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(-) [+]
line wrap: on
line diff
--- /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
Binary file test-data/edgeR_plots.pdf has changed
--- /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
--- a/test-data/tool_wrapper.sh	Tue May 23 18:37:22 2017 -0400
+++ b/test-data/tool_wrapper.sh	Mon May 29 13:11:57 2017 -0400
@@ -1,5 +1,5 @@
-input_base=$1
-baseReference=$2
+input_base=Samp
+baseReference=chrM
 
 bowtie-build ${baseReference}.fa ${baseReference}