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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07 |
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modified:
deseq2.xml test-data/deseq2_out.tab test-data/deseq2_out_filtered.tab |
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added:
deseq2.R test-data/deseq2_tximport_out.tab test-data/deseq2_tximport_out_filtered.tab test-data/genes_sub.gtf test-data/normalized_readcounts.tab test-data/sailfish_quant_result1.tab test-data/sailfish_quant_result2.tab test-data/sailfish_quant_result3.tab test-data/sailfish_quant_result4.tab |
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| diff -r d38fd393402e -r 4939397c4706 deseq2.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2.R Wed Nov 09 17:00:31 2016 -0500 |
| [ |
| b'@@ -0,0 +1,373 @@\n+#!/usr/bin/env Rscript\n+\n+# A command-line interface to DESeq2 for use with Galaxy\n+# written by Bjoern Gruening and modified by Michael Love 2016.03.30\n+#\n+# one of these arguments is required:\n+#\n+# \'factors\' a JSON list object from Galaxy\n+#\n+# \'sample_table\' is a sample table as described in ?DESeqDataSetFromHTSeq\n+# with columns: sample name, filename, then factors (variables)\n+#\n+# the output file has columns:\n+# \n+# baseMean (mean normalized count)\n+# log2FoldChange (by default a moderated LFC estimate)\n+# lfcSE (the standard error)\n+# stat (the Wald statistic)\n+# pvalue (p-value from comparison of Wald statistic to a standard Normal)\n+# padj (adjusted p-value, Benjamini Hochberg correction on genes which pass the mean count filter)\n+# \n+# the first variable in \'factors\' and first column in \'sample_table\' will be the primary factor.\n+# the levels of the primary factor are used in the order of appearance in factors or in sample_table.\n+#\n+# by default, levels in the order A,B,C produces a single comparison of B vs A, to a single file \'outfile\'\n+#\n+# for the \'many_contrasts\' flag, levels in the order A,B,C produces comparisons C vs A, B vs A, C vs B,\n+# to a number of files using the \'outfile\' prefix: \'outfile.condition_C_vs_A\' etc.\n+# all plots will still be sent to a single PDF, named by the arg \'plots\', with extra pages.\n+#\n+# fit_type is an integer valued argument, with the options from ?estimateDisperions\n+# 1 "parametric"\n+# 2 "local"\n+# 3 "mean"\n+\n+# setup R error handling to go to stderr\n+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )\n+\n+# we need that to not crash galaxy with an UTF8 error on German LC settings.\n+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+\n+library("getopt")\n+library("tools")\n+options(stringAsFactors = FALSE, useFancyQuotes = FALSE)\n+args <- commandArgs(trailingOnly = TRUE)\n+\n+# get options, using the spec as defined by the enclosed list.\n+# we read the options from the default: commandArgs(TRUE).\n+spec <- matrix(c(\n+ "quiet", "q", 0, "logical",\n+ "help", "h", 0, "logical",\n+ "outfile", "o", 1, "character",\n+ "countsfile", "n", 1, "character",\n+ "factors", "f", 1, "character",\n+ "plots" , "p", 1, "character",\n+ "sample_table", "s", 1, "character",\n+ "tximport", "i", 0, "logical",\n+ "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)\n+ "fit_type", "t", 1, "integer",\n+ "many_contrasts", "m", 0, "logical",\n+ "outlier_replace_off" , "a", 0, "logical",\n+ "outlier_filter_off" , "b", 0, "logical",\n+ "auto_mean_filter_off", "c", 0, "logical",\n+ "beta_prior_off", "d", 0, "logical"),\n+ byrow=TRUE, ncol=4)\n+opt <- getopt(spec)\n+\n+# if help was asked for print a friendly message\n+# and exit with a non-zero error code\n+if (!is.null(opt$help)) {\n+ cat(getopt(spec, usage=TRUE))\n+ q(status=1)\n+}\n+\n+# enforce the following required arguments\n+if (is.null(opt$outfile)) {\n+ cat("\'outfile\' is required\\n")\n+ q(status=1)\n+}\n+if (is.null(opt$sample_table) & is.null(opt$factors)) {\n+ cat("\'factors\' or \'sample_table\' is required\\n")\n+ q(status=1)\n+}\n+\n+verbose <- if (is.null(opt$quiet)) {\n+ TRUE\n+} else {\n+ FALSE\n+}\n+\n+if (!is.null(opt$tximport)) {\n+ if (is.null(opt$tx2gene)) stop("A transcript-to-gene map or a GTF file is required for tximport")\n+ if (tolower(file_ext(opt$tx2gene)) == "gtf") {\n+ gtfFile <- opt$tx2gene\n+ } else {\n+ gtfFile <- NULL\n+ tx2gene <- read.table(opt$tx2gene, header=FALSE)\n+ }\n+ useTXI <- TRUE\n+} else {\n+ useTXI <- FALSE\n+}\n+\n+suppressPackageStartupMessages({\n+ library("DESeq2")\n+ library("RColorBrewer")\n+ library("gplots")\n+})\n+\n+# build or read sample table\n+\n+trim <- function (x) gsub("^\\\\s+|\\\\s+$", "", x)\n+\n+# switch on if \'factors\' was provided:\n+if (!is.null(opt$factors)) {\n+ library("rjson")\n+ parser <- newJSONParser()\n+ parser$addData(opt$factors)\n+ factorList <- parser$getObject()\n'..b'ace_off)) {\n+ minRep <- 7\n+} else {\n+ minRep <- Inf\n+ if (verbose) cat("outlier replacement off\\n")\n+}\n+if (is.null(opt$outlier_filter_off)) {\n+ cooksCutoff <- TRUE\n+} else { \n+ cooksCutoff <- FALSE\n+ if (verbose) cat("outlier filtering off\\n")\n+}\n+\n+# optional automatic mean filtering\n+if (is.null(opt$auto_mean_filter_off)) {\n+ independentFiltering <- TRUE\n+} else {\n+ independentFiltering <- FALSE\n+ if (verbose) cat("automatic filtering on the mean off\\n")\n+}\n+\n+# shrinkage of LFCs\n+if (is.null(opt$beta_prior_off)) {\n+ betaPrior <- TRUE\n+} else {\n+ betaPrior <- FALSE\n+ if (verbose) cat("beta prior off\\n")\n+}\n+\n+# dispersion fit type\n+if (is.null(opt$fit_type)) {\n+ fitType <- "parametric"\n+} else {\n+ fitType <- c("parametric","local","mean")[opt$fit_type]\n+}\n+\n+if (verbose) cat(paste("using disperion fit type:",fitType,"\\n"))\n+\n+# run the analysis\n+dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep)\n+\n+# create the generic plots and leave the device open\n+if (!is.null(opt$plots)) {\n+ if (verbose) cat("creating plots\\n")\n+ pdf(opt$plots)\n+ generateGenericPlots(dds, factors)\n+}\n+\n+n <- nlevels(colData(dds)[[primaryFactor]])\n+allLevels <- levels(colData(dds)[[primaryFactor]])\n+\n+if (!is.null(opt$countsfile)) {\n+ labs <- paste0(seq_len(ncol(dds)), ": ", do.call(paste, as.list(colData(dds)[factors])))\n+ normalizedCounts<-counts(dds,normalized=TRUE)\n+ colnames(normalizedCounts)<-labs\n+ write.table(normalizedCounts, file=opt$countsfile, sep="\\t", col.names=NA, quote=FALSE)\n+}\n+\n+if (is.null(opt$many_contrasts)) {\n+ # only contrast the first and second level of the primary factor\n+ ref <- allLevels[1]\n+ lvl <- allLevels[2]\n+ res <- results(dds, contrast=c(primaryFactor, lvl, ref),\n+ cooksCutoff=cooksCutoff,\n+ independentFiltering=independentFiltering)\n+ if (verbose) {\n+ cat("summary of results\\n")\n+ cat(paste0(primaryFactor,": ",lvl," vs ",ref,"\\n"))\n+ print(summary(res))\n+ }\n+ resSorted <- res[order(res$padj),]\n+ outDF <- as.data.frame(resSorted)\n+ outDF$geneID <- rownames(outDF)\n+ outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]\n+ filename <- opt$outfile\n+ write.table(outDF, file=filename, sep="\\t", quote=FALSE, row.names=FALSE, col.names=FALSE)\n+ if (independentFiltering) {\n+ threshold <- unname(attr(res, "filterThreshold"))\n+ } else {\n+ threshold <- 0\n+ }\n+ title_suffix <- paste0(primaryFactor,": ",lvl," vs ",ref)\n+ if (!is.null(opt$plots)) {\n+ generateSpecificPlots(res, threshold, title_suffix)\n+ }\n+} else {\n+ # rotate through the possible contrasts of the primary factor\n+ # write out a sorted table of results with the contrast as a suffix\n+ # add contrast specific plots to the device\n+ for (i in seq_len(n-1)) {\n+ ref <- allLevels[i]\n+ contrastLevels <- allLevels[(i+1):n]\n+ for (lvl in contrastLevels) {\n+ res <- results(dds, contrast=c(primaryFactor, lvl, ref),\n+ cooksCutoff=cooksCutoff,\n+ independentFiltering=independentFiltering)\n+ resSorted <- res[order(res$padj),]\n+ outDF <- as.data.frame(resSorted)\n+ outDF$geneID <- rownames(outDF)\n+ outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]\n+ filename <- paste0(opt$outfile,".",primaryFactor,"_",lvl,"_vs_",ref)\n+ write.table(outDF, file=filename, sep="\\t", quote=FALSE, row.names=FALSE, col.names=FALSE)\n+ if (independentFiltering) {\n+ threshold <- unname(attr(res, "filterThreshold"))\n+ } else {\n+ threshold <- 0\n+ }\n+ title_suffix <- paste0(primaryFactor,": ",lvl," vs ",ref)\n+ if (!is.null(opt$plots)) {\n+ generateSpecificPlots(res, threshold, title_suffix)\n+ }\n+ }\n+ }\n+}\n+\n+# close the plot device\n+if (!is.null(opt$plots)) {\n+ cat("closing plot device\\n")\n+ dev.off()\n+}\n+\n+cat("Session information:\\n\\n")\n+\n+sessionInfo()\n+\n' |
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| diff -r d38fd393402e -r 4939397c4706 deseq2.xml --- a/deseq2.xml Thu Sep 22 05:49:52 2016 -0400 +++ b/deseq2.xml Wed Nov 09 17:00:31 2016 -0500 |
| [ |
| b'@@ -1,11 +1,7 @@\n-<tool id="deseq2" name="DESeq2" version="2.1.8.4">\n+<tool id="deseq2" name="DESeq2" version="2.11.38">\n <description>Determines differentially expressed features from count tables</description>\n <requirements>\n- <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->\n- <requirement type="package" version="1.20.0">r-getopt</requirement>\n- <requirement type="package" version="2.17.0">r-gplots</requirement>\n- <requirement type="package" version="0.2.15">r-rjson</requirement>\n- <requirement type="package" version="1.10.1">bioconductor-deseq2</requirement>\n+ <requirement type="package" version="1.12.4">bioconductor-deseq2</requirement> \n </requirements>\n <stdio>\n <regex match="Execution halted"\n@@ -28,13 +24,23 @@\n </version_command>\n <command>\n <![CDATA[\n- R -e \'library(DESeq2); sink("DESEQ2_ROOT_PATH"); cat(file.path(find.package("DESeq2"),"script","deseq2.R"))\' &&\n+\n+ #if $tximport.tximport_selector == \'tximport\':\n+ #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n+ ln -s \'$tximport.mapping_format.gtf_file\' mapping.gtf &&\n+ #else:\n+ ln -s \'$tximport.mapping_format.tabular_file\' mapping.txt &&\n+ #end if\n+ #end if\n \n #import json\n- Rscript \\$(cat DESEQ2_ROOT_PATH)\n- -o "$deseq_out"\n+ Rscript \'${__tool_directory__}/deseq2.R\'\n+ -o \'$deseq_out\'\n #if $pdf:\n- -p "$plots"\n+ -p \'$plots\'\n+ #end if\n+ #if $normCounts:\n+ -n \'$counts_out\'\n #end if\n #set $temp_factor_names = list()\n #for $factor in $rep_factorName:\n@@ -50,7 +56,7 @@\n $temp_factor_names.append([str($factor.factorName), $temp_factor])\n #end for\n -f \'#echo json.dumps(temp_factor_names)#\'\n- -t "$fit_type"\n+ -t \'$fit_type\'\n #if $outlier_replace_off:\n -a\n #end if\n@@ -63,18 +69,27 @@\n #if $many_contrasts:\n -m\n #end if\n+ #if $tximport.tximport_selector == \'tximport\':\n+ -i\n+ #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n+ -x mapping.gtf\n+ #else:\n+ -x mapping.txt\n+ #end if\n+\n+ #end if\n ]]>\n </command>\n <inputs>\n <repeat name="rep_factorName" title="Factor" min="1">\n- <param name="factorName" type="text" value="FactorName" label="Specify a factor name"\n+ <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"\n help="Only letters, numbers and underscores will be retained in this field">\n <sanitizer>\n <valid initial="string.letters,string.digits"><add value="_" /></valid>\n </sanitizer>\n </param>\n <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">\n- <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"\n+ <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be \'tumor\', \'normal\', \'treated\' or \'control\'"\n help="Only letters, numbers and underscores will be retained in this field">\n <sanitizer>\n <valid initial="string.letters,string.digits"><add value="_" /></valid>\n@@ -83,9 +98,33 @@\n <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>\n </repeat>\n </repeat>\n+\n+ <conditional name="tximport">\n+ <param name="tximport_selector" type="select" label="C'..b'TF</option>\n+ <option value="tabular">Transcript-ID and Gene-ID mapping file</option>\n+ </param>\n+ <when value="gtf">\n+ <param name="gtf_file" type="data" format="gtf" label="GTF file with Transcript - Gene mapping"/>\n+ </when>\n+ <when value="tabular">\n+ <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="count" />\n+ </conditional>\n <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"\n label="Visualising the analysis results"\n help="output an additional PDF files" />\n+ <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"\n+ label="Output normalized counts table" />\n <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"\n label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"\n help=" DESeq2 performs independent \xef\xac\x81ltering by default using the mean of normalized counts as a \xef\xac\x81lter statistic" />\n@@ -110,6 +149,9 @@\n <outputs>\n <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">\n <filter>many_contrasts is False</filter>\n+ <actions>\n+ <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />\n+ </actions>\n </data>\n <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">\n <filter>many_contrasts is True</filter>\n@@ -118,6 +160,9 @@\n <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">\n <filter>pdf == True</filter>\n </data>\n+ <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">\n+ <filter>normCounts == True</filter>\n+ </data>\n </outputs>\n <tests>\n <test>\n@@ -132,9 +177,28 @@\n <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>\n </repeat>\n </repeat>\n- <param name="pdf" value="no"/>\n- <output name="deseq_out" file="deseq2_out.tab" compare="sim_size" delta="1000"/>\n- <output name="deseq_out_filtered" file="deseq2_out_filtered.tab" compare="sim_size" delta="1000"/>\n+ <param name="pdf" value="False"/>\n+ <param name="normCounts" value="True"/>\n+ <output name="counts_out" file="normalized_readcounts.tab"/>\n+ <output name="deseq_out" file="deseq2_out.tab"/>\n+ </test>\n+ <test>\n+ <repeat name="rep_factorName">\n+ <param name="factorName" value="Treatment"/>\n+ <repeat name="rep_factorLevel">\n+ <param name="factorLevel" value="Treated"/>\n+ <param name="countsFile" value="sailfish_quant_result1.tab,sailfish_quant_result2.tab"/>\n+ </repeat>\n+ <repeat name="rep_factorLevel">\n+ <param name="factorLevel" value="Untreated"/>\n+ <param name="countsFile" value="sailfish_quant_result3.tab,sailfish_quant_result4.tab"/>\n+ </repeat>\n+ </repeat>\n+ <param name="pdf" value="False"/>\n+ <param name="tximport_selector" value="tximport"/>\n+ <param name="mapping_format_selector" value="gtf"/>\n+ <param name="gtf_file" value="genes_sub.gtf"/>\n+ <output name="deseq_out" file="deseq2_tximport_out.tab"/>\n </test>\n </tests>\n <help>\n' |
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| diff -r d38fd393402e -r 4939397c4706 test-data/deseq2_out.tab --- a/test-data/deseq2_out.tab Thu Sep 22 05:49:52 2016 -0400 +++ b/test-data/deseq2_out.tab Wed Nov 09 17:00:31 2016 -0500 |
| b |
| b'@@ -1,3179 +1,3179 @@\n-FBgn0003360\t1933.95040021558\t-2.83931225259512\t0.131427106250417\t-21.6037036316175\t1.65776764506556e-103\t4.8042106354e-100\n-FBgn0029167\t1648.81894046778\t-2.12846961402501\t0.111026270383108\t-19.1708647573273\t6.48222732792777e-82\t9.39274739816734e-79\n-FBgn0025111\t655.359768612902\t2.56442932254547\t0.137667337786547\t18.6277250928003\t1.91492266642432e-77\t1.84981529576589e-74\n-FBgn0029896\t211.4755450268\t-2.08777266242928\t0.146415559688566\t-14.259226730206\t3.92782602934154e-46\t2.84570995825794e-43\n-FBgn0000071\t151.249383869297\t2.07788820686474\t0.168180792411128\t12.3550863155956\t4.57265091805509e-35\t2.65030847210473e-32\n-FBgn0027279\t1317.42349329018\t-1.15789518800581\t0.0979487486398482\t-11.8214393147923\t3.02457627375306e-32\t1.46087034022273e-29\n-FBgn0023479\t1361.36610109448\t-1.42278093472624\t0.123382435239163\t-11.5314706827462\t9.15659861926778e-31\t3.79083182837686e-28\n-FBgn0026562\t20055.4860668702\t-1.89651458906925\t0.165538620287047\t-11.4566291888905\t2.17828498754631e-30\t7.89083736738651e-28\n-FBgn0003501\t116.651152955291\t1.80587013415947\t0.166034666709106\t10.8764643550215\t1.4923989382969e-27\t4.80552458131602e-25\n-FBgn0001224\t272.471006012668\t1.32281610420226\t0.134495231954035\t9.83541263867513\t7.92420868827822e-23\t2.29643567786303e-20\n-FBgn0001226\t617.110611842554\t1.45833378003199\t0.148670311493448\t9.80917955563887\t1.02800965013455e-22\t2.70833815099084e-20\n-FBgn0011260\t80.9068053807535\t1.72804169137515\t0.182772479814818\t9.45460549162528\t3.24242333829425e-21\t7.83045236198062e-19\n-FBgn0001137\t215.314997012827\t-1.29233946143563\t0.145480311328745\t-8.88326021323463\t6.49288454986043e-19\t1.4474138019612e-16\n-FBgn0003137\t2007.00068863624\t0.88961461517836\t0.104287926638967\t8.53037013822416\t1.45880207669652e-17\t3.01972029876181e-15\n-FBgn0002527\t17292.4505923723\t-0.73741537684446\t0.0906423933125779\t-8.13543585837923\t4.10458911152738e-16\t7.9300661634709e-14\n-FBgn0003748\t480.807341866837\t1.01051140923348\t0.130425339228426\t7.74781507344736\t9.34871517251503e-15\t1.69328603562178e-12\n-FBgn0001258\t671.110480695285\t0.895361035906691\t0.116548074382586\t7.68233229634957\t1.56217979166483e-14\t2.66305708014393e-12\n-FBgn0001225\t193.977269091929\t1.19104458118686\t0.161805985086091\t7.36094267806688\t1.82615977838543e-13\t2.94011724320054e-11\n-FBgn0024288\t23.7733297010346\t-1.57498520895134\t0.214878970749195\t-7.32963864942211\t2.30774118216246e-13\t3.51991260310884e-11\n-FBgn0029002\t744.250236684945\t1.17108784869134\t0.160714198398625\t7.28677279518668\t3.1746761716241e-13\t4.60010577268332e-11\n-FBgn0030237\t915.313685217584\t-0.850733962006436\t0.118429991807523\t-7.18343342781852\t6.79821458130211e-13\t9.38153612219691e-11\n-FBgn0002868\t45.7700929054867\t-1.52440216488712\t0.214738495601196\t-7.09887698812132\t1.25774693967815e-12\t1.59658579154825e-10\n-FBgn0016715\t64.2462306620967\t-1.42223206792763\t0.200375069888307\t-7.09784939174522\t1.26713158059385e-12\t1.59658579154825e-10\n-FBgn0000116\t279.97574453728\t1.11632215948692\t0.158425268315346\t7.04636432910989\t1.83653016084046e-12\t2.21761016921486e-10\n-FBgn0000406\t120.154935949727\t-1.37174695998837\t0.200388894764987\t-6.84542405205206\t7.62496639944616e-12\t8.83886105023799e-10\n-FBgn0003502\t503.917225808725\t0.801327660473763\t0.118268610139101\t6.77548894445694\t1.23986224053237e-11\t1.38196952810108e-09\n-FBgn0024315\t31.3113542635758\t-1.3763209973179\t0.20963230775834\t-6.56540497996374\t5.18916350280528e-11\t5.56970215967767e-09\n-FBgn0027949\t652.544029710057\t0.646429666729111\t0.103801654132743\t6.22754687418032\t4.73795011529377e-10\t4.90377836932905e-08\n-FBgn0003076\t687.758986559078\t0.667050302734252\t0.107718459531582\t6.19253473949538\t5.92042952512063e-10\t5.91634647027572e-08\n-FBgn0029801\t670.98347311978\t-0.754988069284397\t0.123107613719941\t-6.13274879165415\t8.63734806999727e-10\t8.34367823561736e-08\n-FBgn0010591\t719.537870853329\t-0.678169968761112\t0.111477787189876\t-6.08345380596773\t1.17620817098387e-09\t1.09956492887459e-07\n-FBgn0028327\t1677.74174348924\t0.623125753194051\t0.103267516027833\t6.03409258944608\t1.59858392560922e-09\t1'..b'-0.0654391021889628\t0.0865521046682724\t-0.756065984065562\t0.449609635290332\tNA\n-FBgn0030537\t0.0923751652987496\t-0.0204895043498917\t0.0402731934859522\t-0.508762841393214\t0.610918468289372\tNA\n-FBgn0030538\t0.080862070626247\t0.0230872191457161\t0.0399975247953908\t0.577216196847676\t0.563793416904323\tNA\n-FBgn0030539\t0.181391852667795\t0.000922878063802334\t0.043122754627709\t0.0214011853317304\t0.982925628025152\tNA\n+FBgn0030509\t0.105352514349918\t0.00877278360142249\t0.0478917301960402\t0.183179508560495\t0.85465717212165\tNA\n+FBgn0030536\t1.19456732550319\t-0.0642565152437565\t0.0856555300074181\t-0.750173575928975\t0.453150171139533\tNA\n+FBgn0030537\t0.0923751652987496\t-0.0123454843911289\t0.0478917301960402\t-0.257779043283546\t0.796577439055694\tNA\n+FBgn0030538\t0.080862070626247\t0.00877278360142249\t0.0478917301960402\t0.183179508560495\t0.85465717212165\tNA\n+FBgn0030539\t0.181391852667795\t-0.000843866517103429\t0.0479792932290776\t-0.0175881398059446\t0.985967418278688\tNA\n FBgn0030540\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030541\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030542\t0.24813606918961\t0.0328712249937809\t0.0428867883455157\t0.766465064461231\t0.443399631338715\tNA\n+FBgn0030542\t0.24813606918961\t0.00877278360142249\t0.0478917301960402\t0.183179508560495\t0.85465717212165\tNA\n FBgn0030543\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030544\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030551\t0.700889780748892\t0.0020840503355373\t0.0848780550042263\t0.0245534647964486\t0.980411137809293\tNA\n-FBgn0030558\t0.100529782041548\t-0.0209903901435717\t0.0404598159839989\t-0.518795986414596\t0.60390301708516\tNA\n+FBgn0030551\t0.700889780748892\t0.00193134217589185\t0.0855453748238806\t0.022576815869567\t0.981987837369666\tNA\n+FBgn0030558\t0.100529782041548\t-0.0123454843911289\t0.0478917301960402\t-0.257779043283545\t0.796577439055694\tNA\n FBgn0030563\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030566\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030569\t0.953050839550445\t0.0285435775697864\t0.0975885126736503\t0.292489113603361\t0.769912682242256\tNA\n+FBgn0030569\t0.953050839550445\t0.0289002381613761\t0.0976672932821219\t0.295904976888167\t0.767302650179969\tNA\n FBgn0030570\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030577\t0.269423611141796\t-0.0265926243080571\t0.0432208120596076\t-0.615273592531813\t0.53837405408732\tNA\n+FBgn0030577\t0.269423611141796\t-0.0123454843911289\t0.0478917301960402\t-0.257779043283545\t0.796577439055695\tNA\n FBgn0030578\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030595\t0.90385617240921\t0.0140835782063791\t0.0874061821542703\t0.161127941517018\t0.871992633622158\tNA\n+FBgn0030595\t0.90385617240921\t0.0157536607828787\t0.0889518084940061\t0.177103322007672\t0.859427232590287\tNA\n FBgn0030608\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030614\t0.210705028699836\t0.034377529798995\t0.0437741723334843\t0.785338202104588\t0.432255303094221\tNA\n-FBgn0030617\t0.267076655602412\t0.0501740190961892\t0.0527678364632217\t0.950844727756834\t0.341683203371434\tNA\n-FBgn0030618\t0.205882296391466\t0.00423405052771355\t0.0447574735163511\t0.0945998555116551\t0.924632664607429\tNA\n-FBgn0030619\t0.080862070626247\t0.0230872191457161\t0.0399975247953908\t0.577216196847676\t0.563793416904323\tNA\n+FBgn0030614\t0.210705028699836\t0.021620211405579\t0.0480178189263924\t0.450253924250936\t0.652527357960287\tNA\n+FBgn0030617\t0.267076655602412\t0.0312575504218663\t0.0521416848457772\t0.599473348709746\t0.548857277278096\tNA\n+FBgn0030618\t0.205882296391466\t0.000434560838337217\t0.0480145367841427\t0.00905060982449664\t0.992778756741582\tNA\n+FBgn0030619\t0.080862070626247\t0.00877278360142249\t0.0478917301960402\t0.183179508560495\t0.85465717212165\tNA\n FBgn0030620\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030621\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030622\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030623\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030624\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030640\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030663\t1.2590203447849\t0.0316273222798865\t0.104066953284795\t0.303913214345129\t0.761194010092697\tNA\n-FBgn0030688\t0.827337508607711\t0.0122149676539822\t0.0936309991990391\t0.130458584854102\t0.896203618553293\tNA\n+FBgn0030663\t1.2590203447849\t0.0314856851094844\t0.103816486091694\t0.303282130755949\t0.761674862887635\tNA\n+FBgn0030688\t0.827337508607711\t0.0103444390915356\t0.094022066535967\t0.110021396813039\t0.91239240572348\tNA\n' |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/deseq2_out_filtered.tab --- a/test-data/deseq2_out_filtered.tab Thu Sep 22 05:49:52 2016 -0400 +++ b/test-data/deseq2_out_filtered.tab Wed Nov 09 17:00:31 2016 -0500 |
| b |
| b'@@ -1,3 +1,5 @@\n+<<<<<<< 32814b042e5c76fbb4786cff0edf98023718d3b2\n+<<<<<<< c2d5ab40b214e429d8a9d0c5b2b35adfc46a87e6\n FBgn0003360\t1933.95040021558\t-2.83931225259512\t0.131427106250417\t-21.6037036316175\t1.65776764506556e-103\t4.8042106354e-100\n FBgn0029167\t1648.81894046778\t-2.12846961402501\t0.111026270383108\t-19.1708647573273\t6.48222732792777e-82\t9.39274739816734e-79\n FBgn0025111\t655.359768612902\t2.56442932254547\t0.137667337786547\t18.6277250928003\t1.91492266642432e-77\t1.84981529576589e-74\n@@ -2981,10 +2983,5982 @@\n FBgn0001256\t0.594525744008654\t-0.0814845844960409\t0.0740904299552205\t-1.09979905023212\t0.271419686258455\tNA\n FBgn0001269\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0001281\t0.24813606918961\t0.0328712249937809\t0.0428867883455157\t0.766465064461231\t0.443399631338715\tNA\n+=======\n+FBgn0003360\t1933.95040021558\t-2.83931225277355\t0.13142710621978\t-21.6037036380113\t1.65776741559173e-103\t4.80420997038483e-100\n+FBgn0029167\t1648.81894046778\t-2.12846961422629\t0.111026270323124\t-19.1708647694975\t6.4822258114457e-82\t9.39274520078482e-79\n+FBgn0025111\t655.359768612902\t2.56442932272882\t0.137667337750974\t18.6277250989455\t1.91492244659163e-77\t1.84981508340752e-74\n+FBgn0029896\t211.4755450268\t-2.08777266267271\t0.146415559643033\t-14.2592267363031\t3.92782568619497e-46\t2.84570970964826e-43\n+FBgn0000071\t151.249383869297\t2.07788820702293\t0.168180792388495\t12.3550863181989\t4.57265077002907e-35\t2.65030838630885e-32\n+FBgn0027279\t1317.42349329018\t-1.15789518813539\t0.0979487485552853\t-11.8214393263211\t3.02457585863399e-32\t1.46087013972022e-29\n+FBgn0023479\t1361.36610109448\t-1.4227809348361\t0.123382435197198\t-11.5314706875586\t9.15659810735844e-31\t3.79083161644639e-28\n+FBgn0026562\t20055.4860668702\t-1.89651458904389\t0.165538620290002\t-11.4566291885328\t2.17828499653902e-30\t7.89083739996261e-28\n+FBgn0003501\t116.651152955291\t1.80587013436293\t0.166034666673343\t10.8764643585896\t1.49239887989692e-27\t4.80552439326809e-25\n+FBgn0001224\t272.471006012668\t1.32281610434034\t0.134495231900496\t9.83541264361695\t7.92420829921966e-23\t2.29643556511386e-20\n+FBgn0001226\t617.110611842554\t1.45833378008992\t0.148670311476792\t9.80917955712746\t1.02800963497078e-22\t2.70833811104121e-20\n+FBgn0011260\t80.9068053807535\t1.72804169152786\t0.182772479795608\t9.4546054934545\t3.24242328160394e-21\t7.8304522250735e-19\n+FBgn0001137\t215.314997012827\t-1.2923394615637\t0.145480311288172\t-8.88326021659239\t6.49288435379596e-19\t1.4474137582539e-16\n+FBgn0003137\t2007.00068863624\t0.889614615259382\t0.104287926571956\t8.53037014448231\t1.45880199777668e-17\t3.01972013539773e-15\n+FBgn0002527\t17292.4505923723\t-0.73741537691578\t0.0906423932278383\t-8.1354358667717\t4.10458882716588e-16\t7.93006561408447e-14\n+FBgn0003748\t480.807341866837\t1.0105114093244\t0.130425339183444\t7.74781507681658\t9.34871492453577e-15\t1.69328599070654e-12\n+FBgn0001258\t671.110480695285\t0.895361035995726\t0.116548074322099\t7.68233230110052\t1.56217973371195e-14\t2.66305698135131e-12\n+FBgn0001225\t193.977269091929\t1.19104458129442\t0.161805985055831\t7.36094268010821\t1.82615975045602e-13\t2.94011719823418e-11\n+FBgn0024288\t23.7733297010346\t-1.57498520888571\t0.214878970747888\t-7.32963864916123\t2.30774118665459e-13\t3.51991260996052e-11\n+FBgn0029002\t744.250236684945\t1.17108784869797\t0.160714198396003\t7.28677279534683\t3.17467616785188e-13\t4.60010576721737e-11\n+FBgn0030237\t915.313685217584\t-0.850733962079202\t0.118429991755134\t-7.18343343161065\t6.79821439265396e-13\t9.38153586186246e-11\n+FBgn0002868\t45.7700929054867\t-1.52440216456383\t0.214738495602616\t-7.09887698656886\t1.25774695380453e-12\t1.59658579073656e-10\n+FBgn0016715\t64.2462306620967\t-1.42223206793242\t0.200375069886999\t-7.0978493918155\t1.26713157994965e-12\t1.59658579073656e-10\n+FBgn0000116\t279.97574453728\t1.11632215952793\t0.1584252683027\t7.04636432993124\t1.83653015000524e-12\t2.21761015613133e-10\n+FBgn0000406\t120.154935949727\t-1.37174695982313\t0.200388894777049\t-6.84542405081539\t7.6249664653199e-12\t8.83886112659883e-10\n+FBgn0003502\t503.917225808725\t0.801327660544834\t0.1182686100753\t6.77548894871294\t1.23986220403101e-11\t1.3819694'..b'834\t0.341683203371434\tNA\n FBgn0030618\t0.205882296391466\t0.00423405052771355\t0.0447574735163511\t0.0945998555116551\t0.924632664607429\tNA\n FBgn0030619\t0.080862070626247\t0.0230872191457161\t0.0399975247953908\t0.577216196847676\t0.563793416904323\tNA\n+=======\n+=======\n+>>>>>>> add new deseq2\n+FBgn0030443\t0.080862070626247\t0.023087219145506\t0.0399975247950268\t0.577216196847677\t0.563793416904322\tNA\n+FBgn0030449\t0.631222387582343\t-0.069918508729723\t0.0690250631909992\t-1.01294378443742\t0.311087013088738\tNA\n+FBgn0030462\t0.0923751652987496\t-0.0204895043497049\t0.040273193485586\t-0.5087628413932\t0.610918468289381\tNA\n+FBgn0030477\t0.661041167025807\t-0.00819847469940316\t0.0850498198112658\t-0.0963961442551719\t0.923205954303339\tNA\n+FBgn0030491\t1.23119801662681\t0.0641480244241913\t0.107889436871621\t0.594571871762773\t0.552129686837968\tNA\n+FBgn0030492\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030493\t0.105352514349918\t0.0254741503089926\t0.040583050041178\t0.627704183967076\t0.530197743974527\tNA\n+FBgn0030494\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030495\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030509\t0.105352514349918\t0.0254741503089926\t0.040583050041178\t0.627704183967076\t0.530197743974527\tNA\n+FBgn0030536\t1.19456732550319\t-0.0654391021551412\t0.0865521046423288\t-0.756065983901423\t0.449609635388738\tNA\n+FBgn0030537\t0.0923751652987496\t-0.0204895043497049\t0.040273193485586\t-0.5087628413932\t0.610918468289381\tNA\n+FBgn0030538\t0.080862070626247\t0.023087219145506\t0.0399975247950268\t0.577216196847677\t0.563793416904322\tNA\n+FBgn0030539\t0.181391852667795\t0.000922878063793952\t0.0431227546273171\t0.0214011853317305\t0.982925628025152\tNA\n+FBgn0030540\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030541\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030542\t0.24813606918961\t0.0328712249934809\t0.0428867883451263\t0.766465064461196\t0.443399631338737\tNA\n+FBgn0030543\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030544\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030551\t0.700889780748892\t0.0020840503361408\t0.0848780550075907\t0.0245534648025856\t0.980411137804398\tNA\n+FBgn0030558\t0.100529782041548\t-0.0209903901433803\t0.0404598159836309\t-0.518795986414583\t0.603903017085169\tNA\n+FBgn0030563\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030566\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030569\t0.953050839550445\t0.0285435775734393\t0.0975885126788574\t0.292489113625187\t0.76991268222557\tNA\n+FBgn0030570\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030577\t0.269423611141796\t-0.026592624307814\t0.0432208120592152\t-0.615273592531775\t0.538374054087345\tNA\n+FBgn0030578\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030595\t0.90385617240921\t0.0140835782037349\t0.0874061821492121\t0.161127941496091\t0.87199263363864\tNA\n+FBgn0030608\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030614\t0.210705028699836\t0.0343775297986814\t0.043774172333087\t0.785338202104552\t0.432255303094243\tNA\n+FBgn0030617\t0.267076655602412\t0.0501740190928278\t0.0527678364612048\t0.950844727729477\t0.341683203385323\tNA\n+FBgn0030618\t0.205882296391466\t0.00423405052709174\t0.0447574735119474\t0.09459985550707\t0.924632664611071\tNA\n+FBgn0030619\t0.080862070626247\t0.023087219145506\t0.0399975247950268\t0.577216196847677\t0.563793416904322\tNA\n+<<<<<<< 32814b042e5c76fbb4786cff0edf98023718d3b2\n+>>>>>>> add new deseq2\n+=======\n+>>>>>>> add new deseq2\n FBgn0030620\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030621\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030622\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030623\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030624\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030640\t0\tNA\tNA\tNA\tNA\tNA\n+<<<<<<< 32814b042e5c76fbb4786cff0edf98023718d3b2\n+<<<<<<< c2d5ab40b214e429d8a9d0c5b2b35adfc46a87e6\n FBgn0030663\t1.2590203447849\t0.0316273222798865\t0.104066953284795\t0.303913214345129\t0.761194010092697\tNA\n FBgn0030688\t0.827337508607711\t0.0122149676539822\t0.0936309991990391\t0.130458584854102\t0.896203618553293\tNA\n+=======\n+FBgn0030663\t1.2590203447849\t0.0316273222752506\t0.104066953276194\t0.303913214325699\t0.7611940101075\tNA\n+FBgn0030688\t0.827337508607711\t0.0122149676551879\t0.0936309992070552\t0.13045858485581\t0.896203618551941\tNA\n+>>>>>>> add new deseq2\n+=======\n+FBgn0030663\t1.2590203447849\t0.0316273222752506\t0.104066953276194\t0.303913214325699\t0.7611940101075\tNA\n+FBgn0030688\t0.827337508607711\t0.0122149676551879\t0.0936309992070552\t0.13045858485581\t0.896203618551941\tNA\n+>>>>>>> add new deseq2\n' |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/deseq2_tximport_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq2_tximport_out.tab Wed Nov 09 17:00:31 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +WASH7P 9900.55558083217 -4.23770412981225 0.206202033070674 -20.5512238007848 7.50472789083548e-94 3.00189115633419e-93 +DDX11L1 537.947385623122 0.311741396087371 0.207236221043698 1.50428045115548 0.132509170400216 0.265018340800432 +MIR6859-1 1535.69554043224 0.215149819818111 0.188163332682435 1.1434205418822 0.252864027682612 0.337152036910149 +MIR6859-2 80.7433269754715 -0.177756822115013 0.275440925762787 -0.645353705600378 0.51869799671008 0.51869799671008 |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/genes_sub.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes_sub.gtf Wed Nov 09 17:00:31 2016 -0500 |
| b |
| @@ -0,0 +1,15 @@ +chr1 unknown exon 11874 12227 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NM_001168316"; tss_id "TSS16107"; +chr1 unknown exon 12613 12721 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NM_174914"; tss_id "TSS16107"; +chr1 unknown exon 13221 14409 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_031764"; tss_id "TSS16107"; +chr1 unknown exon 14362 14829 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_004503"; tss_id "TSS8151"; +chr1 unknown exon 14970 15038 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_006897"; tss_id "TSS8151"; +chr1 unknown exon 15796 15947 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_014212"; tss_id "TSS8151"; +chr1 unknown exon 16607 16765 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_014620"; tss_id "TSS8151"; +chr1 unknown exon 16858 17055 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_017409"; tss_id "TSS8151"; +chr1 unknown exon 17233 17368 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_017410"; tss_id "TSS8151"; +chr1 unknown exon 17369 17436 . - . gene_id "MIR6859-2"; gene_name "MIR6859-2"; transcript_id "NM_018953"; tss_id "TSS24460"; +chr1 unknown exon 17369 17436 . - . gene_id "MIR6859-1"; gene_name "MIR6859-1"; transcript_id "NM_022658"; tss_id "TSS24460"; +chr1 unknown exon 17606 17742 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_153633"; tss_id "TSS8151"; +chr1 unknown exon 17915 18061 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_153693"; tss_id "TSS8151"; +chr1 unknown exon 18268 18366 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NM_173860"; tss_id "TSS8151"; +chr1 unknown exon 24738 24891 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NR_003084"; tss_id "TSS8151"; |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/normalized_readcounts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/normalized_readcounts.tab Wed Nov 09 17:00:31 2016 -0500 |
| b |
| b'@@ -0,0 +1,4000 @@\n+\t1: Untreated\t2: Untreated\t3: Untreated\t4: Untreated\t5: Treated\t6: Treated\t7: Treated\n+FBgn0000003\t0\t0\t0\t0\t0\t0\t0\n+FBgn0000008\t28.2894791698886\t51.3707186232312\t36.8576909542011\t45.5881872175379\t33.0020972022181\t50.8852644310105\t33.39603516864\n+FBgn0000014\t0\t2.81483389716335\t0\t0\t0\t1.47493520089885\t1.13206898876746\n+FBgn0000015\t0\t0\t0.646626157091247\t0\t0\t0\t0\n+FBgn0000017\t2314.07939609689\t2481.27608034949\t1832.5385291966\t1906.8438308577\t1702.21343464072\t1751.48555106739\t1793.76331270204\n+FBgn0000018\t173.508805575317\t165.371491458347\t176.528940885911\t179.208735958597\t185.853915823018\t173.304886105615\t153.395347977991\n+FBgn0000022\t1.88596527799258\t0\t0\t0\t0\t0\t0\n+FBgn0000024\t0\t2.11112542287251\t1.29325231418249\t4.7160193673315\t1.73695248432727\t1.47493520089885\t0.566034494383729\n+FBgn0000028\t0\t0\t0\t0\t0\t0.737467600449427\t0.566034494383729\n+FBgn0000032\t439.42990977227\t417.299125254467\t419.013749795128\t627.23057585509\t477.661933189999\t407.819583048533\t393.393973596692\n+FBgn0000036\t0\t0\t0\t0\t0\t0\t0\n+FBgn0000037\t3.77193055598515\t4.92595932003587\t0\t6.28802582310867\t6.94780993730908\t6.63720840404485\t4.52827595506983\n+FBgn0000038\t0\t0\t0\t0\t0\t0\t0\n+FBgn0000039\t0\t0\t0\t0\t0\t0.737467600449427\t0\n+FBgn0000042\t30777.0673715608\t32142.5882717083\t32682.4258578629\t45948.1766959108\t35998.3402376827\t45250.2744959764\t45663.1347309242\n+FBgn0000043\t10608.5546887082\t11068.6305921206\t11095.4582295287\t13509.823480949\t16033.808382825\t18477.9881968608\t18723.289005225\n+FBgn0000044\t24.5175486139035\t9.85191864007173\t9.05276619927746\t9.432038734663\t17.3695248432727\t13.2744168080897\t10.1886208989071\n+FBgn0000045\t1.88596527799258\t2.81483389716335\t3.87975694254748\t0\t0\t6.63720840404485\t11.3206898876746\n+FBgn0000046\t7.5438611119703\t3.51854237145419\t3.23313078545624\t0\t15.6325723589454\t17.6992224107863\t10.1886208989071\n+FBgn0000047\t3.77193055598515\t1.40741694858168\t1.93987847127374\t1.57200645577717\t3.47390496865454\t8.84961120539313\t5.66034494383729\n+FBgn0000052\t920.351055660377\t1134.37806055683\t1169.10009202098\t1136.56066752689\t906.689196818835\t1061.21587704673\t1000.18295157605\n+FBgn0000053\t709.122944525208\t880.339301337838\t896.223853728469\t801.723292446355\t918.847864209126\t1175.52335511639\t1119.61622989102\n+FBgn0000054\t267.807069474946\t320.187355802331\t276.109369077963\t345.841420270977\t267.4906825864\t278.762752969884\t323.205696293109\n+FBgn0000055\t0\t0\t0\t0\t0\t0\t0\n+FBgn0000056\t0\t0\t0\t0\t0\t0\t0\n+FBgn0000057\t299.868479200819\t307.520603265096\t343.358489415452\t337.981387992091\t270.964587555054\t348.822175012579\t345.847076068458\n+FBgn0000061\t0\t0\t0.646626157091247\t0\t1.73695248432727\t0.737467600449427\t0\n+FBgn0000063\t188.596527799258\t147.778779601076\t150.663894602261\t185.496761781706\t175.432200917054\t185.104367712806\t178.866900225258\n+FBgn0000064\t3409.82522261058\t3441.83814775649\t3365.68914765994\t3092.13669851369\t3849.08670526923\t3953.56380600938\t4139.41025742821\n+FBgn0000071\t54.6929930617847\t53.4818440461037\t54.3165971956648\t29.8681226597662\t253.595062711781\t283.925026173029\t328.866041236947\n+FBgn0000075\t1.88596527799258\t0\t0.646626157091247\t0\t0\t0\t0.566034494383729\n+FBgn0000077\t75.438611119703\t77.4079321719922\t100.873680506235\t100.608413169739\t74.6889568260726\t82.5963712503359\t104.150346966606\n+FBgn0000078\t9.42982638996288\t14.0741694858168\t19.3987847127374\t7.86003227888584\t3.47390496865454\t8.1121436049437\t9.05655191013967\n+FBgn0000079\t52.8070277837921\t137.926860961004\t129.971857575341\t75.456309877304\t15.6325723589454\t55.310070033707\t52.6412079776868\n+FBgn0000083\t2425.35134749845\t2515.75779558975\t2735.22864449598\t2244.82521884979\t2264.98603956276\t2619.48491679637\t2651.87160618777\n+FBgn0000084\t752.500145919038\t916.228433526671\t941.487684724856\t784.431221432806\t574.931272312326\t761.804031264258\t843.95743112614\n+FBgn0000092\t5.65789583397773\t7.03708474290838\t6.46626157091247\t3.14401291155433\t3.47390496865454\t2.94987040179771\t4.52827595506983\n+FBgn0000094\t7.5438611119703\t9.14821016578089\t2.58650462836499\t1.57200645577717\t13.8956198746182\t3.68733800224714\t3.9622414606861\n+FBgn0000097\t14'..b'9141128\t453.344598409417\t523.601996319093\t483.393458203705\n+FBgn0030659\t209.342145857176\t197.742081275725\t206.920370269199\t193.356794060592\t187.590868307345\t212.390668929435\t220.753452809654\n+FBgn0030660\t56.5789583397773\t61.9263457375937\t58.1963541382123\t95.8923938024072\t81.6367667633817\t84.0713064512347\t66.79207033728\n+FBgn0030661\t7.5438611119703\t15.4815864343984\t6.46626157091247\t7.86003227888584\t19.1064773276\t7.37467600449427\t16.9810348315119\n+FBgn0030662\t254.605312528998\t320.187355802331\t268.996481349959\t169.776697223934\t305.703637241599\t420.356532256174\t442.072940113692\n+FBgn0030663\t0\t3.51854237145419\t0.646626157091247\t0\t0\t2.94987040179771\t1.69810348315119\n+FBgn0030664\t9.42982638996288\t2.81483389716335\t8.40614004218622\t3.14401291155433\t8.68476242163635\t3.68733800224714\t6.22637943822102\n+FBgn0030665\t3.77193055598515\t2.81483389716335\t1.93987847127374\t3.14401291155433\t1.73695248432727\t0.737467600449427\t1.13206898876746\n+FBgn0030666\t9.42982638996288\t10.5556271143626\t10.34601851346\t7.86003227888584\t1.73695248432727\t0.737467600449427\t2.26413797753492\n+FBgn0030667\t62.236854173755\t20.4075457544343\t38.7975694254748\t42.4441743059835\t79.8998142790544\t50.1477968305611\t40.7544835956285\n+FBgn0030668\t122.587743069517\t96.4080609778448\t128.031979104067\t124.188510006396\t85.1106717320362\t102.50799646247\t100.754140000304\n+FBgn0030669\t101.842125011599\t102.037728772172\t118.332586747698\t117.900484183288\t99.0062916066544\t79.6465008485382\t83.7731051687919\n+FBgn0030670\t284.780756976879\t270.927762601973\t307.147424618343\t388.28559457696\t267.4906825864\t238.202034945165\t245.092936068155\n+FBgn0030671\t124.47370834751\t156.223281292566\t154.543651544808\t122.616503550619\t177.169153401382\t130.531765279549\t116.037071348664\n+FBgn0030672\t2595.08822251778\t3063.94669706231\t3163.29516049038\t3188.0290923161\t2079.13212373974\t2461.66685030019\t2495.64608573786\n+FBgn0030673\t41.4912361158367\t28.8520474459244\t38.7975694254748\t48.7322001290922\t36.4760021708727\t32.4485744197748\t37.3582766293261\n+FBgn0030674\t3815.30775737898\t5111.03464877436\t3873.29068097657\t4261.7095016119\t3661.49583696188\t4747.81641169341\t4215.25887967563\n+FBgn0030675\t26.4035138918961\t33.7780067659602\t47.2037094676611\t33.0121355713205\t31.2651447178909\t35.3984448215725\t43.0186215731634\n+FBgn0030676\t7.5438611119703\t6.33337626861754\t3.87975694254748\t0\t12.1586673902909\t0.737467600449427\t5.09431044945356\n+FBgn0030678\t84.8684375096659\t121.037857578024\t89.8810358356834\t119.472490639065\t59.0563844671272\t106.195334464718\t106.414484944141\n+FBgn0030679\t224.429868081116\t172.408576201255\t223.732650353572\t172.920710135488\t125.060578871563\t197.641316920447\t209.998797416364\n+FBgn0030680\t256.49127780699\t264.594386333355\t229.552285767393\t240.516987733907\t218.856013025236\t240.414437746513\t251.885350000759\n+FBgn0030683\t84.8684375096659\t99.2228948750082\t112.512951333877\t160.344658489271\t105.954101543963\t126.106959676852\t109.810691910443\n+FBgn0030684\t0\t5.6296677943267\t0.646626157091247\t4.7160193673315\t0\t1.47493520089885\t0\n+FBgn0030685\t1250.39497930908\t987.302989430046\t914.329386127024\t1183.72086120021\t769.469950556981\t778.765786074595\t796.976568092291\n+FBgn0030686\t237.631625027064\t188.593871109945\t219.206267253933\t216.936890897249\t149.377913652145\t198.378784520896\t189.055521124166\n+FBgn0030687\t275.350930586916\t366.632115105527\t344.005115572544\t400.861646223178\t281.386302461018\t396.757569041792\t382.639318203401\n+FBgn0030688\t0\t0.703708474290838\t0.646626157091247\t1.57200645577717\t1.73695248432727\t0\t1.13206898876746\n+FBgn0030691\t13.201756945948\t11.2593355886534\t5.17300925672998\t14.1480581019945\t12.1586673902909\t14.7493520089885\t7.35844842698848\n+FBgn0030692\t350.789541706619\t343.409735453929\t347.884872515091\t378.853555842297\t295.281922335636\t367.996332624264\t353.771558989831\n+FBgn0030693\t179.166701409295\t128.074942320933\t156.483530016082\t198.072813427923\t217.119060540909\t143.068714487189\t133.58414067456\n+FBgn0030694\t111.271951401562\t99.926603349299\t108.63319439133\t86.4603550677442\t104.217149059636\t81.8589036498864\t119.999312809351\n' |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/sailfish_quant_result1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_quant_result1.tab Wed Nov 09 17:00:31 2016 -0500 |
| [ |
| @@ -0,0 +1,32 @@ +# sailfish (quasi-mapping-based) v0.7.6 +# [ program ] => sailfish +# [ command ] => quant +# [ index ] => { ./index_dir } +# [ mates1 ] => { ./mate1.fastq } +# [ mates2 ] => { ./mate2.fastq } +# [ libType ] => { IU } +# [ output ] => { ./ } +# [ biasCorrect ] => { } +# [ threads ] => { 1 } +# [ fldMean ] => { 200 } +# [ fldSD ] => { 80 } +# [ maxReadOcc ] => { 200 } +# [ maxFragLen ] => { 1000 } +# [ txpAggregationKey ] => { gene_id } +# [ mapping rate ] => { 100% } +# Name Length TPM NumReads +NM_001168316 2283 12398.5 159.361 +NM_174914 2385 111257 1500.04 +NR_031764 1853 10254.5 104.595 +NM_004503 1681 36198.8 330.806 +NM_006897 1541 80244.3 664 +NM_014212 2037 4852.08 55 +NM_014620 2300 45132.7 584.838 +NM_017409 1959 4330.19 47 +NM_017410 2396 3099.5 42 +NM_018953 1612 26168.3 228 +NM_022658 2288 378838 4881 +NM_153633 1666 40578.4 367.074 +NM_153693 2072 6430.57 74.2815 +NM_173860 849 240218 962 +NR_003084 1640 0 0 |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/sailfish_quant_result2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_quant_result2.tab Wed Nov 09 17:00:31 2016 -0500 |
| [ |
| @@ -0,0 +1,32 @@ +# sailfish (quasi-mapping-based) v0.7.6 +# [ program ] => sailfish +# [ command ] => quant +# [ index ] => { ./index_dir } +# [ mates1 ] => { ./mate1.fastq } +# [ mates2 ] => { ./mate2.fastq } +# [ libType ] => { IU } +# [ output ] => { ./ } +# [ biasCorrect ] => { } +# [ threads ] => { 1 } +# [ fldMean ] => { 200 } +# [ fldSD ] => { 80 } +# [ maxReadOcc ] => { 200 } +# [ maxFragLen ] => { 1000 } +# [ txpAggregationKey ] => { gene_id } +# [ mapping rate ] => { 100% } +# Name Length TPM NumReads +NM_001168316 2283 1239.5 159.361 +NM_174914 2385 11125 1505.04 +NR_031764 1853 1025.5 100.595 +NM_004503 1681 3619.8 320.806 +NM_006897 1541 8224.3 660 +NM_014212 2037 485.08 60 +NM_014620 2300 4513.7 580.838 +NM_017409 1959 433.19 45 +NM_017410 2396 3219.5 40 +NM_018953 1612 2616.3 220 +NM_022658 2288 37883 4880 +NM_153633 1666 4057.4 360.074 +NM_153693 2072 643.57 70.2815 +NM_173860 849 2521 960 +NR_003084 1640 1000 10 |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/sailfish_quant_result3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_quant_result3.tab Wed Nov 09 17:00:31 2016 -0500 |
| [ |
| @@ -0,0 +1,32 @@ +# sailfish (quasi-mapping-based) v0.7.6 +# [ program ] => sailfish +# [ command ] => quant +# [ index ] => { ./index_dir } +# [ mates1 ] => { ./mate1.fastq } +# [ mates2 ] => { ./mate2.fastq } +# [ libType ] => { IU } +# [ output ] => { ./ } +# [ biasCorrect ] => { } +# [ threads ] => { 1 } +# [ fldMean ] => { 200 } +# [ fldSD ] => { 80 } +# [ maxReadOcc ] => { 200 } +# [ maxFragLen ] => { 1000 } +# [ txpAggregationKey ] => { gene_id } +# [ mapping rate ] => { 100% } +# Name Length TPM NumReads +NM_001168316 2283 12398.5 15.361 +NM_174914 2385 121257 150.04 +NR_031764 1853 14254.5 10.595 +NM_004503 1681 30198.8 30.806 +NM_006897 1541 70244.3 64 +NM_014212 2037 4452.08 555 +NM_014620 2300 42132.7 54.838 +NM_017409 1959 4230.19 475 +NM_017410 2396 3199.5 423 +NM_018953 1612 29168.3 28 +NM_022658 2288 318838 481 +NM_153633 1666 41578.4 3367.074 +NM_153693 2072 6430.57 742.2815 +NM_173860 849 240218 92 +NR_003084 1640 0 90 |
| b |
| diff -r d38fd393402e -r 4939397c4706 test-data/sailfish_quant_result4.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_quant_result4.tab Wed Nov 09 17:00:31 2016 -0500 |
| [ |
| @@ -0,0 +1,32 @@ +# sailfish (quasi-mapping-based) v0.7.6 +# [ program ] => sailfish +# [ command ] => quant +# [ index ] => { ./index_dir } +# [ mates1 ] => { ./mate1.fastq } +# [ mates2 ] => { ./mate2.fastq } +# [ libType ] => { IU } +# [ output ] => { ./ } +# [ biasCorrect ] => { } +# [ threads ] => { 1 } +# [ fldMean ] => { 200 } +# [ fldSD ] => { 80 } +# [ maxReadOcc ] => { 200 } +# [ maxFragLen ] => { 1000 } +# [ txpAggregationKey ] => { gene_id } +# [ mapping rate ] => { 100% } +# Name Length TPM NumReads +NM_001168316 2283 12398.5 15.361 +NM_174914 2385 111260 120.04 +NR_031764 1853 10300.5 12.595 +NM_004503 1681 36250.8 32.806 +NM_006897 1541 80900.3 75 +NM_014212 2037 4900.08 540 +NM_014620 2300 45300.7 51.838 +NM_017409 1959 4400.19 470 +NM_017410 2396 3500.5 420 +NM_018953 1612 26568.3 30 +NM_022658 2288 378938 480 +NM_153633 1666 40878.4 3350.074 +NM_153693 2072 6830.57 740.2815 +NM_173860 849 240818 90 +NR_003084 1640 20 95 |