| Previous changeset 10:6f4143893463 (2019-02-05) Next changeset 12:89e05f831259 (2024-03-18) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19 |
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modified:
RepEnrich_setup.py edgeR_repenrich.R edger-repenrich.xml repenrich.xml test-data/Normalized_counts_file.tab test-data/edgeR_plots.pdf test-data/edgeR_result_file.tab |
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added:
macros.xml |
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| diff -r 6f4143893463 -r 6bba3e33c2e7 RepEnrich_setup.py --- a/RepEnrich_setup.py Tue Feb 05 17:20:55 2019 -0500 +++ b/RepEnrich_setup.py Sat Mar 09 22:32:46 2024 +0000 |
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| @@ -7,7 +7,6 @@ import sys from Bio import SeqIO -from Bio.Alphabet import IUPAC from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord @@ -242,7 +241,7 @@ print("Unrecognised Chromosome: "+chr) pass # Convert metagenome to SeqRecord object (required by SeqIO.write) - record = SeqRecord(Seq(metagenome, IUPAC.unambiguous_dna), id="repname", + record = SeqRecord(Seq(metagenome), id="repname", name="", description="") print("saving repgenome " + newname + ".fa" + " (" + str(k) + " of " + str(nrepgenomes) + ")") |
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| diff -r 6f4143893463 -r 6bba3e33c2e7 edgeR_repenrich.R --- a/edgeR_repenrich.R Tue Feb 05 17:20:55 2019 -0500 +++ b/edgeR_repenrich.R Sat Mar 09 22:32:46 2024 +0000 |
| [ |
| b'@@ -1,228 +1,192 @@\n-#!/usr/bin/env Rscript\n-\n-# A command-line interface to edgeR for use with Galaxy edger-repenrich\n-# written by Christophe Antoniewski drosofff@gmail.com 2017.05.30\n-\n-\n # setup R error handling to go to stderr\n-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )\n+options(show.error.messages = FALSE, error = function() {\n+ cat(geterrmessage(), file = stderr())\n+ q("no", 1, FALSE)\n+})\n \n # To not crash galaxy with an UTF8 error with not-US LC settings.\n loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n \n+# load libraries\n library("getopt")\n library("tools")\n+library("rjson")\n+suppressPackageStartupMessages({\n+ library("edgeR")\n+ library("limma")\n+})\n+\n options(stringAsFactors = FALSE, useFancyQuotes = FALSE)\n-args <- commandArgs(trailingOnly = TRUE)\n \n # get options, using the spec as defined by the enclosed list.\n # we read the options from the default: commandArgs(TRUE).\n-spec <- matrix(c(\n- "quiet", "q", 0, "logical",\n- "help", "h", 0, "logical",\n- "outfile", "o", 1, "character",\n- "countsfile", "n", 1, "character",\n- "factorName", "N", 1, "character",\n- "levelNameA", "A", 1, "character",\n- "levelNameB", "B", 1, "character",\n- "levelAfiles", "a", 1, "character",\n- "levelBfiles", "b", 1, "character",\n- "alignmentA", "i", 1, "character",\n- "alignmentB", "j", 1, "character",\n- "plots" , "p", 1, "character"),\n- byrow=TRUE, ncol=4)\n+spec <- matrix(\n+ c(\n+ "quiet", "q", 0, "logical",\n+ "outfile", "o", 1, "character",\n+ "countsfile", "n", 1, "character",\n+ "factorName", "N", 1, "character",\n+ "levelNameA", "A", 1, "character",\n+ "levelNameB", "B", 1, "character",\n+ "levelAfiles", "a", 1, "character",\n+ "levelBfiles", "b", 1, "character",\n+ "alignmentA", "i", 1, "character",\n+ "alignmentB", "j", 1, "character",\n+ "plots", "p", 1, "character"\n+ ),\n+ byrow = TRUE, ncol = 4\n+)\n opt <- getopt(spec)\n \n-# if help was asked for print a friendly message\n-# and exit with a non-zero error code\n-if (!is.null(opt$help)) {\n- cat(getopt(spec, usage=TRUE))\n- q(status=1)\n-}\n-\n-# enforce the following required arguments\n-if (is.null(opt$outfile)) {\n- cat("\'outfile\' is required\\n")\n- q(status=1)\n-}\n-if (is.null(opt$levelAfiles) | is.null(opt$levelBfiles)) {\n- cat("input count files are required for both levels\\n")\n- q(status=1)\n-}\n-if (is.null(opt$alignmentA) | is.null(opt$alignmentB)) {\n- cat("total aligned read files are required for both levels\\n")\n- q(status=1)\n-}\n-\n-verbose <- if (is.null(opt$quiet)) {\n- TRUE\n-} else {\n- FALSE\n-}\n-\n-suppressPackageStartupMessages({\n- library("edgeR")\n- library("limma")\n-})\n-\n # build levels A and B file lists\n-\n-library("rjson")\n filesA <- fromJSON(opt$levelAfiles, method = "C", unexpected.escape = "error")\n filesB <- fromJSON(opt$levelBfiles, method = "C", unexpected.escape = "error")\n listA <- list()\n-indice = 0\n+indice <- 0\n listA[["level"]] <- opt$levelNameA\n for (file in filesA) {\n- indice = indice +1\n- listA[[paste0(opt$levelNameA,"_",indice)]] <- read.delim(file, header=FALSE)\n- }\n+ indice <- indice + 1\n+ listA[[paste0(opt$levelNameA, "_", indice)]] <- read.delim(file, header = FALSE)\n+}\n listB <- list()\n-indice = 0\n+indice <- 0\n listB[["level"]] <- opt$levelNameB\n for (file in filesB) {\n- indice = indice +1\n- listB[[paste0(opt$levelNameB,"_",indice)]] <- read.delim(file, header=FALSE)\n- }\n+ indice <- indice + 1\n+ listB[[paste0(opt$levelNameB, "_", indice)]] <- read.delim(file, header = FALSE)\n+}\n \n # build a counts table\n-counts <- data.frame(row.names=listA[[2]][,1])\n+counts <- data.frame(row.names = listA[[2]][, 1])\n for (element in names(listA[-1])) {\n- counts<-cbind(counts, listA[[element]][,4])\n- } \n+ counts <- cbind(counts, listA[[element]][, 4])\n+}\n for (element in names(listB[-1])) {\n- counts<-cbind(counts, listB[[element]][,4])\n- }\n-colnames(count'..b'lts,res[,c(1,5)])\n- logfc <- cbind(logfc,res[c(1)])\n+lrt <- glmLRT(yfit, contrast = my.contrasts[, 1])\n+res <- topTags(lrt, n = dim(c)[1], sort.by = "none")$table\n+results <- cbind(results, res[, c(1, 5)])\n+logfc <- cbind(logfc, res[c(1)])\n \n # Add the repeat types back into the results.\n # We should still have the same order as the input data\n-results$class <- listA[[2]][,2]\n-results$type <- listA[[2]][,3]\n-\n+results$class <- listA[[2]][, 2]\n+results$type <- listA[[2]][, 3]\n # Sort the results table by the FDR\n results <- results[with(results, order(FDR)), ]\n \n-# Save the results\n-write.table(results, opt$outfile, quote=FALSE, sep="\\t", col.names=FALSE)\n-\n # Plot Fold Changes for repeat classes and types\n \n # open the device and plots\n if (!is.null(opt$plots)) {\n- if (verbose) cat("creating plots\\n")\n pdf(opt$plots)\n- plotMDS(y, main="Multidimensional Scaling Plot Of Distances Between Samples")\n- plotBCV(y, xlab="Gene abundance (Average log CPM)", main="Biological Coefficient of Variation Plot")\n+ plotMDS(y, main = "Multidimensional Scaling Plot Of Distances Between Samples")\n+ plotBCV(y, xlab = "Gene abundance (Average log CPM)", main = "Biological Coefficient of Variation Plot")\n logFC <- results[, "logFC"]\n # Plot the repeat classes\n classes <- with(results, reorder(class, -logFC, median))\n classes\n- par(mar=c(6,10,4,1))\n- boxplot(logFC ~ classes, data=results, outline=FALSE, horizontal=TRUE,\n- las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Class"))\n- abline(v=0)\n+ par(mar = c(6, 10, 4, 1))\n+ boxplot(logFC ~ classes,\n+ data = results, outline = FALSE, horizontal = TRUE,\n+ las = 2, xlab = "log2(Fold Change)", ylab = "", cex.axis = 0.7, main = paste0(allcontrasts, ", by Class")\n+ )\n+ abline(v = 0)\n # Plot the repeat types\n types <- with(results, reorder(type, -logFC, median))\n- boxplot(logFC ~ types, data=results, outline=FALSE, horizontal=TRUE,\n- las=2, xlab="log2(Fold Change)", main=paste0(allcontrasts, ", by Type"), yaxt="n")\n- axis(2, cex.axis=(1*28)/(length(levels(types))),\n- at=seq(from=1, to=length(levels(types))),\n- labels=levels(types), las=2)\n- abline(v=0)\n+ boxplot(logFC ~ types,\n+ data = results, outline = FALSE, horizontal = TRUE,\n+ las = 2, xlab = "log2(Fold Change)", ylab = "", cex.axis = 0.7, main = paste0(allcontrasts, ", by Type")\n+ )\n+ abline(v = 0)\n # volcano plot\n- TEdata = cbind(rownames(results), as.data.frame(results), score=-log(results$FDR, 10))\n- colnames(TEdata) = c("Tag","log2FC", "FDR", "Class", "Type", "score")\n- color = ifelse(TEdata$FDR<0.05, "red", "black") \n- s <- subset(TEdata, FDR<0.01)\n- with(TEdata, plot(log2FC, score, pch=20, col=color, main="Volcano plot (all tag types)", ylab="-log10(FDR)"))\n- text(s[,2], s[,6], labels = s[,5], pos = seq(from=1, to=3), cex=0.5)\n+ TEdata <- cbind(rownames(results), as.data.frame(results), score = -log(results$FDR, 10))\n+ colnames(TEdata) <- c("Tag", "log2FC", "FDR", "Class", "Type", "score")\n+ color <- ifelse(TEdata$FDR < 0.05, "red", "black")\n+ s <- subset(TEdata, FDR < 0.01)\n+ with(TEdata, plot(log2FC, score, pch = 20, col = color, main = "Volcano plot (all tag types)", ylab = "-log10(FDR)"))\n+ text(s[, 2], s[, 6], labels = s[, 5], pos = seq(from = 1, to = 3), cex = 0.5)\n }\n \n # close the plot device\n if (!is.null(opt$plots)) {\n- cat("closing plot device\\n")\n- dev.off()\n+ cat("closing plot device\\n")\n+ dev.off()\n }\n \n-cat("Session information:\\n\\n")\n+# Save the results\n+results <- cbind(TE_item = rownames(results), results)\n+colnames(results) <- c("TE_item", "log2FC", "FDR", "Class", "Type")\n+results$log2FC <- format(results$log2FC, digits = 5)\n+results$FDR <- format(results$FDR, digits = 5)\n+write.table(results, opt$outfile, quote = FALSE, sep = "\\t", col.names = TRUE, row.names = FALSE)\n \n+cat("Session information:\\n\\n")\n sessionInfo()\n-\n' |
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| diff -r 6f4143893463 -r 6bba3e33c2e7 edger-repenrich.xml --- a/edger-repenrich.xml Tue Feb 05 17:20:55 2019 -0500 +++ b/edger-repenrich.xml Sat Mar 09 22:32:46 2024 +0000 |
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| @@ -1,11 +1,9 @@ -<tool id="edger-repenrich" name="edgeR-repenrich" version="1.5.2"> +<tool id="edger-repenrich" name="edgeR-repenrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Determines differentially expressed features from RepEnrich counts</description> - <requirements> - <requirement type="package" version="3.16.5">bioconductor-edger</requirement> - <requirement type="package" version="3.30.13">bioconductor-limma</requirement> - <requirement type="package" version="1.20.0">r-getopt</requirement> - <requirement type="package" version="0.2.15">r-rjson</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <stdio> <regex match="Execution halted" source="both" @@ -109,7 +107,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="3"> <param name="factorName" value="Genotype"/> <param name="factorLevel_A" value="Mutant"/> <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/> |
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| diff -r 6f4143893463 -r 6bba3e33c2e7 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Mar 09 22:32:46 2024 +0000 |
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| @@ -0,0 +1,18 @@ +<macros> + <token name="@TOOL_VERSION@">1.83</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.0.2">bioconductor-edger</requirement> + <requirement type="package" version="3.58.1">bioconductor-limma</requirement> + <requirement type="package" version="1.20.4">r-getopt</requirement> + <requirement type="package" version="0.2.21">r-rjson</requirement> + <requirement type="package" version="1.0.0">bowtie</requirement> + <requirement type="package" version="1.19.2">samtools</requirement> + <requirement type="package" version="2.23.0">bedtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">biopython</requirement> + </requirements> + </xml> +</macros> |
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| diff -r 6f4143893463 -r 6bba3e33c2e7 repenrich.xml --- a/repenrich.xml Tue Feb 05 17:20:55 2019 -0500 +++ b/repenrich.xml Sat Mar 09 22:32:46 2024 +0000 |
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| @@ -1,11 +1,9 @@ -<tool id="repenrich" name="RepEnrich" version="1.6.1"> +<tool id="repenrich" name="RepEnrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Repeat Element Profiling</description> - <requirements> - <requirement type="package" version="1.2.0">bowtie</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="2.20.1">bedtools</requirement> - <requirement type="package" version="1.69">biopython</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> @@ -55,11 +53,8 @@ echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && #end if - samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && - samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && - mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && + samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' && samtools index ${input_base}_unique.bam && - rm ${input_base}_unique.sam && #if $seq_method.seq_method_list == "single-read": python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" && #else: |
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| diff -r 6f4143893463 -r 6bba3e33c2e7 test-data/Normalized_counts_file.tab --- a/test-data/Normalized_counts_file.tab Tue Feb 05 17:20:55 2019 -0500 +++ b/test-data/Normalized_counts_file.tab Sat Mar 09 22:32:46 2024 +0000 |
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| @@ -14,18 +14,18 @@ BEL_I-int 1148.97283940843 1304.98396962057 1022.22666828812 1059.36800967358 BEL_LTR 36.3043773308206 51.9691483425779 37.6498857074591 41.5799520722748 Bica_I-int 61.1339083208317 53.0858407863027 79.6886723773878 67.3614608163893 -Bica_LTR 4.81708566525451 5.7552610561202 6.02398171319346 6.05768532521486 +Bica_LTR 4.81708566525452 5.7552610561202 6.02398171319346 6.05768532521486 BLASTOPIA_I-int 539.670247700872 1034.65849882041 443.580196295081 462.322544020398 BLASTOPIA_LTR 40.6515034189771 78.9415658294696 23.6656424446886 23.1645886836216 BLOOD_I-int 1071.58616237963 1140.74428097427 960.825083254357 834.603653366803 -BLOOD_LTR 49.6982252781136 46.55748496145 32.1852737247765 36.1522660208823 +BLOOD_LTR 49.6982252781137 46.55748496145 32.1852737247765 36.1522660208823 BS 203.649150075801 355.194096523239 313.935504138996 242.355874491196 BS2 204.197436249082 179.186187508459 240.744126323696 241.871259665179 BS3_DM 33.3279666758666 38.9124366928724 53.871607892273 42.5007202417075 BS4_DM 0.313306384732001 1.97568663120544 1.46296698748984 1.0176911346361 BURDOCK_I-int 203.257517094886 191.727502645676 134.205706881789 161.473660028927 BURDOCK_LTR 21.2656708636846 16.5785878183761 12.3491625120466 17.930748562636 -Chimpo_I-int 53.4970651929892 31.7827849367832 55.4206317613798 51.369171557822 +Chimpo_I-int 53.4970651929892 31.7827849367832 55.4206317613799 51.369171557822 Chimpo_LTR 4.19047289579051 2.83468081868607 4.04467343600132 5.81537791220627 Chouto_I-int 48.2100199506366 44.4958989114965 72.7180649664068 63.1937733126415 Chouto_LTR 6.34445429082302 13.658007580942 12.8655038017489 13.617676611083 @@ -49,9 +49,9 @@ DM412 1711.00533031955 2019.32353592946 1036.38302531413 1142.04329899211 DM412B_LTR 219.588612399041 257.784155662936 132.441540808639 141.022914371002 DMCR1A 684.926920322246 693.380108134362 876.919623677734 870.222843079066 -DMLTR5 7.40186333929352 8.07454536231789 6.92757897017248 7.75383721627503 +DMLTR5 7.40186333929352 8.07454536231789 6.92757897017248 7.75383721627502 DMRP1 11.5531729369925 12.369516299721 11.2734514918335 11.0007565505902 -DMRPR 8.65508887822152 11.6823209497365 5.50764042349117 9.06229724652144 +DMRPR 8.65508887822153 11.6823209497365 5.50764042349117 9.06229724652144 DMRT1A 148.703042853426 106.085782153857 191.734732242786 171.553648410085 DMRT1B 352.587172717776 353.476108148278 417.634046487541 344.997294641637 DMRT1C 74.6844094604907 57.552610561202 108.861955245568 101.139114189787 @@ -71,11 +71,11 @@ FW2_DM 694.091132075657 761.412447782827 612.466826468541 671.046149586002 FW3_DM 25.3386538652006 32.2981814492716 35.756634311884 44.2453336153694 G_DM 428.759787505743 393.591136703623 383.168265399913 389.388012704811 -G2_DM 48.3666731430026 65.6271559235199 57.1417693937208 54.8583983051458 +G2_DM 48.3666731430027 65.6271559235199 57.1417693937208 54.8583983051458 G3_DM 18.7983830839201 21.4748546870157 34.2936673243942 26.9445843265557 G4_DM 87.0600116574048 105.226787966377 157.828320885669 165.108271224056 G5_DM 106.289191020331 111.669244372481 111.916974542973 123.625242116985 -G5A_DM 61.7996843883872 49.9934617113725 77.6233072185786 77.2960647497417 +G5A_DM 61.7996843883872 49.9934617113725 77.6233072185786 77.2960647497416 G6_DM 112.555318714971 67.5169431359773 207.698283782749 168.30672907577 G7_DM 76.3292679803337 35.9059570366902 6.97060741098101 4.74922529496845 GTWIN_I-int 296.387839956473 251.685296931824 234.418945524843 244.924333069087 @@ -97,7 +97,7 @@ Gypsy2-LTR_DM 45.2336092956826 33.0712762180041 41.5654738210349 33.438422995186 Gypsy3_I-int 225.81557679559 193.960887533126 146.253670308176 133.414461602532 Gypsy3_LTR 26.6702060003116 18.2106767745893 24.354097497625 21.6622827229683 -Gypsy4_I-int 513.587491171932 459.390091464639 521.20350351366 487.328669042885 +Gypsy4_I-int 513.587491171933 459.390091464639 521.20350351366 487.328669042885 Gypsy4_LTR 15.273686255685 18.7260732870777 11.7897927815358 9.40152762473347 Gypsy5_I-int 110.988786791311 88.9917978229929 105.333623099269 105.936800967358 Gypsy5_LTR 19.6599756419331 28.0032105118684 28.0115149663496 21.8561286533752 @@ -106,14 +106,14 @@ Gypsy6A_LTR 31.0564953865596 18.8119727058257 26.5485479788598 27.7684295307849 Gypsy7_I-int 45.5077523823231 63.7373687110625 54.0437216555071 48.8976359451344 Gypsy7_LTR 3.13306384732001 3.35007733117444 4.81918537055477 4.21614898634954 -Gypsy8_I-int 163.545932830104 107.116575178834 206.923771848195 197.868233462818 +Gypsy8_I-int 163.545932830105 107.116575178834 206.923771848195 197.868233462818 Gypsy8_LTR 57.4525583002307 41.7471175115585 56.4102858999759 60.1406999087332 -Gypsy9_I-int 16.8010548812535 16.1490907246358 21.6863341674965 22.9707427532148 +Gypsy9_I-int 16.8010548812536 16.1490907246358 21.6863341674965 22.9707427532148 Gypsy9_LTR 2.42812448167301 0.687195349984501 2.19445048123476 2.03538226927219 HELENA_RT 36.5785204174611 35.7341581991941 28.0975718479666 30.3853495912778 Helitron1_DM 0 0 0.129085322425574 0.290768895610313 HETA 879.568511837001 887.083297411243 990.729849616282 1182.31479103414 -HMSBEAGLE_I-int 307.941012893465 350.383729073348 311.48288301291 286.310439210955 +HMSBEAGLE_I-int 307.941012893465 350.383729073348 311.482883012911 286.310439210955 HOBO 171.339429150313 182.020868327145 216.476085707688 213.42436937797 I_DM 449.55549879233 957.692619622151 343.668156737687 339.860377485855 IDEFIX_I-int 282.837338816814 282.265490006134 266.475133927194 268.815843991735 @@ -134,7 +134,7 @@ Jockey2 71.3946924208047 65.2835582485276 76.1603402310888 76.9568343715296 LINEJ1_DM 974.813652795529 1369.15083542537 302.274796679886 306.712723386279 LmeSINE1c 24.5553879033706 56.0923204424849 25.7740360443063 68.5245363988305 -LOOPER1_DM 8.61592558013002 2.66288198118994 35.3263499037988 28.5438132524124 +LOOPER1_DM 8.61592558013003 2.66288198118994 35.3263499037988 28.5438132524124 LSU-rRNA_Cel 14243.5740259843 21618.3926157437 22382.0179984887 15843.270199567 LSU-rRNA_Dme 218650.181450173 354466.098949349 157455.221275418 149201.031867455 LSU-rRNA_Hsa 0.587449471372502 0.944893606228689 0.215142204042624 0 @@ -152,7 +152,7 @@ MuDR-1_DEl 1.253225538928 0.343597674992251 0.258170644851148 0.43615334341547 NINJA_I-int 143.964283784354 98.4407338852798 226.931996824159 218.22205615554 NINJA_LTR 11.6314995331755 9.79253373727915 21.1269644369856 19.6753619362979 -NOF_FB 8.92923196486203 5.41166338112795 54.7321767084434 46.5230232976501 +NOF_FB 8.92923196486203 5.41166338112795 54.7321767084435 46.5230232976501 NOMAD_I-int 454.842544034682 700.423860471703 708.635391675594 561.862429284329 NOMAD_LTR 29.6466166552656 23.7941389932134 26.6346048604768 39.8353386986129 NTS_DM 2194.82871494194 1868.57005602661 2837.89778508544 1754.54797759523 |
| b |
| diff -r 6f4143893463 -r 6bba3e33c2e7 test-data/edgeR_plots.pdf |
| b |
| Binary file test-data/edgeR_plots.pdf has changed |
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| diff -r 6f4143893463 -r 6bba3e33c2e7 test-data/edgeR_result_file.tab --- a/test-data/edgeR_result_file.tab Tue Feb 05 17:20:55 2019 -0500 +++ b/test-data/edgeR_result_file.tab Sat Mar 09 22:32:46 2024 +0000 |
| b |
| b'@@ -1,210 +1,211 @@\n-DM297_I-int\t2.69047105438237\t4.49448726299278e-21\tLTR\tGypsy\n-DM297_LTR\t1.74961921158059\t1.33970311552449e-18\tLTR\tGypsy\n-Gypsy1-I_DM\t2.37388633230267\t4.48026988291108e-16\tLTR\tGypsy\n-NOF_FB\t-2.79644759297337\t4.48026988291108e-16\tDNA\tMULE-NOF\n-G7_DM\t3.25987374806405\t1.55296802933692e-15\tLINE\tJockey\n-Gypsy_I-int\t1.74702179622354\t4.35250852545265e-12\tLTR\tGypsy\n-LINEJ1_DM\t1.94429217926762\t5.18070558194078e-12\tLINE\tJockey\n-TOM_I-int\t1.33935222283437\t6.6922795621824e-12\tLTR\tGypsy\n-GTWIN_LTR\t1.89490932455113\t8.80590960313784e-12\tLTR\tGypsy\n-Gypsy_LTR\t1.56024435809038\t2.99852403114994e-11\tLTR\tGypsy\n-DM1731_I-int\t1.53134429520835\t6.4920552091728e-10\tLTR\tCopia\n-Gypsy6_LTR\t1.53023046204423\t1.07509345482848e-06\tLTR\tGypsy\n-LOOPER1_DM\t-2.46983670012103\t1.61917280285007e-06\tDNA\tPiggyBac\n-TIRANT_LTR\t1.12203469288475\t1.78012665029166e-06\tLTR\tGypsy\n-Gypsy12_I-int\t-1.12204057066646\t2.19485691074579e-06\tLTR\tGypsy\n-R2_DM\t1.67889583354494\t2.73035057005978e-06\tLINE\tR2\n-TRANSPAC_LTR\t1.49364968145495\t2.9021047542613e-06\tLTR\tGypsy\n-Copia_LTR\t1.66649088148806\t1.18604111278586e-05\tLTR\tCopia\n-ACCORD_LTR\t1.3724059468295\t1.75953804703817e-05\tLTR\tGypsy\n-TIRANT_I-int\t1.17728139313168\t2.04686461971632e-05\tLTR\tGypsy\n-TART_B1\t-1.14695345949677\t3.09658484730011e-05\tLINE\tJockey\n-TRANSIB1\t-1.3902119423097\t6.16503339250305e-05\tDNA\tCMC-Transib\n-DM412B_LTR\t0.803090050933452\t0.00012443453312414\tLTR\tGypsy\n-MICROPIA_LTR\t-1.29556276189806\t0.000129852108160169\tLTR\tGypsy\n-G6_DM\t-1.05894868960943\t0.000138305097075584\tLINE\tJockey\n-NINJA_I-int\t-0.874264518473233\t0.000155536374046075\tLTR\tPao\n-R1_DM\t0.955905154410719\t0.000189845334697796\tLINE\tR1\n-Invader6_LTR\t-1.18865109431199\t0.000212988712815497\tLTR\tGypsy\n-Copia_I-int\t1.9331690527025\t0.000223130721644621\tLTR\tCopia\n-BLASTOPIA_LTR\t1.34881958569428\t0.000364879309201161\tLTR\tGypsy\n-LSU-rRNA_Hsa\t2.61189118344978\t0.000801598301190925\trRNA\trRNA\n-TRANSPAC_I-int\t1.16122217809542\t0.000845313292130344\tLTR\tGypsy\n-G4_DM\t-0.74970144243323\t0.000914365923267624\tLINE\tJockey\n-SSU-rRNA_Hsa\t1.12389968473263\t0.0010425909765405\trRNA\trRNA\n-DOC5_DM\t-0.809872869194368\t0.00162410751644423\tLINE\tJockey\n-Invader1_I-int\t0.749727833008358\t0.00198920329215702\tLTR\tGypsy\n-TRANSIB4\t-1.00230688125284\t0.00206051807311839\tDNA\tCMC-Transib\n-MICROPIA_I-int\t-0.751193028928835\t0.00292932704926266\tLTR\tGypsy\n-PLACW_DM\t1.16310826488548\t0.00305178248567248\tDNA\tP\n-TABOR_I-int\t0.737702190628259\t0.00354953953973759\tLTR\tGypsy\n-I_DM\t1.04141382256571\t0.00457151681951996\tLINE\tI\n-Gypsy3_I-int\t0.586594796021762\t0.00533147146680179\tLTR\tGypsy\n-DOC\t0.94015335715084\t0.00552118010544697\tLINE\tJockey\n-Helitron1_DM\t-5.10401049101919\t0.00636579556275411\tRC\tHelitron\n-Invader5_I-int\t-0.973422642391873\t0.00666026639838213\tLTR\tGypsy\n-ACCORD_I-int\t0.593047691019391\t0.00701363615971209\tLTR\tGypsy\n-LSU-rRNA_Dme\t0.902204791675651\t0.0102101724391352\trRNA\trRNA\n-DM412\t0.775970807845826\t0.0108079710929838\tLTR\tGypsy\n-NINJA_LTR\t-0.923408172476265\t0.0109563169817133\tLTR\tPao\n-BATUMI_I-int\t-0.562867612987509\t0.0148551719821132\tLTR\tPao\n-DMRT1C\t-0.664744166716986\t0.0174563775735471\tLINE\tR1\n-TAHRE\t-0.509503033739914\t0.0198535740576507\tLINE\tJockey\n-Gypsy8_I-int\t-0.578276897527121\t0.0248976847994314\tLTR\tGypsy\n-BLASTOPIA_I-int\t0.796987753936179\t0.0301824235833205\tLTR\tGypsy\n-DM176_LTR\t-0.691384671506076\t0.0432538714324547\tLTR\tGypsy\n-DMRT1A\t-0.509608409844153\t0.0432538714324547\tLINE\tR1\n-Gypsy11_I-int\t-0.734634622561586\t0.0432538714324547\tLTR\tGypsy\n-QUASIMODO2-I_DM\t0.470057940126177\t0.044414105251971\tLTR\tGypsy\n-MuDR-1_DEl\t1.35524442785064\t0.0532319546519159\tDNA\tMULE-NOF\n-DM1731_LTR\t0.752238181600754\t0.0540130070646644\tLTR\tCopia\n-FROGGER_I-int\t-0.60531971025629\t0.0540130070646644\tLTR\tCopia\n-MAX_I-int\t-0.516456091983578\t0.0643402067819527\tLTR\tPao\n-BURDOCK_I-int\t0.418223330277469\t0.0691214301126813\tLTR\tGypsy\n-FROGGER_LTR\t0.888326398013863\t0.0706362756551064\tLTR\tCopia\n-DIVER_I-int\t0.579052226156673\t0.0738156276916979\tLTR\tPao\n-Chouto_I-int\t-0.551029990754245\t0.081511593859774\tLTR\tGypsy\n-DM176_I-int\t0.387'..b'-01\tDNA\tTcMar-Tc1\n+Chimpo_I-int\t-0.31980269\t4.6967e-01\tLTR\tGypsy\n+Gypsy2_LTR\t 0.33740593\t4.6967e-01\tLTR\tGypsy\n+Gypsy6_I-int\t 0.24488785\t4.6967e-01\tLTR\tGypsy\n+NOMAD_LTR\t-0.31070751\t4.6967e-01\tLTR\tGypsy\n+DIVER2_I-int\t-0.21740035\t4.8214e-01\tLTR\tPao\n+DOC3_DM\t-0.22674831\t4.9564e-01\tLINE\tJockey\n+XDMR\t 0.24963373\t5.0355e-01\tUnknown\tUnknown\n+ROO_I-int\t 0.27660875\t5.0509e-01\tLTR\tPao\n+BURDOCK_LTR\t 0.32676718\t5.1078e-01\tLTR\tGypsy\n+BEL_I-int\t 0.23736249\t5.3379e-01\tLTR\tPao\n+Invader6_I-int\t-0.20526694\t5.3379e-01\tLTR\tGypsy\n+ROOA_I-int\t-0.19423348\t5.3379e-01\tLTR\tPao\n+DIVER_LTR\t 0.27103098\t5.3662e-01\tLTR\tPao\n+DOC6_DM\t 0.22207941\t5.3662e-01\tLINE\tJockey\n+GTWIN_I-int\t 0.19380839\t5.3662e-01\tLTR\tGypsy\n+MAX_LTR\t-0.25774945\t5.4015e-01\tLTR\tPao\n+Gypsy10_I-int\t-0.18883467\t5.6847e-01\tLTR\tGypsy\n+Gypsy11_LTR\t-0.30451990\t5.6847e-01\tLTR\tGypsy\n+Transib-N1_DM\t-0.28535954\t5.6847e-01\tDNA\tCMC-Transib\n+Gypsy8_LTR\t-0.22930841\t5.7216e-01\tLTR\tGypsy\n+MDG1_LTR\t-0.22227823\t5.9833e-01\tLTR\tGypsy\n+ARS406_DM\t-0.25396979\t6.1631e-01\tUnknown\tUnknown\n+TRANSIB2\t-0.14622244\t6.2541e-01\tDNA\tCMC-Transib\n+Invader3_I-int\t-0.13800579\t6.3087e-01\tLTR\tGypsy\n+FW2_DM\t 0.18134923\t6.3198e-01\tLINE\tJockey\n+Gypsy9_LTR\t-0.34138672\t6.3739e-01\tLTR\tGypsy\n+PROTOP_A\t 0.12947002\t6.4158e-01\tDNA\tP\n+TART-A\t 0.13700066\t6.4158e-01\tLINE\tJockey\n+Invader2_I-int\t-0.15122431\t6.5337e-01\tLTR\tGypsy\n+MDG3_LTR\t-0.18866858\t6.5337e-01\tLTR\tGypsy\n+Jockey2\t-0.16295961\t6.5457e-01\tLINE\tJockey\n+POGO\t-0.15072772\t6.5549e-01\tDNA\tTcMar-Pogo\n+Baggins1\t-0.13482610\t6.9317e-01\tLINE\tLOA\n+Bica_LTR\t-0.20302797\t7.0764e-01\tLTR\tGypsy\n+HMSBEAGLE_I-int\t 0.13884460\t7.0764e-01\tLTR\tGypsy\n+Stalker3_LTR\t-0.17401807\t7.0764e-01\tLTR\tGypsy\n+NTS_DM\t-0.17655207\t7.1269e-01\tOther\tOther\n+TABOR_LTR\t-0.24324332\t7.1269e-01\tLTR\tGypsy\n+ZAM_LTR\t 0.18588916\t7.1788e-01\tLTR\tGypsy\n+G5_DM\t-0.11225655\t7.2833e-01\tLINE\tJockey\n+BEL_LTR\t 0.15254286\t7.5643e-01\tLTR\tPao\n+FB4_DM\t-0.11461634\t7.5643e-01\tDNA\tTcMar-Tc1\n+Invader1_LTR\t 0.14121996\t7.5643e-01\tLTR\tGypsy\n+QUASIMODO_I-int\t 0.12627126\t7.5643e-01\tLTR\tGypsy\n+DMRT1B\t-0.11123522\t7.6005e-01\tLINE\tR1\n+NOMAD_I-int\t-0.13754670\t7.6005e-01\tLTR\tGypsy\n+LmeSINE1c\t-0.22854353\t7.6030e-01\tSINE\ttRNA-Deu-L2\n+Copia2_LTR_DM\t 0.14797919\t7.6240e-01\tLTR\tCopia\n+Gypsy10_LTR\t-0.15465107\t7.6240e-01\tLTR\tGypsy\n+QUASIMODO2-LTR_DM\t-0.15543048\t7.6240e-01\tLTR\tGypsy\n+BS4_DM\t-0.25325163\t8.1092e-01\tLINE\tJockey\n+G_DM\t 0.09027859\t8.1092e-01\tLINE\tJockey\n+IVK_DM\t-0.08072118\t8.1871e-01\tLINE\tI\n+Gypsy12_LTR\t-0.08320455\t8.3527e-01\tLTR\tGypsy\n+Gypsy5_I-int\t-0.07748073\t8.3527e-01\tLTR\tGypsy\n+Gypsy6A_LTR\t-0.11623997\t8.3527e-01\tLTR\tGypsy\n+IDEFIX_I-int\t 0.07819724\t8.3527e-01\tLTR\tGypsy\n+DMRP1\t 0.10050452\t8.4631e-01\tUnknown\tUnknown\n+PROTOP_B\t-0.07455018\t8.4631e-01\tDNA\tP\n+Copia1-LTR_DM\t-0.09617523\t8.5055e-01\tLTR\tCopia\n+TC1-2_DM\t 0.05957200\t8.5307e-01\tDNA\tTcMar-Tc1\n+Gypsy7_I-int\t 0.08264110\t8.6134e-01\tLTR\tGypsy\n+LSU-rRNA_Cel\t-0.09208250\t8.6134e-01\trRNA\trRNA\n+DMLTR5\t 0.07268948\t9.0549e-01\tLTR\tGypsy\n+Gypsy2-LTR_DM\t 0.06521928\t9.0549e-01\tLTR\tGypsy\n+Gypsy4_I-int\t-0.05162740\t9.0549e-01\tLTR\tGypsy\n+Gypsy5_LTR\t-0.07109800\t9.0549e-01\tLTR\tGypsy\n+QUASIMODO_LTR\t-0.06434677\t9.0549e-01\tLTR\tGypsy\n+Stalker2_LTR\t-0.05232101\t9.1731e-01\tLTR\tGypsy\n+ROVER-I_DM\t-0.04081108\t9.2272e-01\tLTR\tGypsy\n+MDG1_I-int\t-0.04114242\t9.3745e-01\tLTR\tGypsy\n+ALA_DM\t-0.11425480\t9.4292e-01\tUnknown\tUnknown\n+DNAREP1_DM\t 0.03935403\t9.4292e-01\tRC\tHelitron\n+BARI_DM\t 0.03727161\t9.4985e-01\tDNA\tTcMar-Tc1\n+Gypsy2_I-int\t-0.02615993\t9.5197e-01\tLTR\tGypsy\n+DMTOM1_LTR\t 0.03496404\t9.5383e-01\tLTR\tGypsy\n+Gypsy3_LTR\t-0.02988832\t9.5772e-01\tLTR\tGypsy\n+IDEFIX_LTR\t 0.02199611\t9.5772e-01\tLTR\tGypsy\n+MINOS\t 0.03304798\t9.5772e-01\tDNA\tTcMar-Tc1\n+STALKER4_I-int\t 0.02412753\t9.5772e-01\tLTR\tGypsy\n+G2_DM\t 0.02260980\t9.6224e-01\tLINE\tJockey\n+Copia1-I_DM\t 0.01242368\t9.6305e-01\tLTR\tCopia\n+Invader4_LTR\t 0.01649543\t9.6305e-01\tLTR\tGypsy\n+M4DM\t-0.01736598\t9.6305e-01\tDNA\tCMC-Transib\n+BS\t 0.00565217\t9.9786e-01\tLINE\tJockey\n+FTZ_DM\t 0.00000000\t1.0000e+00\tUnknown\tUnknown\n+FUSHI_DM\t 0.00000000\t1.0000e+00\tUnknown\tUnknown\n+ROOA_LTR\t-0.00054251\t1.0000e+00\tLTR\tPao\n' |