changeset 15:9a616afdbda5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
author iuc
date Sat, 19 May 2018 03:55:48 -0400
parents d0c39b5e78cf
children a416957ee305
files deseq2.R deseq2.xml test-data/GSM461176_untreat_single.counts test-data/GSM461176_untreat_single.counts.noheader test-data/GSM461177_untreat_paired.counts test-data/GSM461177_untreat_paired.counts.noheader test-data/GSM461178_untreat_paired.counts test-data/GSM461178_untreat_paired.counts.noheader test-data/GSM461179_treat_single.counts test-data/GSM461179_treat_single.counts.noheader test-data/GSM461180_treat_paired.counts test-data/GSM461180_treat_paired.counts.noheader test-data/GSM461181_treat_paired.counts test-data/GSM461181_treat_paired.counts.noheader test-data/GSM461182_untreat_single.counts test-data/GSM461182_untreat_single.counts.noheader test-data/deseq2_out.tab test-data/normalized_readcounts.tab test-data/sailfish/out_deseq2_sailfish.tab
diffstat 19 files changed, 28135 insertions(+), 8034 deletions(-) [+]
line wrap: on
line diff
--- a/deseq2.R	Thu Apr 12 17:29:45 2018 -0400
+++ b/deseq2.R	Sat May 19 03:55:48 2018 -0400
@@ -8,14 +8,14 @@
 #   'factors' a JSON list object from Galaxy
 #
 # the output file has columns:
-# 
+#
 #   baseMean (mean normalized count)
 #   log2FoldChange (by default a moderated LFC estimate)
 #   lfcSE (the standard error)
 #   stat (the Wald statistic)
 #   pvalue (p-value from comparison of Wald statistic to a standard Normal)
 #   padj (adjusted p-value, Benjamini Hochberg correction on genes which pass the mean count filter)
-# 
+#
 # the first variable in 'factors' will be the primary factor.
 # the levels of the primary factor are used in the order of appearance in factors.
 #
@@ -48,6 +48,7 @@
   "help", "h", 0, "logical",
   "outfile", "o", 1, "character",
   "countsfile", "n", 1, "character",
+  "header", "H", 0, "logical",
   "factors", "f", 1, "character",
   "files_to_labels", "l", 1, "character",
   "plots" , "p", 1, "character",
@@ -86,6 +87,12 @@
   FALSE
 }
 
+if (!is.null(opt$header)) {
+  hasHeader <- TRUE
+} else {
+  hasHeader <- FALSE
+}
+
 if (!is.null(opt$tximport)) {
   if (is.null(opt$tx2gene)) stop("A transcript-to-gene map or a GTF file is required for tximport")
   if (tolower(file_ext(opt$tx2gene)) == "gtf") {
@@ -138,15 +145,6 @@
 primaryFactor <- factors[1]
 designFormula <- as.formula(paste("~", paste(rev(factors), collapse=" + ")))
 
-if (verbose) {
-  cat("DESeq2 run information\n\n")
-  cat("sample table:\n")
-  print(sampleTable[,-c(1:2),drop=FALSE])
-  cat("\ndesign formula:\n")
-  print(designFormula)
-  cat("\n\n")
-}
-
 # these are plots which are made once for each analysis
 generateGenericPlots <- function(dds, factors) {
   library("ggplot2")
@@ -202,13 +200,29 @@
 # For JSON input from Galaxy, path is absolute
 dir <- ""
 
-if (!useTXI) {
+if (!useTXI & hasHeader) {
+    countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
+    tbl <- do.call("cbind", countfiles)
+    rownames(sampleTable) <- colnames(tbl) # 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 = sampleTable[,-c(1:2), drop=FALSE],
+                                  design = designFormula)
+} else if (!useTXI & !hasHeader) {
+
   # construct the object from HTSeq files
   dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
                                     directory = dir,
                                     design =  designFormula)
   labs <- unname(unlist(filenames_to_labels[colnames(dds)]))
   colnames(dds) <- labs
+
 } else {
     # construct the object using tximport
     # first need to make the tx2gene table
@@ -232,7 +246,16 @@
                                     designFormula)
 }
 
-if (verbose) cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
+if (verbose) {
+  cat("DESeq2 run information\n\n")
+  cat("sample table:\n")
+  print(sampleTable[,-c(1:2),drop=FALSE])
+  cat("\ndesign formula:\n")
+  print(designFormula)
+  cat("\n\n")
+  cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
+}
+
 # optional outlier behavior
 if (is.null(opt$outlier_replace_off)) {
   minRep <- 7
@@ -242,7 +265,7 @@
 }
 if (is.null(opt$outlier_filter_off)) {
   cooksCutoff <- TRUE
-} else {  
+} else {
   cooksCutoff <- FALSE
   if (verbose) cat("outlier filtering off\n")
 }
--- a/deseq2.xml	Thu Apr 12 17:29:45 2018 -0400
+++ b/deseq2.xml	Sat May 19 03:55:48 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deseq2" name="DESeq2" version="2.11.40.1">
+<tool id="deseq2" name="DESeq2" version="2.11.40.2">
     <description>Determines differentially expressed features from count tables</description>
     <requirements>
         <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
@@ -58,6 +58,9 @@
         $temp_factor.reverse()
         $temp_factor_names.append([str($factor.factorName), $temp_factor])
     #end for
+
+    $header
+
     -f '#echo json.dumps(temp_factor_names)#'
     -l '#echo json.dumps(filename_to_element_identifiers)#'
     -t $fit_type
@@ -103,6 +106,8 @@
             </repeat>
         </repeat>
 
+        <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>
@@ -174,7 +179,7 @@
         </data>
     </outputs>
     <tests>
-        <!--Ensure tables output works-->
+        <!--Ensure counts files with header works -->
         <test expect_num_outputs="2">
             <repeat name="rep_factorName">
                 <param name="factorName" value="Treatment"/>
@@ -189,8 +194,45 @@
             </repeat>
             <param name="pdf" value="False"/>
             <param name="normCounts" value="True"/>
-            <output name="counts_out" file="normalized_readcounts.tab"/>
-            <output name="deseq_out" file="deseq2_out.tab"/>
+            <output name="counts_out">
+                <assert_contents>
+                    <has_text_matching expression="untreat1\tuntreat2\tuntreat3\tuntreat4\ttreat1\ttreat2\ttreat3" />
+                    <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
+                </assert_contents>
+            </output>
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
+                </assert_contents>
+            </output>
+        </test>
+        <!--Ensure counts files without header works -->
+        <test expect_num_outputs="2">
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment"/>
+                <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>
+            </repeat>
+            <param name="header" value="False"/>
+            <param name="pdf" value="False"/>
+            <param name="normCounts" value="True"/>
+            <output name="counts_out">
+                <assert_contents>
+                    <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
+                    <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
+                </assert_contents>
+            </output>
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
+                </assert_contents>
+            </output>
         </test>
         <!--Ensure Sailfish/Salmon input with tx2gene table works-->
         <test expect_num_outputs="1">
@@ -210,8 +252,12 @@
             <param name="txtype" value="sailfish"/>
             <param name="mapping_format_selector" value="tabular"/>
             <param name="tabular_file" value="tx2gene.tab"/>
-            <output name="deseq_out" file="sailfish/out_deseq2_sailfish.tab"/>
-        </test>               
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="MIR6859-2\t1.1858.*\t-1.5832.*\t1.2956.*\t-1.2219.*\t0.2217.*\t0.8868.*" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
@@ -226,7 +272,7 @@
 
 **Count Files**
 
-DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually, should have no header rows, and rows should be in the same order. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
+DESeq2_ 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. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
 
 The following table gives some examples of factors and their levels:
 
@@ -246,7 +292,7 @@
 
 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
 
-DESeq2_ 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. 
+DESeq2_ 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**
 
@@ -275,17 +321,17 @@
 Example:
 
 ============ ========== =============== =========== ===========
-target_id    length     eff_length      est_counts  tpm 
+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    
+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  
+NM_001198819 9527       7964.62         0           0
+NM_001198820 9410       7855.78         0           0
+NM_014576    9267       7714.88         8.37255     0.0481114
 ============ ========== =============== =========== ===========
 
 -----
--- a/test-data/GSM461176_untreat_single.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461176_untreat_single.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	untreat1
 FBgn0000003	0
 FBgn0000008	15
 FBgn0000014	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461176_untreat_single.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
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+no_feature	172410
+ambiguous	33519
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+alignment_not_unique	8666693
--- a/test-data/GSM461177_untreat_paired.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461177_untreat_paired.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	untreat2
 FBgn0000003	0
 FBgn0000008	73
 FBgn0000014	4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461177_untreat_paired.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
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+no_feature	349912
+ambiguous	83890
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+alignment_not_unique	13300038
--- a/test-data/GSM461178_untreat_paired.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461178_untreat_paired.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	untreat3
 FBgn0000003	0
 FBgn0000008	57
 FBgn0000014	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461178_untreat_paired.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
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+alignment_not_unique	11365569
--- a/test-data/GSM461179_treat_single.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461179_treat_single.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	treat1
 FBgn0000003	0
 FBgn0000008	19
 FBgn0000014	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461179_treat_single.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
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+ambiguous	43070
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+alignment_not_unique	14421559
--- a/test-data/GSM461180_treat_paired.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461180_treat_paired.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	treat2
 FBgn0000003	0
 FBgn0000008	69
 FBgn0000014	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461180_treat_paired.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
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+ambiguous	83194
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+alignment_not_unique	11922916
--- a/test-data/GSM461181_treat_paired.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461181_treat_paired.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	treat3
 FBgn0000003	0
 FBgn0000008	59
 FBgn0000014	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461181_treat_paired.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
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+alignment_not_unique	12749496
--- a/test-data/GSM461182_untreat_single.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461182_untreat_single.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	untreat4
 FBgn0000003	0
 FBgn0000008	29
 FBgn0000014	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461182_untreat_single.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
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+ambiguous	48373
+too_low_aQual	0
+not_aligned	0
+alignment_not_unique	6896814
--- a/test-data/deseq2_out.tab	Thu Apr 12 17:29:45 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3999 +0,0 @@
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-FBgn0025388	167.320611609436	0.00314908728570882	0.15021944713689	0.0209632464086967	0.983274974345384	0.992379372255989
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-FBgn0030269	244.888249313562	0.00261603084368685	0.130587879522223	0.0200327231995651	0.984017268460375	0.992774987118797
-FBgn0001259	4.58029246890164	-0.00305280985773013	0.172757730112872	-0.0176710463591735	0.98590127869887	0.993878453504133
-FBgn0016120	1041.94394787703	0.00210238879857459	0.1210402627432	0.0173693343927634	0.98614197307351	0.993878453504133
-FBgn0030289	461.157009013363	0.00251937867005947	0.145268944261133	0.0173428579857418	0.986163095008335	0.993878453504133
-FBgn0029905	298.198980081934	-0.002674357985816	0.162012683818346	-0.016507090202978	0.986829845695426	0.994196865517539
-FBgn0020388	580.961490983375	-0.00194035721902167	0.120805907964119	-0.016061774227118	0.987185109326296	0.994201350330747
-FBgn0023081	686.565770727805	0.00174484720795943	0.11494110538425	0.0151803586900124	0.987888291352574	0.994556098647671
-FBgn0002441	758.5523891712	-0.00131990995513649	0.0983418112827841	-0.0134216559357552	0.989291389459115	0.995023840801423
-FBgn0004028	2.28788658416954	-0.00184603272353732	0.143453037598221	-0.0128685509518985	0.989732665254118	0.995023840801423
-FBgn0004145	7491.45125397969	-0.00173132067848596	0.130735346083461	-0.0132429425580186	0.989433969431458	0.995023840801423
-FBgn0013753	257.142556697253	0.00176669459661468	0.147060504114112	0.0120133859682937	0.990414935368546	0.995023840801423
-FBgn0029508	9.16870388329025	0.00181163494877155	0.148275321853417	0.0122180476570639	0.990251650951921	0.995023840801423
-FBgn0030594	3.62961762362224	-0.00200184429802549	0.167413079084327	-0.011957514364915	0.990459511256463	0.995023840801423
-FBgn0017545	12846.908740161	0.00194663965106323	0.176329464444646	0.0110397865563434	0.991191703673788	0.99540655145695
-FBgn0024230	108.716502253845	-0.00173422559968481	0.178807465301691	-0.00969884337188475	0.992261563938755	0.996127974566926
-FBgn0012049	1265.58497665408	0.00101117762944179	0.135745746875029	0.00744905569949612	0.994056568430144	0.997576598771611
-FBgn0001330	194.903765892257	-0.000816269237547889	0.14376919601152	-0.00567763651876083	0.995469925818087	0.99758195536367
-FBgn0019968	916.955935302438	0.000652756303083771	0.111176432369112	0.00587135500909567	0.995315363402696	0.99758195536367
-FBgn0026144	5.67468986225991	0.000953027816136364	0.15634695816877	0.0060955955094925	0.995136448572679	0.99758195536367
-FBgn0029128	2.36245282088433	-0.000882240149496632	0.13466626528014	-0.00655130776561855	0.994772850071998	0.99758195536367
-FBgn0029858	84.7675753900815	-0.000900927656668868	0.189266326880986	-0.00476010535796675	0.996201999769985	0.997962696128716
-FBgn0020521	2.3653829049525	-0.000570950637375731	0.141108882116086	-0.00404617079246669	0.996771631603193	0.998180496100158
-FBgn0026619	134.661568577878	-0.000562339849358497	0.167804683312013	-0.00335115706105111	0.997326168524797	0.998383031296106
-FBgn0010504	279.265073900721	-0.000280958492894278	0.124020050305149	-0.00226542798686975	0.998192451531772	0.998897389703758
-FBgn0011327	221.75669985069	-0.000210436168350216	0.13552520454093	-0.00155274562442488	0.998761088737257	0.999113634126857
-FBgn0010602	788.37057626526	-0.000120355421911384	0.117913033701391	-0.00102071347105002	0.999185588621862	0.999185588621862
-FBgn0000003	0	NA	NA	NA	NA	NA
-FBgn0000014	0.774548298118524	0.00827091884508803	0.0792234901769868	0.104399829225027	0.916852058201328	NA
-FBgn0000015	0.0923751652987496	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0000022	0.269423611141796	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055694	NA
-FBgn0000024	1.69975989771377	-0.0649857620871372	0.122161429533376	-0.531966287029922	0.59474934530007	NA
-FBgn0000028	0.186214584976165	0.0201334916603579	0.0477240779962571	0.421872826164121	0.673117845457942	NA
-FBgn0000036	0	NA	NA	NA	NA	NA
-FBgn0000038	0	NA	NA	NA	NA	NA
-FBgn0000039	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000055	0	NA	NA	NA	NA	NA
-FBgn0000056	0	NA	NA	NA	NA	NA
-FBgn0000061	0.445863748838278	0.0236941571706422	0.0652997224824485	0.362852341018919	0.716715190114075	NA
-FBgn0000075	0.442660847066793	-0.0182864656152097	0.0656824086658754	-0.278407354216141	0.780699674746967	NA
-FBgn0000099	0.623359594557074	-0.0517130223359342	0.0811858332134595	-0.636971011924786	0.524143725764871	NA
-FBgn0000114	1.39555611045902	0.0940677834394133	0.109110027229822	0.862136925704137	0.388612173696114	NA
-FBgn0000120	0	NA	NA	NA	NA	NA
-FBgn0000137	0	NA	NA	NA	NA	NA
-FBgn0000157	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0000166	0	NA	NA	NA	NA	NA
-FBgn0000179	0.080862070626247	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000182	1.47923912999568	-0.0477002131031881	0.120568571223928	-0.39562725691255	0.692380026225681	NA
-FBgn0000206	0	NA	NA	NA	NA	NA
-FBgn0000216	0	NA	NA	NA	NA	NA
-FBgn0000227	0	NA	NA	NA	NA	NA
-FBgn0000251	0.192904947340298	-0.0204639299876315	0.0477425687456119	-0.428630685891034	0.668192010513688	NA
-FBgn0000274	0	NA	NA	NA	NA	NA
-FBgn0000280	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000281	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000287	0.173237235924997	-0.000839291635723297	0.0477190025576663	-0.0175882057616156	0.985967365661815	NA
-FBgn0000316	0.921169656371541	0.0172285198615874	0.0926383128097293	0.185976183493035	0.852463438308974	NA
-FBgn0000320	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000355	0.493995961967106	-0.0325960466747746	0.0597096898052577	-0.545908826207039	0.585128610979899	NA
-FBgn0000356	0	NA	NA	NA	NA	NA
-FBgn0000357	1.28471435211849	0.0185043049284226	0.108976417784541	0.169801001947117	0.865166638932622	NA
-FBgn0000358	0	NA	NA	NA	NA	NA
-FBgn0000359	0.24813606918961	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000360	0.197727679648668	0.000574771843391052	0.0477473668015818	0.0120377704969484	0.990395480736373	NA
-FBgn0000411	0	NA	NA	NA	NA	NA
-FBgn0000422	1.68680673237329	0.0656458649828095	0.114483271777059	0.573410105806951	0.56636704939483	NA
-FBgn0000427	0	NA	NA	NA	NA	NA
-FBgn0000439	0	NA	NA	NA	NA	NA
-FBgn0000442	1.10500053352326	0.0805271688225853	0.0950934022533201	0.846821829006269	0.397094439101338	NA
-FBgn0000448	0.919712673906461	-0.00475599192205054	0.0950691985689148	-0.0500266331645046	0.960101164692769	NA
-FBgn0000449	0	NA	NA	NA	NA	NA
-FBgn0000451	0	NA	NA	NA	NA	NA
-FBgn0000459	1.61630997945269	0.0386471964747248	0.122640923395735	0.315124800145371	0.752666899291821	NA
-FBgn0000463	0.726807726566163	0.0241170179953986	0.0823595509751875	0.292826001475704	0.769655152666192	NA
-FBgn0000477	0.254099306551244	0.00860352943176375	0.0494791875154284	0.173881784721728	0.861958368235681	NA
-FBgn0000492	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000497	0.819098094833964	-0.0841694069475181	0.0784495357277188	-1.07291147317496	0.283310837815622	NA
-FBgn0000529	0.080862070626247	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000551	0.286744367017713	0.013782588972083	0.0582379938969298	0.236659748213093	0.81292076418579	NA
-FBgn0000552	0	NA	NA	NA	NA	NA
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-FBgn0000564	0	NA	NA	NA	NA	NA
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-FBgn0000577	0.61589808299179	-0.0180513176085535	0.0734322095907834	-0.245822884932215	0.805819340928424	NA
-FBgn0000591	0	NA	NA	NA	NA	NA
-FBgn0000592	1.00774443238046	-0.0352744888274089	0.0941813361297807	-0.374537995286042	0.708004094021048	NA
-FBgn0000606	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0000625	0.323448282504988	0.0296965510243367	0.0482974150248852	0.614868332167168	0.538641677879811	NA
-FBgn0000639	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0000640	0	NA	NA	NA	NA	NA
-FBgn0000644	1.63017730157817	-0.0308862274780214	0.118954323778342	-0.25964779166476	0.795135467825544	NA
-FBgn0000658	0.846115246948708	0.0742975558345013	0.0874392495942088	0.849704865713099	0.395489192568613	NA
-FBgn0000659	0.328998139815857	0.0252805407520915	0.0533992539071623	0.473424980731813	0.635910011077094	NA
-FBgn0000715	0.269423611141796	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055694	NA
-FBgn0000964	0.0923751652987496	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0001077	0	NA	NA	NA	NA	NA
-FBgn0001099	0	NA	NA	NA	NA	NA
-FBgn0001112	0.348665851231158	0.000502290175296151	0.0540960040618429	0.00928516225934043	0.992591618840199	NA
-FBgn0001120	0.621705744195204	0.0505196485335101	0.08102055776735	0.623541110128826	0.532928995844344	NA
-FBgn0001138	0.43114775239429	0.00967882033274035	0.0587726290686068	0.164682446338108	0.869193934117942	NA
-FBgn0001147	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0001148	0	NA	NA	NA	NA	NA
-FBgn0001170	0.718619244414503	-0.0254649991003843	0.0748975505814948	-0.339997755636564	0.733858218101065	NA
-FBgn0001174	0.0923751652987496	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0001180	1.34748934434486	-0.102400454763687	0.112096130495904	-0.913505705421544	0.36097663428397	NA
-FBgn0001208	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0001216	0.602765157782402	0.0298555626573168	0.0786258744279614	0.37971676467231	0.704155674244981	NA
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-FBgn0001223	0	NA	NA	NA	NA	NA
-FBgn0001228	0	NA	NA	NA	NA	NA
-FBgn0001229	1.0632628384938	0.0961290227900536	0.0889983094852341	1.08012189609065	0.280087902568379	NA
-FBgn0001235	0.369953393183345	-0.028331480308904	0.0557663788864834	-0.508038730048705	0.61142618220108	NA
-FBgn0001253	1.02116918130738	-0.0815290193678546	0.100729934714066	-0.80938223179916	0.418295319301694	NA
-FBgn0001254	0.0923751652987496	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0001256	0.594525744008654	-0.0589579552523139	0.0709349875634939	-0.831154797899142	0.40588618661457	NA
-FBgn0001269	0	NA	NA	NA	NA	NA
-FBgn0001281	0.24813606918961	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0001285	0	NA	NA	NA	NA	NA
-FBgn0001313	0	NA	NA	NA	NA	NA
-FBgn0001314	0	NA	NA	NA	NA	NA
-FBgn0001315	0	NA	NA	NA	NA	NA
-FBgn0001319	0.278589750274915	0.0144150844382529	0.0576582512103723	0.250009047025341	0.802580352249562	NA
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-FBgn0001323	0	NA	NA	NA	NA	NA
-FBgn0001325	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0001560	0	NA	NA	NA	NA	NA
-FBgn0001981	0.952837059856552	0.0194978431030571	0.0854129788985432	0.228277287064503	0.819430680730071	NA
-FBgn0001983	0	NA	NA	NA	NA	NA
-FBgn0001991	0.997208994689418	-0.00528900908300704	0.101016096396459	-0.0523580822431427	0.958243373801215	NA
-FBgn0001992	1.54548015999867	0.0766532509804148	0.115823665195247	0.661809923310561	0.508093045665439	NA
-FBgn0002023	0.9722658189774	-0.0167597176646354	0.0906426368133172	-0.184898831872608	0.853308387225119	NA
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-FBgn0003046	1.22178134551473	-0.0361974104459997	0.111151653030326	-0.325657868858899	0.74468322370699	NA
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-FBgn0003091	0.992386262381048	-0.0421969348604122	0.0958002097441631	-0.440468084288126	0.659598122945602	NA
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-FBgn0004622	0.361798776440546	-0.0277515590377991	0.0554125313766664	-0.500817384594073	0.616499649562129	NA
-FBgn0004623	0.869841813384814	0.0946100025737526	0.0950554699559621	0.99531360601956	0.319583762367972	NA
-FBgn0004644	1.73346014729628	-0.153341845562659	0.114301339927642	-1.3415577250427	0.179739441156126	NA
-FBgn0004649	0.316057543049755	0.0288311662585946	0.0482315781273319	0.59776535162254	0.549996512747037	NA
-FBgn0004666	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0004777	0	NA	NA	NA	NA	NA
-FBgn0004778	0	NA	NA	NA	NA	NA
-FBgn0004779	0	NA	NA	NA	NA	NA
-FBgn0004780	0	NA	NA	NA	NA	NA
-FBgn0004781	0	NA	NA	NA	NA	NA
-FBgn0004782	0	NA	NA	NA	NA	NA
-FBgn0004783	0	NA	NA	NA	NA	NA
-FBgn0004784	0	NA	NA	NA	NA	NA
-FBgn0004795	1.06947387537431	0.0331423527367172	0.0985524704568893	0.336291445390148	0.736651100258597	NA
-FBgn0004841	0.080862070626247	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0004842	0	NA	NA	NA	NA	NA
-FBgn0004854	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0004862	0	NA	NA	NA	NA	NA
-FBgn0004863	0.291567099326083	0.0331827376511504	0.0525664248592149	0.631253461501736	0.527874810982963	NA
-FBgn0004878	1.90151256697438	-0.0748888838845035	0.132965162713141	-0.563221842145743	0.573283831394132	NA
-FBgn0004880	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0004892	0	NA	NA	NA	NA	NA
-FBgn0004895	0.350285681768043	-0.00106704628079156	0.0546374011789264	-0.0195295943395477	0.984418628672992	NA
-FBgn0004897	0	NA	NA	NA	NA	NA
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-FBgn0004910	0.625791347127407	-0.025824241165198	0.0731902527324756	-0.352837163434734	0.724210520943851	NA
-FBgn0004911	0	NA	NA	NA	NA	NA
-FBgn0004956	0.0923751652987496	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0004959	0.515212724792022	0.071859481164667	0.0708243287937146	1.01461577382495	0.310289017254846	NA
-FBgn0005390	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0005391	0.580658421883181	0.00109515646389937	0.0710440982591035	0.0154151645349237	0.987700965315007	NA
-FBgn0005511	0.100529782041548	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0005590	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0005626	1.40653167611223	-0.071682237241511	0.119029737782037	-0.602221248044526	0.547026873749735	NA
-FBgn0005633	0.100529782041548	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0005654	0	NA	NA	NA	NA	NA
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-FBgn0005659	0.47270842001492	0.000544694176491008	0.059321647013884	0.00918204742972703	0.992673889063469	NA
-FBgn0005664	0.100529782041548	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0005775	0.526725819464525	0.0484137890233286	0.0758645259486741	0.638161095952578	0.523368819114499	NA
-FBgn0005778	0	NA	NA	NA	NA	NA
-FBgn0005779	0.269423611141796	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055694	NA
-FBgn0008636	0	NA	NA	NA	NA	NA
-FBgn0008646	0	NA	NA	NA	NA	NA
-FBgn0008651	0	NA	NA	NA	NA	NA
-FBgn0010014	1.62617665009303	0.0294813488728782	0.107391981822488	0.274520950005458	0.783684306027552	NA
-FBgn0010019	0	NA	NA	NA	NA	NA
-FBgn0010109	0.508198613102487	0.0210583051503539	0.0622498619451782	0.338286776746579	0.735147087575933	NA
-FBgn0010114	1.54307226846354	-0.0607968675657761	0.121494246704758	-0.500409436781957	0.616786809979003	NA
-FBgn0010197	0.24813606918961	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0010218	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0010294	0	NA	NA	NA	NA	NA
-FBgn0010295	0	NA	NA	NA	NA	NA
-FBgn0010296	0	NA	NA	NA	NA	NA
-FBgn0010317	1.81472112439536	-0.0157648386397717	0.121659024225016	-0.129582155867152	0.896897021754369	NA
-FBgn0010323	0.316947516124059	-0.0254684613822097	0.0531395169275487	-0.479275365203899	0.631742745090842	NA
-FBgn0010357	0	NA	NA	NA	NA	NA
-FBgn0010358	0.0923751652987496	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0010359	0	NA	NA	NA	NA	NA
-FBgn0010385	0.904833829390668	0.0125575117889076	0.0924098918706927	0.1358892596312	0.891908826286015	NA
-FBgn0010389	1.68803733111829	-0.0349765916327482	0.116715758057488	-0.299673259334191	0.764426397650596	NA
-FBgn0010399	1.46436755739347	0.0247651081756215	0.120222708015791	0.205993597918029	0.836795912188492	NA
-FBgn0010401	0.269423611141796	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055694	NA
-FBgn0010403	0.723441976722873	0.00898914172553057	0.080235830386019	0.112034008774924	0.910796441204979	NA
-FBgn0010414	0	NA	NA	NA	NA	NA
-FBgn0010423	0.316947516124059	-0.0254684613822097	0.0531395169275487	-0.479275365203899	0.631742745090842	NA
-FBgn0010424	0.24813606918961	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0010425	0	NA	NA	NA	NA	NA
-FBgn0010431	0.653373147680216	0.0503535605011472	0.0761445452682074	0.661289135338383	0.50842690766975	NA
-FBgn0010433	0	NA	NA	NA	NA	NA
-FBgn0010452	0.467151290790464	-0.0151644936202665	0.0669523540599429	-0.226496795119251	0.820815051596987	NA
-FBgn0010453	0.181391852667795	-0.000839295029802652	0.0477190025024432	-0.0175882769083382	0.985967308903724	NA
-FBgn0011239	0	NA	NA	NA	NA	NA
-FBgn0011244	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0011270	0	NA	NA	NA	NA	NA
-FBgn0011273	0	NA	NA	NA	NA	NA
-FBgn0011277	0.197727679648668	0.000574771843391052	0.0477473668015818	0.0120377704969484	0.990395480736373	NA
-FBgn0011278	0	NA	NA	NA	NA	NA
-FBgn0011279	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0011281	0	NA	NA	NA	NA	NA
-FBgn0011282	0	NA	NA	NA	NA	NA
-FBgn0011283	1.33308982531269	-0.0627070427014511	0.101935434934045	-0.615164321828072	0.538446207153987	NA
-FBgn0011293	0.186214584976165	0.0201334916603579	0.0477240779962571	0.421872826164121	0.673117845457942	NA
-FBgn0011294	0	NA	NA	NA	NA	NA
-FBgn0011296	0.298257461690216	-0.00979976827821036	0.0588721369117433	-0.166458511483989	0.867796130650196	NA
-FBgn0011554	0	NA	NA	NA	NA	NA
-FBgn0011555	0	NA	NA	NA	NA	NA
-FBgn0011556	0	NA	NA	NA	NA	NA
-FBgn0011559	0.161724141252494	0.0191845119231538	0.0477085916676566	0.402118596516016	0.68759674727182	NA
-FBgn0011569	0	NA	NA	NA	NA	NA
-FBgn0011581	0.305434421451557	-0.000993619243577533	0.0524508457765043	-0.0189438173754413	0.984885924592421	NA
-FBgn0011582	0.24813606918961	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0011668	0	NA	NA	NA	NA	NA
-FBgn0011669	0.765695749521016	0.0249133746362099	0.0675162716754023	0.368998080284792	0.712129155675742	NA
-FBgn0011670	0.742132031156716	-0.0180005124657197	0.0728784071363249	-0.246993769115292	0.804913046240013	NA
-FBgn0011693	0.516139450151393	0.0298537470703593	0.0703056136091385	0.424628212994913	0.671107722828824	NA
-FBgn0011694	0	NA	NA	NA	NA	NA
-FBgn0011701	0.52352291769304	-0.00388125616083362	0.0694473650731291	-0.0558877382424315	0.955431239028139	NA
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-FBgn0011743	0.100529782041548	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0011758	0	NA	NA	NA	NA	NA
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-FBgn0011812	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0011822	0	NA	NA	NA	NA	NA
-FBgn0011832	0	NA	NA	NA	NA	NA
-FBgn0011834	0	NA	NA	NA	NA	NA
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-FBgn0011844	0	NA	NA	NA	NA	NA
-FBgn0011845	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0011848	0	NA	NA	NA	NA	NA
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-FBgn0011850	0	NA	NA	NA	NA	NA
-FBgn0011851	0	NA	NA	NA	NA	NA
-FBgn0011852	0	NA	NA	NA	NA	NA
-FBgn0011853	0	NA	NA	NA	NA	NA
-FBgn0011854	0	NA	NA	NA	NA	NA
-FBgn0011855	0	NA	NA	NA	NA	NA
-FBgn0011858	0.080862070626247	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0011859	0.361798776440546	-0.0277515590377991	0.0554125313766664	-0.500817384594073	0.616499649562129	NA
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-FBgn0011864	0	NA	NA	NA	NA	NA
-FBgn0011865	0	NA	NA	NA	NA	NA
-FBgn0011866	0	NA	NA	NA	NA	NA
-FBgn0011867	0	NA	NA	NA	NA	NA
-FBgn0011868	0	NA	NA	NA	NA	NA
-FBgn0011869	0	NA	NA	NA	NA	NA
-FBgn0011870	0	NA	NA	NA	NA	NA
-FBgn0011871	0	NA	NA	NA	NA	NA
-FBgn0011872	0	NA	NA	NA	NA	NA
-FBgn0011877	0	NA	NA	NA	NA	NA
-FBgn0011878	0	NA	NA	NA	NA	NA
-FBgn0011879	0	NA	NA	NA	NA	NA
-FBgn0011880	0	NA	NA	NA	NA	NA
-FBgn0011881	0	NA	NA	NA	NA	NA
-FBgn0011882	0.201059564083097	-0.0206381168219006	0.0477507634245933	-0.432204960544594	0.665592454350888	NA
-FBgn0011883	0.100529782041548	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0011884	0	NA	NA	NA	NA	NA
-FBgn0011885	0	NA	NA	NA	NA	NA
-FBgn0011887	0	NA	NA	NA	NA	NA
-FBgn0011888	0	NA	NA	NA	NA	NA
-FBgn0011889	0	NA	NA	NA	NA	NA
-FBgn0011890	0	NA	NA	NA	NA	NA
-FBgn0011891	0	NA	NA	NA	NA	NA
-FBgn0011892	0	NA	NA	NA	NA	NA
-FBgn0011893	0	NA	NA	NA	NA	NA
-FBgn0011894	0	NA	NA	NA	NA	NA
-FBgn0011895	0	NA	NA	NA	NA	NA
-FBgn0011896	0	NA	NA	NA	NA	NA
-FBgn0011897	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0011902	0	NA	NA	NA	NA	NA
-FBgn0011904	0	NA	NA	NA	NA	NA
-FBgn0011905	0	NA	NA	NA	NA	NA
-FBgn0011906	0	NA	NA	NA	NA	NA
-FBgn0011909	0	NA	NA	NA	NA	NA
-FBgn0011910	0	NA	NA	NA	NA	NA
-FBgn0011915	0	NA	NA	NA	NA	NA
-FBgn0011916	0	NA	NA	NA	NA	NA
-FBgn0011919	0	NA	NA	NA	NA	NA
-FBgn0011921	0	NA	NA	NA	NA	NA
-FBgn0011927	0	NA	NA	NA	NA	NA
-FBgn0011928	0	NA	NA	NA	NA	NA
-FBgn0011931	0	NA	NA	NA	NA	NA
-FBgn0011932	0	NA	NA	NA	NA	NA
-FBgn0011933	0	NA	NA	NA	NA	NA
-FBgn0011934	0	NA	NA	NA	NA	NA
-FBgn0011935	0	NA	NA	NA	NA	NA
-FBgn0011936	0	NA	NA	NA	NA	NA
-FBgn0011937	0	NA	NA	NA	NA	NA
-FBgn0011938	0	NA	NA	NA	NA	NA
-FBgn0011944	0	NA	NA	NA	NA	NA
-FBgn0011945	0	NA	NA	NA	NA	NA
-FBgn0011948	0	NA	NA	NA	NA	NA
-FBgn0011949	0	NA	NA	NA	NA	NA
-FBgn0011950	0	NA	NA	NA	NA	NA
-FBgn0011951	0	NA	NA	NA	NA	NA
-FBgn0011952	0	NA	NA	NA	NA	NA
-FBgn0011953	0	NA	NA	NA	NA	NA
-FBgn0011954	0	NA	NA	NA	NA	NA
-FBgn0011955	0	NA	NA	NA	NA	NA
-FBgn0011956	0	NA	NA	NA	NA	NA
-FBgn0011957	0	NA	NA	NA	NA	NA
-FBgn0011958	0	NA	NA	NA	NA	NA
-FBgn0011959	0	NA	NA	NA	NA	NA
-FBgn0011960	0	NA	NA	NA	NA	NA
-FBgn0011961	0	NA	NA	NA	NA	NA
-FBgn0011962	0	NA	NA	NA	NA	NA
-FBgn0011963	0	NA	NA	NA	NA	NA
-FBgn0011965	0	NA	NA	NA	NA	NA
-FBgn0011966	0	NA	NA	NA	NA	NA
-FBgn0011970	0	NA	NA	NA	NA	NA
-FBgn0011971	0	NA	NA	NA	NA	NA
-FBgn0011974	0	NA	NA	NA	NA	NA
-FBgn0011975	0	NA	NA	NA	NA	NA
-FBgn0011976	0	NA	NA	NA	NA	NA
-FBgn0011977	0	NA	NA	NA	NA	NA
-FBgn0011980	0	NA	NA	NA	NA	NA
-FBgn0011981	0	NA	NA	NA	NA	NA
-FBgn0011982	0.24813606918961	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0011983	0	NA	NA	NA	NA	NA
-FBgn0011984	0	NA	NA	NA	NA	NA
-FBgn0011985	0	NA	NA	NA	NA	NA
-FBgn0011986	0	NA	NA	NA	NA	NA
-FBgn0011987	0	NA	NA	NA	NA	NA
-FBgn0011993	0	NA	NA	NA	NA	NA
-FBgn0011994	0	NA	NA	NA	NA	NA
-FBgn0011998	0	NA	NA	NA	NA	NA
-FBgn0011999	0	NA	NA	NA	NA	NA
-FBgn0012000	0	NA	NA	NA	NA	NA
-FBgn0012001	0	NA	NA	NA	NA	NA
-FBgn0012002	0	NA	NA	NA	NA	NA
-FBgn0012003	0	NA	NA	NA	NA	NA
-FBgn0012004	0	NA	NA	NA	NA	NA
-FBgn0012009	0	NA	NA	NA	NA	NA
-FBgn0012010	0	NA	NA	NA	NA	NA
-FBgn0012011	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0012016	0	NA	NA	NA	NA	NA
-FBgn0012017	0.100529782041548	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0012018	0	NA	NA	NA	NA	NA
-FBgn0012024	0	NA	NA	NA	NA	NA
-FBgn0012025	0	NA	NA	NA	NA	NA
-FBgn0012026	0	NA	NA	NA	NA	NA
-FBgn0012027	0	NA	NA	NA	NA	NA
-FBgn0012028	0	NA	NA	NA	NA	NA
-FBgn0012344	1.94526892174709	-0.0410561090024572	0.120508344112237	-0.340691006128332	0.73333621012128	NA
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-FBgn0013277	0.201059564083097	-0.0206381168219006	0.0477507634245933	-0.432204960544594	0.665592454350888	NA
-FBgn0013279	0.6557201032196	-0.0111536435700222	0.0722879474871197	-0.154294650183691	0.877377415341611	NA
-FBgn0013300	0	NA	NA	NA	NA	NA
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-FBgn0013307	0	NA	NA	NA	NA	NA
-FBgn0013308	0.269423611141796	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055694	NA
-FBgn0013323	1.85905919381936	-0.0869703553857145	0.121130641752006	-0.717988067493039	0.472764644294456	NA
-FBgn0013342	0.906959263338976	0.00278309331765603	0.0737186247107431	0.0377529196804243	0.96988468223976	NA
-FBgn0013348	0.876318396055054	0.0179264376473448	0.0917580296954572	0.19536641868665	0.845106104046533	NA
-FBgn0013433	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0013467	0.105352514349918	0.00872518825807776	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0013672	32.2343447251885	-0.026574633997878	0.0789974708191096	-0.336398541906857	NA	NA
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-FBgn0013682	49.1512095932707	0.0416127054476129	0.0878441008281923	0.47371087022679	NA	NA
-FBgn0013683	1.06135572369289	0.0507762622659519	0.0809158097805592	0.627519670181332	0.530318646477612	NA
-FBgn0013685	0	NA	NA	NA	NA	NA
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-FBgn0013689	0	NA	NA	NA	NA	NA
-FBgn0013690	0	NA	NA	NA	NA	NA
-FBgn0013691	0	NA	NA	NA	NA	NA
-FBgn0013692	0	NA	NA	NA	NA	NA
-FBgn0013693	0	NA	NA	NA	NA	NA
-FBgn0013694	0	NA	NA	NA	NA	NA
-FBgn0013695	0	NA	NA	NA	NA	NA
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-FBgn0013699	0	NA	NA	NA	NA	NA
-FBgn0013700	0	NA	NA	NA	NA	NA
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-FBgn0013702	0	NA	NA	NA	NA	NA
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-FBgn0013704	0	NA	NA	NA	NA	NA
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-FBgn0013706	0	NA	NA	NA	NA	NA
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-FBgn0013745	0.493995961967106	-0.0325960466747746	0.0597096898052577	-0.545908826207039	0.585128610979899	NA
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-FBgn0015001	0.740918308757009	-0.0383196649863992	0.0898250637581363	-0.426603259526528	0.669668323210144	NA
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-FBgn0015561	0.786061392791026	-0.0179043805280996	0.0862232579564135	-0.207651403489652	0.835501164880218	NA
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-FBgn0017561	1.19754143377002	0.0168245655673626	0.106744686838069	0.15761501640719	0.874760170102237	NA
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-FBgn0022740	0.0923751652987496	-0.0122785059273883	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
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-FBgn0029729	0	NA	NA	NA	NA	NA
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-FBgn0029733	0.100529782041548	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0029740	0	NA	NA	NA	NA	NA
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-FBgn0029775	0.998957646455905	0.130584941512342	0.0908530564199868	1.43732029122594	0.150627005815758	NA
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-FBgn0029963	0	NA	NA	NA	NA	NA
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-FBgn0029987	1.02417521518207	0.122323509404846	0.101449527677389	1.20575730814476	0.227911080991502	NA
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-FBgn0029995	0.22457235082531	-0.0122785059273882	0.0476319012243461	-0.257779043283545	0.796577439055695	NA
-FBgn0030005	1.70512015904143	0.0916781273537025	0.11839802967193	0.774321393757433	0.438740755303333	NA
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-FBgn0030014	0.34051123448836	0.000662461383479205	0.053668118500632	0.0123436670035564	0.990151428772895	NA
-FBgn0030015	0.173237235924997	-0.000839291635723297	0.0477190025576663	-0.0175882057616156	0.985967365661815	NA
-FBgn0030016	1.63163428404325	-0.00787318983378183	0.111475663942514	-0.07062698310406	0.943694634621088	NA
-FBgn0030027	1.21894779257814	-0.0146866484112459	0.106547056206499	-0.137841897600453	0.890365370898224	NA
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-FBgn0030050	1.58908631955764	-0.0847523877989257	0.10392226572933	-0.815536374271002	0.414765352454612	NA
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-FBgn0030074	0.080862070626247	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
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-FBgn0030098	0.080862070626247	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0030102	0	NA	NA	NA	NA	NA
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-FBgn0030167	0.181391852667795	-0.000839295029802652	0.0477190025024432	-0.0175882769083382	0.985967308903724	NA
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-FBgn0030589	1.42239350972207	0.0161168664338161	0.103589708470224	0.155583664360332	0.876361202079661	NA
-FBgn0030591	1.68572973453371	-0.125061769503347	0.120936127191662	-1.03411422547992	0.301082766691791	NA
-FBgn0030595	0.90385617240921	0.0134818947876613	0.0847437711026876	0.159090097268916	0.873597890091336	NA
-FBgn0030608	0	NA	NA	NA	NA	NA
-FBgn0030614	0.210705028699836	0.0215025420644558	0.0477573054627681	0.450246132106831	0.652532975884079	NA
-FBgn0030617	0.267076655602412	0.029926182454707	0.0509056819044001	0.587875092428932	0.556616135941788	NA
-FBgn0030618	0.205882296391466	0.000432195717863538	0.0477540583009715	0.00905045001912948	0.992778884242595	NA
-FBgn0030619	0.080862070626247	0.00872518825807775	0.0476319012243461	0.183179508560495	0.85465717212165	NA
-FBgn0030620	0	NA	NA	NA	NA	NA
-FBgn0030621	0	NA	NA	NA	NA	NA
-FBgn0030622	0	NA	NA	NA	NA	NA
-FBgn0030623	0	NA	NA	NA	NA	NA
-FBgn0030624	0	NA	NA	NA	NA	NA
-FBgn0030640	0	NA	NA	NA	NA	NA
-FBgn0030663	1.2590203447849	0.0303360386139559	0.101522079533499	0.298812226397962	0.765083321606146	NA
-FBgn0030684	1.7810355028069	-0.133155952112686	0.109755683382357	-1.21320325298152	0.225052120743722	NA
-FBgn0030688	0.827337508607711	0.00995313668027199	0.0911280107870993	0.109221485186649	0.913026819537744	NA
--- a/test-data/normalized_readcounts.tab	Thu Apr 12 17:29:45 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4000 +0,0 @@
-	GSM461176_untreat_single.counts	GSM461177_untreat_paired.counts	GSM461178_untreat_paired.counts	GSM461182_untreat_single.counts	GSM461179_treat_single.counts	GSM461180_treat_paired.counts	GSM461181_treat_paired.counts
-FBgn0000003	0	0	0	0	0	0	0
-FBgn0000008	28.2894791698886	51.3707186232312	36.8576909542011	45.5881872175379	33.0020972022181	50.8852644310105	33.39603516864
-FBgn0000014	0	2.81483389716335	0	0	0	1.47493520089885	1.13206898876746
-FBgn0000015	0	0	0.646626157091247	0	0	0	0
-FBgn0000017	2314.07939609689	2481.27608034949	1832.5385291966	1906.8438308577	1702.21343464072	1751.48555106739	1793.76331270204
-FBgn0000018	173.508805575317	165.371491458347	176.528940885911	179.208735958597	185.853915823018	173.304886105615	153.395347977991
-FBgn0000022	1.88596527799258	0	0	0	0	0	0
-FBgn0000024	0	2.11112542287251	1.29325231418249	4.7160193673315	1.73695248432727	1.47493520089885	0.566034494383729
-FBgn0000028	0	0	0	0	0	0.737467600449427	0.566034494383729
-FBgn0000032	439.42990977227	417.299125254467	419.013749795128	627.23057585509	477.661933189999	407.819583048533	393.393973596692
-FBgn0000036	0	0	0	0	0	0	0
-FBgn0000037	3.77193055598515	4.92595932003587	0	6.28802582310867	6.94780993730908	6.63720840404485	4.52827595506983
-FBgn0000038	0	0	0	0	0	0	0
-FBgn0000039	0	0	0	0	0	0.737467600449427	0
-FBgn0000042	30777.0673715608	32142.5882717083	32682.4258578629	45948.1766959108	35998.3402376827	45250.2744959764	45663.1347309242
-FBgn0000043	10608.5546887082	11068.6305921206	11095.4582295287	13509.823480949	16033.808382825	18477.9881968608	18723.289005225
-FBgn0000044	24.5175486139035	9.85191864007173	9.05276619927746	9.432038734663	17.3695248432727	13.2744168080897	10.1886208989071
-FBgn0000045	1.88596527799258	2.81483389716335	3.87975694254748	0	0	6.63720840404485	11.3206898876746
-FBgn0000046	7.5438611119703	3.51854237145419	3.23313078545624	0	15.6325723589454	17.6992224107863	10.1886208989071
-FBgn0000047	3.77193055598515	1.40741694858168	1.93987847127374	1.57200645577717	3.47390496865454	8.84961120539313	5.66034494383729
-FBgn0000052	920.351055660377	1134.37806055683	1169.10009202098	1136.56066752689	906.689196818835	1061.21587704673	1000.18295157605
-FBgn0000053	709.122944525208	880.339301337838	896.223853728469	801.723292446355	918.847864209126	1175.52335511639	1119.61622989102
-FBgn0000054	267.807069474946	320.187355802331	276.109369077963	345.841420270977	267.4906825864	278.762752969884	323.205696293109
-FBgn0000055	0	0	0	0	0	0	0
-FBgn0000056	0	0	0	0	0	0	0
-FBgn0000057	299.868479200819	307.520603265096	343.358489415452	337.981387992091	270.964587555054	348.822175012579	345.847076068458
-FBgn0000061	0	0	0.646626157091247	0	1.73695248432727	0.737467600449427	0
-FBgn0000063	188.596527799258	147.778779601076	150.663894602261	185.496761781706	175.432200917054	185.104367712806	178.866900225258
-FBgn0000064	3409.82522261058	3441.83814775649	3365.68914765994	3092.13669851369	3849.08670526923	3953.56380600938	4139.41025742821
-FBgn0000071	54.6929930617847	53.4818440461037	54.3165971956648	29.8681226597662	253.595062711781	283.925026173029	328.866041236947
-FBgn0000075	1.88596527799258	0	0.646626157091247	0	0	0	0.566034494383729
-FBgn0000077	75.438611119703	77.4079321719922	100.873680506235	100.608413169739	74.6889568260726	82.5963712503359	104.150346966606
-FBgn0000078	9.42982638996288	14.0741694858168	19.3987847127374	7.86003227888584	3.47390496865454	8.1121436049437	9.05655191013967
-FBgn0000079	52.8070277837921	137.926860961004	129.971857575341	75.456309877304	15.6325723589454	55.310070033707	52.6412079776868
-FBgn0000083	2425.35134749845	2515.75779558975	2735.22864449598	2244.82521884979	2264.98603956276	2619.48491679637	2651.87160618777
-FBgn0000084	752.500145919038	916.228433526671	941.487684724856	784.431221432806	574.931272312326	761.804031264258	843.95743112614
-FBgn0000092	5.65789583397773	7.03708474290838	6.46626157091247	3.14401291155433	3.47390496865454	2.94987040179771	4.52827595506983
-FBgn0000094	7.5438611119703	9.14821016578089	2.58650462836499	1.57200645577717	13.8956198746182	3.68733800224714	3.9622414606861
-FBgn0000097	1412.58799321644	1522.82513836537	1222.12343690246	1182.14885474443	1413.8793222424	1382.01428324223	1262.8229569701
-FBgn0000099	0	1.40741694858168	0.646626157091247	1.57200645577717	0	0.737467600449427	0
-FBgn0000100	12322.8971264035	12039.7482866419	13786.0696691854	10573.3154215572	10029.1636445057	11880.6030432403	11372.1990266635
-FBgn0000108	22.6315833359109	26.037213548761	20.6920370269199	3.14401291155433	29.5281922335636	19.9116252121345	21.5093107865817
-FBgn0000109	37.7193055598515	51.3707186232312	64.0159895520335	89.6043679792985	79.8998142790544	44.9855236274151	50.3770700001519
-FBgn0000114	1.88596527799258	1.40741694858168	0	0	3.47390496865454	0.737467600449427	2.26413797753492
-FBgn0000115	279.122861142901	249.816508373247	260.590341307773	265.669091026341	251.858110227454	247.789113751008	290.375695618853
-FBgn0000116	179.166701409295	192.112413481399	166.829548529542	143.052587475722	310.914494694581	491.153421899319	476.6010442711
-FBgn0000117	4692.28161164553	4808.4400048293	4791.49982404614	4308.86969528522	4651.55875302843	5595.90415221025	5544.30787248863
-FBgn0000119	250.833381973013	316.668813430877	298.094658419065	317.545304066988	281.386302461018	280.975155771232	281.319143708713
-FBgn0000120	0	0	0	0	0	0	0
-FBgn0000121	0	1.40741694858168	0.646626157091247	4.7160193673315	3.47390496865454	3.68733800224714	2.83017247191865
-FBgn0000137	0	0	0	0	0	0	0
-FBgn0000139	350.789541706619	241.372006681757	353.057881771821	367.849510651857	204.960393150618	216.078006931682	257.545694944597
-FBgn0000140	439.42990977227	439.817796431774	318.786695445985	493.610027114031	493.294505548945	445.430430671454	352.639490001063
-FBgn0000142	873.201923710562	938.043396229687	791.470416279687	891.327660425654	755.574330682362	822.276374501111	824.14622382271
-FBgn0000146	552.587826451825	593.929952301467	583.903419853396	646.094653324416	965.745581285962	849.56267571774	773.203119328174
-FBgn0000147	135.789500015465	132.297193166678	184.935080928097	172.920710135488	201.486488181963	217.552942132581	204.338452472526
-FBgn0000150	3513.55331290017	3583.28355108895	4053.69937880503	3117.28880180612	4137.42081766756	4733.80452728487	4350.54112383334
-FBgn0000152	188.596527799258	222.371877875905	228.25903345321	262.525078114787	217.119060540909	252.951386954154	258.677763933364
-FBgn0000153	7.5438611119703	5.6296677943267	12.2858969847337	12.5760516462173	6.94780993730908	11.7994816071908	4.52827595506983
-FBgn0000157	0	0	0	1.57200645577717	0	0	0
-FBgn0000158	9.42982638996288	1.40741694858168	0.646626157091247	3.14401291155433	1.73695248432727	4.42480560269656	1.69810348315119
-FBgn0000163	363.991298652567	505.966393015112	417.073871323855	345.841420270977	402.972976363927	366.521397423365	369.054490338191
-FBgn0000166	0	0	0	0	0	0	0
-FBgn0000171	2681.84262530544	3743.72908322726	2935.03612703717	2251.1132446729	2419.57481066789	3232.32049276984	3029.9826484361
-FBgn0000173	629.91240284952	586.189159084268	755.905977639668	710.54691801128	755.574330682362	732.305327246281	722.826049328022
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-FBgn0000180	13.201756945948	11.9630440629442	8.40614004218622	0	5.21085745298181	16.9617548103368	10.7546553932909
-FBgn0000181	7457.10670918264	6052.5965873755	6556.14260674816	5228.49347191486	5709.36281598374	5622.45298582643	5642.23184001701
-FBgn0000182	1.88596527799258	0.703708474290838	2.58650462836499	1.57200645577717	1.73695248432727	0.737467600449427	1.13206898876746
-FBgn0000183	1173.07040291138	1157.60044020843	1160.69395197879	1340.92150677792	1264.50140859025	1106.93886827459	1161.50278247541
-FBgn0000206	0	0	0	0	0	0	0
-FBgn0000210	678.947500077327	798.00540984581	584.550046010488	583.214395093329	623.56594187349	796.465008485382	651.505703035672
-FBgn0000212	1493.68450017012	1448.93574856484	1353.38854679198	1443.10192640344	1464.25094428789	1536.88247933661	1655.65089607241
-FBgn0000216	0	0	0	0	0	0	0
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-FBgn0000227	0	0	0	0	0	0	0
-FBgn0000228	369.649194486545	397.595287974323	351.764629457639	342.697407359422	312.651447178909	348.08470741213	326.601903259412
-FBgn0000229	394.166743100448	358.187613414037	355.644386400186	521.90614331802	479.398885674326	290.562234577074	307.922764944749
-FBgn0000233	1.88596527799258	2.11112542287251	3.87975694254748	0	1.73695248432727	1.47493520089885	2.83017247191865
-FBgn0000239	1035.39493761792	1163.93381647705	1093.4448316413	1229.30904841774	1193.28635673283	1157.8241327056	997.352779104131
-FBgn0000241	3.77193055598515	0.703708474290838	1.29325231418249	1.57200645577717	5.21085745298181	2.94987040179771	1.13206898876746
-FBgn0000242	67.8947500077327	71.7782643776655	67.895746494581	53.4482194964237	33.0020972022181	67.8470192413473	63.3958633709777
-FBgn0000244	250.833381973013	254.742467693283	214.679884154294	281.389155584113	210.1712506036	187.316770514155	187.923452135398
-FBgn0000246	98.0701944556139	54.1855525203945	43.9705786822048	78.6003227888584	116.375816449927	53.8351348328082	49.2450010113844
-FBgn0000247	1208.90374319324	1355.34252148415	1186.55899826244	1296.90532601616	1057.80406295531	1223.4587491456	1100.37105708197
-FBgn0000250	1223.99146541718	1011.22907755593	1060.46689762965	957.351931568295	964.008628801635	946.170931376615	1090.18243618306
-FBgn0000251	0	0.703708474290838	0.646626157091247	0	0	0	0
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-FBgn0000257	316.842166702753	370.854365951272	360.817395656916	292.393200774553	323.073162084872	364.308994622017	410.375008428204
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-FBgn0030676	7.5438611119703	6.33337626861754	3.87975694254748	0	12.1586673902909	0.737467600449427	5.09431044945356
-FBgn0030678	84.8684375096659	121.037857578024	89.8810358356834	119.472490639065	59.0563844671272	106.195334464718	106.414484944141
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-FBgn0030680	256.49127780699	264.594386333355	229.552285767393	240.516987733907	218.856013025236	240.414437746513	251.885350000759
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-FBgn0030685	1250.39497930908	987.302989430046	914.329386127024	1183.72086120021	769.469950556981	778.765786074595	796.976568092291
-FBgn0030686	237.631625027064	188.593871109945	219.206267253933	216.936890897249	149.377913652145	198.378784520896	189.055521124166
-FBgn0030687	275.350930586916	366.632115105527	344.005115572544	400.861646223178	281.386302461018	396.757569041792	382.639318203401
-FBgn0030688	0	0.703708474290838	0.646626157091247	1.57200645577717	1.73695248432727	0	1.13206898876746
-FBgn0030691	13.201756945948	11.2593355886534	5.17300925672998	14.1480581019945	12.1586673902909	14.7493520089885	7.35844842698848
-FBgn0030692	350.789541706619	343.409735453929	347.884872515091	378.853555842297	295.281922335636	367.996332624264	353.771558989831
-FBgn0030693	179.166701409295	128.074942320933	156.483530016082	198.072813427923	217.119060540909	143.068714487189	133.58414067456
-FBgn0030694	111.271951401562	99.926603349299	108.63319439133	86.4603550677442	104.217149059636	81.8589036498864	119.999312809351
--- a/test-data/sailfish/out_deseq2_sailfish.tab	Thu Apr 12 17:29:45 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-MIR6859-2	1.1858265336986	-1.58325519934585	1.29566733255222	-1.22196119294536	0.221722302676964	0.886889210707858
-DDX11L1	1.91972630671259	-0.204757212641591	1.31524142129485	-0.155680325548148	0.876285006005361	0.999999999763967
-MIR6859-1	0.294068009390125	-0.712896459907293	1.28824575367762	-0.55338545294805	0.579999497913718	0.999999999763967
-WASH7P	114.545909292233	-3.75034560711482e-10	1.2677635335979	-2.95823748492859e-10	0.999999999763967	0.999999999763967