T>G]G	8.768503e-03	7.669052e-03	1.102237e-02	9.725885e-03
+G[T>G]T	1.076981e-02	6.207912e-03	6.393167e-03	1.271972e-02
+T[T>G]A	8.496984e-03	2.798437e-03	1.940681e-03	4.645137e-03
+T[T>G]C	2.128895e-03	5.382631e-03	6.346618e-03	5.118158e-03
+T[T>G]G	1.196188e-02	6.471983e-03	1.892812e-02	9.668990e-03
+T[T>G]T	2.241590e-02	2.343561e-02	3.806567e-02	1.368935e-02
--- a/test-data/user_defined_signature.tsv	Mon Oct 25 15:22:14 2021 +0000
+++ b/test-data/user_defined_signature.tsv	Wed Oct 27 00:46:47 2021 +0000
@@ -1,4 +1,4 @@
-Type	SBS1	SBS2	SBS3	SBS4	SBS5	SBS6	SBS7a	SBS8	SBS9	SBS10a	SBS11	SBS12	SBS13	SBS14	SBS15	SBS16	SBS17a	SBS18	SBS19	SBS20	SBS21	SBS22	SBS23	SBS24	SBS25	SBS26	SBS28	SBS29	SBS30
+Type	SBSa	SBSb	SBSc	SBSd	SBSe	SBSf	SBS7a	SBSg	SBSh	SBS10a	SBSi	SBSj	SBSk	SBSl	SBSm	SBSn	SBS17a	SBSo	SBSp	SBSq	SBSr	SBSs	SBSt	SBSu	SBSv	SBSw	SBSx	SBSy	SBSz
 A[C>A]A	0.000876022860356065	5.79005909129116e-07	0.0209197492105927	0.0424507363741909	0.0120520481367051	0.000425145613703031	6.71694562134893e-05	0.0443106405724723	0.000560638966969298	0.00218526226624343	0.000147337461127982	0.00454236809131541	0.00181687918087284	0.00112609260941517	0.000946030090875022	0.0160943727268514	0.00207279918632882	0.0516883199119327	0.00127961346873583	0.000624247512114177	0.000157722171783313	0.00604617162363952	0.000844506730061431	0.0366237270205082	0.00993578471500029	0.000876874614431855	0.000785670933284911	0.0634975968681214	0.00181050219506439
 A[C>A]C	0.0022201195808427	0.000145504532003707	0.0163431921068143	0.0329895820389566	0.00933708706453245	0.000516225985778605	0.000176729831442553	0.0472995640705189	0.00404699056207519	0.00173937218490227	0.000548604298962786	0.00111836131396873	0.000708842466041201	0.0129714099117801	0.000490511447644093	0.00287284286844122	0.000905293428455269	0.015617160603031	0.000636052426566461	0.00138051386891227	0.00233488180943175	9.45179243898909e-05	0.000397419651060091	0.0262583136241544	0.00691870511579565	0.000522296335554948	0.00249692183598218	0.0506605586475702	0.000501229784403264
 A[C>A]G	0.000179727205679816	5.36186073164881e-05	0.00180754877738393	0.0161159612218968	0.00190813974719045	5.34208697464283e-05	7.3305382042244e-05	0.00476727552433761	0.000439559345708089	0.000153712628486902	9.75233896485778e-05	0.000557309553139576	0.000270655854422162	0.000426446913390031	4.74452478520416e-05	0.00105369054278497	4.89499976093771e-05	0.0025046687585242	0.000254547611912212	2.25777938295459e-05	0.000303318754994713	0.000790362401227405	1.02308497833945e-07	0.0152926133494441	0.00149449277081636	0.000117594481949321	0.000363293951337536	0.0198107208240535	9.43096572057688e-05
Binary file test-data/user_output.pdf has changed