Mercurial > repos > drosofff > repenrich
changeset 1:54a3f3a195d6 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d
| author | drosofff |
|---|---|
| date | Mon, 29 May 2017 13:11:57 -0400 |
| parents | 1435d142041b |
| children | aed130b47d36 |
| files | edgeR_repenrich.R edger-repenrich.xml repenrich.xml test-data/353_fraction_counts.tab test-data/354_fraction_counts.tab test-data/355_fraction_counts.tab test-data/356_fraction_counts.tab test-data/Normalized_counts_file.tab test-data/aligned_353.tab test-data/aligned_354.tab test-data/aligned_355.tab test-data/aligned_356.tab test-data/aligned_reads.tab test-data/edgeR_plots.pdf test-data/edgeR_result_file.tab test-data/tool_wrapper.sh |
| diffstat | 16 files changed, 1677 insertions(+), 4 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/edgeR_repenrich.R Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,221 @@ +#!/usr/bin/env Rscript + +# A command-line interface to edgeR for use with Galaxy edger-repenrich +# written by Christophe Antoniewski drosofff@gmail.com 2017.05.30 + + +# setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# To not crash galaxy with an UTF8 error with not-US LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +library("getopt") +library("tools") +options(stringAsFactors = FALSE, useFancyQuotes = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +# get options, using the spec as defined by the enclosed list. +# we read the options from the default: commandArgs(TRUE). +spec <- matrix(c( + "quiet", "q", 0, "logical", + "help", "h", 0, "logical", + "outfile", "o", 1, "character", + "countsfile", "n", 1, "character", + "factorName", "N", 1, "character", + "levelNameA", "A", 1, "character", + "levelNameB", "B", 1, "character", + "levelAfiles", "a", 1, "character", + "levelBfiles", "b", 1, "character", + "alignmentA", "i", 1, "character", + "alignmentB", "j", 1, "character", + "plots" , "p", 1, "character"), + byrow=TRUE, ncol=4) +opt <- getopt(spec) + +# if help was asked for print a friendly message +# and exit with a non-zero error code +if (!is.null(opt$help)) { + cat(getopt(spec, usage=TRUE)) + q(status=1) +} + +# enforce the following required arguments +if (is.null(opt$outfile)) { + cat("'outfile' is required\n") + q(status=1) +} +if (is.null(opt$levelAfiles) | is.null(opt$levelBfiles)) { + cat("input count files are required for both levels\n") + q(status=1) +} +if (is.null(opt$alignmentA) | is.null(opt$alignmentB)) { + cat("total aligned read files are required for both levels\n") + q(status=1) +} + +verbose <- if (is.null(opt$quiet)) { + TRUE +} else { + FALSE +} + +suppressPackageStartupMessages({ + library("edgeR") + library("limma") +}) + +# build levels A and B file lists + +library("rjson") +filesA <- fromJSON(opt$levelAfiles, method = "C", unexpected.escape = "error") +filesB <- fromJSON(opt$levelBfiles, method = "C", unexpected.escape = "error") +listA <- list() +indice = 0 +listA[["level"]] <- opt$levelNameA +for (file in filesA) { + indice = indice +1 + listA[[paste0(opt$levelNameA,"_",indice)]] <- read.delim(file, header=FALSE) + } +listB <- list() +indice = 0 +listB[["level"]] <- opt$levelNameB +for (file in filesB) { + indice = indice +1 + listB[[paste0(opt$levelNameB,"_",indice)]] <- read.delim(file, header=FALSE) + } + +# build a counts table +counts <- data.frame(row.names=listA[[2]][,1]) +for (element in names(listA[-1])) { + counts<-cbind(counts, listA[[element]][,4]) + } +for (element in names(listB[-1])) { + counts<-cbind(counts, listB[[element]][,4]) + } +colnames(counts)=c(names(listA[-1]), names(listB[-1])) + +# build aligned counts vector + +filesi <- fromJSON(opt$alignmentA, method = "C", unexpected.escape = "error") +filesj <- fromJSON(opt$alignmentB, method = "C", unexpected.escape = "error") +sizes <- c() +for (file in filesi) { + sizes <- c(sizes, read.delim(file, header=FALSE)[1,1]) + } +for (file in filesj) { + sizes <- c(sizes, read.delim(file, header=FALSE)[1,1]) + } + +# build a meta data object + +meta <- data.frame( + row.names=colnames(counts), + condition=c(rep(opt$levelNameA,length(filesA)), rep(opt$levelNameB,length(filesB)) ), + libsize=sizes +) + + +# Define the library size and conditions for the GLM +libsize <- meta$libsize +condition <- factor(meta$condition) +design <- model.matrix(~0+condition) +colnames(design) <- levels(meta$condition) + + +# Build a DGE object for the GLM +y <- DGEList(counts=counts, lib.size=libsize) + +# Normalize the data +y <- calcNormFactors(y) +y$samples +# plotMDS(y) latter + +# Estimate the variance +y <- estimateGLMCommonDisp(y, design) +y <- estimateGLMTrendedDisp(y, design) +y <- estimateGLMTagwiseDisp(y, design) +# plotBCV(y) latter + +# Builds and outputs an object to contain the normalized read abundance in counts per million of reads +cpm <- cpm(y, log=FALSE, lib.size=libsize) +cpm <- as.data.frame(cpm) +colnames(cpm) <- colnames(counts) +if (!is.null(opt$countsfile)) { + normalizedAbundance <- data.frame(Tag=rownames(cpm)) + normalizedAbundance <- cbind(normalizedAbundance, cpm) + write.table(normalizedAbundance, file=opt$countsfile, sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) +} + +# test +print(counts) +print(cpm) + +# Conduct fitting of the GLM +yfit <- glmFit(y, design) + +# Initialize result matrices to contain the results of the GLM +results <- matrix(nrow=dim(counts)[1],ncol=0) +logfc <- matrix(nrow=dim(counts)[1],ncol=0) + +# Make the comparisons for the GLM +my.contrasts <- makeContrasts( + paste0(opt$levelNameB,"_",opt$levelNameA," = ", opt$levelNameB, " - ", opt$levelNameA), + levels = design +) + +# Define the contrasts used in the comparisons +allcontrasts = paste0(opt$levelNameB," vs ",opt$levelNameA) + +# Conduct a for loop that will do the fitting of the GLM for each comparison +# Put the results into the results objects + lrt <- glmLRT(yfit, contrast=my.contrasts[,1]) + plotSmear(lrt, de.tags=rownames(y)) + title(allcontrasts) + res <- topTags(lrt,n=dim(c)[1],sort.by="none")$table + results <- cbind(results,res[,c(1,5)]) + logfc <- cbind(logfc,res[c(1)]) + +# Add the repeat types back into the results. +# We should still have the same order as the input data +results$class <- listA[[2]][,2] +results$type <- listA[[2]][,3] + +# Sort the results table by the FDR +results <- results[with(results, order(FDR)), ] + +# Save the results +write.table(results, opt$outfile, quote=FALSE, sep="\t", col.names=FALSE) + +# Plot Fold Changes for repeat classes and types + +# open the device and plots +if (!is.null(opt$plots)) { + if (verbose) cat("creating plots\n") + pdf(opt$plots) + plotMDS(y, main="Multidimensional Scaling Plot Of Distances Between Samples") + plotBCV(y, xlab="Gene abundance (Average log CPM)", main="Biological Coefficient of Variation Plot") + logFC <- results[, "logFC"] + # Plot the repeat classes + classes <- with(results, reorder(class, -logFC, median)) + par(mar=c(6,10,4,1)) + boxplot(logFC ~ classes, data=results, outline=FALSE, horizontal=TRUE, + las=2, xlab="log(Fold Change)", main=paste0(allcontrasts, ", by Class")) + abline(v=0) + # Plot the repeat types + types <- with(results, reorder(type, -logFC, median)) + boxplot(logFC ~ types, data=results, outline=FALSE, horizontal=TRUE, + las=2, xlab="log(Fold Change)", main=paste0(allcontrasts, ", by Type")) + abline(v=0) +} + +# close the plot device +if (!is.null(opt$plots)) { + cat("closing plot device\n") + dev.off() +} + +cat("Session information:\n\n") + +sessionInfo() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/edger-repenrich.xml Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,180 @@ +<tool id="edger-repenrich" name="edgeR-repenrich" version="0.3.0"> + <description>Determines differentially expressed features from RepEnrich counts</description> + <requirements> + <requirement type="package" version="3.16.5-r3.3.1_0">bioconductor-edger</requirement> + <requirement type="package" version="3.30.13-r3.3.1_0">bioconductor-limma</requirement> + <requirement type="package" version="1.20.0-r3.3.1_0">r-getopt</requirement> + <requirement type="package" version="0.2.15-r3.3.1_0">r-rjson</requirement> + </requirements> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + </stdio> + <version_command> + <![CDATA[ + echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR) && + cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]> + </version_command> + <command> + <![CDATA[ + #import json + Rscript '${__tool_directory__}/edgeR_repenrich.R' + --factorName '$factorName' + + --levelNameA '$factorLevel_A' + #set $factorlevelsA = list() + #for $file in $countsFiles_A: + $factorlevelsA.append(str($file)) + #end for + $factorlevelsA.reverse() + --levelAfiles '#echo json.dumps(factorlevelsA)#' + + --levelNameB '$factorLevel_B' + #set $factorlevelsB = list() + #for $file in $countsFiles_B: + $factorlevelsB.append(str($file)) + #end for + $factorlevelsB.reverse() + --levelBfiles '#echo json.dumps(factorlevelsB)#' + + #set $alignedA = list() + #for file in $alignmentFiles_A: + $alignedA.append(str($file)) + #end for + $alignedA.reverse() + --alignmentA '#echo json.dumps(alignedA)#' + + #set $alignedB = list() + #for file in $alignmentFiles_B: + $alignedB.append(str($file)) + #end for + $alignedB.reverse() + --alignmentB '#echo json.dumps(alignedB)#' + + -o 'edger_out' + + -p '$plots' + #if $normCounts: + -n '$counts_out' + #end if + -o '$edger_out' + ]]> + </command> + <inputs> + <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. genotype or age or drug_x" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="factorLevel_A" type="text" value="FactorLevel1" label="Specify a factor level, typical values could be 'wildtype' or 'control'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" /> + <param name="alignmentFiles_A" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/> + <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'mutant' or 'Drug_X'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" /> + <param name="alignmentFiles_B" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/> + <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="Output normalized counts table" /> + </inputs> + <outputs> + <data format="tabular" name="edger_out" label="edgeR result file on ${on_string}"> + <actions> + <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" /> + </actions> + </data> + <data format="pdf" name="plots" label="edgeR plots on ${on_string}" /> + <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> + <filter>normCounts == True</filter> + </data> + </outputs> + <tests> + <test> + <param name="factorName" value="genotype"/> + <param name="factorLevel_A" value="wildtype"/> + <param name="countsFiles_A" value="353_fraction_counts.tab,354_fraction_counts.tab"/> + <param name="alignmentFiles_A" value="aligned_353.tab,aligned_354.tab"/> + <param name="factorLevel_B" value="mutant"/> + <param name="countsFiles_B" value="355_fraction_counts.tab,356_fraction_counts.tab"/> + <param name="alignmentFiles_B" value="aligned_355.tab,aligned_356.tab"/> + <param name="normCounts" value="True"/> + <output name="counts_out" file="Normalized_counts_file.tab"/> + <output name="plots" file="edgeR_plots.pdf"/> + <output name="edger_out" file="edgeR_result_file.tab"/> + + </test> + </tests> + <help> +<![CDATA[ +.. class:: infomark + +**What it does** + +Estimate Distance between samples (MDS) and Biological Coefficient Variation (BCV) in count data from high-throughput sequencing assays and test for differential expression using edgeR_. + +**Inputs** + +edger-repenrich takes count tables generated by repenrich as input. Count tables must be generated for each sample individually. Here, edgeR_ is handling a single factor (genotype, age, treatment, etc) that effect your experiment. This factor has two levels/states (for instance, "wild-type" and "mutant". +You need to select appropriate count table from your history for each factor level. + +The following table gives some examples of factors and their levels: + +========= ============== =============== +Factor Factorlevel1 Factorlevel2 +--------- -------------- --------------- +Treatment Treated Untreated +--------- -------------- --------------- +Genotype Knockdown Wildtype +--------- -------------- --------------- +TimePoint Day4 Day1 +--------- -------------- --------------- +Gender Female Male +========= ============== =============== + +*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples. + +**Output** + +edgeR_ generates a tabular file containing the different columns and results visualized in a PDF: + +====== ============================================================================= +Column Description +------ ----------------------------------------------------------------------------- + 1 Tag (transposon element ID) + 2 the logarithm (to basis 2) of the fold change (See the note in inputs section) + 3 p value adjusted for multiple testing with the Benjamini-Hochberg procedure + which controls false discovery rate (FDR) + 4 Class the transposon belongs to + 5 Type the transposon belongs to +====== ============================================================================= + +.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html +]]> + +**Note**: This edgeR_ wrapper was adapted from code available at https://github.com/nskvir/RepEnrich + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp616</citation> + </citations> +</tool>
--- a/repenrich.xml Tue May 23 18:37:22 2017 -0400 +++ b/repenrich.xml Mon May 29 13:11:57 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="0.2.0"> +<tool id="repenrich" name="RepEnrich" version="0.3.0"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -18,7 +18,10 @@ ln -f -s '$input_fastq' '${input_base}.fastq' && bowtie-build '$genome' ${baseReference} && python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && - bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam && + bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && + ALIGNED=\$(grep 'reads with at least one' bowtie_alignments.txt | cut -d ' ' -f 9) && + NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && + echo \$((\$ALIGNED-\$NONALIGNED)) > bowtie_aligned.numb && 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 && @@ -38,6 +41,8 @@ </inputs> <outputs> + <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb"> + </data> <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular"> </data> <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular"> @@ -51,6 +56,7 @@ <param name="input_fastq" value="Samp.fastq" ftype="fastq"/> <param name="genome" value="chrM.fa" ftype="fasta"/> <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> + <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/> <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/> <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/353_fraction_counts.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,210 @@ +LSU-rRNA_Dme rRNA rRNA 3078755 +FW3_DM LINE Jockey 913 +DMTOM1_LTR LTR Gypsy 1012 +R1_DM LINE R1 5407 +TAHRE LINE Jockey 3914 +G4_DM LINE Jockey 3407 +BS LINE Jockey 5001 +Stalker2_I-int LTR Gypsy 12474 +Stalker3_LTR LTR Gypsy 439 +TABOR_I-int LTR Gypsy 3081 +G7_DM LINE Jockey 98 +BEL_I-int LTR Pao 21860 +Gypsy6_I-int LTR Gypsy 6746 +ACCORD_I-int LTR Gypsy 2165 +DM412B_LTR LTR Gypsy 2910 +G2_DM LINE Jockey 1132 +SSU-rRNA_Hsa rRNA rRNA 172100 +TART_B1 LINE Jockey 21513 +S2_DM DNA TcMar-Tc1 733 +LOOPER1_DM DNA PiggyBac 589 +HOBO DNA hAT-hobo 4404 +ARS406_DM Unknown Unknown 719 +G6_DM LINE Jockey 3473 +DOC2_DM LINE Jockey 4538 +Baggins1 LINE LOA 3893 +NINJA_LTR LTR Pao 406 +TRANSIB2 DNA CMC-Transib 3076 +Gypsy5_LTR LTR Gypsy 451 +MDG3_LTR LTR Gypsy 848 +Gypsy12A_LTR LTR Gypsy 2242 +Gypsy_LTR LTR Gypsy 917 +TIRANT_LTR LTR Gypsy 1279 +I_DM LINE I 7013 +DIVER2_I-int LTR Pao 5627 +P-1_DY DNA P 2 +Invader2_I-int LTR Gypsy 5510 +DOC6_DM LINE Jockey 1240 +BURDOCK_LTR LTR Gypsy 370 +SSU-rRNA_Dme rRNA rRNA 4153 +MAX_LTR LTR Pao 753 +STALKER4_LTR LTR Gypsy 1210 +XDMR_DM Unknown Unknown 4328 +BARI_DM DNA TcMar-Tc1 902 +Transib-N1_DM DNA CMC-Transib 371 +Gypsy5_I-int LTR Gypsy 2186 +XDMR Unknown Unknown 1440 +ACCORD2_LTR LTR Gypsy 192 +POGON1 DNA TcMar-Pogo 403 +BS4_DM LINE Jockey 21 +ALA_DM Unknown Unknown 6 +Gypsy1-I_DM LTR Gypsy 6297 +ACCORD_LTR LTR Gypsy 220 +BURDOCK_I-int LTR Gypsy 3332 +ZAM_I-int LTR Gypsy 4426 +Invader5_I-int LTR Gypsy 335 +G3_DM LINE Jockey 556 +ROOA_I-int LTR Pao 4589 +Gypsy1-LTR_DM LTR Gypsy 795 +DM1731_I-int LTR Copia 4881 +ROO_I-int LTR Pao 28034 +DM412 LTR Gypsy 23566 +PROTOP DNA P 4353 +TART-A LINE Jockey 3408 +ROO_LTR LTR Pao 1851 +DIVER_LTR LTR Pao 429 +Gypsy3_I-int LTR Gypsy 2753 +BATUMI_LTR LTR Pao 403 +IDEFIX_LTR LTR Gypsy 1844 +G5_DM LINE Jockey 2551 +HETA LINE Jockey 24397 +Gypsy11_I-int LTR Gypsy 560 +R1-2_DM LINE R1 177 +Gypsy11_LTR LTR Gypsy 149 +HELENA_RT LINE Jockey 627 +FTZ_DM Unknown Unknown 0 +MICROPIA_I-int LTR Gypsy 10355 +Invader4_I-int LTR Gypsy 1219 +PLACW_DM DNA P 127 +BLOOD_LTR LTR Gypsy 746 +R2_DM LINE R2 8407 +Copia1-I_DM LTR Copia 3518 +Gypsy4_I-int LTR Gypsy 10056 +Chouto_LTR LTR Gypsy 281 +BATUMI_I-int LTR Pao 4789 +DNAREP1_DM RC Helitron 63954 +DMRT1B LINE R1 7119 +DMRT1C LINE R1 2087 +TLD2 LTR Gypsy 17 +DMRT1A LINE R1 3540 +DM1731_LTR LTR Copia 440 +LSU-rRNA_Cel rRNA rRNA 326925 +Copia_LTR LTR Copia 1129 +Gypsy6_LTR LTR Gypsy 484 +Gypsy12_I-int LTR Gypsy 9627 +BLASTOPIA_LTR LTR Gypsy 478 +Bica_LTR LTR Gypsy 125 +Gypsy8_LTR LTR Gypsy 1241 +NINJA_I-int LTR Pao 4503 +PROTOP_B DNA P 8285 +PROTOP_A DNA P 3384 +Invader3_LTR LTR Gypsy 608 +Chimpo_LTR LTR Gypsy 120 +Invader2_LTR LTR Gypsy 472 +BLASTOPIA_I-int LTR Gypsy 9540 +FROGGER_LTR LTR Copia 54 +NOMAD_I-int LTR Gypsy 11594 +QUASIMODO_LTR LTR Gypsy 1174 +TABOR_LTR LTR Gypsy 273 +Stalker2_LTR LTR Gypsy 672 +MICROPIA_LTR LTR Gypsy 863 +Gypsy9_I-int LTR Gypsy 474 +STALKER4_I-int LTR Gypsy 5741 +TRANSIB1 DNA CMC-Transib 2116 +DOC LINE Jockey 16414 +TRANSIB3 DNA CMC-Transib 1132 +Copia_I-int LTR Copia 26733 +TRANSIB4 DNA CMC-Transib 571 +Gypsy10_LTR LTR Gypsy 368 +Invader3_I-int LTR Gypsy 3722 +Invader1_I-int LTR Gypsy 1672 +BS3_DM LINE Jockey 877 +Gypsy2-LTR_DM LTR Gypsy 690 +LSU-rRNA_Hsa rRNA rRNA 0 +NOMAD_LTR LTR Gypsy 822 +Helitron1_DM RC Helitron 6 +LINEJ1_DM LINE Jockey 6329 +Invader4_LTR LTR Gypsy 1228 +MDG3_I-int LTR Gypsy 4971 +LmeSINE1c SINE tRNA-Deu-L2 1414 +ROVER-LTR_DM LTR Gypsy 415 +S_DM DNA TcMar-Tc1 3476 +Invader6_I-int LTR Gypsy 6701 +ROVER-I_DM LTR Gypsy 5589 +QUASIMODO_I-int LTR Gypsy 13018 +Chouto_I-int LTR Gypsy 1304 +NTS_DM Other Other 36205 +Gypsy3_LTR LTR Gypsy 447 +SSU-rRNA_Cel rRNA rRNA 2183 +MINOS DNA TcMar-Tc1 226 +DOC4_DM LINE Jockey 830 +ZAM_LTR LTR Gypsy 225 +QUASIMODO2-LTR_DM LTR Gypsy 200 +Gypsy2-I_DM LTR Gypsy 3896 +TRANSPAC_I-int LTR Gypsy 14982 +Bica_I-int LTR Gypsy 1390 +BS2 LINE Jockey 4991 +BLOOD_I-int LTR Gypsy 17222 +DMCR1A LINE CR1 17957 +QUASIMODO2-I_DM LTR Gypsy 2225 +HMSBEAGLE_I-int LTR Gypsy 5908 +DMLTR5 LTR Gypsy 160 +Gypsy7_LTR LTR Gypsy 87 +G5A_DM LINE Jockey 1595 +MDG1_I-int LTR Gypsy 13740 +Gypsy2_I-int LTR Gypsy 3453 +BARI1 DNA TcMar-Tc1 322 +Invader5_LTR LTR Gypsy 64 +DM176_LTR LTR Gypsy 872 +DOC3_DM LINE Jockey 10659 +Copia1-LTR_DM LTR Copia 566 +TOM_I-int LTR Gypsy 2311 +NOF_FB DNA MULE-NOF 960 +Chimpo_I-int LTR Gypsy 1060 +DIVER_I-int LTR Pao 15627 +TIRANT_I-int LTR Gypsy 8559 +Gypsy2_LTR LTR Gypsy 485 +FB4_DM DNA TcMar-Tc1 6939 +GTWIN_LTR LTR Gypsy 467 +Invader6_LTR LTR Gypsy 588 +Gypsy8_I-int LTR Gypsy 4083 +G_DM LINE Jockey 8035 +TRANSPAC_LTR LTR Gypsy 555 +FUSHI_DM Unknown Unknown 0 +Transib5 DNA CMC-Transib 965 +MuDR-1_DEl DNA MULE-NOF 9 +Mariner2_DM DNA TcMar-Tc1 1591 +DOC5_DM LINE Jockey 2183 +TC1_DM DNA TcMar-Tc1 1960 +Gypsy9_LTR LTR Gypsy 42 +DMRP1 Unknown Unknown 227 +Gypsy10_I-int LTR Gypsy 1930 +Gypsy4_LTR LTR Gypsy 194 +DM297_LTR LTR Gypsy 1478 +ACCORD2_I-int LTR Gypsy 2458 +Invader1_LTR LTR Gypsy 1931 +BEL_LTR LTR Pao 858 +IVK_DM LINE I 2921 +M4DM DNA CMC-Transib 1650 +FW2_DM LINE Jockey 13847 +Copia2_I-int LTR Copia 3455 +MDG1_LTR LTR Gypsy 582 +Gypsy12_LTR LTR Gypsy 5934 +Gypsy7_I-int LTR Gypsy 1009 +FROGGER_I-int LTR Copia 1361 +Gypsy_I-int LTR Gypsy 5634 +5S_DM RNA RNA 10392 +GTWIN_I-int LTR Gypsy 5054 +CIRCE LTR Gypsy 3323 +DIVER2_LTR LTR Pao 535 +POGO DNA TcMar-Pogo 2492 +Gypsy6A_LTR LTR Gypsy 573 +MAX_I-int LTR Pao 9201 +ROOA_LTR LTR Pao 483 +DM176_I-int LTR Gypsy 2813 +Copia2_LTR_DM LTR Copia 486 +DM297_I-int LTR Gypsy 11530 +IDEFIX_I-int LTR Gypsy 5547 +Jockey2 LINE Jockey 1588 +TC1-2_DM DNA TcMar-Tc1 3948 +DMRPR Unknown Unknown 187
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/354_fraction_counts.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,210 @@ +LSU-rRNA_Dme rRNA rRNA 3659329 +FW3_DM LINE Jockey 831 +DMTOM1_LTR LTR Gypsy 1004 +R1_DM LINE R1 7343 +TAHRE LINE Jockey 4560 +G4_DM LINE Jockey 3668 +BS LINE Jockey 7296 +Stalker2_I-int LTR Gypsy 12252 +Stalker3_LTR LTR Gypsy 593 +TABOR_I-int LTR Gypsy 3947 +G7_DM LINE Jockey 162 +BEL_I-int LTR Pao 23757 +Gypsy6_I-int LTR Gypsy 7489 +ACCORD_I-int LTR Gypsy 2723 +DM412B_LTR LTR Gypsy 3078 +G2_DM LINE Jockey 1328 +SSU-rRNA_Hsa rRNA rRNA 318045 +TART_B1 LINE Jockey 25248 +S2_DM DNA TcMar-Tc1 765 +LOOPER1_DM DNA PiggyBac 821 +HOBO DNA hAT-hobo 5031 +ARS406_DM Unknown Unknown 563 +G6_DM LINE Jockey 4827 +DOC2_DM LINE Jockey 4438 +Baggins1 LINE LOA 5136 +NINJA_LTR LTR Pao 491 +TRANSIB2 DNA CMC-Transib 3197 +Gypsy5_LTR LTR Gypsy 651 +MDG3_LTR LTR Gypsy 1037 +Gypsy12A_LTR LTR Gypsy 3059 +Gypsy_LTR LTR Gypsy 1306 +TIRANT_LTR LTR Gypsy 1371 +I_DM LINE I 7987 +DIVER2_I-int LTR Pao 6679 +P-1_DY DNA P 8 +Invader2_I-int LTR Gypsy 6823 +DOC6_DM LINE Jockey 1259 +BURDOCK_LTR LTR Gypsy 287 +SSU-rRNA_Dme rRNA rRNA 7113 +MAX_LTR LTR Pao 1017 +STALKER4_LTR LTR Gypsy 1292 +XDMR_DM Unknown Unknown 3317 +BARI_DM DNA TcMar-Tc1 990 +Transib-N1_DM DNA CMC-Transib 308 +Gypsy5_I-int LTR Gypsy 2448 +XDMR Unknown Unknown 1249 +ACCORD2_LTR LTR Gypsy 235 +POGON1 DNA TcMar-Pogo 331 +BS4_DM LINE Jockey 34 +ALA_DM Unknown Unknown 5 +Gypsy1-I_DM LTR Gypsy 8160 +ACCORD_LTR LTR Gypsy 295 +BURDOCK_I-int LTR Gypsy 3119 +ZAM_I-int LTR Gypsy 5129 +Invader5_I-int LTR Gypsy 416 +G3_DM LINE Jockey 797 +ROOA_I-int LTR Pao 4985 +Gypsy1-LTR_DM LTR Gypsy 1042 +DM1731_I-int LTR Copia 5180 +ROO_I-int LTR Pao 31793 +DM412 LTR Gypsy 24086 +PROTOP DNA P 4942 +TART-A LINE Jockey 3697 +ROO_LTR LTR Pao 1639 +DIVER_LTR LTR Pao 469 +Gypsy3_I-int LTR Gypsy 3399 +BATUMI_LTR LTR Pao 554 +IDEFIX_LTR LTR Gypsy 2191 +G5_DM LINE Jockey 2601 +HETA LINE Jockey 23025 +Gypsy11_I-int LTR Gypsy 671 +R1-2_DM LINE R1 267 +Gypsy11_LTR LTR Gypsy 134 +HELENA_RT LINE Jockey 653 +FTZ_DM Unknown Unknown 0 +MICROPIA_I-int LTR Gypsy 10149 +Invader4_I-int LTR Gypsy 1439 +PLACW_DM DNA P 149 +BLOOD_LTR LTR Gypsy 748 +R2_DM LINE R2 15327 +Copia1-I_DM LTR Copia 3588 +Gypsy4_I-int LTR Gypsy 12113 +Chouto_LTR LTR Gypsy 299 +BATUMI_I-int LTR Pao 6395 +DNAREP1_DM RC Helitron 67821 +DMRT1B LINE R1 9706 +DMRT1C LINE R1 2530 +TLD2 LTR Gypsy 65 +DMRT1A LINE R1 4456 +DM1731_LTR LTR Copia 577 +LSU-rRNA_Cel rRNA rRNA 520168 +Copia_LTR LTR Copia 1408 +Gypsy6_LTR LTR Gypsy 428 +Gypsy12_I-int LTR Gypsy 9778 +BLASTOPIA_LTR LTR Gypsy 550 +Bica_LTR LTR Gypsy 140 +Gypsy8_LTR LTR Gypsy 1311 +NINJA_I-int LTR Pao 5274 +PROTOP_B DNA P 8690 +PROTOP_A DNA P 3533 +Invader3_LTR LTR Gypsy 657 +Chimpo_LTR LTR Gypsy 94 +Invader2_LTR LTR Gypsy 492 +BLASTOPIA_I-int LTR Gypsy 10309 +FROGGER_LTR LTR Copia 41 +NOMAD_I-int LTR Gypsy 16469 +QUASIMODO_LTR LTR Gypsy 1332 +TABOR_LTR LTR Gypsy 384 +Stalker2_LTR LTR Gypsy 726 +MICROPIA_LTR LTR Gypsy 797 +Gypsy9_I-int LTR Gypsy 504 +STALKER4_I-int LTR Gypsy 6207 +TRANSIB1 DNA CMC-Transib 2082 +DOC LINE Jockey 17883 +TRANSIB3 DNA CMC-Transib 1184 +Copia_I-int LTR Copia 27612 +TRANSIB4 DNA CMC-Transib 635 +Gypsy10_LTR LTR Gypsy 314 +Invader3_I-int LTR Gypsy 4667 +Invader1_I-int LTR Gypsy 1832 +BS3_DM LINE Jockey 1252 +Gypsy2-LTR_DM LTR Gypsy 966 +LSU-rRNA_Hsa rRNA rRNA 5 +NOMAD_LTR LTR Gypsy 619 +Helitron1_DM RC Helitron 3 +LINEJ1_DM LINE Jockey 7025 +Invader4_LTR LTR Gypsy 1420 +MDG3_I-int LTR Gypsy 5392 +LmeSINE1c SINE tRNA-Deu-L2 599 +ROVER-LTR_DM LTR Gypsy 564 +S_DM DNA TcMar-Tc1 3612 +Invader6_I-int LTR Gypsy 6931 +ROVER-I_DM LTR Gypsy 6513 +QUASIMODO_I-int LTR Gypsy 14906 +Chouto_I-int LTR Gypsy 1690 +NTS_DM Other Other 65954 +Gypsy3_LTR LTR Gypsy 566 +SSU-rRNA_Cel rRNA rRNA 3463 +MINOS DNA TcMar-Tc1 173 +DOC4_DM LINE Jockey 813 +ZAM_LTR LTR Gypsy 259 +QUASIMODO2-LTR_DM LTR Gypsy 313 +Gypsy2-I_DM LTR Gypsy 4606 +TRANSPAC_I-int LTR Gypsy 9674 +Bica_I-int LTR Gypsy 1852 +BS2 LINE Jockey 5595 +BLOOD_I-int LTR Gypsy 22330 +DMCR1A LINE CR1 20380 +QUASIMODO2-I_DM LTR Gypsy 2717 +HMSBEAGLE_I-int LTR Gypsy 7239 +DMLTR5 LTR Gypsy 161 +Gypsy7_LTR LTR Gypsy 112 +G5A_DM LINE Jockey 1804 +MDG1_I-int LTR Gypsy 16315 +Gypsy2_I-int LTR Gypsy 3190 +BARI1 DNA TcMar-Tc1 395 +Invader5_LTR LTR Gypsy 69 +DM176_LTR LTR Gypsy 899 +DOC3_DM LINE Jockey 11941 +Copia1-LTR_DM LTR Copia 771 +TOM_I-int LTR Gypsy 2563 +NOF_FB DNA MULE-NOF 1272 +Chimpo_I-int LTR Gypsy 1288 +DIVER_I-int LTR Pao 13178 +TIRANT_I-int LTR Gypsy 10917 +Gypsy2_LTR LTR Gypsy 479 +FB4_DM DNA TcMar-Tc1 7149 +GTWIN_LTR LTR Gypsy 598 +Invader6_LTR LTR Gypsy 649 +Gypsy8_I-int LTR Gypsy 4809 +G_DM LINE Jockey 8905 +TRANSPAC_LTR LTR Gypsy 538 +FUSHI_DM Unknown Unknown 0 +Transib5 DNA CMC-Transib 1123 +MuDR-1_DEl DNA MULE-NOF 6 +Mariner2_DM DNA TcMar-Tc1 2011 +DOC5_DM LINE Jockey 3037 +TC1_DM DNA TcMar-Tc1 1840 +Gypsy9_LTR LTR Gypsy 51 +DMRP1 Unknown Unknown 262 +Gypsy10_I-int LTR Gypsy 2258 +Gypsy4_LTR LTR Gypsy 274 +DM297_LTR LTR Gypsy 1489 +ACCORD2_I-int LTR Gypsy 2934 +Invader1_LTR LTR Gypsy 3346 +BEL_LTR LTR Pao 875 +IVK_DM LINE I 3349 +M4DM DNA CMC-Transib 1727 +FW2_DM LINE Jockey 14234 +Copia2_I-int LTR Copia 4218 +MDG1_LTR LTR Gypsy 690 +Gypsy12_LTR LTR Gypsy 6292 +Gypsy7_I-int LTR Gypsy 1256 +FROGGER_I-int LTR Copia 1611 +Gypsy_I-int LTR Gypsy 6822 +5S_DM RNA RNA 6317 +GTWIN_I-int LTR Gypsy 5448 +CIRCE LTR Gypsy 3767 +DIVER2_LTR LTR Pao 793 +POGO DNA TcMar-Pogo 2427 +Gypsy6A_LTR LTR Gypsy 617 +MAX_I-int LTR Pao 12395 +ROOA_LTR LTR Pao 400 +DM176_I-int LTR Gypsy 3627 +Copia2_LTR_DM LTR Copia 891 +DM297_I-int LTR Gypsy 11837 +IDEFIX_I-int LTR Gypsy 6193 +Jockey2 LINE Jockey 1770 +TC1-2_DM DNA TcMar-Tc1 3807 +DMRPR Unknown Unknown 128
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/355_fraction_counts.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,210 @@ +LSU-rRNA_Dme rRNA rRNA 4126525 +FW3_DM LINE Jockey 376 +DMTOM1_LTR LTR Gypsy 458 +R1_DM LINE R1 6019 +TAHRE LINE Jockey 1417 +G4_DM LINE Jockey 1225 +BS LINE Jockey 4135 +Stalker2_I-int LTR Gypsy 4814 +Stalker3_LTR LTR Gypsy 235 +TABOR_I-int LTR Gypsy 3691 +G7_DM LINE Jockey 418 +BEL_I-int LTR Pao 15192 +Gypsy6_I-int LTR Gypsy 3763 +ACCORD_I-int LTR Gypsy 2031 +DM412B_LTR LTR Gypsy 3001 +G2_DM LINE Jockey 764 +SSU-rRNA_Hsa rRNA rRNA 301813 +TART_B1 LINE Jockey 5089 +S2_DM DNA TcMar-Tc1 205 +LOOPER1_DM DNA PiggyBac 31 +HOBO DNA hAT-hobo 2119 +ARS406_DM Unknown Unknown 230 +G6_DM LINE Jockey 786 +DOC2_DM LINE Jockey 2052 +Baggins1 LINE LOA 1832 +NINJA_LTR LTR Pao 114 +TRANSIB2 DNA CMC-Transib 1484 +Gypsy5_LTR LTR Gypsy 326 +MDG3_LTR LTR Gypsy 454 +Gypsy12A_LTR LTR Gypsy 1077 +Gypsy_LTR LTR Gypsy 1737 +TIRANT_LTR LTR Gypsy 1596 +I_DM LINE I 11149 +DIVER2_I-int LTR Pao 2668 +P-1_DY DNA P 4 +Invader2_I-int LTR Gypsy 3157 +DOC6_DM LINE Jockey 768 +BURDOCK_LTR LTR Gypsy 193 +SSU-rRNA_Dme rRNA rRNA 3822 +MAX_LTR LTR Pao 343 +STALKER4_LTR LTR Gypsy 803 +XDMR_DM Unknown Unknown 1587 +BARI_DM DNA TcMar-Tc1 522 +Transib-N1_DM DNA CMC-Transib 130 +Gypsy5_I-int LTR Gypsy 1036 +XDMR Unknown Unknown 903 +ACCORD2_LTR LTR Gypsy 76 +POGON1 DNA TcMar-Pogo 256 +BS4_DM LINE Jockey 23 +ALA_DM Unknown Unknown 0 +Gypsy1-I_DM LTR Gypsy 22753 +ACCORD_LTR LTR Gypsy 344 +BURDOCK_I-int LTR Gypsy 2232 +ZAM_I-int LTR Gypsy 2892 +Invader5_I-int LTR Gypsy 117 +G3_DM LINE Jockey 250 +ROOA_I-int LTR Pao 2579 +Gypsy1-LTR_DM LTR Gypsy 576 +DM1731_I-int LTR Copia 6873 +ROO_I-int LTR Pao 22941 +DM412 LTR Gypsy 23508 +PROTOP DNA P 2059 +TART-A LINE Jockey 1825 +ROO_LTR LTR Pao 1453 +DIVER_LTR LTR Pao 328 +Gypsy3_I-int LTR Gypsy 2258 +BATUMI_LTR LTR Pao 169 +IDEFIX_LTR LTR Gypsy 1012 +G5_DM LINE Jockey 1300 +HETA LINE Jockey 10327 +Gypsy11_I-int LTR Gypsy 168 +R1-2_DM LINE R1 68 +Gypsy11_LTR LTR Gypsy 48 +HELENA_RT LINE Jockey 416 +FTZ_DM Unknown Unknown 0 +MICROPIA_I-int LTR Gypsy 3327 +Invader4_I-int LTR Gypsy 1180 +PLACW_DM DNA P 204 +BLOOD_LTR LTR Gypsy 542 +R2_DM LINE R2 15128 +Copia1-I_DM LTR Copia 1946 +Gypsy4_I-int LTR Gypsy 5348 +Chouto_LTR LTR Gypsy 159 +BATUMI_I-int LTR Pao 1842 +DNAREP1_DM RC Helitron 36953 +DMRT1B LINE R1 4115 +DMRT1C LINE R1 670 +TLD2 LTR Gypsy 1 +DMRT1A LINE R1 1235 +DM1731_LTR LTR Copia 321 +LSU-rRNA_Cel rRNA rRNA 251671 +Copia_LTR LTR Copia 3075 +Gypsy6_LTR LTR Gypsy 760 +Gypsy12_I-int LTR Gypsy 2466 +BLASTOPIA_LTR LTR Gypsy 919 +Bica_LTR LTR Gypsy 67 +Gypsy8_LTR LTR Gypsy 486 +NINJA_I-int LTR Pao 1146 +PROTOP_B DNA P 4300 +PROTOP_A DNA P 1988 +Invader3_LTR LTR Gypsy 227 +Chimpo_LTR LTR Gypsy 33 +Invader2_LTR LTR Gypsy 213 +BLASTOPIA_I-int LTR Gypsy 12045 +FROGGER_LTR LTR Copia 57 +NOMAD_I-int LTR Gypsy 8154 +QUASIMODO_LTR LTR Gypsy 528 +TABOR_LTR LTR Gypsy 88 +Stalker2_LTR LTR Gypsy 356 +MICROPIA_LTR LTR Gypsy 149 +Gypsy9_I-int LTR Gypsy 188 +STALKER4_I-int LTR Gypsy 3132 +TRANSIB1 DNA CMC-Transib 289 +DOC LINE Jockey 21700 +TRANSIB3 DNA CMC-Transib 741 +Copia_I-int LTR Copia 87220 +TRANSIB4 DNA CMC-Transib 153 +Gypsy10_LTR LTR Gypsy 162 +Invader3_I-int LTR Gypsy 2022 +Invader1_I-int LTR Gypsy 1768 +BS3_DM LINE Jockey 453 +Gypsy2-LTR_DM LTR Gypsy 385 +LSU-rRNA_Hsa rRNA rRNA 11 +NOMAD_LTR LTR Gypsy 277 +Helitron1_DM RC Helitron 0 +LINEJ1_DM LINE Jockey 15939 +Invader4_LTR LTR Gypsy 679 +MDG3_I-int LTR Gypsy 3770 +LmeSINE1c SINE tRNA-Deu-L2 653 +ROVER-LTR_DM LTR Gypsy 168 +S_DM DNA TcMar-Tc1 2041 +Invader6_I-int LTR Gypsy 3298 +ROVER-I_DM LTR Gypsy 3069 +QUASIMODO_I-int LTR Gypsy 8000 +Chouto_I-int LTR Gypsy 518 +NTS_DM Other Other 21753 +Gypsy3_LTR LTR Gypsy 212 +SSU-rRNA_Cel rRNA rRNA 1817 +MINOS DNA TcMar-Tc1 93 +DOC4_DM LINE Jockey 658 +ZAM_LTR LTR Gypsy 118 +QUASIMODO2-LTR_DM LTR Gypsy 105 +Gypsy2-I_DM LTR Gypsy 2658 +TRANSPAC_I-int LTR Gypsy 16760 +Bica_I-int LTR Gypsy 618 +BS2 LINE Jockey 2086 +BLOOD_I-int LTR Gypsy 13280 +DMCR1A LINE CR1 8072 +QUASIMODO2-I_DM LTR Gypsy 1811 +HMSBEAGLE_I-int LTR Gypsy 4079 +DMLTR5 LTR Gypsy 94 +Gypsy7_LTR LTR Gypsy 39 +G5A_DM LINE Jockey 582 +MDG1_I-int LTR Gypsy 8043 +Gypsy2_I-int LTR Gypsy 1552 +BARI1 DNA TcMar-Tc1 125 +Invader5_LTR LTR Gypsy 23 +DM176_LTR LTR Gypsy 330 +DOC3_DM LINE Jockey 5205 +Copia1-LTR_DM LTR Copia 389 +TOM_I-int LTR Gypsy 3390 +NOF_FB DNA MULE-NOF 63 +Chimpo_I-int LTR Gypsy 370 +DIVER_I-int LTR Pao 11751 +TIRANT_I-int LTR Gypsy 12728 +Gypsy2_LTR LTR Gypsy 250 +FB4_DM DNA TcMar-Tc1 3348 +GTWIN_LTR LTR Gypsy 938 +Invader6_LTR LTR Gypsy 146 +Gypsy8_I-int LTR Gypsy 1247 +G_DM LINE Jockey 4582 +TRANSPAC_LTR LTR Gypsy 979 +FUSHI_DM Unknown Unknown 0 +Transib5 DNA CMC-Transib 328 +MuDR-1_DEl DNA MULE-NOF 4 +Mariner2_DM DNA TcMar-Tc1 926 +DOC5_DM LINE Jockey 752 +TC1_DM DNA TcMar-Tc1 1485 +Gypsy9_LTR LTR Gypsy 8 +DMRP1 Unknown Unknown 144 +Gypsy10_I-int LTR Gypsy 927 +Gypsy4_LTR LTR Gypsy 218 +DM297_LTR LTR Gypsy 2516 +ACCORD2_I-int LTR Gypsy 1200 +Invader1_LTR LTR Gypsy 1903 +BEL_LTR LTR Pao 605 +IVK_DM LINE I 1769 +M4DM DNA CMC-Transib 918 +FW2_DM LINE Jockey 8864 +Copia2_I-int LTR Copia 1892 +MDG1_LTR LTR Gypsy 281 +Gypsy12_LTR LTR Gypsy 2680 +Gypsy7_I-int LTR Gypsy 742 +FROGGER_I-int LTR Copia 546 +Gypsy_I-int LTR Gypsy 11161 +5S_DM RNA RNA 4146 +GTWIN_I-int LTR Gypsy 2930 +CIRCE LTR Gypsy 1570 +DIVER2_LTR LTR Pao 240 +POGO DNA TcMar-Pogo 1032 +Gypsy6A_LTR LTR Gypsy 219 +MAX_I-int LTR Pao 3905 +ROOA_LTR LTR Pao 276 +DM176_I-int LTR Gypsy 2298 +Copia2_LTR_DM LTR Copia 460 +DM297_I-int LTR Gypsy 42705 +IDEFIX_I-int LTR Gypsy 3286 +Jockey2 LINE Jockey 760 +TC1-2_DM DNA TcMar-Tc1 2287 +DMRPR Unknown Unknown 136
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/356_fraction_counts.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,210 @@ +LSU-rRNA_Dme rRNA rRNA 5583038 +FW3_DM LINE Jockey 647 +DMTOM1_LTR LTR Gypsy 1403 +R1_DM LINE R1 15424 +TAHRE LINE Jockey 3806 +G4_DM LINE Jockey 2223 +BS LINE Jockey 5200 +Stalker2_I-int LTR Gypsy 10966 +Stalker3_LTR LTR Gypsy 543 +TABOR_I-int LTR Gypsy 5504 +G7_DM LINE Jockey 1949 +BEL_I-int LTR Pao 29338 +Gypsy6_I-int LTR Gypsy 11381 +ACCORD_I-int LTR Gypsy 4103 +DM412B_LTR LTR Gypsy 5607 +G2_DM LINE Jockey 1235 +SSU-rRNA_Hsa rRNA rRNA 563673 +TART_B1 LINE Jockey 13382 +S2_DM DNA TcMar-Tc1 716 +LOOPER1_DM DNA PiggyBac 220 +HOBO DNA hAT-hobo 4375 +ARS406_DM Unknown Unknown 755 +G6_DM LINE Jockey 2874 +DOC2_DM LINE Jockey 4511 +Baggins1 LINE LOA 5500 +NINJA_LTR LTR Pao 297 +TRANSIB2 DNA CMC-Transib 3357 +Gypsy5_LTR LTR Gypsy 502 +MDG3_LTR LTR Gypsy 926 +Gypsy12A_LTR LTR Gypsy 2436 +Gypsy_LTR LTR Gypsy 3771 +TIRANT_LTR LTR Gypsy 3225 +I_DM LINE I 11479 +DIVER2_I-int LTR Pao 6446 +P-1_DY DNA P 13 +Invader2_I-int LTR Gypsy 5970 +DOC6_DM LINE Jockey 1718 +BURDOCK_LTR LTR Gypsy 543 +SSU-rRNA_Dme rRNA rRNA 9958 +MAX_LTR LTR Pao 958 +STALKER4_LTR LTR Gypsy 2040 +XDMR_DM Unknown Unknown 4049 +BARI_DM DNA TcMar-Tc1 1117 +Transib-N1_DM DNA CMC-Transib 366 +Gypsy5_I-int LTR Gypsy 2834 +XDMR Unknown Unknown 1771 +ACCORD2_LTR LTR Gypsy 213 +POGON1 DNA TcMar-Pogo 641 +BS4_DM LINE Jockey 8 +ALA_DM Unknown Unknown 9 +Gypsy1-I_DM LTR Gypsy 36962 +ACCORD_LTR LTR Gypsy 790 +BURDOCK_I-int LTR Gypsy 5190 +ZAM_I-int LTR Gypsy 6896 +Invader5_I-int LTR Gypsy 191 +G3_DM LINE Jockey 480 +ROOA_I-int LTR Pao 4103 +Gypsy1-LTR_DM LTR Gypsy 1432 +DM1731_I-int LTR Copia 18829 +ROO_I-int LTR Pao 34023 +DM412 LTR Gypsy 43689 +PROTOP DNA P 4775 +TART-A LINE Jockey 5092 +ROO_LTR LTR Pao 2219 +DIVER_LTR LTR Pao 547 +Gypsy3_I-int LTR Gypsy 5766 +BATUMI_LTR LTR Pao 348 +IDEFIX_LTR LTR Gypsy 2538 +G5_DM LINE Jockey 2714 +HETA LINE Jockey 22459 +Gypsy11_I-int LTR Gypsy 487 +R1-2_DM LINE R1 184 +Gypsy11_LTR LTR Gypsy 159 +HELENA_RT LINE Jockey 934 +FTZ_DM Unknown Unknown 0 +MICROPIA_I-int LTR Gypsy 6941 +Invader4_I-int LTR Gypsy 1888 +PLACW_DM DNA P 277 +BLOOD_LTR LTR Gypsy 1269 +R2_DM LINE R2 54042 +Copia1-I_DM LTR Copia 4100 +Gypsy4_I-int LTR Gypsy 13114 +Chouto_LTR LTR Gypsy 162 +BATUMI_I-int LTR Pao 4723 +DNAREP1_DM RC Helitron 76851 +DMRT1B LINE R1 9003 +DMRT1C LINE R1 1907 +TLD2 LTR Gypsy 33 +DMRT1A LINE R1 3797 +DM1731_LTR LTR Copia 1274 +LSU-rRNA_Cel rRNA rRNA 363697 +Copia_LTR LTR Copia 2612 +Gypsy6_LTR LTR Gypsy 1423 +Gypsy12_I-int LTR Gypsy 5002 +BLASTOPIA_LTR LTR Gypsy 1038 +Bica_LTR LTR Gypsy 123 +Gypsy8_LTR LTR Gypsy 1467 +NINJA_I-int LTR Pao 3676 +PROTOP_B DNA P 9371 +PROTOP_A DNA P 4465 +Invader3_LTR LTR Gypsy 506 +Chimpo_LTR LTR Gypsy 107 +Invader2_LTR LTR Gypsy 417 +BLASTOPIA_I-int LTR Gypsy 13780 +FROGGER_LTR LTR Copia 85 +NOMAD_I-int LTR Gypsy 11614 +QUASIMODO_LTR LTR Gypsy 1625 +TABOR_LTR LTR Gypsy 443 +Stalker2_LTR LTR Gypsy 790 +MICROPIA_LTR LTR Gypsy 460 +Gypsy9_I-int LTR Gypsy 429 +STALKER4_I-int LTR Gypsy 7287 +TRANSIB1 DNA CMC-Transib 1229 +DOC LINE Jockey 29082 +TRANSIB3 DNA CMC-Transib 1802 +Copia_I-int LTR Copia 50888 +TRANSIB4 DNA CMC-Transib 364 +Gypsy10_LTR LTR Gypsy 363 +Invader3_I-int LTR Gypsy 4411 +Invader1_I-int LTR Gypsy 2993 +BS3_DM LINE Jockey 851 +Gypsy2-LTR_DM LTR Gypsy 1155 +LSU-rRNA_Hsa rRNA rRNA 15 +NOMAD_LTR LTR Gypsy 757 +Helitron1_DM RC Helitron 0 +LINEJ1_DM LINE Jockey 24891 +Invader4_LTR LTR Gypsy 1624 +MDG3_I-int LTR Gypsy 7857 +LmeSINE1c SINE tRNA-Deu-L2 627 +ROVER-LTR_DM LTR Gypsy 415 +S_DM DNA TcMar-Tc1 4974 +Invader6_I-int LTR Gypsy 6566 +ROVER-I_DM LTR Gypsy 6947 +QUASIMODO_I-int LTR Gypsy 17910 +Chouto_I-int LTR Gypsy 1231 +NTS_DM Other Other 56043 +Gypsy3_LTR LTR Gypsy 681 +SSU-rRNA_Cel rRNA rRNA 3855 +MINOS DNA TcMar-Tc1 273 +DOC4_DM LINE Jockey 1030 +ZAM_LTR LTR Gypsy 377 +QUASIMODO2-LTR_DM LTR Gypsy 298 +Gypsy2-I_DM LTR Gypsy 7374 +TRANSPAC_I-int LTR Gypsy 28474 +Bica_I-int LTR Gypsy 1561 +BS2 LINE Jockey 5214 +BLOOD_I-int LTR Gypsy 27362 +DMCR1A LINE CR1 17489 +QUASIMODO2-I_DM LTR Gypsy 3977 +HMSBEAGLE_I-int LTR Gypsy 7863 +DMLTR5 LTR Gypsy 189 +Gypsy7_LTR LTR Gypsy 80 +G5A_DM LINE Jockey 1578 +MDG1_I-int LTR Gypsy 16306 +Gypsy2_I-int LTR Gypsy 4226 +BARI1 DNA TcMar-Tc1 370 +Invader5_LTR LTR Gypsy 47 +DM176_LTR LTR Gypsy 560 +DOC3_DM LINE Jockey 11067 +Copia1-LTR_DM LTR Copia 600 +TOM_I-int LTR Gypsy 6929 +NOF_FB DNA MULE-NOF 228 +Chimpo_I-int LTR Gypsy 1366 +DIVER_I-int LTR Pao 24742 +TIRANT_I-int LTR Gypsy 23165 +Gypsy2_LTR LTR Gypsy 869 +FB4_DM DNA TcMar-Tc1 7840 +GTWIN_LTR LTR Gypsy 2533 +Invader6_LTR LTR Gypsy 312 +Gypsy8_I-int LTR Gypsy 4176 +G_DM LINE Jockey 10948 +TRANSPAC_LTR LTR Gypsy 1457 +FUSHI_DM Unknown Unknown 0 +Transib5 DNA CMC-Transib 973 +MuDR-1_DEl DNA MULE-NOF 32 +Mariner2_DM DNA TcMar-Tc1 1096 +DOC5_DM LINE Jockey 1793 +TC1_DM DNA TcMar-Tc1 2618 +Gypsy9_LTR LTR Gypsy 62 +DMRP1 Unknown Unknown 295 +Gypsy10_I-int LTR Gypsy 2236 +Gypsy4_LTR LTR Gypsy 390 +DM297_LTR LTR Gypsy 6128 +ACCORD2_I-int LTR Gypsy 2286 +Invader1_LTR LTR Gypsy 2525 +BEL_LTR LTR Pao 927 +IVK_DM LINE I 3025 +M4DM DNA CMC-Transib 1880 +FW2_DM LINE Jockey 17723 +Copia2_I-int LTR Copia 3614 +MDG1_LTR LTR Gypsy 650 +Gypsy12_LTR LTR Gypsy 7572 +Gypsy7_I-int LTR Gypsy 1162 +FROGGER_I-int LTR Copia 1075 +Gypsy_I-int LTR Gypsy 24082 +5S_DM RNA RNA 6331 +GTWIN_I-int LTR Gypsy 7568 +CIRCE LTR Gypsy 3676 +DIVER2_LTR LTR Pao 648 +POGO DNA TcMar-Pogo 2909 +Gypsy6A_LTR LTR Gypsy 793 +MAX_I-int LTR Pao 8914 +ROOA_LTR LTR Pao 435 +DM176_I-int LTR Gypsy 4726 +Copia2_LTR_DM LTR Copia 747 +DM297_I-int LTR Gypsy 82387 +IDEFIX_I-int LTR Gypsy 7222 +Jockey2 LINE Jockey 1823 +TC1-2_DM DNA TcMar-Tc1 4438 +DMRPR Unknown Unknown 221
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Normalized_counts_file.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,211 @@ +Tag wildtype_1 wildtype_2 mutant_1 mutant_2 +LSU-rRNA_Dme 157455.221275418 149201.031867455 218650.181450173 354466.098949349 +FW3_DM 35.756634311884 44.2453336153694 25.3386538652006 32.2981814492716 +DMTOM1_LTR 43.2005545717588 49.0430203929395 54.9461072223747 39.3419337866127 +R1_DM 315.957840856997 262.031236427494 604.054709763298 517.028601444589 +TAHRE 196.209690086873 189.678242903128 149.055512536249 121.719476366005 +G4_DM 157.828320885669 165.108271224056 87.0600116574048 105.226787966377 +BS 313.935504138996 242.355874491196 203.649150075801 355.194096523239 +Stalker2_I-int 527.184456786045 604.508533973842 429.46472687139 413.519801853174 +Stalker3_LTR 25.5158653994552 21.2745908621546 21.2656708636846 20.1863634057947 +TABOR_I-int 169.833255871247 149.309827895896 215.554792695617 317.054754599099 +G7_DM 6.97060741098101 4.74922529496845 76.3292679803337 35.9059570366902 +BEL_I-int 1022.22666828812 1059.36800967358 1148.97283940843 1304.98396962057 +Gypsy6_I-int 322.239993215042 326.921161631196 445.717495579363 323.23951274896 +ACCORD_I-int 117.166444321613 104.919109832721 160.687012069425 174.461719477315 +DM412B_LTR 132.441540808639 141.022914371002 219.588612399041 257.784155662936 +G2_DM 57.1417693937208 54.8583983051458 48.3666731430026 65.6271559235199 +SSU-rRNA_Hsa 13684.9804569472 8340.22115575582 22075.2937251301 25925.561270609 +TART_B1 1086.38207353363 1042.55187521078 524.083255060455 437.142142008891 +S2_DM 32.9167572185214 35.52226674706 28.0409214335141 17.6093808433528 +LOOPER1_DM 35.3263499037988 28.5438132524124 8.61592558013002 2.66288198118994 +HOBO 216.476085707688 213.42436937797 171.339429150313 182.020868327145 +ARS406_DM 24.2250121751994 34.8438059906359 29.5682900590826 19.7568663120544 +G6_DM 207.698283782749 168.30672907577 112.555318714971 67.5169431359773 +DOC2_DM 190.960220308233 219.9182080466 176.665637690757 176.265607271025 +Baggins1 220.994071992583 188.660551768492 215.398139503251 157.367735146451 +NINJA_LTR 21.1269644369856 19.6753619362979 11.6314995331755 9.79253373727915 +TRANSIB2 137.561925264854 149.067520482887 131.471191693166 127.474737422125 +Gypsy5_LTR 28.0115149663496 21.8561286533752 19.6599756419331 28.0032105118684 +MDG3_LTR 44.6204931184401 41.0953372462576 36.2652140327291 38.9983361116205 +Gypsy12A_LTR 131.624000433277 108.650643993054 95.4017941508943 92.5136739916635 +Gypsy_LTR 56.1951436959333 44.4391795457762 147.684797103047 149.207290365385 +TIRANT_LTR 58.9919923484874 61.9822362475985 126.301636345088 137.095472321908 +I_DM 343.668156737687 339.860377485855 449.55549879233 957.692619622151 +DIVER2_I-int 287.386956160137 272.692762599872 252.44661949781 229.179649219831 +P-1_DY 0.344227526468198 0.0969229652034378 0.509122875189502 0.343597674992251 +Invader2_I-int 293.583051636564 267.022769135471 233.804889606256 271.184464987634 +DOC6_DM 54.1728069779326 60.0922384261314 67.2825461211972 65.9707535985121 +BURDOCK_LTR 12.3491625120466 17.930748562636 21.2656708636846 16.5785878183761 +SSU-rRNA_Dme 306.061299471036 201.260537244939 389.988122395158 328.307578455096 +MAX_LTR 43.7599243022696 36.4914963990943 37.5184395716571 29.4635006305855 +STALKER4_LTR 55.5927455246139 58.6383939480799 79.8931281066602 68.9772332546943 +XDMR_DM 142.725338161877 209.741296700239 158.572193972484 136.322377553175 +BARI_DM 42.5981564004395 43.7122573067505 43.7454039682056 44.8394965864887 +Transib-N1_DM 13.2527597690256 17.9792100452377 14.333767101489 11.1669244372481 +Gypsy5_I-int 105.333623099269 105.936800967358 110.988786791311 88.9917978229929 +XDMR 53.7425225698474 69.7845349464752 69.3582009200467 77.5671751295006 +ACCORD2_LTR 10.1116835900033 9.30460465953003 8.34178249348953 6.52835582485276 +POGON1 14.2424139076217 19.5299774884927 25.1036740766516 21.990251199504 +BS4_DM 1.46296698748984 1.0176911346361 0.313306384732001 1.97568663120544 +ALA_DM 0.215142204042624 0.290768895610313 0.352469682823501 0 +Gypsy1-I_DM 351.112076997562 305.161955943024 1447.55382405803 1954.46947477467 +ACCORD_LTR 12.6933900385148 10.6615261723782 30.9390054922851 29.5494000493336 +BURDOCK_I-int 134.205706881789 161.473660028927 203.257517094886 191.727502645676 +ZAM_I-int 220.692872906923 214.490521995208 270.070103638985 248.421119019397 +Invader5_I-int 17.8998313763463 16.2345966715758 7.48018993547652 10.0502319935233 +G3_DM 34.2936673243942 26.9445843265557 18.7983830839201 21.4748546870157 +ROOA_I-int 214.496777430496 222.389743659288 160.687012069425 221.534600951254 +Gypsy1-LTR_DM 44.8356353224828 38.5268786683665 56.0818428670282 49.4780651988841 +DM1731_I-int 222.887323388158 236.54049657899 737.405739764856 590.386705055435 +ROO_I-int 1368.00321862543 1358.56920325659 1332.45289096711 1970.61856549931 +DM412 1036.38302531413 1142.04329899211 1711.00533031955 2019.32353592946 +PROTOP 212.646554475729 210.952833765282 187.004748386913 176.866903202261 +TART-A 159.076145669116 165.156732706658 199.419513881919 156.766439215214 +ROO_LTR 70.523614485172 89.7022042957817 86.9033584650388 124.811855440935 +DIVER_LTR 20.1803387391981 20.7899760361374 21.4223240560506 28.1750093493646 +Gypsy3_I-int 146.253670308176 133.414461602532 225.81557679559 193.960887533126 +BATUMI_LTR 23.8377562079227 19.5299774884927 13.628827735842 14.5170017684226 +IDEFIX_LTR 94.2753138114777 89.3629739175697 99.3964505562273 86.9302117730394 +G5_DM 111.916974542973 123.625242116985 106.289191020331 111.669244372481 +HETA 990.729849616282 1182.31479103414 879.568511837001 887.083297411243 +Gypsy11_I-int 28.8720837825201 27.1384302569626 19.0725261705606 14.4311023496745 +R1-2_DM 11.4885936958761 8.57768242050425 7.20604684883602 5.84116047486826 +Gypsy11_LTR 5.76581106834231 7.22076090765612 6.22696439654852 4.12317209990701 +HELENA_RT 28.0975718479666 30.3853495912778 36.5785204174611 35.7341581991941 +FTZ_DM 0 0 0 0 +MICROPIA_I-int 436.695645765717 501.818652340799 271.832452053102 285.787366174805 +Invader4_I-int 61.9179263234671 59.0745472914953 73.9403067967522 101.361314122714 +PLACW_DM 6.41123768047018 6.1546082904183 10.8482335713455 17.5234814246048 +BLOOD_LTR 32.1852737247765 36.1522660208823 49.6982252781136 46.55748496145 +R2_DM 659.496912272258 407.415684232651 2116.46295546085 1299.48640682069 +Copia1-I_DM 154.386045620987 170.487495792847 160.56952217515 167.16026888373 +Gypsy4_I-int 521.20350351366 487.328669042885 513.587491171932 459.390091464639 +Chouto_LTR 12.8655038017489 13.617676611083 6.34445429082302 13.658007580942 +BATUMI_I-int 275.166878970516 232.082040179632 184.968256886155 158.226729333931 +DNAREP1_DM 2918.23188407496 3099.30565831033 3009.73862162988 3174.24122099716 +DMRT1B 417.634046487541 344.997294641637 352.587172717776 353.476108148278 +DMRT1C 108.861955245568 101.139114189787 74.6844094604907 57.552610561202 +TLD2 2.79684865255411 0.823845204229221 1.2923888370195 0.0858994187480627 +DMRT1A 191.734732242786 171.553648410085 148.703042853426 106.085782153857 +DM1731_LTR 24.8274103465188 21.3230523447563 49.8940417685711 27.5737134181281 +LSU-rRNA_Cel 22382.0179984887 15843.270199567 14243.5740259843 21618.3926157437 +Copia_LTR 60.5840446584028 54.7130138573406 102.294534614998 264.140712650293 +Gypsy6_LTR 18.4161726660486 23.455357579232 55.7293731842047 65.2835582485276 +Gypsy12_I-int 420.732094225755 466.538693006748 195.894817053684 211.827966632723 +BLASTOPIA_LTR 23.6656424446886 23.1645886836216 40.6515034189771 78.9415658294696 +Bica_LTR 6.02398171319346 6.05768532521486 4.81708566525451 5.7552610561202 +Gypsy8_LTR 56.4102858999759 60.1406999087332 57.4525583002307 41.7471175115585 +NINJA_I-int 226.931996824159 218.22205615554 143.964283784354 98.4407338852798 +PROTOP_B 373.91715062608 401.503383355241 366.999266415448 369.367500616669 +PROTOP_A 152.019481376518 163.993657124217 174.864125978548 170.768044471149 +Invader3_LTR 28.2696856112007 29.4645814218451 19.8166288342991 19.4991680558102 +Chimpo_LTR 4.04467343600132 5.81537791220627 4.19047289579051 2.83468081868607 +Invader2_LTR 21.1699928777942 22.8738197880113 16.3310953041555 18.2965761933373 +BLASTOPIA_I-int 443.580196295081 462.322544020398 539.670247700872 1034.65849882041 +FROGGER_LTR 1.76416607314951 2.61692006049282 3.32888033777751 4.89626686863957 +NOMAD_I-int 708.635391675594 561.862429284329 454.842544034682 700.423860471703 +QUASIMODO_LTR 57.3138831569549 56.893780574418 63.6403593986877 45.3548930989771 +TABOR_LTR 16.5229212704735 13.2299847502693 17.3493410545346 7.55914884982952 +Stalker2_LTR 31.238648026989 32.5661163083551 30.9390054922851 30.5801930743103 +MICROPIA_LTR 34.2936673243942 41.8222594852834 18.0151171220901 12.7990133934613 +Gypsy9_I-int 21.6863341674965 22.9707427532148 16.8010548812535 16.1490907246358 +STALKER4_I-int 267.077532098513 278.217371616468 285.382953192761 269.036979518932 +TRANSIB1 89.5852137633485 102.544497185237 48.1316933544536 24.8249320181901 +DOC 769.477606978848 795.446775424614 1138.94703509701 1864.01738683296 +TRANSIB3 50.9456739172933 54.8583983051458 70.5722631608832 63.6514692923144 +Copia_I-int 1188.10130760498 1295.52081439175 1992.94191328026 7492.14730320603 +TRANSIB4 27.3230599134132 27.6715065655815 14.255440505306 13.1426110684536 +Gypsy10_LTR 13.5109304138768 17.8338255974326 14.2162772072145 13.9157058371862 +Invader3_I-int 200.813733253385 180.373638243598 172.749307881607 173.688624708583 +Invader1_I-int 78.8281035612173 81.027598910074 117.21575118786 151.870172346575 +BS3_DM 53.871607892273 42.5007202417075 33.3279666758666 38.9124366928724 +Gypsy2-LTR_DM 41.5654738210349 33.438422995186 45.2336092956826 33.0712762180041 +LSU-rRNA_Hsa 0.215142204042624 0 0.587449471372502 0.944893606228689 +NOMAD_LTR 26.6346048604768 39.8353386986129 29.6466166552656 23.7941389932134 +Helitron1_DM 0.129085322425574 0.290768895610313 0 0 +LINEJ1_DM 302.274796679886 306.712723386279 974.813652795529 1369.15083542537 +Invader4_LTR 61.1003859481051 59.5107006349108 63.6011961005962 58.3257053299346 +MDG3_I-int 232.009352839565 240.902030013145 307.706033104916 323.840808680196 +LmeSINE1c 25.7740360443063 68.5245363988305 24.5553879033706 56.0923204424849 +ROVER-LTR_DM 24.2680406160079 20.1115152797133 16.2527687079725 14.4311023496745 +S_DM 155.418728200391 168.452113523575 194.798244707122 175.320713664796 +Invader6_I-int 298.230123243885 324.740394914118 257.14621526879 283.296283031111 +ROVER-I_DM 280.244234985922 270.851226261007 272.067431841651 263.625316137804 +QUASIMODO_I-int 641.38193869187 630.871580509177 701.414668818767 687.195349984501 +Chouto_I-int 72.7180649664068 63.1937733126415 48.2100199506366 44.4958989114965 +NTS_DM 2837.89778508544 1754.54797759523 2194.82871494194 1868.57005602661 +Gypsy3_LTR 24.354097497625 21.6622827229683 26.6702060003116 18.2106767745893 +SSU-rRNA_Cel 149.007490519921 105.791416519552 150.974514142733 156.07924386523 +MINOS 7.44392025987478 10.9522950679885 10.6915803789795 7.98864594356983 +DOC4_DM 34.9821223773306 40.2230305594267 40.3381970342451 56.5218175362252 +ZAM_LTR 11.1443661694079 10.9038335853868 14.7645633804955 10.1361314122714 +QUASIMODO2-LTR_DM 13.4679019730682 9.69229652034378 11.670662831267 9.01943896854658 +Gypsy2-I_DM 198.188998364065 188.805936216297 288.790160126722 228.320655032351 +TRANSPAC_I-int 416.257136381668 726.049932338953 1115.13574985737 1439.67425821753 +Bica_I-int 79.6886723773878 67.3614608163893 61.1339083208317 53.0858407863027 +BS2 240.744126323696 241.871259665179 204.197436249082 179.186187508459 +BLOOD_I-int 960.825083254357 834.603653366803 1071.58616237963 1140.74428097427 +DMCR1A 876.919623677734 870.222843079066 684.926920322246 693.380108134362 +QUASIMODO2-I_DM 116.908273676762 107.826798788825 155.752436509896 155.563847352742 +HMSBEAGLE_I-int 311.48288301291 286.310439210955 307.941012893465 350.383729073348 +DMLTR5 6.92757897017248 7.75383721627503 7.40186333929352 8.07454536231789 +Gypsy7_LTR 4.81918537055477 4.21614898634954 3.13306384732001 3.35007733117444 +G5A_DM 77.6233072185786 77.2960647497417 61.7996843883872 49.9934617113725 +MDG1_I-int 702.009011791081 665.860770947618 638.596738680001 690.889024990668 +Gypsy2_I-int 137.260726179194 167.337499423735 165.50409773468 133.315897896993 +BARI1 16.9962341193673 15.6045973977535 14.490420293855 10.7374273435078 +Invader5_LTR 2.96896241578821 3.10153488651001 1.84067501030051 1.97568663120544 +DM176_LTR 38.6825682868637 42.2584128286989 21.9314469312401 28.3468081868607 +DOC3_DM 513.802611694594 516.550943051722 433.420219978632 447.106474583666 +Copia1-LTR_DM 33.1749278633726 27.4291991525729 23.4979788549001 33.4148738929964 +TOM_I-int 110.281893792249 111.994486292572 271.362492476004 291.199029555932 +NOF_FB 54.7321767084434 46.5230232976501 8.92923196486203 5.41166338112795 +Chimpo_I-int 55.4206317613798 51.369171557822 53.4970651929892 31.7827849367832 +DIVER_I-int 567.028792974739 757.307588617061 968.978321379896 1009.40406970848 +TIRANT_I-int 469.741488306664 414.781829588112 907.2178002896 1093.32780182534 +Gypsy2_LTR 20.6106231472833 23.5038190618337 34.0329060415136 21.4748546870157 +FB4_DM 307.610323340143 336.274227773327 307.040257037361 287.591253968514 +GTWIN_LTR 25.7310076034978 22.6315123750027 99.2006340657698 80.5736547856828 +Invader6_LTR 27.9254580847325 28.4953517698107 12.218949004548 12.5413151372172 +Gypsy8_I-int 206.923771848195 197.868233462818 163.545932830104 107.116575178834 +G_DM 383.168265399913 389.388012704811 428.759787505743 393.591136703623 +TRANSPAC_LTR 23.1493011549863 26.896122843954 57.0609253193157 84.0955309543534 +FUSHI_DM 0 0 0 0 +Transib5 48.3209390279733 46.7653307106587 38.1058890430296 28.1750093493646 +MuDR-1_DEl 0.258170644851148 0.43615334341547 1.253225538928 0.343597674992251 +Mariner2_DM 86.5301944659432 77.1022188193348 42.9229747082841 79.542861760706 +DOC5_DM 130.67737473549 105.791416519552 70.2197934780597 64.5963628985431 +TC1_DM 79.1723310876855 94.9845058993691 102.529514403547 127.560636840873 +Gypsy9_LTR 2.19445048123476 2.03538226927219 2.42812448167301 0.687195349984501 +DMRP1 11.2734514918335 11.0007565505902 11.5531729369925 12.369516299721 +Gypsy10_I-int 97.1582193456488 93.5306614213175 87.5691345325943 79.6287611794541 +Gypsy4_LTR 11.7897927815358 9.40152762473347 15.273686255685 18.7260732870777 +DM297_LTR 64.0693483638933 71.6260712853405 239.992690704713 216.122937570126 +ACCORD2_I-int 126.245445332212 119.118324235025 89.5272994371693 103.079302497675 +Invader1_LTR 143.973162945324 93.5791229039192 98.8873276810378 163.466593877563 +BEL_LTR 37.6498857074591 41.5799520722748 36.3043773308206 51.9691483425779 +IVK_DM 144.102248267749 141.555990679621 118.468976726788 151.956071765323 +M4DM 74.3101172763222 79.9614462928362 73.6270004120202 78.8556664107215 +FW2_DM 612.466826468541 671.046149586002 694.091132075657 761.412447782827 +Copia2_I-int 181.493963330357 167.434422388939 141.536159302681 162.521700271335 +MDG1_LTR 29.6896241578821 28.2045828742004 25.4561437594751 24.1377366682056 +Gypsy12_LTR 270.734949567238 287.5704377586 296.544493148839 230.210442244808 +Gypsy7_I-int 54.0437216555071 48.8976359451344 45.5077523823231 63.7373687110625 +FROGGER_I-int 69.3188181425333 65.9560778209394 42.1005454483626 46.9010826364422 +Gypsy_I-int 293.540023195756 273.031992978084 943.130544639506 958.723412647127 +5S_DM 271.810660587451 503.611727197063 247.942840217287 356.138990129468 +GTWIN_I-int 234.418945524843 244.924333069087 296.387839956473 251.685296931824 +CIRCE 162.088136525713 161.037506685512 143.964283784354 134.862087434458 +DIVER2_LTR 34.1215535611601 25.9268931919196 25.3778171632921 20.615860499535 +POGO 104.43002584229 120.766014643484 113.926034148174 88.6482001480007 +Gypsy6A_LTR 26.5485479788598 27.7684295307849 31.0564953865596 18.8119727058257 +MAX_I-int 533.337523821664 445.894101418416 349.101639187632 335.437230211185 +ROOA_LTR 17.2113763234099 23.4068960966302 17.0360346698026 23.7082395744653 +DM176_I-int 156.064154812519 136.322150558635 185.08574678043 197.396864283048 +Copia2_LTR_DM 38.3383407603955 23.5522805444354 29.2549836743506 39.5137326241088 +DM297_I-int 509.327653850507 558.760894397819 3226.54663986442 3668.33467763602 +IDEFIX_I-int 266.475133927194 268.815843991735 282.837338816814 282.265490006134 +Jockey2 76.1603402310888 76.9568343715296 71.3946924208047 65.2835582485276 +TC1-2_DM 163.809274158054 191.325933311586 173.806716930078 196.451970676819 +DMRPR 5.50764042349117 9.06229724652144 8.65508887822152 11.6823209497365
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligned_353.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,1 @@ +15862067
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligned_354.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,1 @@ +28421096
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligned_355.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,1 @@ +10808170
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligned_356.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,1 @@ +29256707
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligned_reads.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,1 @@ +2500
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edgeR_result_file.tab Mon May 29 13:11:57 2017 -0400 @@ -0,0 +1,210 @@ +DM297_I-int 2.69047105438237 4.49448726299278e-21 LTR Gypsy +DM297_LTR 1.74961921158059 1.33970311551615e-18 LTR Gypsy +Gypsy1-I_DM 2.37388633230267 4.48026988289666e-16 LTR Gypsy +NOF_FB -2.79644759297337 4.48026988289666e-16 DNA MULE-NOF +G7_DM 3.25987374806405 1.55296802933851e-15 LINE Jockey +Gypsy_I-int 1.74702179622354 4.35250852544863e-12 LTR Gypsy +LINEJ1_DM 1.94429217926762 5.18070558191679e-12 LINE Jockey +TOM_I-int 1.33935222283437 6.69227956217608e-12 LTR Gypsy +GTWIN_LTR 1.89490932455113 8.80590960311443e-12 LTR Gypsy +Gypsy_LTR 1.56024435809038 2.99852403113839e-11 LTR Gypsy +DM1731_I-int 1.53134429520835 6.4920552091728e-10 LTR Copia +Gypsy6_LTR 1.53023046204423 1.07509345482697e-06 LTR Gypsy +LOOPER1_DM -2.46983670012103 1.61917280285007e-06 DNA PiggyBac +TIRANT_LTR 1.12203469288475 1.7801266502904e-06 LTR Gypsy +Gypsy12_I-int -1.12204057066646 2.19485691074398e-06 LTR Gypsy +R2_DM 1.67889583354494 2.73035057005978e-06 LINE R2 +TRANSPAC_LTR 1.49364968145495 2.90210475425899e-06 LTR Gypsy +Copia_LTR 1.66649088148806 1.186041112787e-05 LTR Copia +ACCORD_LTR 1.3724059468295 1.75953804703817e-05 LTR Gypsy +TIRANT_I-int 1.17728139313168 2.04686461971632e-05 LTR Gypsy +TART_B1 -1.14695345949677 3.0965848472869e-05 LINE Jockey +TRANSIB1 -1.3902119423097 6.16503339250287e-05 DNA CMC-Transib +DM412B_LTR 0.803090050933452 0.00012443453312394 LTR Gypsy +MICROPIA_LTR -1.29556276189806 0.000129852108160169 LTR Gypsy +G6_DM -1.05894868960943 0.000138305097075555 LINE Jockey +NINJA_I-int -0.874264518473233 0.000155536374045889 LTR Pao +R1_DM 0.955905154410719 0.000189845334696753 LINE R1 +Invader6_LTR -1.18865109431199 0.000212988712815497 LTR Gypsy +Copia_I-int 1.9331690527025 0.000223130721644621 LTR Copia +BLASTOPIA_LTR 1.34881958569428 0.000364879309201074 LTR Gypsy +LSU-rRNA_Hsa 2.61189118344978 0.000801598301190925 rRNA rRNA +TRANSPAC_I-int 1.16122217809542 0.000845313292127692 LTR Gypsy +G4_DM -0.74970144243323 0.000914365923267139 LINE Jockey +SSU-rRNA_Hsa 1.12389968473263 0.0010425909765405 rRNA rRNA +DOC5_DM -0.809872869194368 0.00162410751644232 LINE Jockey +Invader1_I-int 0.749727833008358 0.00198920329215514 LTR Gypsy +TRANSIB4 -1.00230688125284 0.00206051807311839 DNA CMC-Transib +MICROPIA_I-int -0.751193028928835 0.00292932704926266 LTR Gypsy +PLACW_DM 1.16310826488548 0.00305178248567248 DNA P +TABOR_I-int 0.737702190628259 0.00354953953974351 LTR Gypsy +I_DM 1.04141382256571 0.00457151681951996 LINE I +Gypsy3_I-int 0.586594796021762 0.00533147146680049 LTR Gypsy +DOC 0.94015335715084 0.00552118010545893 LINE Jockey +Helitron1_DM -5.10401049101919 0.00636579556275411 RC Helitron +Invader5_I-int -0.973422642391873 0.00666026639838213 LTR Gypsy +ACCORD_I-int 0.593047691019391 0.00701363615971111 LTR Gypsy +LSU-rRNA_Dme 0.902204791675651 0.0102101724391352 rRNA rRNA +DM412 0.775970807845826 0.0108079710929838 LTR Gypsy +NINJA_LTR -0.923408172476265 0.0109563169817133 LTR Pao +BATUMI_I-int -0.562867612987509 0.0148551719821076 LTR Pao +DMRT1C -0.664744166716986 0.0174563775735501 LINE R1 +TAHRE -0.509503033739914 0.0198535740576257 LINE Jockey +Gypsy8_I-int -0.578276897527121 0.0248976847994196 LTR Gypsy +BLASTOPIA_I-int 0.796987753936179 0.0301824235833281 LTR Gypsy +Gypsy11_I-int -0.734634622561586 0.0432538714324547 LTR Gypsy +DMRT1A -0.509608409844153 0.0432538714324547 LINE R1 +DM176_LTR -0.691384671506076 0.0432538714324547 LTR Gypsy +QUASIMODO2-I_DM 0.470057940126177 0.044414105251961 LTR Gypsy +MuDR-1_DEl 1.35524442785064 0.053231954651916 DNA MULE-NOF +DM1731_LTR 0.752238181600754 0.0540130070646255 LTR Copia +FROGGER_I-int -0.60531971025629 0.0540130070646255 LTR Copia +MAX_I-int -0.516456091983578 0.064340206781843 LTR Pao +BURDOCK_I-int 0.418223330277469 0.0691214301126655 LTR Gypsy +FROGGER_LTR 0.888326398013863 0.0706362756551064 LTR Copia +DIVER_I-int 0.579052226156673 0.0738156276915433 LTR Pao +Chouto_I-int -0.551029990754245 0.0815115938596914 LTR Gypsy +DM176_I-int 0.387008766766431 0.0918637211505558 LTR Gypsy +Invader4_I-int 0.532747054501905 0.0948962153499253 LTR Gypsy +G3_DM -0.607648157164968 0.103160664266056 LINE Jockey +Gypsy4_LTR 0.67676362702008 0.105307005535582 LTR Gypsy +BATUMI_LTR -0.625598883331715 0.112325719453317 LTR Pao +Gypsy2-I_DM 0.418860685191156 0.127538985839663 LTR Gypsy +Invader3_LTR -0.553726127316243 0.130228544874336 LTR Gypsy +SSU-rRNA_Dme 0.50182621141568 0.130837858091619 rRNA rRNA +MDG3_I-int 0.417195433411295 0.130837858091619 LTR Gypsy +G5A_DM -0.468375220785066 0.142388172856161 LINE Jockey +S2_DM -0.576444154651049 0.154380925206595 DNA TcMar-Tc1 +Stalker2_I-int -0.424817076156048 0.157921464286182 LTR Gypsy +R1-2_DM -0.611853226580459 0.158635278613665 LINE R1 +BLOOD_LTR 0.494999752604753 0.158635278613665 LTR Gypsy +Invader5_LTR -0.675984091871337 0.158635278613665 LTR Gypsy +Transib5 -0.51646991193603 0.158635278613665 DNA CMC-Transib +TLD2 -1.24823548505769 0.158665416598185 LTR Gypsy +TC1_DM 0.400572910860442 0.167626897114744 DNA TcMar-Tc1 +BS2 -0.331386491833491 0.185478101135177 LINE Jockey +ROVER-LTR_DM -0.529681787599071 0.188737381603441 LTR Gypsy +ACCORD2_I-int -0.350572607465432 0.191790844708865 LTR Gypsy +Gypsy12A_LTR -0.354465506898828 0.204428444984683 LTR Gypsy +FW3_DM -0.476342557702003 0.216920256528965 LINE Jockey +ROO_LTR 0.400232536676205 0.244465267215694 LTR Pao +STALKER4_LTR 0.383349427659289 0.248258091824802 LTR Gypsy +POGON1 0.482507112501569 0.255779427421414 DNA TcMar-Pogo +HOBO -0.283220815078204 0.273166685685483 DNA hAT-hobo +BS3_DM -0.418041606433149 0.277910060681488 LINE Jockey +P-1_DY 0.969417874734635 0.280951304168472 DNA P +Gypsy9_I-int -0.437336296478435 0.280951304168472 LTR Gypsy +Bica_I-int -0.363151852276852 0.287621291763233 LTR Gypsy +DMCR1A -0.342108879038489 0.320538100201857 LINE CR1 +Mariner2_DM -0.422114252836712 0.320538100201857 DNA TcMar-Tc1 +TRANSIB3 0.344232145502121 0.322658401361327 DNA CMC-Transib +Gypsy7_LTR -0.484940393339899 0.322658401361327 LTR Gypsy +DMRPR 0.474671090698546 0.369600785239272 Unknown Unknown +DIVER2_LTR -0.381362071713278 0.384462351162869 LTR Pao +Gypsy1-LTR_DM 0.341547880045558 0.384860099197011 LTR Gypsy +SSU-rRNA_Cel 0.268693361351043 0.389414554540408 rRNA rRNA +DOC4_DM 0.362114244909638 0.389414554540408 LINE Jockey +ZAM_I-int 0.25296287202699 0.397202788288859 LTR Gypsy +XDMR_DM -0.256211211677393 0.40891453273183 Unknown Unknown +Chimpo_LTR -0.460515218470088 0.409319591327129 LTR Gypsy +DOC2_DM -0.219218822289782 0.412039231991164 LINE Jockey +PROTOP -0.21894181311432 0.412039231991164 DNA P +HETA -0.298692871636692 0.412039231991164 LINE Jockey +HELENA_RT 0.306716860759321 0.412039231991164 LINE Jockey +Invader2_LTR -0.349451178427879 0.412039231991164 LTR Gypsy +BLOOD_I-int 0.301193505006723 0.412039231991164 LTR Gypsy +5S_DM -0.36064468671157 0.412039231991164 RNA RNA +CIRCE -0.21220098912431 0.412039231991164 LTR Gypsy +ACCORD2_LTR -0.373877436518785 0.415323684742582 LTR Gypsy +BARI1 -0.361825471165769 0.439062969216072 DNA TcMar-Tc1 +Copia2_I-int -0.199651272204726 0.454016393979065 LTR Copia +Chouto_LTR -0.42256718750228 0.457631460799645 LTR Gypsy +S_DM 0.193275098711318 0.466588891241469 DNA TcMar-Tc1 +Gypsy6_I-int 0.244887845096584 0.469668398060558 LTR Gypsy +NOMAD_LTR -0.310707505731374 0.469668398060558 LTR Gypsy +Chimpo_I-int -0.3198026895528 0.469668398060558 LTR Gypsy +Gypsy2_LTR 0.337405927915915 0.469668398060558 LTR Gypsy +DIVER2_I-int -0.217400353167491 0.48214327316296 LTR Pao +DOC3_DM -0.226748306440889 0.495640056966085 LINE Jockey +XDMR 0.249633734746355 0.503551868695272 Unknown Unknown +ROO_I-int 0.276608752749181 0.505091620203207 LTR Pao +BURDOCK_LTR 0.32676718204459 0.510777537217992 LTR Gypsy +BEL_I-int 0.237362494177496 0.533794803142518 LTR Pao +ROOA_I-int -0.194233478923581 0.533794803142518 LTR Pao +Invader6_I-int -0.205266937253198 0.533794803142518 LTR Gypsy +DOC6_DM 0.222079405295424 0.536617484807693 LINE Jockey +DIVER_LTR 0.271030983517942 0.536617484807693 LTR Pao +GTWIN_I-int 0.193808394449743 0.536617484807693 LTR Gypsy +MAX_LTR -0.257749452683052 0.540151898310394 LTR Pao +Transib-N1_DM -0.285359544492984 0.568470618173646 DNA CMC-Transib +Gypsy11_LTR -0.304519901682671 0.568470618173646 LTR Gypsy +Gypsy10_I-int -0.188834668589015 0.568470618173646 LTR Gypsy +Gypsy8_LTR -0.22930840819102 0.572155988619216 LTR Gypsy +MDG1_LTR -0.222278232633914 0.598330807400729 LTR Gypsy +ARS406_DM -0.253969785738388 0.616310720407917 Unknown Unknown +TRANSIB2 -0.146222438911029 0.625405183746989 DNA CMC-Transib +Invader3_I-int -0.138005789457227 0.630870214463397 LTR Gypsy +FW2_DM 0.18134923098773 0.631976090646791 LINE Jockey +Gypsy9_LTR -0.341386719736692 0.637388403082853 LTR Gypsy +TART-A 0.137000662462686 0.641582941743804 LINE Jockey +PROTOP_A 0.129470019526978 0.641582941743804 DNA P +MDG3_LTR -0.188668582948884 0.653366733777971 LTR Gypsy +Invader2_I-int -0.151224307192946 0.653366733777971 LTR Gypsy +Jockey2 -0.162959614427421 0.654568430062825 LINE Jockey +POGO -0.150727724968995 0.655487951512125 DNA TcMar-Pogo +Baggins1 -0.134826103211095 0.693165877069107 LINE LOA +Stalker3_LTR -0.174018068430168 0.707635948527927 LTR Gypsy +Bica_LTR -0.203027970314789 0.707635948527927 LTR Gypsy +HMSBEAGLE_I-int 0.13884460350775 0.707635948527927 LTR Gypsy +TABOR_LTR -0.243243320673685 0.7126900116144 LTR Gypsy +NTS_DM -0.176552072990723 0.7126900116144 Other Other +ZAM_LTR 0.185889162361338 0.717882303973929 LTR Gypsy +G5_DM -0.112256553949312 0.728328879400811 LINE Jockey +QUASIMODO_I-int 0.126271255526405 0.756425760963745 LTR Gypsy +FB4_DM -0.114616335459739 0.756425760963745 DNA TcMar-Tc1 +Invader1_LTR 0.141219962488351 0.756425760963745 LTR Gypsy +BEL_LTR 0.152542861711851 0.756425760963745 LTR Pao +DMRT1B -0.111235216287692 0.760051744799183 LINE R1 +NOMAD_I-int -0.137546703453753 0.760051744799183 LTR Gypsy +LmeSINE1c -0.228543531933743 0.76029602974523 SINE tRNA-Deu-L2 +Gypsy10_LTR -0.154651074858764 0.762401782894161 LTR Gypsy +QUASIMODO2-LTR_DM -0.155430480903998 0.762401782894161 LTR Gypsy +Copia2_LTR_DM 0.147979193864449 0.762401782894161 LTR Copia +BS4_DM -0.253251631796478 0.81092436860891 LINE Jockey +G_DM 0.0902785903431559 0.81092436860891 LINE Jockey +IVK_DM -0.0807211765160779 0.81870908545043 LINE I +Gypsy5_I-int -0.0774807293903186 0.835273508730751 LTR Gypsy +Gypsy12_LTR -0.0832045482918072 0.835273508730751 LTR Gypsy +Gypsy6A_LTR -0.116239966704279 0.835273508730751 LTR Gypsy +IDEFIX_I-int 0.0781972363147815 0.835273508730751 LTR Gypsy +PROTOP_B -0.0745501769371703 0.846311908195535 DNA P +DMRP1 0.100504519100353 0.846311908195535 Unknown Unknown +Copia1-LTR_DM -0.0961752276665428 0.850550157756422 LTR Copia +TC1-2_DM 0.0595720035046981 0.853067020850901 DNA TcMar-Tc1 +LSU-rRNA_Cel -0.0920825033469626 0.861339242540399 rRNA rRNA +Gypsy7_I-int 0.0826410967604942 0.861339242540399 LTR Gypsy +Gypsy5_LTR -0.0710979993807782 0.905487490634908 LTR Gypsy +Gypsy4_I-int -0.0516274039610208 0.905487490634908 LTR Gypsy +QUASIMODO_LTR -0.0643467685962964 0.905487490634908 LTR Gypsy +Gypsy2-LTR_DM 0.0652192786223383 0.905487490634908 LTR Gypsy +DMLTR5 0.0726894766496021 0.905487490634908 LTR Gypsy +Stalker2_LTR -0.0523210063310555 0.917308330496028 LTR Gypsy +ROVER-I_DM -0.0408110836395496 0.922716163337709 LTR Gypsy +MDG1_I-int -0.0411424164719924 0.937452811422426 LTR Gypsy +ALA_DM -0.11425480149938 0.942917068804402 Unknown Unknown +DNAREP1_DM 0.039354033592028 0.942917068804402 RC Helitron +BARI_DM 0.0372716083617889 0.94985097135805 DNA TcMar-Tc1 +Gypsy2_I-int -0.0261599267227275 0.95196577198178 LTR Gypsy +DMTOM1_LTR 0.0349640382618226 0.953829042791583 LTR Gypsy +IDEFIX_LTR 0.0219961145617681 0.957715681080671 LTR Gypsy +STALKER4_I-int 0.0241275307638275 0.957715681080671 LTR Gypsy +Gypsy3_LTR -0.0298883238815861 0.957715681080671 LTR Gypsy +MINOS 0.0330479824589295 0.957715681080671 DNA TcMar-Tc1 +G2_DM 0.0226097987515835 0.962242582650612 LINE Jockey +Copia1-I_DM 0.0124236833262227 0.963045943681216 LTR Copia +Invader4_LTR 0.016495431966038 0.963045943681216 LTR Gypsy +M4DM -0.0173659751457427 0.963045943681216 DNA CMC-Transib +BS 0.00565217021634194 0.997858051773989 LINE Jockey +FTZ_DM 0 1 Unknown Unknown +FUSHI_DM 0 1 Unknown Unknown +ROOA_LTR -0.0005425128837839 1 LTR Pao