| Previous changeset 3:8b1020c25f0f (2019-04-12) Next changeset 5:bcff1eb6fdb5 (2023-10-06) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c |
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modified:
cpm_tpm_rpk.R cpm_tpm_rpk.xml test-data/counts.tab test-data/cpm.tab test-data/logcpm.tab test-data/logrpk.tab test-data/logtpm.tab test-data/none.tab test-data/none_pca.pdf test-data/none_tsne.pdf test-data/pca.nolab.pdf test-data/pca.pdf test-data/rpk.tab test-data/tpm.tab test-data/tsne.nolab.pdf test-data/tsne.pdf |
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added:
infos.txt |
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removed:
README.md |
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| diff -r 8b1020c25f0f -r be358a1ebf67 README.md --- a/README.md Fri Apr 12 12:01:35 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -#Creation of test files - -- count table : count.tab -Subset of RSEM results of Patel et al. (2014) which was aligned with hg38 CuratedRefSeq annotation. - -- gene length : length_gene.tab -Feature length determined by FeatureCounts with RSEM genome bam results of Patel et al. (2014) in hg38 CuratedRefSeq annotation. - - |
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| diff -r 8b1020c25f0f -r be358a1ebf67 cpm_tpm_rpk.R --- a/cpm_tpm_rpk.R Fri Apr 12 12:01:35 2019 -0400 +++ b/cpm_tpm_rpk.R Thu Oct 05 13:50:22 2023 +0000 |
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| b'@@ -1,142 +1,150 @@\n if (length(commandArgs(TRUE)) == 0) {\n- system("Rscript cpm_tpm_rpk.R -h", intern = F)\n+ system("Rscript cpm_tpm_rpk.R -h", intern = FALSE)\n q("no")\n }\n \n \n # load packages that are provided in the conda env\n-options( show.error.messages=F,\n- error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )\n-loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+options(show.error.messages = FALSE,\n+ error = function() {\n+ cat(geterrmessage(), file = stderr())\n+ q("no", 1, FALSE)\n+ }\n+)\n+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") # nolint\xe2\x81\xa0\n warnings()\n library(optparse)\n library(ggplot2)\n library(reshape2)\n-library(Rtsne)\n+library(Rtsne) # nolint\xe2\x81\xa0\n library(ggfortify)\n \n \n \n #Arguments\n-option_list = list(\n+option_list <- list(\n make_option(\n c("-d", "--data"),\n default = NA,\n- type = \'character\',\n+ type = "character",\n help = "Input file that contains count values to transform"\n ),\n make_option(\n c("-t", "--type"),\n- default = \'cpm\',\n- type = \'character\',\n+ default = "cpm",\n+ type = "character",\n help = "Transformation type, either cpm, tpm, rpk or none[default : \'%default\' ]"\n ),\n make_option(\n c("-s", "--sep"),\n- default = \'\\t\',\n- type = \'character\',\n+ default = "\\t",\n+ type = "character",\n help = "File separator [default : \'%default\' ]"\n ),\n make_option(\n c("-c", "--colnames"),\n default = TRUE,\n- type = \'logical\',\n+ type = "logical",\n help = "Consider first line as header ? [default : \'%default\' ]"\n ),\n make_option(\n c("-f", "--gene"),\n default = NA,\n- type = \'character\',\n+ type = "character",\n help = "Two column of gene length file"\n ),\n make_option(\n c("-a", "--gene_sep"),\n- default = \'\\t\',\n- type = \'character\',\n+ default = "\\t",\n+ type = "character",\n help = "Gene length file separator [default : \'%default\' ]"\n ),\n make_option(\n c("-b", "--gene_header"),\n default = TRUE,\n- type = \'logical\',\n+ type = "logical",\n help = "Consider first line of gene length as header ? [default : \'%default\' ]"\n ),\n make_option(\n c("-l", "--log"),\n default = FALSE,\n- type = \'logical\',\n+ type = "logical",\n help = "Should be log transformed as well ? (log2(data +1)) [default : \'%default\' ]"\n ),\n make_option(\n c("-o", "--out"),\n default = "res.tab",\n- type = \'character\',\n+ type = "character",\n help = "Output name [default : \'%default\' ]"\n ),\n make_option(\n "--visu",\n default = FALSE,\n- type = \'logical\',\n+ type = "logical",\n help = "performs T-SNE [default : \'%default\' ]"\n ),\n make_option(\n "--tsne_labels",\n default = FALSE,\n- type = \'logical\',\n+ type = "logical",\n help = "add labels to t-SNE plot [default : \'%default\' ]"\n ),\n make_option(\n "--seed",\n default = 42,\n- type = \'integer\',\n+ type = "integer",\n help = "Seed value for reproducibility [default : \'%default\' ]"\n ),\n make_option(\n "--perp",\n default = 5.0,\n- type = \'numeric\',\n+ type = "numeric",\n help = "perplexity [default : \'%default\' ]"\n ),\n make_option(\n "--theta",\n default = 1.0,\n- type = \'numeric\',\n+ type = "numeric",\n help = "theta [default : \'%default\' ]"\n ),\n make_option(\n c("-D", "--tsne_out"),\n default = "tsne.pdf",\n- type = \'character\',\n+ type = "character",\n help = "T-SNE pdf [default : \'%default\' ]"\n ),\n make_option(\n "--pca_out",\n default = "pca.pdf",\n- type = \'character\',\n+ type = "character",\n help = "PCA pdf [default : \'%default\' ]"\n )\n \n )\n \n-opt = parse_args(OptionParser(option_list = option_list),\n- args = commandArgs(trailingOnly = TRUE))\n+opt <- parse_args(OptionParser(option_list = option_list),\n+ args = commandArgs(trailingOnly = TRUE))\n \n-if (opt$data == "" & !(opt$help)) {\n+if (opt$data == "" && !(opt$help)) {\n stop'..b'es(res) = colnames(data)\n-\n+ res <- data\n+colnames(res) <- colnames(data)\n \n if (opt$log == TRUE) {\n- res = log2(res + 1)\n+ res <- log2(res + 1)\n }\n \n+if (opt$visu == TRUE) {\n+ df <- res\n+ # filter and transpose df for tsne and pca\n+ df <- df[rowSums(df) != 0, ] # remove lines without information (with only 0 counts)\n+ tdf <- t(df)\n+ # make tsne and plot results\n+ set.seed(opt$seed) ## Sets seed for reproducibility\n+ tsne_out <- Rtsne(tdf, perplexity = opt$perp, theta = opt$theta)\n+ embedding <- as.data.frame(tsne_out$Y)\n+ embedding$Class <- as.factor(sub("Class_", "", rownames(tdf)))\n+ gg_legend <- theme(legend.position = "none")\n+ ggplot(embedding, aes(x = V1, y = V2)) +\n+ geom_point(size = 1, color = "red") +\n+ gg_legend +\n+ xlab("") +\n+ ylab("") +\n+ ggtitle("t-SNE") +\n+ if (opt$tsne_labels == TRUE) {\n+ geom_text(aes(label = Class), hjust = -0.2, vjust = -0.5, size = 2.5, color = "darkblue")\n+ }\n+ ggsave(file = opt$tsne_out, device = "pdf")\n+ # make PCA and plot result with ggfortify (autoplot)\n+ tdf_pca <- prcomp(tdf, center = TRUE, scale. = TRUE)\n+ if (opt$tsne_labels == TRUE) {\n+ autoplot(tdf_pca, shape = FALSE, label = TRUE, label.size = 2.5, label.vjust = 1.2,\n+ label.hjust = 1.2,\n+ colour = "darkblue") +\n+ geom_point(size = 1, color = "red") +\n+ xlab(paste("PC1", summary(tdf_pca)$importance[2, 1] * 100, "%")) +\n+ ylab(paste("PC2", summary(tdf_pca)$importance[2, 2] * 100, "%")) +\n+ ggtitle("PCA")\n+ ggsave(file = opt$pca_out, device = "pdf")\n+ } else {\n+ autoplot(tdf_pca, shape = TRUE, colour = "darkblue") +\n+ geom_point(size = 1, color = "red") +\n+ xlab(paste("PC1", summary(tdf_pca)$importance[2, 1] * 100, "%")) +\n+ ylab(paste("PC2", summary(tdf_pca)$importance[2, 2] * 100, "%")) +\n+ ggtitle("PCA")\n+ ggsave(file = opt$pca_out, device = "pdf")\n+ }\n+}\n+\n+# at this stage, we select numeric columns and round theirs values to 8 decimals for cleaner output\n+is_num <- sapply(res, is.numeric)\n+res[is_num] <- lapply(res[is_num], round, 8)\n+\n write.table(\n cbind(Features = rownames(res), res),\n opt$out,\n col.names = opt$colnames,\n- row.names = F,\n- quote = F,\n+ row.names = FALSE,\n+ quote = FALSE,\n sep = "\\t"\n )\n-\n-## \n-if (opt$visu == TRUE) {\n- df = res\n- # filter and transpose df for tsne and pca\n- df = df[rowSums(df) != 0,] # remove lines without information (with only 0 counts)\n- tdf = t(df)\n- # make tsne and plot results\n- set.seed(opt$seed) ## Sets seed for reproducibility\n- tsne_out <- Rtsne(tdf, perplexity=opt$perp, theta=opt$theta) # \n- embedding <- as.data.frame(tsne_out$Y)\n- embedding$Class <- as.factor(sub("Class_", "", rownames(tdf)))\n- gg_legend = theme(legend.position="none")\n- ggplot(embedding, aes(x=V1, y=V2)) +\n- geom_point(size=1, color=\'red\') +\n- gg_legend +\n- xlab("") +\n- ylab("") +\n- ggtitle(\'t-SNE\') +\n- if (opt$tsne_labels == TRUE) {\n- geom_text(aes(label=Class),hjust=-0.2, vjust=-0.5, size=2.5, color=\'darkblue\')\n- }\n- ggsave(file=opt$tsne_out, device="pdf")\n- # make PCA and plot result with ggfortify (autoplot)\n- tdf.pca <- prcomp(tdf, center = TRUE, scale. = T)\n- if (opt$tsne_labels == TRUE) {\n- autoplot(tdf.pca, shape=F, label=T, label.size=2.5, label.vjust=1.2,\n- label.hjust=1.2,\n- colour="darkblue") +\n- geom_point(size=1, color=\'red\') +\n- xlab(paste("PC1",summary(tdf.pca)$importance[2,1]*100, "%")) +\n- ylab(paste("PC2",summary(tdf.pca)$importance[2,2]*100, "%")) +\n- ggtitle(\'PCA\')\n- ggsave(file=opt$pca_out, device="pdf") \n- } else {\n- autoplot(tdf.pca, shape=T, colour="darkblue") +\n- geom_point(size=1, color=\'red\') +\n- xlab(paste("PC1",summary(tdf.pca)$importance[2,1]*100, "%")) +\n- ylab(paste("PC2",summary(tdf.pca)$importance[2,2]*100, "%")) +\n- ggtitle(\'PCA\') \n- ggsave(file=opt$pca_out, device="pdf")\n- }\n-}\n- \n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n' |
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| diff -r 8b1020c25f0f -r be358a1ebf67 cpm_tpm_rpk.xml --- a/cpm_tpm_rpk.xml Fri Apr 12 12:01:35 2019 -0400 +++ b/cpm_tpm_rpk.xml Thu Oct 05 13:50:22 2023 +0000 |
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| @@ -1,10 +1,11 @@ -<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.4.0"> +<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.5.0"> <description>from raw counts expression values</description> <requirements> - <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> - <requirement type="package" version="0.13=r3.3.2_0">r-rtsne</requirement> - <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement> - <requirement type="package" version="0.4.1=r3.3.2_0">r-ggfortify</requirement> + <requirement type="package" version="1.7.1">r-optparse</requirement> + <requirement type="package" version="0.16">r-rtsne</requirement> + <requirement type="package" version="3.3.6">r-ggplot2</requirement> + <requirement type="package" version="0.4.14">r-ggfortify</requirement> + <requirement type="package" version="1.4.4">r-reshape2</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -138,7 +139,7 @@ </outputs> <tests> <!-- test t-SNE --> - <test> + <test expect_num_outputs="3"> <param name="input" value="none.tab" ftype="tabular"/> <param name="type_transfo" value="none"/> <param name="log" value="FALSE"/> @@ -147,11 +148,11 @@ <param name="perp" value="10"/> <param name="theta" value="1" /> <param name="tsne_labels" value="yes" /> - <output name="output" file="none.tab" ftype="tabular"/> - <output name="tsne_out" file="none_tsne.pdf" ftype="pdf"/> - <output name="pca_out" file="none_pca.pdf" ftype="pdf"/> + <output name="output" file="none.tab" ftype="tabular" /> + <output name="tsne_out" file="none_tsne.pdf" ftype="pdf" compare="sim_size" delta="1000" /> + <output name="pca_out" file="none_pca.pdf" ftype="pdf" /> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="cpm"/> <param name="log" value="TRUE"/> @@ -160,11 +161,11 @@ <param name="perp" value="2"/> <param name="theta" value="1" /> <param name="tsne_labels" value="yes" /> - <output name="output" file="logcpm.tab" ftype="tabular"/> - <output name="tsne_out" file="tsne.pdf" ftype="pdf"/> - <output name="pca_out" file="pca.pdf" ftype="pdf"/> + <output name="output" file="logcpm.tab" ftype="tabular" /> + <output name="tsne_out" file="tsne.pdf" ftype="pdf" compare="sim_size" delta="1000" /> + <output name="pca_out" file="pca.pdf" ftype="pdf" /> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="tpm"/> <param name="gene_file" value="gene_length.tab" ftype="tabular"/> @@ -174,51 +175,51 @@ <param name="perp" value="2"/> <param name="theta" value="1" /> <param name="tsne_labels" value="no" /> - <output name="output" file="logtpm.tab" ftype="tabular"/> - <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf"/> - <output name="pca_out" file="pca.nolab.pdf" ftype="pdf"/> + <output name="output" file="logtpm.tab" ftype="tabular" /> + <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf" compare="sim_size" delta="1000" /> + <output name="pca_out" file="pca.nolab.pdf" ftype="pdf" /> </test> <!-- test without t-SNE --> - <test> + <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="cpm"/> <output name="output" file="cpm.tab" ftype="tabular"/> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="cpm"/> <param name="log" value="TRUE"/> - <output name="output" file="logcpm.tab" ftype="tabular"/> + <output name="output" file="logcpm.tab" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="tpm"/> <param name="gene_file" value="gene_length.tab" ftype="tabular"/> <param name="gene_header" value="TRUE"/> <output name="output" file="tpm.tab" ftype="tabular"/> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="tpm"/> <param name="gene_file" value="gene_length.tab" ftype="tabular"/> <param name="gene_header" value="TRUE"/> <param name="log" value="TRUE"/> - <output name="output" file="logtpm.tab" ftype="tabular"/> + <output name="output" file="logtpm.tab" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="rpk"/> <param name="gene_file" value="gene_length.tab" ftype="tabular"/> <param name="gene_header" value="TRUE"/> - <output name="output" file="rpk.tab" ftype="tabular"/> + <output name="output" file="rpk.tab" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="rpk"/> <param name="gene_file" value="gene_length.tab" ftype="tabular"/> <param name="gene_header" value="TRUE"/> <param name="log" value="TRUE"/> - <output name="output" file="logrpk.tab" ftype="tabular"/> + <output name="output" file="logrpk.tab" ftype="tabular" /> </test> </tests> <help> @@ -240,4 +241,24 @@ Computed values may be log-transformed (log2([CPM or RPK or TPM]+1)) </help> + <citations> + <citation type="bibtex">@Article{, + title = {Visualizing High-Dimensional Data Using t-SNE}, + volume = {9}, + pages = {2579-2605}, + year = {2008}, + author = {L.J.P. {van der Maaten} and G.E. Hinton}, + journal = {Journal of Machine Learning Research}, + } + </citation> + <citation type="bibtex">@Manual{, + title = {{ClusterR}: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, + K-Medoids and Affinity Propagation Clustering}, + author = {Lampros Mouselimis}, + year = {2019}, + note = {R package version 1.1.9}, + url = {https://github.com/mlampros/ClusterR}, + } + </citation> + </citations> </tool> |
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| diff -r 8b1020c25f0f -r be358a1ebf67 infos.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/infos.txt Thu Oct 05 13:50:22 2023 +0000 |
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| @@ -0,0 +1,9 @@ +#Creation of test files + +- count table : count.tab +Subset of RSEM results of Patel et al. (2014) which was aligned with hg38 CuratedRefSeq annotation. + +- gene length : length_gene.tab +Feature length determined by FeatureCounts with RSEM genome bam results of Patel et al. (2014) in hg38 CuratedRefSeq annotation. + + |
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| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/counts.tab --- a/test-data/counts.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/counts.tab Thu Oct 05 13:50:22 2023 +0000 |
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| b'@@ -1,5066 +1,469 @@\n gene\tWt1\tWt2\tWt3\tCA1\tCA2\tCA3\tKK1\tKK2\tKK3\n-0610005C13Rik\t68\t49\t54\t49\t50\t56\t78\t62\t71\n-0610006L08Rik\t0\t0\t0\t0\t0\t1\t0\t0\t0\n-0610009B22Rik\t446\t432\t542\t412\t405\t448\t488\t503\t542\n-0610009E02Rik\t188\t156\t180\t179\t199\t229\t175\t164\t186\n-0610009L18Rik\t28\t27\t15\t20\t19\t20\t12\t16\t11\n-0610009O20Rik\t729\t748\t845\t852\t873\t883\t799\t819\t1004\n-0610010F05Rik\t705\t592\t744\t576\t711\t689\t735\t710\t760\n-0610010K14Rik\t17\t8\t15\t21\t24\t29\t18\t21\t20\n-0610012D04Rik\t2\t0\t1\t0\t1\t2\t3\t3\t0\n-0610012G03Rik\t496\t524\t602\t396\t480\t442\t460\t571\t553\n-0610030E20Rik\t400\t338\t360\t354\t350\t408\t385\t365\t441\n-0610033M10Rik\t0\t0\t0\t2\t0\t1\t2\t1\t1\n-0610037L13Rik\t407\t423\t386\t435\t404\t449\t404\t505\t451\n-0610038B21Rik\t38\t26\t39\t65\t54\t76\t47\t47\t48\n-0610039K10Rik\t17\t15\t16\t21\t31\t43\t34\t34\t32\n-0610040B10Rik\t10\t17\t15\t23\t11\t20\t17\t19\t10\n-0610040F04Rik\t27\t27\t24\t23\t33\t45\t29\t33\t31\n-0610040J01Rik\t22\t15\t22\t45\t49\t54\t50\t54\t52\n-0610043K17Rik\t7\t3\t11\t4\t2\t4\t6\t8\t4\n-1010001B22Rik\t6\t6\t7\t4\t8\t9\t4\t6\t5\n-1010001N08Rik\t2\t3\t4\t2\t0\t0\t4\t3\t4\n-1110002E22Rik\t0\t0\t0\t2\t0\t0\t1\t0\t1\n-1110002J07Rik\t84\t74\t92\t210\t200\t262\t151\t143\t168\n-1110002L01Rik\t402\t366\t398\t337\t351\t409\t378\t403\t378\n-1110002O04Rik\t0\t0\t0\t1\t0\t1\t0\t0\t0\n-1110003F10Rik\t16\t5\t18\t11\t7\t7\t5\t8\t8\n-1110004E09Rik\t378\t437\t415\t425\t401\t393\t385\t413\t516\n-1110004F10Rik\t972\t1039\t1082\t860\t962\t996\t1112\t1026\t1223\n-1110006O24Rik\t9\t16\t13\t6\t13\t10\t12\t10\t20\n 1110008F13Rik\t1583\t1546\t1746\t1720\t1845\t1699\t1671\t1893\t2018\n-1110008L16Rik\t827\t799\t924\t734\t882\t849\t954\t905\t999\n-1110008P14Rik\t252\t273\t267\t258\t284\t327\t243\t271\t286\n-1110012L19Rik\t230\t237\t260\t206\t234\t227\t249\t264\t253\n-1110017D15Rik\t3\t0\t3\t2\t0\t2\t2\t2\t2\n-1110018N20Rik\t9\t9\t7\t11\t10\t9\t9\t9\t5\n-1110019B22Rik\t1\t0\t0\t0\t0\t0\t0\t1\t0\n-1110019D14Rik\t77\t53\t55\t53\t59\t81\t85\t81\t83\n-1110020A21Rik\t3\t3\t6\t7\t9\t9\t4\t6\t5\n-1110025L11Rik\t0\t0\t1\t0\t0\t0\t0\t0\t0\n-1110025M09Rik\t23\t17\t16\t9\t18\t16\t9\t14\t19\n-1110028F11Rik\t0\t0\t0\t0\t0\t0\t2\t0\t1\n-1110028F18Rik\t1\t0\t0\t0\t0\t2\t0\t1\t0\n-1110032A03Rik\t211\t231\t224\t186\t183\t217\t233\t178\t246\n-1110032F04Rik\t38\t38\t49\t13\t16\t13\t27\t38\t40\n-1110034G24Rik\t125\t127\t142\t93\t84\t129\t126\t128\t111\n-1110035H17Rik\t70\t57\t63\t54\t47\t60\t61\t57\t64\n-1110036E04Rik\t0\t1\t0\t0\t0\t0\t0\t0\t0\n 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No newline at end of file\n' |
| b |
| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/cpm.tab --- a/test-data/cpm.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/cpm.tab Thu Oct 05 13:50:22 2023 +0000 |
| b |
| b'@@ -1,35194 +1,3962 @@\n Features\tWt1\tWt2\tWt3\tCA1\tCA2\tCA3\tKK1\tKK2\tKK3\n-0610005C13Rik\t3.71891459102467\t2.77720061125619\t2.82163106264664\t2.58592405542131\t2.56876269482524\t2.66134714065576\t4.05855136773181\t3.07119054354673\t3.11787622918428\n-0610006L08Rik\t0\t0\t0\t0\t0\t0.0475240560831386\t0\t0\t0\n-0610009B22Rik\t24.3917045234854\t24.4847074298505\t28.3208154806385\t21.7428716496649\t20.8069778280844\t21.2907771252461\t25.3919624032452\t24.9162716678066\t23.8012523410969\n-0610009E02Rik\t10.2817050457741\t8.84169990522378\t9.40543687548879\t9.446538896335\t10.2236755254044\t10.8830088430387\t9.10572422247522\t8.12379434099458\t8.16795744546867\n-0610009L18Rik\t1.53131777277487\t1.53029421436565\t0.783786406290732\t1.05547920629441\t0.97612982403359\t0.950481121662772\t0.624392518112586\t0.792565301560447\t0.483051246775029\n-0610009O20Rik\t39.8689520126027\t42.3948174942781\t44.1533008877113\t44.963414188142\t44.8505966516487\t41.9637415214114\t41.5741351643297\t40.5694363736254\t44.0894047056481\n-0610010F05Rik\t38.5563939216529\t33.5531175890543\t38.8758057520203\t30.3978011412791\t36.5278055204149\t32.7440746412825\t38.2440417343959\t35.1700852567448\t33.3744497771838\n-0610010K14Rik\t0.929728647756168\t0.453420507960194\t0.783786406290732\t1.10825316660913\t1.23300609351611\t1.37819762641102\t0.936588777168879\t1.04024195829809\t0.878274994136417\n-0610012D04Rik\t0.10937984091249\t0\t0.0522524270860488\t0\t0.0513752538965048\t0.0950481121662772\t0.156098129528147\t0.148605994042584\t0\n-0610012G03Rik\t27.1262005462976\t29.6990432713927\t31.4559611058014\t20.8984882846294\t24.6601218703223\t21.0056327887473\t23.9350465276491\t28.2846741994385\t24.2843035878719\n-0610030E20Rik\t21.8759681824981\t19.1570164613182\t18.8108737509776\t18.6819819514111\t17.9813388637767\t19.3898148819205\t20.0325932894455\t18.0803959418477\t19.365963620708\n-0610033M10Rik\t0\t0\t0\t0.105547920629441\t0\t0.0475240560831386\t0.104065419685431\t0.0495353313475279\t0.0439137497068208\n-0610037L13Rik\t22.2587976256918\t23.9746093583952\t20.1694368552148\t22.9566727369035\t20.7556025741879\t21.3383011813292\t21.0212147764571\t25.0153423305016\t19.8051011177762\n-0610038B21Rik\t2.07821697733732\t1.47361665087063\t2.0378446563559\t3.43030742045684\t2.77426371041126\t3.61182826231853\t2.44553736260763\t2.32816057333381\t2.1078599859274\n-0610039K10Rik\t0.929728647756168\t0.850163452425363\t0.836038833376781\t1.10825316660913\t1.59263287079165\t2.04353441157496\t1.76911213465233\t1.68420126581595\t1.40523999061827\n-0610040B10Rik\t0.546899204562452\t0.963518579415412\t0.783786406290732\t1.21380108723858\t0.565127792861552\t0.950481121662772\t0.884556067326164\t0.941171295603031\t0.439137497068208\n-0610040F04Rik\t1.47662785231862\t1.53029421436565\t1.25405825006517\t1.21380108723858\t1.69538337858466\t2.13858252374124\t1.50894858543875\t1.63466593446842\t1.36132624091145\n-0610040J01Rik\t1.20317825003739\t0.850163452425363\t1.14955339589307\t2.37482821416243\t2.51738744092873\t2.56629902848948\t2.60163549213578\t2.67490789276651\t2.28351498475468\n-0610043K17Rik\t0.382829443193716\t0.170032690485073\t0.574776697946537\t0.211095841258883\t0.10275050779301\t0.190096224332554\t0.312196259056293\t0.396282650780224\t0.175654998827283\n-1010001B22Rik\t0.328139522737471\t0.340065380970145\t0.365766989602342\t0.211095841258883\t0.411002031172038\t0.427716504748247\t0.208130839370862\t0.297211988085168\t0.219568748534104\n-1010001N08Rik\t0.10937984091249\t0.170032690485073\t0.209009708344195\t0.105547920629441\t0\t0\t0.208130839370862\t0.148605994042584\t0.175654998827283\n-1110002E22Rik\t0\t0\t0\t0.105547920629441\t0\t0\t0.0520327098427155\t0\t0.0439137497068208\n-1110002J07Rik\t4.5939533183246\t4.19413969863179\t4.80722329191649\t11.0825316660913\t10.275050779301\t12.4513026937823\t7.85693918625004\t7.0835523826965\t7.3775099507459\n-1110002L01Rik\t21.9853480234106\t20.7439882391789\t20.7964659802474\t17.7848246260609\t18.0327141176732\t19.4373389380037\t19.6683643205465\t19.9627385330538\t16.5993973891783\n-1110002O04Rik\t0\t0\t0\t0.0527739603147207\t0\t0.0475240560831386\t0\t0\t0\n-1110003F10Rik\t0.875038727299923\t0.283387817475121\t0.940543687548879\t0.580513563461928\t0.359626777275533\t0.33266839258'..b'29a\t78.50366377\t61.08893088\t76.40267735\t70.17418751\t73.73091158\t92.24138817\t87.11003949\t78.11472147\t91.27740194\n+Zfp740\t298.14318856\t336.13188339\t326.21514192\t298.94838143\t387.97286901\t430.87073252\t343.10644896\t393.91629707\t434.09837132\n+Zfp850\t118.49396957\t102.2267218\t105.8169944\t119.7041651\t124.04181656\t122.72321348\t125.68351797\t124.9369085\t128.32326218\n+Zfp871\t101.46808193\t72.05393861\t100.06793019\t115.04284554\t106.63490489\t127.77487012\t107.81956828\t96.25765802\t121.6192314\n+Zfp91\t121.13334752\t130.46566038\t151.1107214\t124.11930638\t137.82685304\t141.39841193\t131.30469406\t141.96668072\t150.96933312\n+Zfp930\t102.86312377\t95.74905167\t104.57400585\t90.73769816\t94.83399984\t95.52751144\t103.66559964\t95.84150294\t94.8048719\n+Zfp936\t133.6887135\t94.00358822\t115.22675722\t216.29497335\t216.48846222\t248.69104726\t177.90104833\t151.09526459\t195.66355065\n+Zfp958\t123.58746146\t115.49660911\t138.11922798\t174.93095247\t218.10337834\t207.04546314\t162.66637808\t193.91655467\t215.25538684\n+Zfp961\t102.67864431\t95.42425295\t98.44809777\t247.89310807\t245.16711635\t231.25457255\t196.92138777\t194.01781523\t199.57480329\n+Zfp979\t304.2426869\t262.79192477\t324.36228035\t508.47836947\t497.44608197\t632.69206701\t497.175151\t417.96362035\t466.57391857\n+Zfp990\t104.41096154\t88.43826012\t104.75552135\t154.72870602\t208.45156129\t209.35206185\t170.65573619\t150.57735487\t164.68061798\n+Zfr\t205.40284625\t183.02186741\t180.83358525\t214.670867\t243.11620112\t241.39110951\t233.69173712\t213.86837723\t241.13090944\n+Zfx\t122.01457828\t97.09673496\t141.85607422\t130.01713332\t136.15229751\t142.6167241\t130.31477018\t120.3524953\t150.544527\n+Zic3\t305.71217241\t372.59930432\t424.03151454\t386.25236746\t426.02867203\t449.64170324\t354.79039439\t380.08503372\t425.53374424\n+Zkscan17\t72.6750331\t75.15940597\t77.91527963\t85.81290116\t87.35746043\t88.28689114\t74.67380911\t78.645666\t79.20902328\n+Zmat2\t88.26190778\t86.82368191\t92.76158734\t89.45613816\t79.52513213\t92.22847127\t80.98480558\t82.73066651\t121.10176189\n+Zmat3\t297.70018958\t255.4148143\t287.12534668\t299.17756289\t367.84996615\t393.03867002\t259.87491123\t322.7050989\t408.19332554\n+Zmym1\t188.82886034\t175.82984341\t186.97837111\t170.75898646\t169.99854973\t155.6230916\t200.83465878\t214.60746092\t222.3776539\n+Zmym2\t356.44729538\t290.96341381\t373.56853034\t491.34575252\t466.25438473\t626.19324193\t506.6780644\t441.03239341\t506.98423917\n+Zmym4\t175.17433467\t171.55692565\t188.83810638\t149.64188801\t214.25158797\t225.04626731\t198.90999715\t205.89699241\t226.32927624\n+Zmynd19\t74.07535472\t65.62234832\t67.58201069\t86.23172197\t80.91874743\t77.64935718\t82.57467847\t86.17695421\t85.97476029\n+Zmynd8\t165.1306106\t133.4311493\t185.88037312\t238.8686868\t226.6324132\t248.33120218\t191.17642429\t184.66624026\t232.66576854\n+Znrf2\t132.53676372\t161.00315025\t179.04352745\t141.53722725\t153.47826269\t157.46641329\t139.94476198\t152.20690031\t156.91201206\n+Zpr1\t79.45337753\t92.5094221\t83.63261244\t85.81290116\t79.88092103\t84.14939383\t86.24392735\t86.16884466\t85.30202507\n+Zranb1\t298.69384615\t239.99501661\t274.03459474\t289.15844072\t280.98474383\t339.92209454\t285.24858921\t227.90062661\t316.62555286\n+Zranb2\t201.0373768\t176.21328446\t209.67102177\t147.12453672\t178.33940875\t170.12498971\t165.68492942\t205.44672819\t235.84503254\n+Zscan10\t138.29909385\t136.93872176\t125.82859468\t154.73370774\t148.06121364\t148.80340153\t167.64173501\t175.2999555\t196.25077259\n+Zscan26\t109.39357658\t106.41886465\t123.81356417\t100.26690215\t98.04701964\t132.35241605\t132.03290283\t122.19136857\t141.1325387\n+Zswim4\t91.08578638\t100.54033782\t100.5197821\t93.96638541\t113.41497954\t120.01027754\t98.65723121\t109.76225644\t133.20045206\n+Zwilch\t114.2382939\t99.44504229\t101.06557098\t130.95481926\t135.70448301\t137.88079348\t136.67998251\t126.57650048\t132.58245059\n+Zwint\t82.31242535\t76.13457283\t100.76672859\t109.93143\t104.37456401\t114.82197938\t103.42546179\t101.18614746\t123.94655403\n+Zyg11b\t105.9846917\t129.48734263\t148.37503421\t127.24389523\t149.36302136\t150.05545756\t131.79145845\t143.5625591\t161.14775131\n+Zzz3\t175.048998\t149.7428778\t154.70038883\t158.06574483\t155.17098452\t158.80688207\t164.17598815\t154.06711257\t153.66662314\n' |
| b |
| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/logcpm.tab --- a/test-data/logcpm.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/logcpm.tab Thu Oct 05 13:50:22 2023 +0000 |
| b |
| b'@@ -1,35194 +1,3962 @@\n Features\tWt1\tWt2\tWt3\tCA1\tCA2\tCA3\tKK1\tKK2\tKK3\n-0610005C13Rik\t2.23845505996379\t1.91731740892465\t1.93418850835685\t1.84234493437827\t1.83542397244854\t1.87237456532778\t2.33872429523358\t2.02545074537792\t2.04190046760359\n-0610006L08Rik\t0\t0\t0\t0\t0\t0.0669833753741182\t0\t0\t0\n-0610009B22Rik\t4.66628534001215\t4.67155988576351\t4.87385332364942\t4.50734252383895\t4.44671793939391\t4.47837500916089\t4.72202672270845\t4.69578628096291\t4.63234106633311\n-0610009E02Rik\t3.49591321893519\t3.2989075262378\t3.37926563323017\t3.3849531286591\t3.48847330148664\t3.57082827558175\t3.3371008104431\t3.18963392729766\t3.19660034761207\n-0610009L18Rik\t1.33988862970429\t1.33930514655114\t0.834942874768512\t1.03947477733719\t0.982677729481796\t0.96383003485809\t0.699900287394128\t0.842025675982355\t0.568568450921874\n-0610009O20Rik\t5.35293334422573\t5.43945085134167\t5.49675955325264\t5.52241406104713\t5.51886860255227\t5.42504773158453\t5.41190531870063\t5.37745128195265\t5.4947165577597\n-0610010F05Rik\t5.30583900661438\t5.11074397995404\t5.31744176593288\t4.97259162235934\t5.22988802440403\t5.07656228635046\t5.2944017269107\t5.17672509347099\t5.10326471575511\n-0610010K14Rik\t0.948397994612813\t0.539452168200853\t0.834942874768512\t1.0760481213778\t1.15898718804954\t1.24986860692394\t0.953517638957561\t1.02874025579343\t0.909408300282999\n-0610012D04Rik\t0.14975341489191\t0\t0.0734808373491687\t0\t0.0722776838678355\t0.130994257642744\t0.209263858889789\t0.199883995613306\t0\n-0610012G03Rik\t4.8138427729139\t4.940121789925\t5.02041157366506\t4.45275937478025\t4.6814561172749\t4.45980095301208\t4.64010298989544\t4.87207393901999\t4.66017013737629\n-0610030E20Rik\t4.51576089894109\t4.33321020917173\t4.30822060602863\t4.29880360049849\t4.2465098524733\t4.34977677214734\t4.39455483821255\t4.25401920425035\t4.34808817232356\n-0610033M10Rik\t0\t0\t0\t0.144761560980538\t0\t0.0669833753741182\t0.142825659307661\t0.0697507340449269\t0.0620025184110997\n-0610037L13Rik\t4.5397046128383\t4.6423902070947\t4.40391098648157\t4.58235564578128\t4.44331507125803\t4.48144756851238\t4.46082215069385\t4.70129078645212\t4.37886539513063\n-0610038B21Rik\t1.62209492792856\t1.30662193574653\t1.60304809787323\t2.14740681132666\t1.91619522855864\t2.20533879015479\t1.78472900177206\t1.7347250406797\t1.6359215094862\n-0610039K10Rik\t0.948397994612813\t0.887652731058775\t0.876596572982451\t1.0760481213778\t1.37441792813978\t1.60574767766981\t1.46942347654025\t1.42449285123566\t1.26618085075248\n-0610040B10Rik\t0.62937919432059\t0.973441249292143\t0.834942874768512\t1.14652560001178\t0.64628045818068\t0.96383003485809\t0.914224717183301\t0.956927432020159\t0.525204435623763\n-0610040F04Rik\t1.30837709993252\t1.33930514655114\t1.17252479855995\t1.14652560001178\t1.43049048969242\t1.65011314265591\t1.32708290666077\t1.39762004526308\t1.23959737813155\n-0610040J01Rik\t1.13958622224797\t0.887652731058775\t1.10403694797339\t1.75481406782762\t1.81450425686275\t1.83442767571444\t1.84865217894046\t1.87770809095193\t1.71524103918457\n-0610043K17Rik\t0.467623226891532\t0.226548838989738\t0.655147270133281\t0.276313038638934\t0.141106424760476\t0.251078226268554\t0.391983513242642\t0.481591017194141\t0.233464757024114\n-1010001B22Rik\t0.409406711585629\t0.422303390608671\t0.449711369704472\t0.276313038638934\t0.496720064731575\t0.513709538332349\t0.27277670556514\t0.375414261523614\t0.286371086853762\n-1010001N08Rik\t0.14975341489191\t0.226548838989738\t0.273825829470238\t0.144761560980538\t0\t0\t0.27277670556514\t0.199883995613306\t0.233464757024114\n-1110002E22Rik\t0\t0\t0\t0.144761560980538\t0\t0\t0.073179561658965\t0\t0.0620025184110997\n-1110002J07Rik\t2.48386821453942\t2.3768848164447\t2.5378485077701\t3.59485087069609\t3.49506202582972\t3.74967399249095\t3.14680821302994\t3.01498943637089\t3.06652149505353\n-1110002L01Rik\t4.52264260519467\t4.44254467578508\t4.44602233419789\t4.23149574201992\t4.25040940347267\t4.35313545599306\t4.36935231432273\t4.38975529506319\t4.1374541261063\n-1110002O04Rik\t0\t0\t0\t0.0741957104952366\t0\t0.0669833753741182\t0\t0\t0\n-1110003F10Rik\t0.906920393532013\t0.35995719365727\t0.956460912948477\t0.660393416042979\t0.443210680541945\t0.414317839771467\t0.333610984'..b'64\t7.13754089\t7.40437875\t7.6207155\t7.2621562\t7.45997592\t7.48640887\t7.29860247\t7.40908219\t7.55511017\n+Zfp7\t6.93028793\t6.90432052\t6.9377333\t6.87413502\t6.91751488\t6.91289721\t6.95746896\t6.90665035\t6.87506645\n+Zfp704\t7.56421409\t7.1665889\t7.37223054\t6.84693956\t6.81260347\t7.09011975\t7.15915359\t6.91904643\t7.4876239\n+Zfp706\t7.08699226\t7.09381975\t7.23265712\t7.12835927\t7.31099873\t7.38929052\t7.02625247\t7.34608772\t7.5669554\n+Zfp710\t7.54112235\t7.60584817\t7.54034509\t7.59967704\t7.6366609\t7.56939201\t7.58744751\t7.86881877\t7.95675857\n+Zfp729a\t6.31294944\t5.95626418\t6.27431156\t6.15328221\t6.22363322\t6.54289858\t6.46123451\t6.30587427\t6.52790548\n+Zfp740\t8.2246924\t8.39716926\t8.3540957\t8.22857044\t8.60352572\t8.75445574\t8.42671112\t8.62540309\t8.76519781\n+Zfp850\t6.900794\t6.68967267\t6.73899739\t6.91533165\t6.96626683\t6.9509724\t6.98508503\t6.97655735\t7.01483799\n+Zfp871\t6.67903078\t6.19089015\t6.65918148\t6.85851377\t6.75000219\t7.00870727\t6.7657942\t6.60373995\t6.93804146\n+Zfp91\t6.93231336\t7.0385422\t7.24897803\t6.96716061\t7.11714284\t7.15378925\t7.04772044\t7.15953515\t7.24763641\n+Zfp930\t6.69853971\t6.59617561\t6.72211085\t6.5194428\t6.58246568\t6.59286828\t6.70964354\t6.59755356\t6.58202712\n+Zfp936\t7.07348515\t6.5699101\t6.86079843\t7.76351099\t7.76479506\t7.96400028\t7.48301803\t7.24883143\t7.61958579\n+Zfp958\t6.96101507\t6.86414415\t7.12017802\t7.45886552\t7.77546792\t7.70075502\t7.35461417\t7.60671282\t7.75659226\n+Zfp961\t6.69597495\t6.59132416\t6.63587187\t7.95938247\t7.94349425\t7.85956319\t7.62878371\t7.60746211\t7.64799657\n+Zfp979\t8.25381292\t8.04325659\t8.3459032\t8.99287709\t8.96129364\t9.30763814\t8.96050925\t8.71068117\t8.86905065\n+Zfp990\t6.71988109\t6.48282022\t6.72458918\t7.2828911\t7.71047283\t7.71666215\t7.42337426\t7.24391043\t7.37226103\n+Zfr\t7.68931906\t7.5237334\t7.50647488\t7.7526875\t7.93142423\t7.92119297\t7.87462324\t7.74730936\t7.91964345\n+Zfx\t6.94268549\t6.61613321\t7.15841857\t7.03361168\t7.09963498\t7.16607995\t7.03688539\t6.92305996\t7.24359794\n+Zic3\t8.26074161\t8.54534796\t8.73142601\t8.59713025\t8.73818913\t8.81583702\t8.47488375\t8.57396914\t8.73651607\n+Zkscan17\t6.2031039\t6.25095032\t6.30223276\t6.43983755\t6.46528005\t6.48037647\t6.24172216\t6.31552395\t6.32569264\n+Zmat2\t6.47997274\t6.45653811\t6.55092509\t6.4991465\t6.33136722\t6.54269871\t6.35728465\t6.3876842\t6.93194021\n+Zmat3\t8.22255434\t8.00233581\t8.17055277\t8.22967233\t8.52689029\t8.62219341\t8.02721439\t8.33853628\t8.6766388\n+Zmym1\t7.56855554\t7.46621797\t7.55442286\t7.42424177\t7.41784028\t7.29115312\t7.65703012\t7.75226329\t7.80334106\n+Zmym2\t8.48158673\t8.18964378\t8.54908589\t8.943528\t8.86806439\t9.2927662\t8.98777012\t8.78800829\t8.98863993\n+Zmym4\t7.46085996\t7.43092857\t7.5686258\t7.23497918\t7.74988007\t7.82047428\t7.64320681\t7.69276886\t7.82863968\n+Zmynd19\t6.23026748\t6.0579343\t6.0997583\t6.44678096\t6.35612175\t6.29736307\t6.38499399\t6.44587489\t6.44252489\n+Zmynd8\t7.37617411\t7.07072366\t7.54597125\t7.90610103\t7.83056219\t7.96191963\t7.58628755\t7.5365677\t7.86830259\n+Znrf2\t7.06109317\t7.33987806\t7.49220193\t7.15519496\t7.27126003\t7.30803329\t7.13898605\t7.25933747\t7.30297711\n+Zpr1\t6.33008108\t6.54703983\t6.4031418\t6.43983755\t6.33772752\t6.41192435\t6.44698281\t6.44574068\t6.43132251\n+Zranb1\t8.22734565\t7.9128595\t8.10346929\t8.18069709\t8.1394733\t8.41329829\t8.16112477\t7.8385776\t8.31118317\n+Zranb2\t7.65847841\t7.46934295\t7.71884807\t7.21066683\t7.48654874\t7.41890664\t7.38097986\t7.68962574\t7.8877996\n+Zscan10\t7.12204206\t7.10788369\t6.98673624\t7.28293743\t7.2197611\t7.22692657\t7.3978178\t7.4618883\t7.62388714\n+Zscan26\t6.78651242\t6.74710357\t6.96363092\t6.66201891\t6.63004166\t7.05910015\t7.0556393\t6.94475737\t7.15109306\n+Zswim4\t6.52490659\t6.66590915\t6.66561707\t6.56934504\t6.83813214\t6.91898577\t6.63890259\t6.79132254\t7.06824572\n+Zwilch\t6.8484764\t6.65026255\t6.67335248\t7.04390023\t7.09491674\t7.11770329\t7.10517501\t6.9952188\t7.06158668\n+Zwint\t6.38045977\t6.26930574\t6.66912216\t6.79352437\t6.71938285\t6.85576525\t6.70632971\t6.67505583\t6.9651673\n+Zyg11b\t6.74126057\t7.02776606\t7.22279523\t7.00274634\t7.232306\t7.2389345\t7.05301854\t7.17555014\t7.34116521\n+Zzz3\t7.45983321\t7.23594603\t7.28262874\t7.31347937\t7.28698263\t7.32018573\t7.36786017\t7.27674893\t7.27301809\n' |
| b |
| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/logrpk.tab --- a/test-data/logrpk.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/logrpk.tab Thu Oct 05 13:50:22 2023 +0000 |
| b |
| b'@@ -1,35194 +1,3962 @@\n Features\tWt1\tWt2\tWt3\tCA1\tCA2\tCA3\tKK1\tKK2\tKK3\n-0610005C13Rik\t4.32037705883187\t3.87535650523183\t4.00640300474817\t3.87535650523183\t3.90253540825548\t4.05566081635216\t4.5090286107558\t4.1940819485886\t4.37960688006834\n-0610006L08Rik\t0\t0\t0\t0\t0\t0.555742361806163\t0\t0\t0\n-0610009B22Rik\t8.80701284548234\t8.76110483031773\t9.08769135332551\t8.69287926431069\t8.66821708962038\t8.81345348779313\t8.93657303367178\t8.98016247783306\t9.08769135332551\n-0610009E02Rik\t6.71795958858224\t6.4515814257575\t6.65583279918893\t6.64787540908288\t6.79923761634092\t7.00011876940119\t6.6155995476456\t6.52292690385482\t6.70267690205874\n-0610009L18Rik\t5.53089004288733\t5.47957786527661\t4.65721886881995\t5.05789114553272\t4.98616828816104\t5.05789114553272\t4.34951436797712\t4.74675035507611\t4.23040268753524\n-0610009O20Rik\t8.24908781043004\t8.28608681183049\t8.46146923239503\t8.47333769492555\t8.50836826985129\t8.52475518485638\t8.38094900435004\t8.41651126656745\t8.70955695001347\n-0610010F05Rik\t7.08642724071711\t6.83642603911999\t7.16355003066172\t6.79724830565135\t7.09856395656247\t7.05355446279364\t7.14611487545405\t7.0965482476521\t7.19403495792499\n-0610010K14Rik\t3.3170500004989\t2.38388653607811\t3.15565087046019\t3.59406470782841\t3.77169840131091\t4.02638920005239\t3.39144754331865\t3.59406470782841\t3.5296364704667\n-0610012D04Rik\t2.25292374130653\t0\t1.52769051669563\t0\t1.52769051669563\t2.25292374130653\t2.73329305495545\t2.73329305495545\t0\n-0610012G03Rik\t8.42732371996404\t8.50632645765883\t8.70600898195919\t8.10354192545267\t8.38015769187882\t8.2615418767774\t8.31894539918667\t8.62992378407673\t8.58383105164184\n-0610030E20Rik\t6.12074809671541\t5.88156929093785\t5.97104674591309\t5.94718896183673\t5.93106172822866\t6.14891067755124\t6.06641406523421\t5.99063121312767\t6.25959797864409\n-0610033M10Rik\t0\t0\t0\t1.49307446246493\t0\t0.931638445391021\t1.49307446246493\t0.931638445391021\t0.931638445391021\n-0610037L13Rik\t6.19481192243803\t6.24969564404845\t6.11945505344139\t6.28953026397036\t6.18428466160796\t6.33465512564479\t6.18428466160796\t6.50223949408945\t6.3409878423591\n-0610038B21Rik\t3.74133965717268\t3.24280028150652\t3.7760456930001\t4.4702598864352\t4.21597742476091\t4.68636825290365\t4.02719485126934\t4.02719485126934\t4.05572389071175\n-0610039K10Rik\t4.23703919730085\t4.06663193109025\t4.15435010906423\t4.52724700286487\t5.06880085413603\t5.52882343176791\t5.19826962713627\t5.19826962713627\t5.11326064756031\n-0610040B10Rik\t2.52768198277205\t3.18633497977981\t3.02674099595288\t3.58048582078792\t2.64225995313468\t3.39682922004363\t3.18633497977981\t3.33001966107816\t2.52768198277205\n-0610040F04Rik\t3.7610873184984\t3.7610873184984\t3.60440238154484\t3.54814983510343\t4.03111612437044\t4.454849205973\t3.8568235983219\t4.03111612437044\t3.94660030541049\n-0610040J01Rik\t3.34414996384191\t2.85642747157719\t3.34414996384191\t4.3020698124664\t4.41894400737223\t4.55286334610071\t4.44674085286231\t4.55286334610071\t4.5007776560898\n-0610043K17Rik\t3.33498424771281\t2.29163417257376\t3.93411206434354\t2.63105891531061\t1.84695562535429\t2.63105891531061\t3.1362254828801\t3.50964649174983\t2.63105891531061\n-1010001B22Rik\t3.48371998759562\t3.48371998759562\t3.68757025555163\t2.96184026758181\t3.86615063189005\t4.02504083079194\t2.96184026758181\t3.48371998759562\t3.24625063583233\n-1010001N08Rik\t0.978835390001958\t1.29649304751109\t1.55667345628973\t0.978835390001958\t0\t0\t1.55667345628973\t1.29649304751109\t1.55667345628973\n-1110002E22Rik\t0\t0\t0\t0.263082504486581\t0\t0\t0.137529759577519\t0\t0.137529759577519\n-1110002J07Rik\t5.10543436134688\t4.92822231450868\t5.23303020533712\t6.40199661609766\t6.33246004104006\t6.71778414665972\t5.93280635161994\t5.85559356651946\t6.08432725382066\n-1110002L01Rik\t6.61931028203217\t6.48540110194761\t6.60503068636649\t6.36769099421861\t6.42571643078501\t6.64396444895718\t6.53143242923409\t6.62285820574675\t6.53143242923409\n-1110002O04Rik\t0\t0\t0\t1.46821025445916\t0\t1.46821025445916\t0\t0\t0\n-1110003F10Rik\t4.45025419288102\t2.91052253955419\t4.61282765853723\t3.93937616379084\t3.34005898311833\t3.34005898311833\t2.91052253955419\t3.51478476512484\t3.51478476512484\n-1110004E09Rik\t8.12381'..b'918606\t8.37648572\t8.44362934\t8.36312131\t8.3462398\t8.56532675\n+Zfp7\t8.22220194\t8.15329938\t8.30139241\t8.2163756\t8.30060591\t8.40381789\t8.32091691\t8.34247517\t8.48775159\n+Zfp704\t7.42977668\t7.14644331\t7.33103435\t6.84625465\t6.91917584\t7.06967353\t7.21105956\t7.14711068\t7.3959241\n+Zfp706\t8.6743642\t8.66011511\t8.84026773\t8.84342395\t8.89908606\t9.0504228\t8.86283987\t8.86283987\t9.04165585\n+Zfp710\t8.63472773\t8.74029749\t8.78253614\t8.71424849\t8.82403291\t8.93373836\t8.63052915\t8.86972276\t9.07252206\n+Zfp729a\t6.94843\t6.69700986\t6.88987355\t6.84048179\t7.08737056\t7.08845588\t6.96388839\t6.9218863\t7.12382122\n+Zfp740\t9.91211512\t9.95699855\t9.98662899\t10.0382074\t10.09216508\t10.20041314\t9.98690828\t10.16481386\t10.34555771\n+Zfp850\t8.18062974\t8.04095938\t8.26751523\t8.12385783\t8.13222536\t8.23136256\t8.24454388\t8.27660232\t8.42292034\n+Zfp871\t8.22664872\t7.91150791\t8.06268865\t8.22036393\t8.22575257\t8.46477668\t8.26117147\t8.20589504\t8.41454053\n+Zfp91\t7.7596069\t7.54569902\t7.71382557\t7.54569902\t7.67500096\t7.75229889\t7.75363038\t7.7382436\t7.89909434\n+Zfp930\t8.14572121\t7.99991356\t8.24113509\t8.01603064\t8.12010268\t8.23839009\t8.22828016\t8.18806543\t8.34940674\n+Zfp936\t9.15024509\t8.75784866\t9.02980074\t9.97775285\t10.0871234\t10.15903062\t9.74902985\t9.69103788\t9.74184273\n+Zfp958\t9.62091446\t9.50222771\t9.80067821\t10.24930199\t10.43928949\t10.43709016\t10.26674493\t10.19827052\t10.30583993\n+Zfp961\t8.46015583\t8.39539524\t8.548156\t9.75016323\t9.80700937\t9.90018069\t9.34697386\t9.28268863\t9.43809043\n+Zfp979\t10.14138668\t10.03836479\t10.21380001\t10.93476585\t11.08060446\t11.10550513\t10.7150038\t10.57960973\t10.71709009\n+Zfp990\t8.94124143\t8.57446966\t8.89086998\t9.62991996\t9.73770875\t9.70101562\t9.52130188\t9.31985025\t9.4895244\n+Zfr\t9.03227999\t8.9388881\t9.09878147\t9.02433358\t9.16064729\t9.26509569\t9.19728072\t9.11030922\t9.39112528\n+Zfx\t7.96504368\t7.81368197\t8.03763811\t7.86963709\t8.05032584\t8.09591558\t8.00686907\t8.00034514\t8.19446476\n+Zic3\t10.20447073\t10.16790186\t10.3113739\t10.29166006\t10.41181259\t10.53031339\t10.29686108\t10.26814674\t10.50378526\n+Zkscan17\t7.83555668\t7.84107067\t8.0072342\t8.12491941\t8.191182\t8.31423056\t7.9458642\t8.09292354\t8.28013155\n+Zmat2\t9.08799033\t9.17902384\t9.25317566\t9.24160675\t9.18012618\t9.26569138\t9.151188\t9.35917348\t9.58652721\n+Zmat3\t8.61693372\t8.37542509\t8.58443507\t8.75152942\t8.92118005\t9.08926953\t8.67086444\t8.66123595\t8.95665519\n+Zmym1\t9.39487037\t9.33282442\t9.52941555\t9.27079685\t9.3371163\t9.38712964\t9.43296302\t9.48562441\t9.65161524\n+Zmym2\t9.4356199\t9.25123846\t9.48332862\t9.95099917\t10.05283419\t10.15617959\t9.80803078\t9.72284229\t9.90253621\n+Zmym4\t8.4705733\t8.31284784\t8.52355569\t8.36592951\t8.56111514\t8.5890019\t8.52596208\t8.55452992\t8.73134572\n+Zmynd19\t8.06756597\t7.96601687\t8.18520836\t8.21463609\t8.08041093\t8.13560836\t8.20293693\t8.30496326\t8.4094398\n+Zmynd8\t7.89352747\t7.76414292\t7.91968933\t8.23739491\t8.27630201\t8.38670727\t8.05123766\t8.10922323\t8.31377638\n+Znrf2\t8.58836025\t8.5471143\t8.65709626\t8.43346653\t8.52888929\t8.60645316\t8.54461415\t8.53771632\t8.65420007\n+Zpr1\t8.31438768\t8.49040171\t8.45985137\t8.47577302\t8.41336813\t8.59615022\t8.50377471\t8.57518933\t8.73775464\n+Zranb1\t9.56838119\t9.36790006\t9.53784847\t9.65595695\t9.72269271\t9.86914736\t9.68923171\t9.54315905\t9.69528681\n+Zranb2\t8.80865361\t8.59785777\t8.8887401\t8.48681583\t8.63591492\t8.64073594\t8.77980604\t8.76810355\t8.92388331\n+Zscan10\t9.48942074\t9.51588201\t9.50201554\t9.6720291\t9.68128763\t9.86584588\t9.71593796\t9.73740122\t10.01487613\n+Zscan26\t8.58136277\t8.64959933\t8.73970409\t8.50883097\t8.65370755\t8.76423032\t8.71789618\t8.72103185\t8.90736277\n+Zswim4\t8.34285549\t8.35719533\t8.42954811\t8.50961454\t8.45909926\t8.49758216\t8.33031129\t8.46264044\t8.78180273\n+Zwilch\t8.65148483\t8.52460414\t8.72497087\t8.77657706\t8.78500143\t8.92255473\t8.88884345\t8.81896149\t8.99366175\n+Zwint\t8.20280976\t8.26759129\t8.34967601\t8.43205871\t8.4720088\t8.58816013\t8.47840886\t8.55480517\t8.71900512\n+Zyg11b\t7.71833012\t7.685393\t7.83816712\t7.73189756\t7.94104209\t7.98828404\t7.9095502\t7.90489966\t8.1435465\n+Zzz3\t7.77376581\t7.50688509\t7.6679306\t7.6777679\t7.69179252\t7.83273978\t7.75297816\t7.73424539\t7.90727686\n' |
| b |
| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/logtpm.tab --- a/test-data/logtpm.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/logtpm.tab Thu Oct 05 13:50:22 2023 +0000 |
| b |
| b'@@ -1,35194 +1,3962 @@\n Features\tWt1\tWt2\tWt3\tCA1\tCA2\tCA3\tKK1\tKK2\tKK3\n-0610005C13Rik\t1.75437893850878\t1.43582117845318\t1.46881127291061\t1.4049317795927\t1.4068644557087\t1.46344410753876\t1.84743084078508\t1.54116398828653\t1.58645453061248\n-0610006L08Rik\t0\t0\t0\t0\t0\t0.0742960420246607\t0\t0\t0\n-0610009B22Rik\t5.83027989003174\t5.78079393615334\t6.01585480037125\t5.66532089348757\t5.61557398395503\t5.68601033693279\t5.89162687256367\t5.82376643843323\t5.80473853447764\n-0610009E02Rik\t3.81168228791554\t3.55941432145841\t3.66801392073697\t3.69644728802654\t3.81382238986891\t3.93389851994426\t3.65374302301661\t3.46487768470313\t3.51452587634149\n-0610009L18Rik\t2.7350560656578\t2.68689596956154\t1.94209452709424\t2.29092211070079\t2.21189421782652\t2.21212217754358\t1.72861265390193\t1.94618505479304\t1.48355151159737\n-0610009O20Rik\t5.28279154583289\t5.31470459799798\t5.40028982103187\t5.44988289355049\t5.45876165660497\t5.40281152981312\t5.34602175233191\t5.27090593678026\t5.4335396158057\n-0610010F05Rik\t4.1597454868512\t3.91895918702218\t4.14569930299784\t3.83616133349221\t4.09610152313001\t3.98428463778308\t4.15285926215789\t3.99985236752756\t3.97275128963184\n-0610010K14Rik\t1.0850763383522\t0.609907260652211\t0.947144804100218\t1.22327345020402\t1.32085993664056\t1.44365840925843\t1.0930495851296\t1.15234240571155\t1.04705702101638\n-0610012D04Rik\t0.55690203225034\t0\t0.287962874929156\t0\t0.290292942688663\t0.509517094886943\t0.743642564781588\t0.699292629515445\t0\n-0610012G03Rik\t5.45725432189924\t5.5304452428532\t5.6401205355235\t5.08854359996926\t5.33323644444025\t5.14564323940305\t5.28538921135379\t5.47974042439855\t5.31054354039142\n-0610030E20Rik\t3.25984455369363\t3.04039041304668\t3.04283794465449\t3.05569642937443\t3.01842998995638\t3.1485254124668\t3.15057910296433\t2.98353901885427\t3.11167673289755\n-0610033M10Rik\t0\t0\t0\t0.285355796551298\t0\t0.140189316659718\t0.28290195623384\t0.137737249376783\t0.126615825973188\n-0610037L13Rik\t3.32729903391107\t3.37352790882418\t3.17606105888849\t3.36543735230334\t3.24615913172795\t3.31671953109823\t3.25718147910124\t3.44586805668217\t3.18481326729418\n-0610038B21Rik\t1.34919729798065\t1.03966401876568\t1.31598360950505\t1.82809381855702\t1.62345291020874\t1.91956496642696\t1.49920551925437\t1.42736878241074\t1.36736360698302\n-0610039K10Rik\t1.6931194561572\t1.56794148978472\t1.57120496757067\t1.87117375529432\t2.27916181840473\t2.60396367671794\t2.39592906397748\t2.30530768237065\t2.13680052030566\n-0610040B10Rik\t0.674624659642521\t1.00751126573613\t0.87868466179578\t1.21482466869664\t0.696474281728301\t1.05106378646807\t0.976170986157913\t0.999838942105185\t0.567372039047931\n-0610040F04Rik\t1.36219373471759\t1.35952244811072\t1.20755641933386\t1.19482644312205\t1.49395142701318\t1.74579179991716\t1.38409746105418\t1.42999422633573\t1.29720455799721\n-0610040J01Rik\t1.10106163693089\t0.830582390266678\t1.05238930020581\t1.70342627586307\t1.77119846207837\t1.81850861826549\t1.80063623445415\t1.79942637219052\t1.67241054823605\n-0610043K17Rik\t1.09564132916\t0.571283489951577\t1.41996963302482\t0.7013486537619\t0.386714437105333\t0.663755872081123\t0.9487083722722\t1.10230578411672\t0.608925857361369\n-1010001B22Rik\t1.18532618210411\t1.18287689231087\t1.25950030057595\t0.862670894005152\t1.3826795728261\t1.44275013821219\t0.856509041967767\t1.08717856716748\t0.893841658810624\n-1010001N08Rik\t0.165347023143866\t0.240744423787841\t0.296050283337913\t0.159628737097256\t0\t0\t0.300748613028777\t0.215083948497564\t0.258559858260622\n-1110002E22Rik\t0\t0\t0\t0.0343661053307504\t0\t0\t0.0171226600260526\t0\t0.0145133310255185\n-1110002J07Rik\t2.37320530441238\t2.22404978394489\t2.40450156841683\t3.46864113235583\t3.38119000416462\t3.66956122103894\t3.03078766184025\t2.86433625328483\t2.95565759032665\n-1110002L01Rik\t3.71938057749821\t3.59075012578566\t3.62079804337177\t3.43709094627194\t3.46678469421167\t3.60101475916473\t3.57562749153857\t3.55700915756166\t3.35751264843787\n-1110002O04Rik\t0\t0\t0\t0.278477930376228\t0\t0.261459143059931\t0\t0\t0\n-1110003F10Rik\t1.85168194637519\t0.858306200601577\t1.90802197275744\t1.44800226476244\t1.05668913709851\t1.01888441114945\t0.830378356922877\t1.10531722367811\t1.0'..b'3\t5.70138297\t5.7912643\t5.60052595\t5.7459406\t5.75814617\t5.74973561\t5.61687888\t5.70877981\n+Zfp7\t5.67268417\t5.58651411\t5.65078214\t5.61742043\t5.67128128\t5.71896629\t5.70819896\t5.61317967\t5.63252096\n+Zfp704\t4.89738104\t4.60472204\t4.70347332\t4.28580131\t4.32757589\t4.41968885\t4.6249158\t4.44984527\t4.56885286\n+Zfp706\t6.11850146\t6.0858919\t6.18208861\t6.23576414\t6.26165381\t6.35716687\t6.2428524\t6.12592186\t6.17838996\n+Zfp710\t6.07934612\t6.16511617\t6.12504106\t6.10809013\t6.1874449\t6.24173755\t6.01333184\t6.13272099\t6.20889172\n+Zfp729a\t4.43189722\t4.17325431\t4.27892155\t4.28027687\t4.48910506\t4.43773253\t4.38688467\t4.23409074\t4.30761312\n+Zfp740\t7.34626777\t7.37223098\t7.31923309\t7.42148762\t7.44580767\t7.49894513\t7.35824351\t7.41739758\t7.47201269\n+Zfp850\t5.63179973\t5.47620078\t5.61748029\t5.52653228\t5.50584539\t5.54945365\t5.63308424\t5.54847928\t5.56884441\n+Zfp871\t5.67705853\t5.34928502\t5.41642966\t5.62134079\t5.59769539\t5.77896494\t5.64943227\t5.47909039\t5.5606176\n+Zfp91\t5.21895688\t4.99197079\t5.07533957\t4.96124113\t5.05854451\t5.08062936\t5.15202463\t5.02194906\t5.05647144\n+Zfp930\t5.59748395\t5.43593495\t5.59155744\t5.42073847\t5.49394802\t5.55635438\t5.61709705\t5.46160336\t5.49670329\n+Zfp936\t6.58952022\t6.18246454\t6.36955705\t7.36133475\t7.44079035\t7.45775917\t7.12168708\t6.94641352\t6.87194219\n+Zfp958\t7.05671593\t6.92014929\t7.13433008\t7.63162223\t7.79144299\t7.73459971\t7.63677868\t7.45068943\t7.43249091\n+Zfp961\t5.90705569\t5.82473582\t5.89373303\t7.1350006\t7.16217211\t7.20027462\t6.7224222\t6.54132057\t6.57068234\n+Zfp979\t7.5744551\t7.45319884\t7.54529363\t8.31477929\t8.4307911\t8.40088572\t8.08341207\t7.83039599\t7.84194979\n+Zfp990\t6.38245819\t6.00132964\t6.23211315\t7.01550454\t7.0932883\t7.00233904\t6.89544474\t6.57814662\t6.62165685\n+Zfr\t6.47261665\t6.36154856\t6.43785054\t6.41478244\t6.5205904\t6.56977745\t6.57398197\t6.37061477\t6.52415114\n+Zfx\t5.42011\t5.25352874\t5.39187807\t5.27735519\t5.4255048\t5.41657264\t5.39977152\t5.27775326\t5.34488865\n+Zic3\t7.63726969\t7.58214607\t7.64244145\t7.67380395\t7.7640714\t7.82746389\t7.66676915\t7.52023347\t7.62951058\n+Zkscan17\t5.29325303\t5.28032407\t5.36209125\t5.52757457\t5.56373236\t5.63086446\t5.34000468\t5.36836135\t5.42878575\n+Zmat2\t6.52781494\t6.59943846\t6.59081955\t6.63007368\t6.53989205\t6.57036783\t6.52830171\t6.61712397\t6.71783611\n+Zmat3\t6.06177238\t5.80506159\t5.92950379\t6.14492401\t6.28350743\t6.39561755\t6.05315031\t5.92695466\t6.09443369\n+Zmym1\t6.83220031\t6.75198353\t6.86485797\t6.65901935\t6.69553699\t6.69076771\t6.80774785\t6.74252395\t6.78240153\n+Zmym2\t6.87265644\t6.67104703\t6.81910989\t7.33471864\t7.4066691\t7.4549219\t7.18033964\t6.97800065\t7.03151323\n+Zmym4\t5.91732924\t5.74343816\t5.86948465\t5.76454798\t5.92785147\t5.90135297\t5.91017294\t5.82179842\t5.87220516\n+Zmynd19\t5.52070803\t5.402699\t5.5366278\t5.61571062\t5.45500711\t5.45548884\t5.59219086\t5.57632898\t5.55561044\n+Zmynd8\t5.35001773\t5.20509131\t5.27639602\t5.6380836\t5.64738184\t5.70213243\t5.44327139\t5.38432678\t5.46176322\n+Znrf2\t6.03355829\t5.97433384\t6.00118403\t5.83106785\t5.89607578\t5.9185584\t5.9285664\t5.80523949\t5.79622822\n+Zpr1\t5.76341263\t5.91838847\t5.80671963\t5.87276066\t5.78225221\t5.90840024\t5.88829753\t5.84214889\t5.87851972\n+Zranb1\t7.00451696\t6.78679096\t6.87323004\t7.04137444\t7.07836523\t7.16942194\t7.06225678\t6.79960982\t6.82573534\n+Zranb2\t6.25125457\t6.02441562\t6.23000719\t5.88364619\t6.00164386\t5.95236672\t6.16076528\t6.03237935\t6.06208098\n+Zscan10\t6.9260823\t6.93370999\t6.83765812\t7.05734493\t7.03722154\t7.16613991\t7.08879688\t6.9924617\t7.14313904\n+Zscan26\t6.0266499\t6.07550573\t6.08273427\t5.90535129\t6.01920435\t6.07424126\t6.09959716\t5.98593023\t6.04577534\n+Zswim4\t5.79144863\t5.7871055\t5.77687773\t5.9061239\t5.82729527\t5.81127002\t5.71744303\t5.73133707\t5.92193041\n+Zwilch\t6.09589822\t5.95212465\t6.06818532\t6.16967764\t6.14886992\t6.23067956\t6.2685704\t6.0825868\t6.13097808\n+Zwint\t5.65361038\t5.69889727\t5.69826836\t5.82968075\t5.84001441\t5.90052313\t5.86329417\t5.82206953\t5.8600474\n+Zyg11b\t5.17861516\t5.12817049\t5.19669779\t5.14273427\t5.31844106\t5.31115537\t5.30445235\t5.18447281\t5.29507204\n+Zzz3\t5.23280102\t4.95418773\t5.03061068\t5.08991202\t5.07491469\t5.15911062\t5.15138781\t5.01805582\t5.06444205\n' |
| b |
| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/none.tab --- a/test-data/none.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/none.tab Thu Oct 05 13:50:22 2023 +0000 |
| b |
| b'@@ -1,216 +1,216 @@\n Features\t20nM_1\t20sM_4\t32nM_7\t32sM_10\t40nM_13\t40sM_16\t20n1d_a\t20n1d_b\t30n5h_c1\t30n5h_c2\t30s5h_c3\t30s5h_c4\t40n5h_c5\t40n5h_c6\t40s5h_c7\t40s5h_c8\t20n1d_c\t20s1d_d\t20s1d_e\t20s1d_f\t30n1d_g\t30n1d_h\t30n1d_i\t30s1d_j\t30s1d_k\t30s1d_l\t40n1d_m\t40n1d_n\t40n1d_o\t40s1d_p\t40s1d_q\t40s1d_r\n-5S_DM\t0\t0\t0\t0\t2.52271103749722\t0\t0\t1.46876851779219\t1.10607886502204\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.51278181441303\t2.52260597944523\t0\t0\t0\t2.05794942496048\t0.646139123391797\n-ACCORD2_I-int\t13.4694287027486\t19.7873189245625\t17.5674602110498\t50.6988197972739\t17.6589772624805\t19.313391508794\t18.1589910793351\t13.2189166601297\t12.1668675152425\t18.2343843151734\t26.0100186444685\t27.0989940048899\t23.1050300244153\t31.4819885379018\t24.4065408703064\t27.0644930469596\t9.83737686997288\t16.0386739801143\t14.5565923551731\t13.0633061628418\t25.016895793462\t24.992288899494\t17.9393955029792\t28.3792668127381\t19.8019745551662\t35.5503726387062\t17.6582418561166\t22.6167312355617\t26.939353284346\t26.4137500118019\t25.7243678120059\t41.9990430204668\n-ACCORD2_LTR\t0\t0.860318214111411\t0\t2.25328087987884\t3.78406655624583\t2.75905592982771\t1.13493694245845\t0\t2.21215773004408\t0\t4.0640654131982\t3.69531736430316\t1.84840240195322\t4.49742693398597\t1.10938822137756\t2.00477726273775\t0\t1.33655616500952\t0.970439490344876\t2.61266123256835\t4.46730282026107\t3.22481147090245\t2.4462812049517\t2.74638065929724\t2.47524681939578\t1.51278181441303\t0\t10.3660018162991\t2.78682965010476\t0\t1.02897471248024\t5.16911298713437\n-ACCORD_I-int\t16.1633144432983\t28.3905010656766\t29.6450891061465\t33.7992131981826\t18.9203327812291\t43.2252095673008\t30.643297446378\t19.0939907312984\t11.0607886502204\t53.8743172948305\t18.6947009007117\t23.4036766405867\t36.0438468380879\t25.1855908303214\t25.5159290916839\t48.114654305706\t16.3956281166215\t17.3752301451238\t16.4974713358629\t24.8202817093994\t36.6318831261408\t29.8295061058477\t34.2479368693238\t26.5483463732066\t24.7524681939578\t21.9353363089889\t31.5325747430654\t21.6743674340799\t22.2946372008381\t40.0760345006649\t40.1300137867293\t58.7986602286535\n-ACCORD_LTR\t0.897961913516572\t2.58095464233423\t0\t0\t0\t0\t0\t0\t0\t3.3153426027588\t0.812813082639639\t2.46354490953544\t1.84840240195322\t0\t1.10938822137756\t6.01433178821325\t0\t0\t0\t1.30633061628418\t0\t1.61240573545123\t1.63085413663447\t0.915460219765745\t0.825082273131927\t0\t0\t1.88472760296347\t0\t0\t5.14487356240119\t1.93841737017539\n-ALA_DM\t1.79592382703314\t0\t0\t0\t0\t0\t1.13493694245845\t0\t0\t0\t0\t0\t0\t0\t1.10938822137756\t0\t0\t0\t0\t0\t0\t0\t0\t1.83092043953149\t0\t0\t0\t0\t0\t0\t0\t0.646139123391797\n-ARS406_DM\t4.48980956758286\t8.60318214111411\t10.9796626319061\t14.6463257192125\t16.3976217437319\t8.27716778948314\t13.6192433095013\t2.93753703558437\t12.1668675152425\t14.0902060617249\t16.2562616527928\t8.62240718337405\t16.635621617579\t7.19588309437755\t15.5314350992859\t17.0406067332709\t21.8608374888286\t12.0290054850857\t14.5565923551731\t15.6759673954101\t12.508447896731\t18.5426659576891\t14.6776872297102\t11.9009828569547\t8.25082273131927\t18.1533817729563\t18.9195448458392\t14.1354570222261\t13.0052050338222\t6.37573276146942\t7.20282298736166\t14.8611998380113\n-BARI1\t16.1633144432983\t8.60318214111411\t17.5674602110498\t9.01312351951536\t16.3976217437319\t17.4740208889088\t10.214432482126\t10.2813796245453\t4.42431546008817\t11.6036991096558\t7.31531774375675\t17.2448143667481\t6.46940840683628\t8.99485386797193\t4.43755288551025\t14.0334408391642\t14.2095443677386\t13.3655616500952\t17.4679108262078\t23.5139510931152\t5.36076338431329\t11.2868401481586\t8.96969775148958\t15.5628237360177\t11.551151823847\t10.5894727008912\t6.30651494861307\t1.88472760296347\t10.2183753837175\t9.10818965924203\t9.26077241232214\t10.3382259742687\n-BARI_DM\t27.8368193190137\t18.0666824963396\t14.2735614214779\t15.7729661591519\t22.7043993374749\t14.7149649590811\t19.2939280217936\t36.7192129448047\t23.2276561654629\t18.2343843151734\t17.0690747354324\t13.5494970024449\t17.5598228185556\t17.0902223491467\t12.2032704351532\t25.0597157842219\t15.30258624218\t13.3655616500952\t17.4679108262078\t9.14431431398924\t18.7626718450965\t17.7364630899635\t17.9393955029792\t1'..b'4\t15.13626622\t11.03622372\t20.42886496\t22.03152777\t6.63647319\t7.45952086\t11.37938316\t20.94013173\t12.93881681\t18.88919312\t15.5314351\t9.02149768\t21.86083749\t2.67311233\t20.3792293\t27.43294294\t16.08229015\t12.09304302\t16.30854137\t11.90098286\t9.075905\t7.56390907\t23.9647568\t22.61673124\t8.36048895\t8.19737069\t9.26077241\t18.09189545\n+TRANSIB3\t76.32676265\t70.54609356\t72.46577337\t63.09186464\t100.9084415\t95.64727223\t60.15165795\t73.43842589\t85.16807261\t77.08171551\t69.08911202\t84.99229938\t94.2685225\t69.26037478\t99.84493992\t113.26991534\t88.53639183\t52.12569044\t76.66471974\t67.92919205\t107.21526769\t83.03889538\t89.69697751\t91.54602198\t57.75575912\t78.66465435\t52.97472557\t77.27383172\t110.54424279\t78.33043107\t116.27414251\t73.65986007\n+TRANSIB4\t18.85720018\t11.18413678\t34.03695416\t14.64632572\t11.35219967\t26.67087399\t4.53974777\t14.68768518\t15.48510411\t4.9730139\t4.06406541\t20.94013173\t12.93881681\t17.98970774\t21.07837621\t18.04299536\t12.02346062\t32.07734796\t20.3792293\t19.59495924\t6.25422395\t11.28684015\t8.96969775\t13.7319033\t4.95049364\t14.37142724\t2.52260598\t8.48127421\t10.21837538\t1.82163793\t5.14487356\t8.3998086\n+TRANSPAC_I-int\t27.83681932\t72.26672999\t46.11458305\t75.48490948\t31.53388797\t49.66300674\t61.28659489\t27.90660184\t33.18236595\t53.04548164\t41.45346721\t49.27089819\t46.21006005\t37.77838625\t46.5943053\t54.12898609\t45.90775873\t68.16436442\t70.8420828\t16.98229801\t50.92725215\t67.72104089\t48.9256241\t52.18123253\t48.67985411\t37.06315445\t34.05518072\t55.59946429\t50.1629337\t50.09504313\t23.66641839\t59.44479935\n+TRANSPAC_LTR\t8.08165722\t15.48572785\t9.88169637\t32.67257276\t10.09084415\t6.43779717\t17.02405414\t5.87507407\t9.95470979\t21.54972692\t14.63063549\t17.24481437\t23.10503002\t9.89433925\t16.64082332\t32.0764362\t10.93041874\t22.72145481\t22.32010828\t1.30633062\t12.5084479\t23.37988316\t24.46281205\t9.1546022\t18.97689228\t15.88420905\t12.6130299\t17.90491223\t25.08146685\t20.03801725\t10.28974712\t27.13784318\n+Transib-N1_DM\t14.36739062\t12.90477321\t7.68576384\t4.50656176\t10.09084415\t12.87559434\t10.21443248\t11.75014814\t17.69726184\t3.3153426\t12.19219624\t4.92708982\t11.09041441\t3.59794155\t4.43755289\t11.02627495\t3.27912562\t13.36556165\t7.76351592\t6.53165308\t10.72152677\t4.83721721\t8.15427068\t15.56282374\t4.95049364\t13.61503633\t20.18084784\t4.71181901\t10.21837538\t4.55409483\t9.26077241\t9.04594773\n+Transib5\t1.79592383\t6.88254571\t0\t5.6332022\t0\t4.59842655\t2.26987388\t5.87507407\t4.42431546\t4.14417825\t0\t1.23177245\t3.6968048\t0.89948539\t0\t7.01672042\t0\t8.01933699\t8.73395541\t1.30633062\t5.36076338\t4.03101434\t4.07713534\t3.66184088\t4.12541137\t0.75639091\t0\t3.76945521\t2.78682965\t4.55409483\t1.02897471\t1.93841737\n+XDMR\t9.87758105\t12.90477321\t6.58779758\t1.12664044\t6.30677759\t6.43779717\t11.34936942\t11.75014814\t14.37902525\t4.14417825\t10.56657007\t0\t2.7726036\t8.99485387\t7.76571755\t3.00716589\t9.83737687\t10.69244932\t5.82263694\t15.6759674\t8.93460564\t4.03101434\t8.15427068\t17.39374418\t11.55115182\t12.85864542\t5.04521196\t8.48127421\t5.5736593\t2.7324569\t2.05794942\t5.16911299\n+XDMR_DM\t7.18369531\t5.16190928\t8.78373011\t0\t13.87491071\t3.67874124\t9.07949554\t8.81261111\t1.10607887\t3.3153426\t4.8768785\t9.85417964\t2.7726036\t8.99485387\t22.18776443\t5.01194316\t12.02346062\t10.69244932\t4.85219745\t9.14431431\t6.25422395\t4.83721721\t7.33884361\t5.49276132\t4.95049364\t7.56390907\t0\t9.42363801\t4.64471608\t8.19737069\t6.17384827\t3.87683474\n+ZAM_I-int\t35.02051463\t32.69209214\t35.13492042\t40.55905584\t22.70439934\t33.10867116\t35.18304522\t11.75014814\t32.07628709\t34.81109733\t33.32533639\t51.7344431\t44.36165765\t26.08507622\t32.17225842\t39.09315662\t31.69821436\t41.43324112\t43.66977707\t54.86588588\t28.59073805\t29.02330324\t37.50964514\t25.63288615\t39.60394911\t33.28119992\t23.9647568\t34.86746065\t37.15772867\t48.27340519\t33.95616551\t35.53765179\n+ZAM_LTR\t1.79592383\t1.72063643\t2.19593253\t3.37992132\t3.78406656\t1.83937062\t2.26987388\t0\t7.74255206\t17.40554866\t4.06406541\t1.23177245\t12.93881681\t4.49742693\t7.76571755\t3.00716589\t5.46520937\t2.67311233\t2.91131847\t6.53165308\t5.36076338\t0\t0.81542707\t0\t3.30032909\t4.53834544\t10.09042392\t7.53891041\t7.43154573\t7.28655173\t3.08692414\t3.87683474\n' 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| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/rpk.tab --- a/test-data/rpk.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/rpk.tab Thu Oct 05 13:50:22 2023 +0000 |
| b |
| b'@@ -1,35194 +1,3962 @@\n Features\tWt1\tWt2\tWt3\tCA1\tCA2\tCA3\tKK1\tKK2\tKK3\n-0610005C13Rik\t18.9785096288027\t13.6756907619313\t15.071169411108\t13.6756907619313\t13.9547864917667\t15.6293608707787\t21.769466927156\t17.3039352497907\t19.8157968183087\n-0610006L08Rik\t0\t0\t0\t0\t0\t0.469924812030075\t0\t0\t0\n-0610009B22Rik\t446.89378757515\t432.865731462926\t543.086172344689\t412.825651302605\t405.811623246493\t448.897795591182\t488.977955911824\t504.008016032064\t543.086172344689\n-0610009E02Rik\t104.270660011093\t86.522462562396\t99.8336106489185\t99.2789794786467\t110.371602884082\t127.010537992235\t97.0604547975596\t90.9595119245702\t103.161397670549\n-0610009L18Rik\t45.2342487883683\t43.6187399030695\t24.232633279483\t32.3101777059774\t30.6946688206785\t32.3101777059774\t19.3861066235864\t25.8481421647819\t17.7705977382876\n-0610009O20Rik\t303.24459234609\t311.148086522463\t351.497504159734\t354.409317803661\t363.144758735441\t367.304492512479\t332.362728785358\t340.682196339434\t417.637271214642\n-0610010F05Rik\t134.902411021814\t113.2797550708\t142.365097588978\t110.218140068886\t136.050516647532\t131.8407960199\t140.642939150402\t135.859165709912\t145.426712590892\n-0610010K14Rik\t8.9662447257384\t4.21940928270042\t7.91139240506329\t11.0759493670886\t12.6582278481013\t15.295358649789\t9.49367088607595\t11.0759493670886\t10.5485232067511\n-0610012D04Rik\t3.76647834274953\t0\t1.88323917137476\t0\t1.88323917137476\t3.76647834274953\t5.64971751412429\t5.64971751412429\t0\n-0610012G03Rik\t343.252595155709\t362.629757785467\t416.608996539792\t274.048442906574\t332.179930795848\t305.882352941176\t318.339100346021\t395.155709342561\t382.698961937716\n-0610030E20Rik\t68.5871056241427\t57.9561042524006\t61.7283950617284\t60.6995884773663\t60.0137174211248\t69.9588477366255\t66.0150891632373\t62.5857338820302\t75.6172839506173\n-0610033M10Rik\t0\t0\t0\t1.81488203266788\t0\t0.907441016333938\t1.81488203266788\t0.907441016333938\t0.907441016333938\n-0610037L13Rik\t72.2527960234333\t75.0932007811113\t68.524764778981\t77.2235043493698\t71.7202201313687\t79.708858512338\t71.7202201313687\t89.6502751642109\t80.0639091070477\n-0610038B21Rik\t12.3738196027353\t8.46629762292413\t12.6994464343862\t21.1657440573103\t17.5838489091501\t24.7476392054705\t15.3044610875936\t15.3044610875936\t15.6300879192445\n-0610039K10Rik\t17.8571428571429\t15.7563025210084\t16.8067226890756\t22.0588235294118\t32.563025210084\t45.1680672268908\t35.7142857142857\t35.7142857142857\t33.6134453781513\n-0610040B10Rik\t4.76644423260248\t8.10295519542421\t7.14966634890372\t10.9628217349857\t5.24308865586273\t9.53288846520496\t8.10295519542421\t9.05624404194471\t4.76644423260248\n-0610040F04Rik\t12.5581395348837\t12.5581395348837\t11.1627906976744\t10.6976744186047\t15.3488372093023\t20.9302325581395\t13.4883720930233\t15.3488372093023\t14.4186046511628\n-0610040J01Rik\t9.15522263836871\t6.24219725343321\t9.15522263836871\t18.7265917602996\t20.3911776945485\t22.4719101123595\t20.8073241781107\t22.4719101123595\t21.6396171452351\n-0610043K17Rik\t9.09090909090909\t3.8961038961039\t14.2857142857143\t5.19480519480519\t2.5974025974026\t5.19480519480519\t7.79220779220779\t10.3896103896104\t5.19480519480519\n-1010001B22Rik\t10.1867572156197\t10.1867572156197\t11.8845500848896\t6.7911714770798\t13.5823429541596\t15.2801358234295\t6.7911714770798\t10.1867572156197\t8.48896434634975\n-1010001N08Rik\t0.970873786407767\t1.45631067961165\t1.94174757281553\t0.970873786407767\t0\t0\t1.94174757281553\t1.45631067961165\t1.94174757281553\n-1110002E22Rik\t0\t0\t0\t0.2000400080016\t0\t0\t0.1000200040008\t0\t0.1000200040008\n-1110002J07Rik\t33.4261838440111\t29.4468762435336\t36.6096299243932\t83.5654596100279\t79.5861520095503\t104.257859132511\t60.0875447672105\t56.9040986868285\t66.8523676880223\n-1110002L01Rik\t97.3129992737836\t88.5984023238925\t96.3447107237957\t81.5783103364803\t84.9673202614379\t99.0075042362624\t91.5032679738562\t97.5550714112806\t91.5032679738562\n-1110002O04Rik\t0\t0\t0\t1.76678445229682\t0\t1.76678445229682\t0\t0\t0\n-1110003F10Rik\t20.8604954367666\t6.51890482398957\t23.4680573663625\t14.3415906127771\t9.1264667535854\t9.1264667535854\t6.51890482398957\t10.4302477183833\t10.4302477183833\n-1110004E09Rik\t277.94117647058'..b'8557\n+Zfp740\t962.48281281\t992.9286977\t1013.5533294\t1050.48124141\t1090.55195443\t1175.60400707\t1013.74975447\t1146.92594775\t1300.13749754\n+Zfp850\t289.14489697\t262.37222132\t307.15560604\t277.94905079\t279.57163719\t299.52944994\t302.28784683\t309.10270972\t342.20347233\n+Zfp871\t298.54910714\t239.76934524\t266.36904762\t297.24702381\t298.36309524\t352.30654762\t305.80357143\t294.27083333\t340.21577381\n+Zfp91\t215.70774438\t185.84511248\t208.93888115\t185.84511248\t203.36452319\t214.61278121\t214.81186542\t212.52239697\t237.70654987\n+Zfp930\t282.20858896\t254.98466258\t301.57208589\t257.86042945\t277.22392638\t300.99693252\t298.88803681\t290.64417178\t325.15337423\n+Zfp936\t567.19609041\t431.88759927\t521.686011\t1007.33048259\t1086.74404398\t1142.33353696\t859.49908369\t825.59560171\t855.22296885\n+Zfp958\t786.37901861\t724.1962775\t890.86294416\t1216.15905245\t1387.47884941\t1385.36379019\t1230.96446701\t1173.85786802\t1264.80541455\n+Zfp961\t351.17674204\t335.71758191\t373.32718043\t860.17535764\t894.78541763\t954.54545455\t650.20766036\t621.82741117\t692.66266728\n+Zfp979\t1128.43590367\t1050.59596205\t1186.57261007\t1956.45828266\t2164.68012649\t2202.38384821\t1679.88324009\t1529.31160302\t1682.31573826\n+Zfp990\t490.56603774\t380.21726701\t473.69925672\t791.30931961\t852.77301315\t831.33218982\t733.84791309\t638.07890223\t717.83876501\n+Zfr\t522.585011\t489.7648452\t547.2847234\t519.70901709\t571.30773135\t614.27846388\t586.02605312\t551.68330232\t670.44493318\n+Zfx\t248.87169568\t223.98452611\t261.76660219\t232.88201161\t264.08768536\t272.59832366\t256.22179239\t255.06125081\t291.94068343\n+Zic3\t1178.91787023\t1149.38564346\t1269.67018754\t1252.42509161\t1361.28475965\t1477.90472085\t1256.9519293\t1232.1621039\t1450.95925846\n+Zkscan17\t227.42182375\t228.29652307\t256.28690138\t278.15438443\t291.27487426\t317.29717909\t245.57183468\t272.03148918\t309.86223486\n+Zmat2\t543.19893664\t578.64421799\t609.21577315\t604.34204696\t579.08728401\t614.53256535\t567.56756757\t655.73770492\t767.83340718\n+Zmat3\t391.60472234\t331.08876257\t382.85964145\t429.99562746\t483.77787495\t543.68167906\t406.55881067\t403.84783559\t495.84608658\n+Zmym1\t672.19020173\t643.85206532\t737.99231508\t616.71469741\t645.77329491\t668.58789625\t690.20172911\t715.89817483\t803.31412104\n+Zmym2\t691.47582697\t608.39694656\t714.75826972\t988.80407125\t1061.19592875\t1140.07633588\t895.41984733\t844.02035623\t956.10687023\n+Zmym4\t353.72895933\t316.99225949\t366.99840275\t328.91018553\t376.70475488\t384.0766679\t367.61272884\t374.98464185\t424.00786337\n+Zmynd19\t267.27447217\t249.0403071\t290.0671785\t296.06525912\t269.67370441\t280.2303263\t293.66602687\t315.25911708\t339.01151631\n+Zmynd8\t236.78723597\t216.39017315\t241.13860937\t300.78868643\t309.03816517\t333.69594778\t264.25528057\t275.13371408\t317.1969903\n+Znrf2\t383.90544041\t373.05699482\t402.68782383\t344.72150259\t368.36139896\t388.76295337\t372.40932642\t370.62823834\t401.87823834\n+Zpr1\t317.33184482\t358.63801284\t351.10242813\t355.00976835\t339.93859894\t385.98939436\t361.9871616\t380.40747977\t425.90008373\n+Zranb1\t758.22368421\t659.72222222\t742.3245614\t805.73830409\t843.93274854\t934.21052632\t824.56140351\t745.06578947\t828.03362573\n+Zranb2\t447.40346205\t386.44769936\t472.99896434\t357.74522858\t396.80426099\t398.13581891\t438.52640923\t434.9755881\t484.68708389\n+Zscan10\t717.78711485\t731.09243697\t724.08963585\t814.77591036\t820.0280112\t932.07282913\t839.9859944\t852.59103641\t1033.61344538\n+Zscan26\t382.04306001\t400.59551077\t426.47732478\t363.26156665\t401.74072377\t433.80668804\t420.06413193\t420.98030234\t479.15712322\n+Zswim4\t323.67567568\t326.91891892\t343.78378378\t363.45945946\t350.91891892\t360.43243243\t320.86486486\t351.78378378\t439.13513514\n+Zwilch\t401.12070978\t367.26593509\t422.13401821\t437.54377773\t440.11207098\t484.24001868\t473.03292085\t450.61872519\t508.75554518\n+Zwint\t293.64005413\t307.17185386\t325.2142535\t344.38430311\t354.08209292\t383.85205232\t355.66080289\t375.0563825\t420.38791159\n+Zyg11b\t209.59540128\t204.84191908\t227.83550741\t211.58523104\t244.74906036\t252.92947159\t239.44284767\t238.66902498\t281.7820031\n+Zzz3\t217.84503\t180.88529437\t202.36542308\t203.75684842\t205.75702235\t226.97625881\t214.71432298\t211.9314723\t239.06426646\n' |
| b |
| diff -r 8b1020c25f0f -r be358a1ebf67 test-data/tpm.tab --- a/test-data/tpm.tab Fri Apr 12 12:01:35 2019 -0400 +++ b/test-data/tpm.tab Thu Oct 05 13:50:22 2023 +0000 |
| b |
| b'@@ -1,35194 +1,3962 @@\n Features\tWt1\tWt2\tWt3\tCA1\tCA2\tCA3\tKK1\tKK2\tKK3\n-0610005C13Rik\t2.37381049023012\t1.70536111275201\t1.76793731889918\t1.64805259994156\t1.65160238516669\t1.75765907070531\t2.59858775626434\t1.91029215561158\t2.00310419383368\n-0610006L08Rik\t0\t0\t0\t0\t0\t0.0528471775169269\t0\t0\t0\n-0610009B22Rik\t55.8969688196476\t53.9784350443719\t63.7072204071056\t49.7494715108448\t48.0293586202636\t50.482504611921\t58.3685458889474\t55.6406704887002\t54.8985337007296\n-0610009E02Rik\t13.0420560622898\t10.7893667385481\t11.7110730516098\t11.9640742904764\t13.0629015847409\t14.28345189691\t11.5859570791675\t10.0416026527761\t10.42819676697\n-0610009L18Rik\t5.65784860833049\t5.43926475911583\t2.84263122133178\t3.8936879533089\t3.63283152100137\t3.63356361085688\t2.31408970565307\t2.85354183899371\t1.79636272933552\n-0610009O20Rik\t37.9294901705155\t38.8002226943942\t41.2327363692096\t42.7097400648851\t42.9795719226589\t41.3066201691206\t39.6736273125208\t37.6100879845593\t42.2173772340238\n-0610010F05Rik\t16.8734407866737\t14.1260059563187\t16.7002680462719\t13.2823486186813\t16.1020992998207\t14.8266568882315\t16.7883311476663\t14.9983627872578\t14.7006381099503\n-0610010K14Rik\t1.12148773556099\t0.52616110109278\t0.928053125529734\t1.33475869475375\t1.49814970786133\t1.72009758382099\t1.13324487958801\t1.22274493555773\t1.06631044251888\n-0610012D04Rik\t0.471106845380222\t0\t0.220915094288057\t0\t0.222888562939821\t0.423573611133787\t0.674398082768008\t0.623708473989091\t0\n-0610012G03Rik\t42.9336458508171\t45.219996416962\t48.8706995642276\t33.0254797877817\t39.3147660360564\t34.399160443018\t37.9996483729905\t43.6237677097962\t38.6855952683646\n-0610030E20Rik\t8.57879749303491\t7.22713668795237\t7.24110586833076\t7.31488568635773\t7.10285312454829\t7.867487629022\t7.880119573084\t6.90923970542957\t7.64386615368628\n-0610033M10Rik\t0\t0\t0\t0.218710784310182\t0\t0.102049722101652\t0.216639674500794\t0.100178221321297\t0.091729791243911\n-0610037L13Rik\t9.03729789659485\t9.36413572619426\t8.03836023714644\t9.30617687509072\t8.48836252016724\t8.96396207996683\t8.56113227455614\t9.89706762782086\t8.09335872675418\n-0610038B21Rik\t1.54770334192154\t1.0557488456313\t1.48972018482949\t2.55067624228889\t2.08111581039935\t2.78308965335641\t1.82686996110292\t1.68955740641981\t1.57998666155582\n-0610039K10Rik\t2.23355120443659\t1.96481377561432\t1.97152798431863\t2.65830092988773\t3.8539586497399\t5.07954635662697\t4.26315930892634\t3.94272856771675\t3.39785646893412\n-0610040B10Rik\t0.59618144637011\t1.01043997917198\t0.838698153481589\t1.3211257242912\t0.62053960730767\t1.07205713780763\t0.967237288393201\t0.999776738810922\t0.481821877744471\n-0610040F04Rik\t1.57075787028285\t1.56600227250823\t1.30946137749163\t1.28917291607579\t1.81659362250906\t2.35378870652136\t1.61008621341776\t1.69445637049781\t1.45752238533697\n-0610040J01Rik\t1.14512487884556\t0.778403127084824\t1.07396176923557\t2.2567348718148\t2.41337391557686\t2.52716390462967\t2.4837382573853\t2.48081797519256\t2.18746731479029\n-0610043K17Rik\t1.13708061316772\t0.485844860879177\t1.67579878667083\t0.626024115090444\t0.307412537457259\t0.584201526005301\t0.930143849220292\t1.14697558333578\t0.525123272471636\n-1010001B22Rik\t1.27414805550203\t1.27029046817306\t1.39412802286708\t0.818401644515521\t1.60752226717888\t1.71838564313104\t0.810651685228777\t1.12458132321972\t0.858117401959168\n-1010001N08Rik\t0.121435793639271\t0.181602205280081\t0.227778475858171\t0.116999652577583\t0\t0\t0.231783418737743\t0.160771456159324\t0.196283941652019\n-1110002E22Rik\t0\t0\t0\t0.0241067497809383\t0\t0\t0.0119392339117761\t0\t0.0101106451241038\n-1110002J07Rik\t4.18090921833256\t3.67203079624559\t4.29452613854364\t10.0704436341151\t9.41932566025028\t11.7247130776273\t7.17255772309612\t6.2820076343565\t6.75785381286618\n-1110002L01Rik\t12.1717997371766\t11.0482368024667\t11.3018044533162\t9.83097298625147\t10.0562075161672\t11.1342644992041\t10.9226042424779\t10.7697286754093\t9.24972038765399\n-1110002O04Rik\t0\t0\t0\t0.212914562111149\t0\t0.198690448332191\t0\t0\t0\n-1110003F10Rik\t2.60920714364431\t0.812908611205925\t2.75294194420502\t1.72829995267799\t1.08015226655452\t1.02635144236264\t0.778151633963086\t1.15146179813371\t1.'..b'5\t71.42369926\n+Zfp710\t66.61850036\t70.76040701\t68.79448128\t67.97923066\t71.87968896\t74.67461621\t63.59416063\t69.16701048\t72.97119727\n+Zfp729a\t20.58410287\t17.04158652\t18.41260136\t18.43084683\t21.45718301\t20.6715815\t19.92106901\t17.81864359\t18.80253361\n+Zfp740\t161.7222554\t164.67716704\t158.70139338\t170.43140566\t173.34578396\t179.88702684\t163.07862647\t169.94608563\t176.54152526\n+Zfp850\t48.58389599\t43.51441772\t48.09418631\t45.09480566\t44.43856565\t45.83300318\t48.62806293\t45.80138384\t46.46671838\n+Zfp871\t50.16404897\t39.76573203\t41.70785866\t48.22573321\t47.42551186\t53.90877966\t49.19362612\t43.60366625\t46.19681514\n+Zfp91\t36.24453597\t30.82240115\t32.71548779\t30.15174618\t32.32526663\t32.83933612\t34.55608626\t31.49056794\t32.27741447\n+Zfp930\t47.41841505\t42.28919153\t47.21992306\t41.83560231\t44.06539153\t46.0575525\t48.08114655\t43.06628462\t44.15153992\n+Zfp936\t95.30376\t71.62853334\t81.68519055\t163.43057195\t172.74050769\t174.79608982\t138.26482265\t122.33286822\t116.12800003\n+Zfp958\t132.13221763\t120.10791071\t139.49062811\t197.31118333\t220.54300843\t211.98377328\t198.02125093\t173.93673074\t171.74389436\n+Zfp961\t59.00686642\t55.67874153\t58.45528005\t139.5559383\t142.22823504\t146.06138016\t104.59679196\t92.13945737\t94.05445501\n+Zfp979\t189.60670984\t174.2412795\t185.79261801\t317.41826705\t344.0809693\t337.00147331\t270.23735415\t226.60619123\t228.43628997\n+Zfp990\t82.42790935\t63.05901173\t74.17146183\t128.38302516\t135.55026508\t127.20769497\t118.05172744\t94.54752678\t97.47303705\n+Zfr\t87.80793328\t81.22747123\t85.69341707\t84.31824846\t90.81070019\t93.99485358\t94.27210551\t81.74583365\t91.03757974\n+Zfx\t41.81694613\t37.14782069\t40.98721133\t37.7830722\t41.97735529\t41.71209155\t41.21756655\t37.79377496\t39.64169454\n+Zic3\t198.08899895\t190.62554244\t198.80397217\t203.19503141\t216.37939659\t226.14407962\t202.20176948\t182.57597784\t197.02113127\n+Zkscan17\t38.21280731\t37.86296514\t40.12920403\t45.12811925\t46.29882256\t48.55176218\t39.50434249\t40.30834497\t42.07520486\n+Zmat2\t91.27161129\t95.96811006\t95.39053275\t98.0492183\t92.04727828\t94.03373535\t91.30274896\t97.164125\t104.2616501\n+Zmat3\t65.79982321\t54.91105211\t59.9478654\t69.76303462\t76.89762478\t83.19236767\t65.40179381\t59.84027041\t67.32935907\n+Zmym1\t112.94551345\t106.78282777\t115.5542637\t100.05657276\t102.64717569\t102.30510283\t111.03050775\t106.07842011\t109.0794631\n+Zmym2\t116.18600229\t100.90259837\t111.91629492\t160.42482354\t168.67957502\t174.4507004\t144.04327909\t125.06296157\t129.82670333\n+Zmym4\t59.43570559\t52.57314789\t57.46432496\t53.36280463\t59.8781019\t58.77013812\t59.13666428\t55.56345828\t57.5746758\n+Zmynd19\t44.90909331\t41.30332052\t45.4184936\t48.03400222\t42.86526608\t42.87991528\t47.24109879\t46.71361129\t46.03329285\n+Zmynd8\t39.78644121\t35.88829769\t37.75729623\t48.80033704\t49.1223392\t51.06104739\t42.50988767\t40.76801804\t43.07116792\n+Znrf2\t64.50614271\t61.871481\t63.0525468\t55.92805272\t58.55190596\t59.48721798\t59.90827733\t54.91794693\t54.56976458\n+Zpr1\t53.32003956\t59.48009367\t54.97534559\t57.59723397\t54.03403542\t59.06281718\t58.23169757\t56.36698887\t57.83161437\n+Zranb1\t127.40138595\t109.41489237\t116.23260347\t130.72400186\t134.14508434\t142.94979688\t132.64451165\t110.40033989\t112.43604582\n+Zranb2\t75.1754691\t64.09232857\t74.06181059\t58.0410385\t63.07296541\t60.92142278\t70.54431744\t64.45263418\t65.81411368\n+Zscan10\t120.60698598\t121.25163836\t113.37739298\t132.19027454\t130.34537043\t142.62269354\t135.12581543\t126.3329246\t140.35107403\n+Zscan26\t64.19321416\t66.43874227\t66.77748839\t58.93601617\t63.85762772\t66.37966089\t67.57435093\t62.37887864\t65.06321795\n+Zswim4\t54.38596886\t54.21948378\t53.82939794\t58.96812254\t55.77938296\t55.15217561\t51.61648741\t52.1256644\t59.6287598\n+Zwilch\t67.39875768\t60.91103408\t66.09741682\t70.98765607\t69.95684311\t74.09680191\t76.09526776\t66.77056056\t69.08229329\n+Zwint\t49.33919982\t50.94443418\t50.92179531\t55.87334505\t56.28217687\t58.73576819\t57.21399681\t55.57408848\t57.08313409\n+Zyg11b\t35.21750266\t33.97302042\t35.67430685\t34.32785558\t38.90343561\t38.70242902\t38.51839228\t35.36485214\t38.26227973\n+Zzz3\t36.60365578\t29.9998156\t31.68622083\t33.05776888\t32.70555997\t34.73115446\t34.54039493\t31.4030075\t32.46177448\n' 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