# HG changeset patch # User drosofff # Date 1496077917 14400 # Node ID 54a3f3a195d6ee57724dafeb4c25ada6bf48946c # Parent 1435d142041bb6f8519793375f94d7a96cb745ff planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 114b47cc624e39b4f485c8623458fc98494c564d diff -r 1435d142041b -r 54a3f3a195d6 edgeR_repenrich.R --- /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() + diff -r 1435d142041b -r 54a3f3a195d6 edger-repenrich.xml --- /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 @@ + + Determines differentially expressed features from RepEnrich counts + + bioconductor-edger + bioconductor-limma + r-getopt + r-rjson + + + + + + + + /dev/null | grep -v -i "WARNING: ") + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + normCounts == True + + + + + + + + + + + + + + + + + + + + + +**Note**: This edgeR_ wrapper was adapted from code available at https://github.com/nskvir/RepEnrich + + + + 10.1093/bioinformatics/btp616 + + diff -r 1435d142041b -r 54a3f3a195d6 repenrich.xml --- 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 @@ - + Repeat Element Profiling bowtie @@ -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 @@ + + @@ -51,6 +56,7 @@ + diff -r 1435d142041b -r 54a3f3a195d6 test-data/353_fraction_counts.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/354_fraction_counts.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/355_fraction_counts.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/356_fraction_counts.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/Normalized_counts_file.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/aligned_353.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/aligned_354.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/aligned_355.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/aligned_356.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/aligned_reads.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/edgeR_plots.pdf Binary file test-data/edgeR_plots.pdf has changed diff -r 1435d142041b -r 54a3f3a195d6 test-data/edgeR_result_file.tab --- /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 diff -r 1435d142041b -r 54a3f3a195d6 test-data/tool_wrapper.sh --- 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}