Mercurial > repos > iuc > ruvseq
changeset 0:61dffb20b6f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_deseq_dataset.R Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,69 @@ +get_deseq_dataset <- function(sampleTable, header, designFormula, tximport, txtype, tx2gene) { + + dir <- "" + + if (!is.null(header)) { + hasHeader <- TRUE + } else { + hasHeader <- FALSE + } + + if (!is.null(tximport)) { + if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF file is required for tximport") + if (tolower(file_ext(opt$tx2gene)) == "gtf") { + gtfFile <-tx2gene + } else { + gtfFile <- NULL + tx2gene <- read.table(tx2gene, header=FALSE) + } + useTXI <- TRUE + } else { + useTXI <- FALSE + } + + if (!useTXI & hasHeader) { + countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)}) + tbl <- do.call("cbind", countfiles) + colnames(tbl) <- rownames(sampleTable) # take sample ids from header + + # check for htseq report lines (from DESeqDataSetFromHTSeqCount function) + oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual", + "not_aligned", "alignment_not_unique") + specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames + tbl <- tbl[!specialRows, , drop = FALSE] + + dds <- DESeqDataSetFromMatrix(countData = tbl, + colData = subset(sampleTable, select=-(filename)), + design = designFormula) + } else if (!useTXI & !hasHeader) { + + # construct the object from HTSeq files + dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, + directory = dir, + design = designFormula) + colnames(dds) <- row.names(sampleTable) + + } else { + # construct the object using tximport + # first need to make the tx2gene table + # this takes ~2-3 minutes using Bioconductor functions + if (!is.null(gtfFile)) { + suppressPackageStartupMessages({ + library("GenomicFeatures") + }) + txdb <- makeTxDbFromGFF(gtfFile, format="gtf") + k <- keys(txdb, keytype = "GENEID") + df <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME") + tx2gene <- df[, 2:1] # tx ID, then gene ID + } + library("tximport") + txiFiles <- as.character(sampleTable$filename) + labs <- row.names(sampleTable) + names(txiFiles) <- labs + txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene) + dds <- DESeqDataSetFromTximport(txi, + subset(sampleTable, select=-c(filename)), + designFormula) + } + return(dds) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ruvseq.R Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,198 @@ +# setup R error handling to go to stderr +library("getopt") +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(stringAsFactors = FALSE, useFancyQuotes = FALSE) + +setup_cmdline_options <- function() { + args <- commandArgs(trailingOnly = TRUE) + spec <- matrix(c( + "help", "h", 0, "logical", + "alpha", "a", 1, "double", + "min_mean_count", "min_c", 1, "double", + "min_k", "min_k", 1, "double", + "max_k", "max_k", 1, "double", + "sample_json", "s", 1, "character", + "plots" , "p", 1, "character", + "header", "H", 0, "logical", + "txtype", "y", 1, "character", + "tx2gene", "x", 1, "character"), # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF) + byrow=TRUE, ncol=4) + + opt <- getopt(spec) + # if help was asked for print a friendly message + # and exit with a non-zero error code + if (!is.null(opt$help)) { + cat(getopt(spec, usage=TRUE)) + q(status=1) + } else { + load_libraries() + } + return(opt) +} + +load_libraries <- function() { + # Allows displaying help without waiting for libraries to load + library("tools") + library("jsonlite") + library("reshape2") + library("RUVSeq") + library("RColorBrewer") + library("tximport") + library("DESeq2") + library("ggrepel") +} + +source_local <- function(fname){ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +# Source get_deseq_dataset.R for getting deseq dataset from htseq/featurecounts/tximport +source_local('get_deseq_dataset.R') + +# RUVseq function definitions + +plot_pca_rle <- function (set, title) { + x <- pData(set)[,1] + colors <- brewer.pal(3, "Set2") + label <- paste0(' for ', title) + plotRLE(set, outline=FALSE, ylim=c(-4, 4), col=colors[x]) + title(main=paste0("RLE", label)) + plotPCA(set, col=colors[x], cex=1.2) + title(main=paste0("PCA", label)) +} + +plot_factors_of_unwanted_variation <- function(set, method, k){ + pd <- pData(set) + pd['sample'] <- row.names(pd) + colnames(pd)[1] <- 'condition' + d = melt(pd, id.vars = c('sample', 'condition')) + d['x'] <- 1 # There is no information on the X, so we just fake it to be able to do a scatterplot + print(ggplot(d, aes(x=x, y=value, color=condition, label=sample)) + + geom_point() + + ggtitle(paste0('Factors of unwanted variation for method: ', method, ", k=", k)) + + facet_wrap( ~ variable, scales = "free_x") + + geom_text_repel() + + theme(axis.title.x=element_blank(), + axis.text.x=element_blank(), + axis.ticks.x=element_blank(), + plot.title = element_text(hjust = 0.5)) + ) +} + +create_seq_expression_set <- function (dds, min_mean_count) { + count_values <- counts(dds) + filter <- apply(count_values, 1, function(x) mean(x) > min_mean_count) + filtered <- count_values[filter,] + set = newSeqExpressionSet(as.matrix(count_values), + phenoData = data.frame(colData(dds)$condition, row.names=colnames(filtered))) + plot_pca_rle(set = set, title = 'raw data') + set <- betweenLaneNormalization(set, which="upper") + plot_pca_rle(set = set, title = 'upper quartile normalized') + return(set) +} + +get_empirical_control_genes <- function(set, cutoff_p) { + x <- pData(set)[,1] + design <- model.matrix(~x, data=pData(set)) + y <- DGEList(counts=counts(set), group=x) + y <- calcNormFactors(y, method="upperquartile") + y <- estimateGLMCommonDisp(y, design) + y <- estimateGLMTagwiseDisp(y, design) + fit <- glmFit(y, design) + lrt <- glmLRT(fit, coef=2) + top <- topTags(lrt, n=nrow(set))$table + top_rows <- rownames(top)[which(top$PValue > cutoff_p)] + empirical <- rownames(set)[which(!(rownames(set) %in% top_rows))] + return(empirical) +} + +ruv_control_gene_method <- function(set, k, control_genes='empirical', cutoff_p=0.2) { + if (control_genes == 'empirical') { + control_genes = get_empirical_control_genes(set, cutoff_p=cutoff_p) + } + set <- RUVg(set, control_genes, k=k) + plot_pca_rle(set, paste0("RUVg with empirical control genes, k=", k)) + plot_factors_of_unwanted_variation(set, method="RUVg with empirical control genes", k=k) + return(set) +} + +ruv_residual_method <- function(set, k) { + genes <- rownames(counts(set)) + x <- pData(set)[,1] + # Initial edger residuals + design <- model.matrix(~x, data=pData(set)) + y <- DGEList(counts=counts(set), group=x) + y <- calcNormFactors(y, method="upperquartile") + y <- estimateGLMCommonDisp(y, design) + y <- estimateGLMTagwiseDisp(y, design) + fit <- glmFit(y, design) + res <- residuals(fit, type="deviance") + set <- RUVr(set, genes, k=k, res) + plot_pca_rle(set = set, title = paste0('RUVr using residuals, k=', k)) + plot_factors_of_unwanted_variation(set, method="RUVr using residuals", k=k) + return(set) +} + +ruv_replicate_method <- function (set, k) { + genes <- rownames(counts(set)) + x <- pData(set)[,1] + differences <- makeGroups(x) + set <- RUVs(set, genes, k=k, differences) + plot_pca_rle(set, paste0('RUVs with replicate samples, k=', k)) + plot_factors_of_unwanted_variation(set, method="RUVs using replicates", k=k) + return(set) +} + +get_differentially_expressed_genes <- function(dds, contrast, alpha=0.01) { + r <- results(dds, contrast=contrast, alpha=alpha) + return(rownames(r[which(r$padj < alpha),])) +} + +opt <- setup_cmdline_options() +alpha <- opt$alpha +min_k <- opt$min_k +max_k <- opt$max_k +sample_json <- fromJSON(opt$sample_json) +sample_paths <- sample_json$path +sample_names <- sample_json$label +condition <- as.factor(sample_json$condition) +sampleTable <- data.frame(samplename=sample_names, + filename = sample_paths, + condition=condition) +rownames(sampleTable) <- sample_names + +dds <- get_deseq_dataset(sampleTable, header=opt$header, designFormula= ~ condition, tximport=opt$txtype, txtype=opt$txtype, tx2gene=opt$tx2gene) +if (!is.null(opt$plots)) { + pdf(opt$plots) +} + +# Run through the ruvseq variants +set <- create_seq_expression_set(dds, min_mean_count = opt$min_mean_count) +result <- list(no_correction = set) +for (k in seq(min_k, max_k)) { + result[[paste0('residual_method_k', k)]] <- ruv_residual_method(set, k=k) + result[[paste0('replicate_method_k', k)]] <- ruv_replicate_method(set, k=k) + result[[paste0('control_method_k', k)]] <- ruv_control_gene_method(set, k=k, cutoff_p=0.5) +} + +for (name in names(result)) { + if (!startsWith(name, "no_correction")) { + set <- result[[name]] + unwanted_variation <- pData(set) + df <- data.frame(identifier = rownames(unwanted_variation)) + df <- cbind(df, unwanted_variation) + colnames(df)[2] <- 'condition' + write.table(df, file=paste0("batch_effects_", name, ".tabular"), sep="\t", quote=F, row.names=F) + } +} + +# 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/ruvseq.xml Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,307 @@ +<tool id="ruvseq" name="Remove Unwanted Variation" version="1.12.0"> + <description>from RNA-seq data</description> + <requirements> + <requirement type="package" version="1.12.0">bioconductor-ruvseq</requirement> + <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> + <requirement type="package" version="1.6.0">bioconductor-tximport</requirement> + <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement> + <requirement type="package" version="0.6.5">r-ggrepel</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)", RUVSeq version" $(R --vanilla --slave -e "library(RUVSeq); cat(sessionInfo()\$otherPkgs\$RUVSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + <command><![CDATA[ +#if $tximport.tximport_selector == 'tximport': + #if $tximport.mapping_format.mapping_format_selector == 'gtf': + ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && + #else: + ln -s '$tximport.mapping_format.tabular_file' mapping.txt && + #end if +#end if + +Rscript '${__tool_directory__}/ruvseq.R' +#if $pdf: + -p '$plots' +#end if + +--sample_json '$sampleTable' + +$header + +--min_k $min_k +--max_k $max_k + +#if $tximport.tximport_selector == 'tximport': + --txtype $tximport.txtype + #if $tximport.mapping_format.mapping_format_selector == 'gtf': + --tx2gene mapping.gtf + #else: + --tx2gene mapping.txt + #end if +#end if +]]></command> + <configfiles> + <configfile name="sampleTable"> +#import json +#set sample_table = [] +#for $level in $rep_factorLevel: + #for $file in $level.countsFile: + #silent $sample_table.append({"path": str($file), "label": str($file.element_identifier), "condition": str($level.factorLevel)}) + #end for +#end for +#echo json.dumps($sample_table) + </configfile> + </configfiles> + <inputs> + <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> + <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' 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="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> + </repeat> + <param name="min_k" type="integer" value="1" min="1" label="Try to find at least this many factors of unwanted variation" /> + <param name="max_k" type="integer" value="1" min="1" label="Try to find at most this many factors of unwanted variation" /> + <param name="min_mean_count" type="integer" value="5" min="0" label="Ignore genes with fewer than this many counts on average" /> + <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" /> + + <conditional name="tximport"> + <param name="tximport_selector" type="select" label="Choice of Input data"> + <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option> + <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option> + </param> + <when value="tximport"> + <param name="txtype" type="select" label="Program used to generate TPMs"> + <option value="kallisto">kallisto</option> + <option value="sailfish">Sailfish</option> + <option value="salmon">Salmon</option> + </param> + <conditional name="mapping_format"> + <param name="mapping_format_selector" type="select" label="Gene mapping format"> + <option value="gtf" selected="True">GTF</option> + <option value="tabular">Transcript-ID and Gene-ID mapping file</option> + </param> + <when value="gtf"> + <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/> + </when> + <when value="tabular"> + <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/> + </when> + </conditional> + </when> + <when value="count" /> + </conditional> + <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="Visualising the analysis results" + help="output an additional PDF files" /> + </inputs> + <outputs> + <collection name="unwanted_variation" type="list" label="RUVSeq covariate files on ${on_string}"> + <discover_datasets pattern="(?P<designation>.+)\.tabular" format="tabular" directory="." visible="false"/> + </collection> + <data format="pdf" name="plots" label="RUVSeq diagonstic plots on ${on_string}"> + <filter>pdf == True</filter> + </data> + </outputs> + <tests> + <!--Ensure counts files with header works --> + <test> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Treated"/> + <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Untreated"/> + <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> + </repeat> + <param name="pdf" value="true"/> + <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> + <output_collection name="unwanted_variation" type="list"> + <element name="batch_effects_control_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="GSM461179.*\tTreated\t-0.49.*"/> + </assert_contents> + </element> + <element name="batch_effects_replicate_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="GSM461179.*\tTreated\t-0.25.*"/> + </assert_contents> + </element> + <element name="batch_effects_residual_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="GSM461179.*\tTreated\t-0.60.*"/> + </assert_contents> + </element> + </output_collection> + </test> + <!--Ensure counts files without header works --> + <test> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Treated"/> + <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Untreated"/> + <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/> + </repeat> + <param name="pdf" value="true"/> + <param name="header" value="false"/> + <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> + <output_collection name="unwanted_variation" type="list"> + <element name="batch_effects_control_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="GSM461179.*\tTreated\t-0.49.*"/> + </assert_contents> + </element> + <element name="batch_effects_replicate_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="GSM461179.*\tTreated\t-0.25.*"/> + </assert_contents> + </element> + <element name="batch_effects_residual_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="GSM461179.*\tTreated\t-0.60.*"/> + </assert_contents> + </element> + </output_collection> + </test> + <!--Ensure sailfish files work --> + <test> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Treated"/> + <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Untreated"/> + <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> + </repeat> + <param name="pdf" value="true"/> + <param name="tximport_selector" value="tximport"/> + <param name="txtype" value="sailfish"/> + <param name="mapping_format_selector" value="tabular"/> + <param name="tabular_file" value="tx2gene.tab"/> + <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/> + <output_collection name="unwanted_variation" type="list"> + <element name="batch_effects_control_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.28.*"/> + </assert_contents> + </element> + <element name="batch_effects_replicate_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.44.*"/> + </assert_contents> + </element> + <element name="batch_effects_residual_method_k1"> + <assert_contents> + <has_text_matching expression="identifier\tcondition\tW_1"/> + <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.22.*"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +RUVSeq normalizes RNA-seq data using factor analysis of control genes or samples. RUVSeq has been designed for detecting unwanted variation using replicate sample information. The current RUVSeq Galaxy tool only implements estimating unwanted variation for primary factors. +RUVSeq implements 3 different methods for the estimation of unwanted variation: + +RUVg estimates the factors of unwanted variation using control genes + +RUVs estimates the factors of unwanted variation using replicate samples + +RUVr estimating the factors of unwanted variation using residuals. + +This tool runs all RUV methods and outputs diagnostic plots and tables with covariates that +may be used for differential expression analsys. + +----- + +**Inputs** + +**Count Files** + +RUVSeq_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. + +RUVSeq_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2. + +**Salmon or Sailfish Files** + +Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below. + +Example: + +============ ========== =============== =========== =========== +Name Length EffectiveLength TPM NumReads +------------ ---------- --------------- ----------- ----------- +NR_001526 164 20.4518 0 0 +NR_001526_1 164 20.4518 0 0 +NR_001526_2 164 20.4518 0 0 +NM_130786 1764 1956.04 2.47415 109.165 +NR_015380 2129 2139.53 1.77331 85.5821 +NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05 +NM_001198819 9527 7964.62 0 0 +NM_001198820 9410 7855.78 0 0 +NM_014576 9267 7714.88 0.0481114 8.37255 +============ ========== =============== =========== =========== + +**kallisto Files** + +kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below. + +Example: + +============ ========== =============== =========== =========== +target_id length eff_length est_counts tpm +------------ ---------- --------------- ----------- ----------- +NR_001526 164 20.4518 0 0 +NR_001526_1 164 20.4518 0 0 +NR_001526_2 164 20.4518 0 0 +NM_130786 1764 1956.04 109.165 2.47415 +NR_015380 2129 2139.53 85.5821 1.77331 +NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07 +NM_001198819 9527 7964.62 0 0 +NM_001198820 9410 7855.78 0 0 +NM_014576 9267 7714.88 8.37255 0.0481114 +============ ========== =============== =========== =========== + +----- + +**Output** + +RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF. + +.. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html +.. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html + ]]></help> + <citations> + <citation type="doi">10.1038/nbt.2931</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461176_untreat_single.counts Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,4005 @@ +GeneID untreat1 +FBgn0000003 0 +FBgn0000008 15 +FBgn0000014 0 +FBgn0000015 0 +FBgn0000017 1227 +FBgn0000018 92 +FBgn0000022 1 +FBgn0000024 0 +FBgn0000028 0 +FBgn0000032 233 +FBgn0000036 0 +FBgn0000037 2 +FBgn0000038 0 +FBgn0000039 0 +FBgn0000042 16319 +FBgn0000043 5625 +FBgn0000044 13 +FBgn0000045 1 +FBgn0000046 4 +FBgn0000047 2 +FBgn0000052 488 +FBgn0000053 376 +FBgn0000054 142 +FBgn0000055 0 +FBgn0000056 0 +FBgn0000057 159 +FBgn0000061 0 +FBgn0000063 100 +FBgn0000064 1808 +FBgn0000071 29 +FBgn0000075 1 +FBgn0000077 40 +FBgn0000078 5 +FBgn0000079 28 +FBgn0000083 1286 +FBgn0000084 399 +FBgn0000092 3 +FBgn0000094 4 +FBgn0000097 749 +FBgn0000099 0 +FBgn0000100 6534 +FBgn0000108 12 +FBgn0000109 20 +FBgn0000114 1 +FBgn0000115 148 +FBgn0000116 95 +FBgn0000117 2488 +FBgn0000119 133 +FBgn0000120 0 +FBgn0000121 0 +FBgn0000137 0 +FBgn0000139 186 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf1.tab Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1759.2 0 0 +NM_014212 2035 1837.2 0 0 +NM_173860 847 649.348 0 0 +NM_017410 2395 2555.05 0.0173509 1 +NM_014620 2305 2261.56 0.114436 5.83783 +NM_153633 1665 1561.63 3.55316 125.162 +NM_018953 1610 1412.2 0 0 +NR_003084 1644 1446.2 0 0 +NM_004503 1680 1482.2 0 0 +NM_153693 2077 1879.2 0 0 +NM_022658 2286 2088.2 0 0 +NM_006897 1539 1341.2 0 0 +NM_001168316 2281 2071 0.085625 4 +NM_174914 2383 2153.11 0 0 +NR_031764 1851 1659.15 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf2.tab Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1764.64 0 0 +NM_014212 2035 2171.69 0.0161522 1 +NM_173860 847 655.215 0 0 +NM_017410 2395 2567.91 0.01366 1 +NM_014620 2305 2235.74 0 0 +NM_153633 1665 1576.16 1.7359 78 +NM_018953 1610 1726.1 1.31761e-06 6.48367e-05 +NR_003084 1644 1704.36 0.0411608 1.99994 +NM_004503 1680 1679.47 0.10443 5 +NM_153693 2077 2069.83 0 0 +NM_022658 2286 2093.64 0 0 +NM_006897 1539 1557.46 0.0675669 3 +NM_001168316 2281 2088.64 0 0 +NM_174914 2383 2190.64 0 0 +NR_031764 1851 1658.64 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf3.tab Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1760.44 0 0 +NM_014212 2035 2127.85 0.0280759 2 +NM_173860 847 650.573 0 0 +NM_017410 2395 2198.44 0 0 +NM_014620 2305 2223.92 0.0661957 4.92838 +NM_153633 1665 1536.71 2.08127 107.072 +NM_018953 1610 1685.74 1.23894e-08 6.99193e-07 +NR_003084 1644 1658.72 0.0720329 4 +NM_004503 1680 1638.79 0.0546819 3 +NM_153693 2077 2026.99 0 0 +NM_022658 2286 2089.44 0 0 +NM_006897 1539 1342.44 0 0 +NM_001168316 2281 2047.58 0 0 +NM_174914 2383 2143.36 0 0 +NR_031764 1851 1659.97 0.0359895 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf4.tab Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1738.38 0 0 +NM_014212 2035 1816.38 0 0 +NM_173860 847 628.444 0 0 +NM_017410 2395 2176.38 0 0 +NM_014620 2305 2086.38 0 0 +NM_153633 1665 1510.43 2.31417 89.0334 +NM_018953 1610 1391.38 0 0 +NR_003084 1644 1425.38 0 0 +NM_004503 1680 1612.63 0.0730348 3 +NM_153693 2077 1998.27 0 0 +NM_022658 2286 2067.38 0 0 +NM_006897 1539 1320.38 0 0 +NM_001168316 2281 2033.58 0 0 +NM_174914 2383 2129.01 0 0 +NR_031764 1851 1639.11 0.071855 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf5.tab Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1781.23 0 0 +NM_014212 2035 1859.23 0 0 +NM_173860 847 671.305 0 0 +NM_017410 2395 2219.23 0 0 +NM_014620 2305 2195.37 0 0 +NM_153633 1665 1545.8 3.39643 119.002 +NM_018953 1610 1715.91 0.128558 5 +NR_003084 1644 1468.23 0 0 +NM_004503 1680 1654.16 0.0800141 3 +NM_153693 2077 2034.63 0 0 +NM_022658 2286 2148.18 0.0205378 1 +NM_006897 1539 1363.23 0 0 +NM_001168316 2281 2061.52 0 0 +NM_174914 2383 2156.64 0 0 +NR_031764 1851 1671.47 0.0527904 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf6.tab Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1747.9 0 0 +NM_014212 2035 1825.9 0 0 +NM_173860 847 638.159 0 0 +NM_017410 2395 2562.99 0.0171188 1 +NM_014620 2305 2272.12 0.152979 7.92213 +NM_153633 1665 1572.52 3.54659 127.112 +NM_018953 1610 1731.28 0.0760279 3 +NR_003084 1644 1434.9 0 0 +NM_004503 1680 1673.79 0.104853 4 +NM_153693 2077 2057.73 0 0 +NM_022658 2286 2185.1 0.0200793 1 +NM_006897 1539 1329.9 0 0 +NM_001168316 2281 2047.55 0 0 +NM_174914 2383 2143.62 0 0 +NR_031764 1851 1663.05 0.0263825 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tx2gene.tab Wed Sep 05 15:54:16 2018 -0400 @@ -0,0 +1,16 @@ +TXNAME GENEID +NM_001168316 DDX11L1 +NM_174914 DDX11L1 +NR_031764 DDX11L1 +NM_004503 WASH7P +NM_006897 WASH7P +NM_014212 WASH7P +NM_014620 WASH7P +NM_017409 WASH7P +NM_017410 WASH7P +NM_018953 MIR6859-2 +NM_022658 MIR6859-1 +NM_153633 WASH7P +NM_153693 WASH7P +NM_173860 WASH7P +NR_003084 WASH7P