# HG changeset patch
# User iuc
# Date 1517130279 18000
# Node ID 6e8b61c54ff385bf0bcc3f725498940631f15d25
# Parent  f1c406f9554cdc80abbd3f8a57f4c6009a229dcf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c

diff -r f1c406f9554c -r 6e8b61c54ff3 dexseq.R
--- a/dexseq.R	Sun Jan 29 06:59:35 2017 -0500
+++ b/dexseq.R	Sun Jan 28 04:04:39 2018 -0500
@@ -3,9 +3,11 @@
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
-library("DEXSeq")
-library('getopt')
-library('rjson')
+suppressPackageStartupMessages({
+    library("DEXSeq")
+    library('getopt')
+    library('rjson')
+})
 
 
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
@@ -90,7 +92,7 @@
 BPPARAM=MulticoreParam(workers=opt$threads)
 dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM)
 print("Estimated dispersions")
-dxd <- testForDEU(dxd, fullModel=formulaFullModel, BPPARAM=BPPARAM)
+dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM)
 print("tested for DEU")
 dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM)
 print("Estimated fold changes")
@@ -111,7 +113,7 @@
 if ( !is.null(opt$reportdir) ) {
     save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData"))
     save.image()
-    DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
+    DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
     unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData"))
 }
 sessionInfo()
diff -r f1c406f9554c -r 6e8b61c54ff3 dexseq.xml
--- a/dexseq.xml	Sun Jan 29 06:59:35 2017 -0500
+++ b/dexseq.xml	Sun Jan 28 04:04:39 2018 -0500
@@ -1,10 +1,12 @@
-<tool id="dexseq" name="DEXSeq" version="1.20.1">
+<tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
     <description>Determines differential exon usage from count tables</description>
-    <requirements>
-        <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
+     <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="0.2.15">r-rjson</requirement>
-    </requirements>
+    </expand>
     <code file="dexseq_helper.py" />
     <stdio>
         <regex match="Execution halted"
@@ -24,50 +26,45 @@
             level="fatal"
             description="Error in the R script." />
     </stdio>
-    <version_command>
-    <![CDATA[
-        echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
-    ]]>
-    </version_command>
-    <command>
-    <![CDATA[
-        mkdir ./html_out &&
-        #import json
-        Rscript '$__tool_directory__/dexseq.R'
-            -o '$dexseq_out'
-            -p \${GALAXY_SLOTS:-4}
-            #set $temp_factor_names = list()
-            #for $factor in $rep_factorName:
-                #set $temp_factor = list()
-                #set $count_files1 = list()
-                #for $file in $factor.countFiles1:
-                    $count_files1.append(str($file))
-                #end for
-                $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
+    <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
+    ]]></version_command>
+    <command><![CDATA[
+ mkdir ./html_out &&
+ #import json
+ Rscript '$__tool_directory__/dexseq.R'
+     -o '$dexseq_out'
+     -p \${GALAXY_SLOTS:-4}
+     #set $temp_factor_names = list()
+     #for $factor in $rep_factorName:
+         #set $temp_factor = list()
+         #set $count_files1 = list()
+         #for $file in $factor.countFiles1:
+             $count_files1.append(str($file))
+         #end for
+         $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
 
-                #set $count_files2 = list()
-                #for $file in $factor.countFiles2:
-                    $count_files2.append(str($file))
-                #end for
-                $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
-                $temp_factor_names.append([str($factor.factorName), $temp_factor])
-            #end for
-            -f '#echo json.dumps(temp_factor_names)#'
-            -a $gtf
-            -c $fdr_cutoff
+         #set $count_files2 = list()
+         #for $file in $factor.countFiles2:
+             $count_files2.append(str($file))
+         #end for
+         $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
+         $temp_factor_names.append([str($factor.factorName), $temp_factor])
+     #end for
+     -f '#echo json.dumps(temp_factor_names)#'
+     -a $gtf
+     -c $fdr_cutoff
 
-            #if $report:
-                -r ./html_out
-                &&
-                mkdir '$htmlreport.extra_files_path'
-                &&
-                cp ./html_out/testForDEU.html $htmlreport
-                &&
-                cp -r ./html_out/* '$htmlreport.extra_files_path'
-            #end if
-
-    ]]>
-    </command>
+     #if $report:
+         -r ./html_out
+         &&
+         mkdir '$htmlreport.extra_files_path'
+         &&
+         cp ./html_out/testForDEU.html $htmlreport
+         &&
+         cp -r ./html_out/* '$htmlreport.extra_files_path'
+     #end if
+    ]]></command>
     <inputs>
         <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
         <repeat name="rep_factorName" title="Factor" min="1">
@@ -105,7 +102,36 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <!-- Ensure default output works-->
+        <test expect_num_outputs="1">
+            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="condition"/>
+                <param name="factorLevel1" value="knockdown"/>
+                <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
+                <param name="factorLevel2" value="control"/>
+                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
+            </repeat>
+            <param name="report" value="False"/>
+            <param name="fdr_cutoff" value="1"/>
+            <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
+        </test>
+        <!-- Ensure report works-->
+        <test expect_num_outputs="2">
+            <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment"/>
+                <param name="factorLevel1" value="knockdown"/>
+                <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
+                <param name="factorLevel2" value="control"/>
+                <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
+            </repeat>
+            <param name="report" value="True"/>
+            <param name="fdr_cutoff" value="1"/>
+            <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
+        </test>
+        <!-- Ensure two factors works-->
+        <test expect_num_outputs="1">
             <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
             <repeat name="rep_factorName">
                 <param name="factorName" value="condition"/>
@@ -123,11 +149,10 @@
             </repeat>
             <param name="report" value="False"/>
             <param name="fdr_cutoff" value="0.05"/>
-            <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
+            <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/>
         </test>
     </tests>
-    <help>
-    <![CDATA[
+    <help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -139,7 +164,7 @@
 
 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
 DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary
-factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might
+factor that affects gene expressions. You also input several 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.
 
@@ -186,8 +211,7 @@
 
 
 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
-    ]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1101/gr.133744.111</citation>
     </citations>
diff -r f1c406f9554c -r 6e8b61c54ff3 dexseq_count.xml
--- a/dexseq_count.xml	Sun Jan 29 06:59:35 2017 -0500
+++ b/dexseq_count.xml	Sun Jan 28 04:04:39 2018 -0500
@@ -1,9 +1,11 @@
-<tool id="dexseq_count" name="DEXSeq-Count" version="1.20.1">
+<tool id="dexseq_count" name="DEXSeq-Count" version="@VERSION@.0">
     <description>Prepare and count exon abundancies from RNA-seq data</description>
-    <requirements>
-        <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
-        <requirement type="package" version="0.6.1.post1">htseq</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="0.9.1">htseq</requirement>
+    </expand>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
@@ -12,26 +14,24 @@
         <regex match="Error:" />
         <regex match="Exception:" />
     </stdio>
-    <command>
-    <![CDATA[
-        #if $mode.mode_select == "prepare":
-            dexseq_prepare_annotation.py
-                -r $mode.aggregate
-                '$mode.gtffile'
-                '$flattened_gtf_out'
-        #elif $mode.mode_select == "count":
-            dexseq_count.py
-                -f bam
-                -p $mode.paired
-                -s $mode.stranded
-                -a $mode.qual
-                -r $mode.order
-                $mode.flattened_gtf_in
-                '$mode.bamfile'
-                '$counts_file'
-        #end if
-    ]]>
-    </command>
+    <command><![CDATA[
+#if $mode.mode_select == "prepare":
+    dexseq_prepare_annotation.py
+        -r $mode.aggregate
+        '$mode.gtffile'
+        '$flattened_gtf_out'
+#elif $mode.mode_select == "count":
+    dexseq_count.py
+        -f bam
+        -p $mode.paired
+        -s $mode.stranded
+        -a $mode.qual
+        -r $mode.order
+        $mode.flattened_gtf_in
+        '$mode.bamfile'
+        '$counts_file'
+#end if
+    ]]></command>
     <inputs>
         <conditional name="mode">
             <param name="mode_select" type="select" label="Mode of operation">
@@ -76,33 +76,31 @@
             <param name="mode_select" value="prepare" />
             <param name="gtffile" ftype="gff" value="original.gtf"/>
             <param name="aggregate" value="True"/>
-            <output name="flattened_gtf_out" file="flattened.gtf" ftype="gtf"/>
+            <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/>
         </test>
     </tests>
 
-    <help>
-    <![CDATA[
+    <help><![CDATA[
 .. class:: infomark
 
 **What it does**
 
-The main goal of this tol is to count the number of reads/fragments per exon of each gene in RNA-seq sample. In addition it also prepares your annotation gtf file compatible for counting.
+The main goal of this tool is to count the number of reads/fragments per exon of each gene in RNA-seq samples. In addition, it also prepares your annotation GTF file, making it compatible for counting.
 
 
 **Inputs**
 
-Mode-preprare: Takes a normal gtf file as input. For example from ensembl database.
-Mode-count: Inputs are flattened gtf file and BAM file. The flattened gtf file can be generated from 'prepare' mode of this tool.
+Mode-preprare: Takes a normal gtf file as input. For example from Ensembl database.
+Mode-count: Inputs are flattened GTF file and BAM file. The flattened GTF file can be generated from 'prepare' mode of this tool.
 
 **Output**
 
-Mode-preprare: Flattened gtf file that contains only exons with corresponding gene ids from given gtf file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used.
-Mode-count: Two column tab-delimeted file with exon ids and their read counts.
+Mode-prepare: Flattened GTF file that contains only exons with corresponding gene ids from given GTF file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used.
+Mode-count: Two column tab-delimited file with exon ids and their read counts.
 
 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
 
-    ]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1101/gr.133744.111</citation>
     </citations>
diff -r f1c406f9554c -r 6e8b61c54ff3 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Jan 28 04:04:39 2018 -0500
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@VERSION@">1.24.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">bioconductor-dexseq</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/gr.133744.111</citation>
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff -r f1c406f9554c -r 6e8b61c54ff3 test-data/dexseq_result.tabular
--- a/test-data/dexseq_result.tabular	Sun Jan 29 06:59:35 2017 -0500
+++ b/test-data/dexseq_result.tabular	Sun Jan 28 04:04:39 2018 -0500
@@ -1,183 +1,214 @@
-FBgn0000064:E005	FBgn0000064	E005	859.822533198768	0.00400580335097871	103.648404274913	3.11196699769697e-23	5.44594224596969e-21	27.5051135091719	27.9888903359156	0.0251544333390813	3R	22082655	22082854	200	-	746	952	1227	542	790	802	722	FBtr0085000, FBtr0085001, FBtr0084995, FBtr0084994, FBtr0306657, FBtr0114544, FBtr0310661, FBtr0310660, FBtr0084999
-FBgn0000042:E001	FBgn0000042	E001	963.266257907235	0.0494674041791383	58.6864023046738	1.80471928079693e-13	1.57912937069731e-11	29.2361793929567	27.8104974337299	-0.0721252413332429	X	5794894	5795046	153	+	3322	262	275	1633	3139	244	129	FBtr0100662, FBtr0100663, FBtr0070822
-FBgn0000064:E002	FBgn0000064	E002	7.3266084748515	0.0174415205517328	52.6891313145547	3.61993278740899e-12	2.11162745932191e-10	4.57344268891687	4.36382559042999	-0.0676871299306827	3R	22080926	22081153	228	-	0	7	12	0	0	10	12	FBtr0310660, FBtr0084995, FBtr0084994, FBtr0084999
-FBgn0000084:E003	FBgn0000084	E003	12.7120572355022	0.0837118156540486	50.7217207682862	9.68095672648681e-12	4.23541856783798e-10	6.0094928632898	6.08050302516378	0.0169474311496155	X	20066074	20066255	182	-	0	16	13	0	0	29	11	FBtr0070025, FBtr0301931
-FBgn0000042:E005	FBgn0000042	E005	33.8277404051372	0.00974672760676001	34.3730215558909	3.43552573377072e-08	1.20243400681975e-06	9.60659972691163	11.2480627165693	0.227578761693847	X	5798498	5798821	324	+	119	20	29	45	52	14	8	FBtr0100662, FBtr0070823
-FBgn0000032:E005	FBgn0000032	E005	50.5080907808574	0.00563866250172629	33.6728457313117	4.87567169377265e-08	1.42207091068369e-06	11.2003987427418	11.7345634802096	0.0672140810963772	3R	25818551	25818649	99	-	42	53	56	38	55	45	53	FBtr0085609, FBtr0085610
-FBgn0000117:E003	FBgn0000117	E003	651.648249450539	0.00646832336464667	32.2394513365441	9.98371310442968e-08	2.49592827610742e-06	25.6842059292453	26.4526242482609	0.0425293818432292	X	1788541	1788813	273	-	676	728	799	493	606	574	569	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000042:E003	FBgn0000042	E003	37923.6657937205	0.0382188253738751	28.9809820787994	5.09166358707019e-07	9.9004569748587e-06	51.8034875214762	51.7296029759846	-0.0020591075753989	X	5796723	5798206	1484	+	53623	37301	41337	47230	50144	22833	26327	FBtr0100662, FBtr0100663, FBtr0070822, FBtr0070823
-FBgn0000117:E004	FBgn0000117	E004	566.705805129229	0.00396420686097515	29.062938884796	4.88723257919492e-07	9.9004569748587e-06	25.3467671419344	24.9167412697074	-0.0246863519994665	X	1788874	1789074	201	-	541	507	690	417	761	498	535	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000084:E006	FBgn0000084	E006	59.8440945905321	0.0203559407131398	22.0440165999181	1.6338140100348e-05	0.000285917451756091	12.8331207213348	12.5225760471869	-0.0353406706853485	X	20067507	20067552	46	-	132	23	34	71	150	35	46	FBtr0070025
-FBgn0000042:E004	FBgn0000042	E004	2902.21264539337	0.0406433600957287	19.0532609703125	7.28847971089997e-05	0.00115953086309772	36.1678574007083	34.6381912225652	-0.06234453895514	X	5798207	5798497	291	+	7007	1635	1666	3678	8835	1202	1091	FBtr0100662, FBtr0100663, FBtr0070823
-FBgn0000017:E004	FBgn0000017	E004	118.685044393895	0.009449205970161	18.6151588688678	9.07339069495662e-05	0.00132320280968117	15.9518565653778	15.5132175490521	-0.0402264002183915	3L	16619373	16619627	255	-	103	108	87	107	162	144	104	FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000140:E002	FBgn0000140	E002	24.0938527740886	0.0069964414120799	18.2356967741571	0.000109690434972442	0.00147660200924441	8.83210929556324	7.9081263929815	-0.159422095913981	3R	20579850	20580026	177	+	19	23	22	24	32	25	21	FBtr0084692
-FBgn0000064:E011	FBgn0000064	E011	121.014747579775	0.0162642835242919	17.7465902170453	0.000140080246746098	0.00175100308432622	17.4845083643665	14.7073531559126	-0.249539598513264	3R	22086876	22086879	4	-	154	77	97	210	219	76	86	FBtr0085001
-FBgn0000117:E001	FBgn0000117	E001	1110.87821042994	0.00687680447260985	17.5318496824093	0.000155957840381502	0.00181950813778419	29.3482463186276	29.5968478676698	0.0121692348940674	X	1785434	1786152	719	-	1892	943	1111	1063	2137	670	737	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000097:E005	FBgn0000097	E005	205.994534916873	0.00454354511647642	16.4248478874543	0.000271262398953368	0.00296693248855246	19.3225099650976	19.4350345512854	0.00837716220794239	2L	2159312	2160582	1271	-	436	153	131	240	419	142	115	FBtr0330658, FBtr0330660, FBtr0077850, FBtr0077851, FBtr0330659
-FBgn0000054:E006	FBgn0000054	E006	186.13192889271	0.00325650963556041	15.6279894460111	0.000404040788685943	0.00415924341294353	18.6379892993821	18.6223635946701	-0.00121003298514359	2R	2554225	2554518	294	+	295	134	161	246	299	133	134	FBtr0330252, FBtr0330251, FBtr0086111, FBtr0086113, FBtr0086112
-FBgn0000083:E006	FBgn0000083	E006	222.094875801226	0.0282144821764667	14.940494527649	0.000569787391648398	0.00553959964102609	19.6402471081571	19.7714356703552	0.00960455244682029	3R	16895035	16895476	442	+	474	152	158	241	525	133	120	FBtr0089519
-FBgn0000064:E007	FBgn0000064	E007	39.9808634639801	0.0062635457310716	14.2262484910615	0.000814346794247482	0.00750056257859523	11.137048316394	10.794710781542	-0.0450423314512158	3R	22083764	22083999	236	-	74	33	39	53	76	18	22	FBtr0085000, FBtr0084999
-FBgn0000097:E003	FBgn0000097	E003	558.924889184516	0.00477032321464317	13.8339482613023	0.000990823511663669	0.0086697057270571	25.4143335226138	24.7289723478422	-0.0394401099076157	2L	2157427	2158405	979	-	725	462	477	524	1052	491	412	FBtr0330658, FBtr0330660, FBtr0077850, FBtr0077851, FBtr0330659
-FBgn0000140:E003	FBgn0000140	E003	26.5896581030249	0.0237371081245122	13.4350351109632	0.00120953709887615	0.0100794758239679	9.09784552498195	8.46305955371732	-0.104345620107048	3R	20580079	20580291	213	+	27	25	22	29	20	32	23	FBtr0084692
-FBgn0000097:E001	FBgn0000097	E001	461.645239176362	0.00776603592820706	13.2691241865316	0.00131415409610414	0.0104534984917375	23.7756652578164	24.4181091948569	0.0384657810682183	2L	2156484	2156791	308	-	1032	322	349	473	887	310	283	FBtr0330658, FBtr0077850, FBtr0077851
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-FBgn0000084:E005	FBgn0000084	E005	179.51917351967	0.0173004033915315	12.3993034429457	0.00203013756650583	0.0148030864224384	18.4431452434105	18.2828675285912	-0.0125923461272008	X	20067402	20067506	105	-	307	96	143	186	408	128	138	FBtr0070025, FBtr0301931
-FBgn0000053:E004	FBgn0000053	E004	6.32535175423168	0.0456261671191675	12.1706258518488	0.00227605197713583	0.0159323638399508	3.09087160680815	5.79810356406846	0.907567375993392	2L	7018085	7018148	64	-	13	7	15	0	3	3	4	FBtr0100353
-FBgn0000017:E003	FBgn0000017	E003	68.6033909674033	0.0107581701281203	11.2334191254965	0.00363658740658779	0.024477030621264	13.3760421189947	12.3288124266712	-0.11761745657376	3L	16616737	16618374	1638	-	60	55	46	48	132	83	62	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000117:E008	FBgn0000117	E008	20.8971168975998	0.00873566782374951	10.9956404097371	0.00409568947916862	0.0255980592448039	7.84395553008213	8.8800688429932	0.178989504705197	X	1793414	1793431	18	-	53	16	19	22	31	11	13	FBtr0089990, FBtr0089989, FBtr0332583
-FBgn0000139:E007	FBgn0000139	E007	17.4740062043893	0.0174768417948426	11.0131663629035	0.00405995584334216	0.0255980592448039	8.06218952054063	5.57421707504838	-0.532402511522416	3R	20478032	20478312	281	+	12	5	9	24	28	24	19	FBtr0084660, FBtr0084659, FBtr0306171
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-FBgn0000053:E005	FBgn0000053	E005	62.2147652508149	0.00520872685589504	10.459838484334	0.00535395765922015	0.0312314196787842	12.1816850585854	13.0688962458535	0.101423590166876	2L	7018149	7018374	226	-	77	70	85	38	72	45	51	FBtr0079431, FBtr0100353
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-FBgn0000064:E004	FBgn0000064	E004	27.138007646805	0.0443836809195189	9.83341754725546	0.00732319351484911	0.0400487145343311	7.41146867159234	10.6361473256527	0.521144302474263	3R	22082196	22082345	150	-	74	30	39	9	25	20	9	FBtr0085000, FBtr0114544
-FBgn0000097:E002	FBgn0000097	E002	400.358490752986	0.00705203047871159	9.39930720468379	0.00909842823012389	0.0480777516251865	23.1566918837733	23.0147612426682	-0.00886969168929183	2L	2156792	2157426	635	-	517	327	402	386	671	348	286	FBtr0330658, FBtr0330659, FBtr0077850, FBtr0077851
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-FBgn0000032:E006	FBgn0000032	E006	70.8660693183917	0.00448195162960696	8.8242841765894	0.0121291687320675	0.0589612368919947	13.2060237459434	13.2580538524779	0.00567287283016373	3R	25818708	25818903	196	-	79	62	69	80	95	56	64	FBtr0085609, FBtr0085610
-FBgn0000115:E001	FBgn0000115	E001	52.3822474504571	0.00559723657507901	8.86650303908063	0.0118758123908506	0.0589612368919947	12.3502096098012	11.7375055306327	-0.0734096900094162	3L	15976235	15976380	146	+	88	34	41	72	99	33	38	FBtr0075517
-FBgn0000108:E011	FBgn0000108	E011	4.33255157059706	0.0264868115849274	8.59169964424735	0.0136249879597176	0.0644425106202857	3.93750073669012	4.48950960388759	0.189277672328548	X	466182	466322	141	+	13	4	2	1	14	1	3	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
-FBgn0000063:E004	FBgn0000063	E004	30.7202523491883	0.0364269486568578	8.53129752471595	0.0140427537671149	0.0646705765590816	9.95769482216841	9.62790970457965	-0.048589189625067	3R	13499271	13499298	28	+	71	19	19	59	52	9	20	FBtr0331348
-FBgn0000017:E006	FBgn0000017	E006	198.426283439389	0.00367947435954157	8.36350985046133	0.0152716833739159	0.0685267843701354	18.8017086792816	18.7123216723935	-0.00687521092268594	3L	16619843	16619963	121	-	226	135	183	182	354	208	152	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000108:E006	FBgn0000108	E006	0.864384408056277	0.083878044911284	8.26877758279237	0.0160124490861451	0.0700544647518848	0.0346924353144438	2.77171428746935	6.32001362227144	X	465164	465166	3	+	4	2	1	0	0	0	0	FBtr0307295, FBtr0307293
-FBgn0000139:E006	FBgn0000139	E006	30.3520375086607	0.0116274381407471	7.89919960412463	0.0192624090094349	0.0822175994305147	8.82025867848813	10.4918887018724	0.250381536124665	3R	20477583	20477963	381	+	44	29	34	39	45	15	21	FBtr0084660, FBtr0084659, FBtr0306171
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-FBgn0000064:E001	FBgn0000064	E001	545.837147870255	0.0491710542194309	6.86071090713355	0.0323754307650502	0.128765917815541	23.9994733202863	26.1245576620754	0.122403864297361	3R	22079791	22080925	1135	-	1709	361	542	439	682	328	303	FBtr0084994
-FBgn0000008:E013	FBgn0000008	E013	3.91734100140517	0.0320033734758953	6.7393113524931	0.0344014805513144	0.128984660601894	4.06591806011259	3.71815540394307	-0.12899407067252	2R	18060002	18060339	338	+	11	1	1	5	10	5	0	FBtr0071764, FBtr0071763, FBtr0100521
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-FBgn0000053:E008	FBgn0000053	E008	108.804134854617	0.00528121377833344	6.6380640765292	0.0361878432539731	0.131934845196777	15.7455388976597	15.7190233752978	-0.00243154958532595	2L	7023529	7023940	412	-	179	115	101	127	164	57	76	FBtr0079431, FBtr0100353
-FBgn0000032:E009	FBgn0000032	E009	32.7707234445176	0.0436133929003002	6.52577304843769	0.0382777487496753	0.133972120623863	10.1826457944236	9.68770235039865	-0.0718860261245491	3R	25818999	25819130	132	-	54	25	20	73	61	10	18	FBtr0085609
-FBgn0000083:E005	FBgn0000083	E005	519.429405568491	0.00727975670956911	6.56576261159233	0.0375199943362794	0.133972120623863	24.6220444769406	24.6509381812779	0.00169199453694345	3R	16894560	16894741	182	+	567	413	615	536	584	399	524	FBtr0089518, FBtr0089519, FBtr0089520, FBtr0089517
-FBgn0000018:E001	FBgn0000018	E001	75.3353185482626	0.00688049005044877	6.29011506097068	0.0430644464570576	0.142193926980851	13.797288702704	14.0248135568527	0.0235968003742886	2L	10973443	10974210	768	-	152	41	62	106	141	37	57	FBtr0080168
-FBgn0000018:E002	FBgn0000018	E002	143.582443967402	0.00680569274651789	6.31888170929696	0.0424494698697242	0.142193926980851	17.2138103638839	17.0393859081877	-0.0146931381438143	2L	10974268	10975273	1006	-	217	109	114	182	242	98	117	FBtr0080168
-FBgn0000119:E007	FBgn0000119	E007	2.5085164052321	0.0302895085977079	6.31369911005051	0.0425596118087543	0.142193926980851	3.61109594027176	2.37438082996638	-0.60488540135279	2R	9370660	9370723	64	-	3	2	0	6	8	1	1	FBtr0087702
-FBgn0000052:E005	FBgn0000052	E005	5.95928508029525	0.022424760639996	6.12845750402229	0.0466898374251495	0.148558573625476	4.72619009192154	4.83985525090261	0.034286243343325	2L	6045894	6045920	27	-	12	2	7	10	15	2	2	FBtr0079219
-FBgn0000109:E002	FBgn0000109	E002	33.7700649662137	0.0071253840865294	6.15490833352075	0.046076410315864	0.148558573625476	9.888287109767	10.0658339502451	0.0256741658052705	3L	1884323	1884560	238	-	57	15	38	41	40	26	31	FBtr0089420
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-FBgn0000017:E001	FBgn0000017	E001	1147.17152215341	0.00537176046048132	5.98573979690622	0.0501433237803977	0.150902869611528	29.5218215528231	29.3808374361025	-0.00690622385959656	3L	16615470	16616388	919	-	1564	806	875	1289	2492	911	820	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000064:E010	FBgn0000064	E010	4.52637441420982	0.0437214032379316	5.92813953704285	0.051608454732001	0.150902869611528	4.30701936539805	4.17953764513061	-0.043346455067476	3R	22085524	22085552	29	-	10	5	3	5	14	1	1	FBtr0084995
-FBgn0000083:E003	FBgn0000083	E003	84.235857406506	0.0446153232097599	5.92312061689381	0.0517381267239523	0.150902869611528	14.9504769658546	13.4571539369455	-0.151818185925153	3R	16893168	16893221	54	+	119	60	55	93	238	36	74	FBtr0089518, FBtr0089519, FBtr0089520, FBtr0089517
-FBgn0000115:E002	FBgn0000115	E002	121.3964552666	0.00373776217287953	5.95670016312975	0.0508767070708118	0.150902869611528	15.9168284972858	16.469254074607	0.0492223132405372	3L	15976478	15976694	217	+	156	119	129	121	183	82	96	FBtr0075517
-FBgn0000100:E003	FBgn0000100	E003	12136.5601437149	0.0500118773684073	5.72888339903898	0.0570149537239837	0.163567490191756	44.9679093182512	43.7559333118909	-0.039417150807591	3L	22069192	22069236	45	+	14672	9830	10238	12925	20934	9117	11258	FBtr0078481, FBtr0334113
-FBgn0000117:E005	FBgn0000117	E005	3117.72913507179	0.00320956063907167	5.67821952775645	0.0584777017614175	0.165058029165291	36.0119626216585	35.7724047666012	-0.00962912191259871	X	1789147	1790786	1640	-	4350	2733	3196	3198	4668	2293	2428	FBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988
-FBgn0000064:E003	FBgn0000064	E003	103.865948679456	0.0457993509089639	5.57308501769916	0.0616339447641539	0.168530317714483	16.4842636030222	14.1885107567455	-0.216366269000727	3R	22081688	22082029	342	-	167	48	93	85	279	77	76	FBtr0310661, FBtr0085000, FBtr0085001, FBtr0306657, FBtr0114544
-FBgn0000100:E002	FBgn0000100	E002	750.225086408109	0.0507878607465631	5.58897675153813	0.0611461501832268	0.168530317714483	26.8636788609185	27.1320437955451	0.0143408377288523	3L	22069135	22069191	57	+	1225	809	496	1366	1073	336	423	FBtr0334113
-FBgn0000139:E004	FBgn0000139	E004	6.44700256941908	0.0176034848693448	5.45727294942567	0.0653082784742573	0.175829980507616	4.02487716793681	5.66490154905787	0.493106128086209	3R	20476902	20476973	72	+	14	7	6	3	10	4	5	FBtr0306171
-FBgn0000140:E005	FBgn0000140	E005	32.5533299591785	0.0116035749464937	5.34032370881407	0.0692410174385289	0.183593606844584	9.30107040522959	10.5583070516634	0.182909865367515	3R	20585313	20585614	302	+	51	37	38	35	47	22	13	FBtr0084692
-FBgn0000024:E009	FBgn0000024	E009	0.979078995544713	0.180157587463826	5.1838665228174	0.0748751468403384	0.195569413388944	1.0461614485153	2.32078781300609	1.1495091125474	3R	9071532	9072376	845	-	1	2	3	0	1	0	0	FBtr0082780, FBtr0300486
-FBgn0000083:E007	FBgn0000083	E007	32.2876781486623	0.0280506934179046	4.74692311709902	0.0931576966862745	0.239364908836656	10.2527226633941	9.29229265427618	-0.141900579070407	3R	16896000	16896261	262	+	60	20	15	42	51	26	30	FBtr0089517
-FBgn0000116:E003	FBgn0000116	E003	0.40181652404165	0.124257443990387	4.72089109111607	0.0943781640555958	0.239364908836656	1.88137763970372	0.888011469584649	-1.08313924732248	3L	9044818	9045001	184	-	1	0	0	1	2	0	0	FBtr0076546
-FBgn0000052:E006	FBgn0000052	E006	8.05272056492012	0.120258621084705	4.64986629247866	0.0977899814608388	0.244474953652097	5.17319612420627	5.72232070022577	0.145544466471973	2L	6045921	6045970	50	-	18	1	12	13	19	2	3	FBtr0079219, FBtr0079220
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-FBgn0000121:E001	FBgn0000121	E001	1.0078404227901	0.0861392173223703	4.30207955498123	0.116363103114092	0.282826986735641	1.39252009759596	2.69308239768829	0.951560221823747	3L	8640361	8640745	385	-	4	0	1	0	1	1	1	FBtr0076599
-FBgn0000119:E003	FBgn0000119	E003	13.5729072769284	0.0106973360022192	4.22131361964496	0.121158362291424	0.288402784805717	6.04206299054636	7.32057524661987	0.276915794388541	2R	9343488	9343757	270	-	21	15	16	15	13	7	11	FBtr0087702
-FBgn0000139:E003	FBgn0000139	E003	3.61191788404307	0.0554283109029367	4.20823619656839	0.121953177574989	0.288402784805717	3.58421889064816	3.97567075355025	0.149539538155875	3R	20476372	20476716	345	+	8	4	1	3	12	1	2	FBtr0084660
-FBgn0000008:E009	FBgn0000008	E009	18.1387053226442	0.0134208671839162	4.1718159002826	0.124194306720702	0.289786715681639	7.90822920392252	7.02917803999041	-0.169998688266701	2R	18056749	18058222	1474	+	16	17	15	18	33	21	10	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000063:E003	FBgn0000063	E003	67.8567676254432	0.00729115874342759	4.08933603320588	0.129423149182829	0.29037245008968	13.1545892369739	13.2587464105378	0.0113781779532254	3R	13498643	13499198	556	+	104	63	62	60	109	54	50	FBtr0083478, FBtr0331348
-FBgn0000083:E008	FBgn0000083	E008	148.254009682968	0.0445517432277652	4.11897151932777	0.127519528722191	0.29037245008968	16.2072657192566	18.5789867348968	0.197031103335557	3R	16896446	16896639	194	+	317	119	178	86	149	110	129	FBtr0089518, FBtr0089520
-FBgn0000121:E003	FBgn0000121	E003	2.30524126345099	0.0760584685668236	4.10059497351291	0.128696612354743	0.29037245008968	3.20199555239281	2.10868711098508	-0.60262626139748	3L	8641070	8642036	967	-	2	0	1	3	11	2	1	FBtr0076599
-FBgn0000064:E008	FBgn0000064	E008	14.3346630236921	0.010898402227785	3.95784289793482	0.138218232364304	0.302472808359457	6.48047864060362	7.52397296983254	0.215394293111666	3R	22084709	22084991	283	-	33	12	18	10	21	6	11	FBtr0310660, FBtr0114544
-FBgn0000094:E001	FBgn0000094	E001	7.82839415860988	0.0302231009983838	3.957046469044	0.138273283821466	0.302472808359457	5.07595611217118	5.38583999838945	0.0854917757639793	3R	26035670	26035802	133	+	17	6	9	8	9	7	3	FBtr0085611
-FBgn0000008:E010	FBgn0000008	E010	12.8536495497367	0.0237390052895966	3.75619648490175	0.15288057125236	0.322338553845337	5.99731872230532	7.11313374593812	0.246167644702723	2R	18058283	18059490	1208	+	17	17	15	9	20	8	8	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000017:E005	FBgn0000017	E005	271.37662534133	0.0200462458821176	3.78095939472558	0.150999357466835	0.322338553845337	20.5183508372078	20.8382368812244	0.0223184376939397	3L	16619628	16619716	89	-	296	210	261	313	372	242	237	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000094:E002	FBgn0000094	E002	2.87825776924099	0.0423625191779128	3.75784548367269	0.152754573265081	0.322338553845337	3.65776570087601	3.19371864931671	-0.19572544173404	3R	26035865	26036011	147	+	9	2	0	3	8	2	1	FBtr0085611
-FBgn0000052:E002	FBgn0000052	E002	684.815325547703	0.0044258929726073	3.67735196690472	0.159027842273644	0.324191898203593	26.3610247153598	26.3053553810938	-0.00304991162253238	2L	6042075	6044351	2277	-	1005	523	566	843	1051	505	577	FBtr0079219, FBtr0079221, FBtr0079220
-FBgn0000064:E009	FBgn0000064	E009	1.15788898853292	0.253220426035808	3.68669840995403	0.158286403740723	0.324191898203593	1.87088113460232	2.58733759746854	0.467750409419456	3R	22084992	22084996	5	-	5	2	0	0	4	0	0	FBtr0114544
-FBgn0000108:E008	FBgn0000108	E008	7.08361924991647	0.0231352560739625	3.67371667556259	0.159317161402908	0.324191898203593	4.88854227595858	4.67715486561185	-0.063773130505351	X	465460	466091	632	+	5	8	7	0	14	8	7	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
-FBgn0000083:E004	FBgn0000083	E004	2097.66378510688	0.0082192100965237	3.58192358585089	0.16679966575516	0.335516569047736	33.4243999154547	33.2719514319111	-0.00659517499157958	3R	16893791	16894499	709	+	2447	1834	2126	2309	2810	1533	1952	FBtr0089518, FBtr0089519, FBtr0089520, FBtr0089517
-FBgn0000139:E005	FBgn0000139	E005	13.2470390620692	0.0204750976815376	3.43784726013855	0.179258993096476	0.356480952180492	5.98381242317213	7.21152310472912	0.269239043824083	3R	20477139	20477352	214	+	18	13	14	10	17	5	18	FBtr0084659
-FBgn0000053:E002	FBgn0000053	E002	211.729712208868	0.00813215374237342	3.38164868121731	0.184367479733011	0.362520325317718	19.8763125531366	18.7814062941478	-0.0817450418025216	2L	7016437	7017486	1050	-	295	164	223	247	282	155	176	FBtr0079431
-FBgn0000037:E001	FBgn0000037	E001	4.93059492840277	0.0433545626419766	3.33467852742846	0.188748608377574	0.362978093033796	4.50509603818302	3.9758304407979	-0.180301630388726	2R	20266159	20269379	3221	-	9	5	4	5	9	3	3	FBtr0072367, FBtr0072368
-FBgn0000117:E007	FBgn0000117	E007	4.5734995655629	0.0692001428034552	3.35394623889906	0.186938962444411	0.362978093033796	4.27085107278792	4.1520346978032	-0.0407050911031689	X	1793337	1793413	77	-	10	5	2	3	15	1	3	FBtr0332583
-FBgn0000119:E005	FBgn0000119	E005	187.898456532462	0.00767209784304948	3.09113088609446	0.213191289602673	0.405526909570301	18.6862261764732	18.524577013669	-0.0125346347072856	2R	9344041	9347030	2990	-	264	142	176	218	266	139	168	FBtr0087702
-FBgn0000139:E009	FBgn0000139	E009	96.3385782859831	0.00706444345490435	3.06649078166551	0.215834063551355	0.406139366897712	14.8501418965559	14.5649462805297	-0.0279763359405313	3R	20478820	20479098	279	+	92	64	93	95	166	87	94	FBtr0084660, FBtr0084659, FBtr0306171
-FBgn0000108:E007	FBgn0000108	E007	2.0755759309234	0.0642861300205324	2.89420878951182	0.235250495380735	0.437966347783283	2.91238758305937	2.1358063865339	-0.447421492537865	X	465167	465385	219	+	0	3	1	0	5	2	3	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
-FBgn0000008:E011	FBgn0000008	E011	1.99928611112699	0.0399098641425767	2.61232557984533	0.270857401607045	0.483002957250999	3.17239271273564	2.10797686314985	-0.589712342086156	2R	18059587	18059757	171	+	2	0	2	3	6	1	2	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000032:E002	FBgn0000032	E002	80.2953101927857	0.0644639564540266	2.6290692215714	0.26859929737214	0.483002957250999	13.2060234286795	15.1029765652259	0.19363680011898	3R	25816863	25817415	553	-	213	67	51	112	71	52	51	FBtr0085609, FBtr0085610
-FBgn0000045:E002	FBgn0000045	E002	2.68093910810214	0.0643568697407604	2.59705339793862	0.272933610331822	0.483002957250999	3.07205233502172	3.15145867625879	0.0368169516036241	3L	21978349	21978424	76	+	2	3	6	4	4	0	1	FBtr0334090
-FBgn0000053:E001	FBgn0000053	E001	296.253588782233	0.0039965303078777	2.59479725292871	0.273241672959136	0.483002957250999	21.6645776637671	20.9797943738213	-0.0463375746142072	2L	7014861	7016374	1514	-	414	275	301	312	429	184	257	FBtr0079431
-FBgn0000139:E002	FBgn0000139	E002	1.96739811366688	0.132123520575205	2.65965992394747	0.26452223631495	0.483002957250999	2.66402320924572	2.94591105463036	0.14510722062368	3R	20476127	20476311	185	+	4	3	0	2	7	1	0	FBtr0084660
-FBgn0000032:E008	FBgn0000032	E008	11.0767227240209	0.0798401902564677	2.51035424382931	0.285025359515854	0.498794379152745	6.63698895635649	5.48812645254999	-0.274215150459407	3R	25818984	25818998	15	-	12	11	4	17	35	5	6	FBtr0085609, FBtr0085610
-FBgn0000032:E007	FBgn0000032	E007	2.52959384340906	0.0437715617848693	2.47128531992908	0.290647914556016	0.50259553586095	3.21611753752064	3.02524297355984	-0.0882691151406223	3R	25818904	25818983	80	-	5	3	0	4	7	2	0	FBtr0085610
-FBgn0000045:E003	FBgn0000045	E003	1.90232166678076	0.0787624998990938	2.45556539328512	0.292941398044668	0.50259553586095	2.87240938522751	2.78434375492635	-0.0449240442218055	3L	21978425	21979375	951	+	6	1	2	1	6	1	0	FBtr0334090, FBtr0078478
-FBgn0000097:E004	FBgn0000097	E004	38.4345935077677	0.0142078050074908	2.33129736058348	0.311720389561415	0.529622021099492	10.0680428228478	11.2290968845631	0.157458643784659	2L	2158468	2159245	778	-	72	36	37	46	50	27	21	FBtr0330658, FBtr0330660, FBtr0077850, FBtr0077851, FBtr0330659
-FBgn0000119:E001	FBgn0000119	E001	71.3729832029852	0.0111406512484234	2.30453522009596	0.315919574126152	0.531595437231506	13.4756219149392	13.5887769276739	0.0120637541514785	2R	9341159	9342741	1583	-	126	62	49	77	133	44	57	FBtr0087702
-FBgn0000032:E004	FBgn0000032	E004	261.378773499601	0.00819643654624059	2.27934155985812	0.319924329991185	0.533207216651975	20.7181627248029	20.3170316382605	-0.0282064346216979	3R	25817805	25818494	690	-	385	165	234	328	450	197	204	FBtr0085609, FBtr0085610
-FBgn0000109:E003	FBgn0000109	E003	18.3940473673953	0.0293726892708863	2.16278611657816	0.339122778641522	0.554640058525854	8.02551651194346	7.52140194471521	-0.0935926484572927	3L	1884691	1884885	195	-	32	6	19	38	29	9	11	FBtr0089420
-FBgn0000139:E008	FBgn0000139	E008	112.43808666746	0.00404936398532356	2.16746950134991	0.338329586481378	0.554640058525854	15.8044531515159	15.3206807560228	-0.0448507144365468	3R	20478504	20478761	258	+	130	73	89	133	199	85	116	FBtr0084660, FBtr0084659, FBtr0306171
-FBgn0000024:E007	FBgn0000024	E007	0.609263156530486	0.154791971978235	2.12653291257313	0.345325973855703	0.556218835938167	2.07969685417277	0.938775096472096	-1.14752177394572	3R	9069308	9069853	546	-	0	1	0	2	2	0	0	FBtr0082780, FBtr0300486
-FBgn0000064:E006	FBgn0000064	E006	2814.5524025292	0.0148313047423681	2.12006312809046	0.346444874955772	0.556218835938167	35.5129874212414	35.0408493230973	-0.0193089842346954	3R	22082947	22083763	817	-	3729	2672	3078	2786	4155	2022	2100	FBtr0085000, FBtr0085001, FBtr0084995, FBtr0084994, FBtr0306657, FBtr0114544, FBtr0310661, FBtr0310660, FBtr0084999
-FBgn0000108:E001	FBgn0000108	E001	2.75903382413077	0.0366991339272361	1.94502755702236	0.378131304033761	0.60157252914462	3.44284073669307	2.5702566105764	-0.421687041303464	X	424503	424567	65	+	4	1	1	1	6	5	2	FBtr0307294, FBtr0307295, FBtr0070109, FBtr0307292, FBtr0307293
-FBgn0000017:E002	FBgn0000017	E002	40.9148553776179	0.00690769240104033	1.91987762593712	0.382916314770926	0.603696892656866	10.9002145864032	10.3185296079471	-0.0791191356659471	3L	16616389	16616736	348	-	47	29	29	36	83	48	28	FBtr0330136, FBtr0075357, FBtr0330133, FBtr0112790, FBtr0330130
-FBgn0000008:E005	FBgn0000008	E005	1.32353144265853	0.050525535811173	1.85771764772981	0.395004222657933	0.617194097903021	2.06623618045511	2.56503260674538	0.311971995100583	2R	18025505	18025756	252	+	4	1	1	2	2	0	1	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000008:E012	FBgn0000008	E012	0.661887298226701	0.100488589471993	1.80188103473211	0.406187453678996	0.62905136631703	1.59896822605591	1.80439102626633	0.174370745721675	2R	18059821	18059938	118	+	3	0	0	0	2	1	0	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000108:E009	FBgn0000108	E009	1.57262265911296	0.0574831454050284	1.71077127925619	0.425119216650181	0.652595288717383	2.2899365369098	2.10859472100666	-0.11902578521893	X	466092	466103	12	+	2	0	2	0	1	3	2	FBtr0307291, FBtr0070109, FBtr0307292, FBtr0307293
-FBgn0000071:E002	FBgn0000071	E002	14.9999389961672	0.0169925164413192	1.68846878346913	0.429886356800612	0.654174890783541	6.45162657998662	6.3313761300616	-0.0271438330035983	3R	2589128	2589222	95	+	57	24	18	3	10	5	3	FBtr0081619, FBtr0081620
-FBgn0000084:E001	FBgn0000084	E001	53.2358303205052	0.169187365684348	1.54671914624413	0.461460152080192	0.696168332879601	10.9561997974025	13.3028763313918	0.279990736782523	X	20065478	20065681	204	-	144	41	40	12	73	50	45	FBtr0070025, FBtr0301931
-FBgn0000054:E001	FBgn0000054	E001	30.2913156353099	0.0164154025261545	1.52842959451606	0.46569945593967	0.696559015294378	9.27312824348917	9.91601168294666	0.0967038642697362	2R	2549775	2549941	167	+	56	22	27	43	33	21	23	FBtr0330252, FBtr0086111, FBtr0086113, FBtr0086112
-FBgn0000108:E003	FBgn0000108	E003	0.764700251448577	0.179709597123131	1.45403971669405	0.483347289247638	0.716828606935056	1.86652914982048	1.06880098673065	-0.804364794727211	X	425660	425909	250	+	0	1	0	1	1	0	2	FBtr0307294, FBtr0307295, FBtr0307291, FBtr0070109, FBtr0307293, FBtr0307292
-FBgn0000046:E003	FBgn0000046	E003	16.8641331350762	0.0304076600665358	1.40850407699274	0.494478286696399	0.718402311980629	7.51983697185383	7.48410660821892	-0.00687127562089203	3R	9252305	9253811	1507	+	35	16	17	5	33	12	12	FBtr0082785, FBtr0082786
-FBgn0000047:E002	FBgn0000047	E002	4.10256379465508	0.0620316849890141	1.39047340164907	0.498956330631583	0.718402311980629	3.60291386909344	4.05474112086033	0.170445643775757	3R	11266322	11267262	941	+	7	5	6	2	7	3	1	FBtr0083143
-FBgn0000054:E003	FBgn0000054	E003	8.66762333263177	0.0136425866260374	1.35346638599388	0.508274718565623	0.718402311980629	5.67769951248285	4.927274303207	-0.204516708390074	2R	2549954	2550073	120	+	10	5	7	8	16	9	8	FBtr0086112
-FBgn0000071:E004	FBgn0000071	E004	155.00489061648	0.0158148642841528	1.33439556076939	0.513144508557592	0.718402311980629	16.3018801829894	16.18370162011	-0.0104967415862467	3R	2589555	2590983	1429	+	460	234	286	29	93	42	43	FBtr0081619, FBtr0081618, FBtr0081620
-FBgn0000114:E010	FBgn0000114	E010	0.576335917111657	0.445222873374312	1.36507504985869	0.505333068800794	0.718402311980629	1.4344000730277	1.62504099513689	0.180028646901177	2L	12287223	12287808	586	+	1	0	2	0	2	0	0	FBtr0080347
-FBgn0000117:E009	FBgn0000117	E009	75.1849884692702	0.0237545180603618	1.34155847035672	0.511309991777952	0.718402311980629	13.9198045041616	13.5504648364156	-0.0387966067132283	X	1793432	1793557	126	-	102	64	78	105	107	37	64	FBtr0332583, FBtr0089990, FBtr0089989, FBtr0089988
-FBgn0000140:E006	FBgn0000140	E006	29.5385944102884	0.012884838120785	1.3843884211833	0.500476712094224	0.718402311980629	9.30487036834726	9.98811550742641	0.102226454003351	3R	20585679	20586235	557	+	67	21	26	34	46	15	22	FBtr0084692
-FBgn0000017:E007	FBgn0000017	E007	179.862650955019	0.00549771753124386	1.24520064469985	0.536547425778282	0.734958988426926	18.0759031169376	18.6697835787123	0.0466374742523522	3L	16620022	16620292	271	-	263	128	157	167	345	176	112	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000043:E001	FBgn0000043	E001	15041.3064055878	0.109391490489995	1.22701427401194	0.541448600841827	0.734958988426926	46.3608599292243	45.4640180890262	-0.0281821320561008	2R	1901415	1902927	1513	-	27313	15297	16802	15915	20887	8188	9110	FBtr0086029
-FBgn0000043:E002	FBgn0000043	E002	391.125850028855	0.109498173366373	1.22582829789303	0.541769768611849	0.734958988426926	22.5505327893937	23.4220179607712	0.0547038591842883	2R	1903082	1903190	109	-	1145	374	378	570	190	188	174	FBtr0086029
-FBgn0000047:E003	FBgn0000047	E003	1.47614278023545	0.10976579155014	1.25400753132076	0.534189963889714	0.734958988426926	2.67112273008178	1.94251452859415	-0.459520876026365	3R	11267324	11267895	572	+	1	2	1	4	2	0	1	FBtr0083143
-FBgn0000017:E008	FBgn0000017	E008	4.44081189153106	0.159408388210514	1.15366230173669	0.561675414128889	0.756101519019658	3.44294742838657	4.44922827109496	0.369910966954586	3L	16620602	16621188	587	-	5	1	10	5	3	2	5	FBtr0075357, FBtr0330136, FBtr0112790, FBtr0330135, FBtr0330134, FBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130
-FBgn0000008:E014	FBgn0000008	E014	0.55498474117927	0.0991668497318665	1.10098592369296	0.576665466227803	0.759871696251732	1.59211259869536	1.4936182600799	-0.0921309006460141	2R	18060340	18060346	7	+	1	0	1	1	2	0	0	FBtr0071763, FBtr0071764
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-FBgn0000008:E002	FBgn0000008	E002	0.205235479273134	0.345148736432819	1.16175946814889	0.559406021492231	NA	0.946221351097568	0.0418458188899677	-4.4990223297576	2R	18024496	18024531	36	+	0	0	0	0	0	1	0	FBtr0071763, FBtr0100521
-FBgn0000008:E006	FBgn0000008	E006	0.0933261680585749	0.63292012026371	0.386447055483558	0.824297700141234	NA	0.0313582667327381	1.03141680776109	5.03963783099287	2R	18039159	18039200	42	+	1	0	0	0	0	0	0	FBtr0071764, FBtr0071763, FBtr0100521
-FBgn0000014:E001	FBgn0000014	E001	0.298561647331709	14	0.0441608888174834	0.978161544259054	NA	1.27264365403058	0.805558937331108	-0.659766464456778	3R	12632936	12633348	413	-	1	0	0	0	0	1	0	FBtr0306337
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@@ -185,10 +216,8 @@
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-FBgn0000014:E009	FBgn0000014	E009	0.0933261680585749	14	0.0441538225664857	0.978165000232653	NA	0.0483561576507068	0.805558937309304	4.05821862641954	3R	12653620	12653845	226	-	1	0	0	0	0	0	0	FBtr0083388
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-FBgn0000015:E002	FBgn0000015	E002	0.0933261680585749	14	0.381778750542054	0.826223983900076	NA	0.0362778896152491	1.03426437561497	4.83337066726416	3R	12753395	12755302	1908	-	1	0	0	0	0	0	0	FBtr0330709, FBtr0083385, FBtr0083384, FBtr0083383, FBtr0083382, FBtr0083381
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@@ -199,41 +228,28 @@
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-FBgn0000024:E011	FBgn0000024	E011	0.2572924167311	0.375188972952962	0.5808743295506	0.747936524595224	NA	1.03704268244909	0.947941602938094	-0.129605182516137	3R	9084148	9084590	443	-	0	1	0	0	1	0	0	FBtr0082780
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-FBgn0000028:E006	FBgn0000028	E006	0.15316821713762	14	0.0448649614922942	0.977817256456086	NA	0.0665935882332338	0.733003872592276	3.46036563692957	X	15248260	15248491	232	-	0	0	1	0	0	0	0	FBtr0305195, FBtr0305189, FBtr0305196, FBtr0074015, FBtr0305194, FBtr0100328, FBtr0290063, FBtr0305191, FBtr0305190, FBtr0305193, FBtr0305192, FBtr0290064, FBtr0100326
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-FBgn0000036:E001	FBgn0000036	E001	0.225143209263807	14	0.0753841619066407	0.963009424186269	NA	0.744388050549727	1.15690288516914	0.636140962694898	3R	20226948	20227667	720	-	1	0	0	1	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E002	FBgn0000036	E002	0	NA	NA	NA	NA	NA	NA	NA	3R	20228937	20229232	296	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E003	FBgn0000036	E003	0	NA	NA	NA	NA	NA	NA	NA	3R	20230404	20230615	212	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E004	FBgn0000036	E004	0	NA	NA	NA	NA	NA	NA	NA	3R	20230691	20231151	461	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E005	FBgn0000036	E005	0	NA	NA	NA	NA	NA	NA	NA	3R	20233040	20233220	181	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E006	FBgn0000036	E006	0	NA	NA	NA	NA	NA	NA	NA	3R	20238230	20238339	110	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E007	FBgn0000036	E007	0	NA	NA	NA	NA	NA	NA	NA	3R	20240569	20240613	45	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
-FBgn0000036:E008	FBgn0000036	E008	0.0883366573889214	14	0.0753821435284827	0.963010396045353	NA	0.640643943923777	0.0784399443423851	-3.02986234384538	3R	20247417	20247626	210	-	0	0	0	0	1	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E009	FBgn0000036	E009	0	NA	NA	NA	NA	NA	NA	NA	3R	20277617	20278355	739	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000036:E010	FBgn0000036	E010	0	NA	NA	NA	NA	NA	NA	NA	3R	20282157	20282651	495	-	0	0	0	0	0	0	0	FBtr0084619, FBtr0330310
 FBgn0000037:E002	FBgn0000037	E002	0	NA	NA	NA	NA	NA	NA	NA	2R	20270713	20270763	51	-	0	0	0	0	0	0	0	FBtr0072368
 FBgn0000037:E003	FBgn0000037	E003	0	NA	NA	NA	NA	NA	NA	NA	2R	20270764	20270900	137	-	0	0	0	0	0	0	0	FBtr0072367, FBtr0072368
-FBgn0000037:E004	FBgn0000037	E004	0.131817041205232	0.638713869754204	0.621336919360012	0.732956840336235	NA	1.0361289221476	0.0551771658418421	-4.2309883588067	2R	20270959	20271142	184	-	0	0	0	1	0	0	0	FBtr0072367, FBtr0072368
 FBgn0000037:E006	FBgn0000037	E006	0	NA	NA	NA	NA	NA	NA	NA	2R	20277121	20277235	115	-	0	0	0	0	0	0	0	FBtr0072367, FBtr0072368
 FBgn0000038:E001	FBgn0000038	E001	0	NA	NA	NA	NA	NA	NA	NA	3L	4429349	4429502	154	+	0	0	0	0	0	0	0	FBtr0073299, FBtr0073300
 FBgn0000038:E002	FBgn0000038	E002	0	NA	NA	NA	NA	NA	NA	NA	3L	4429566	4429715	150	+	0	0	0	0	0	0	0	FBtr0073299, FBtr0073300
@@ -254,11 +270,9 @@
 FBgn0000039:E009	FBgn0000039	E009	0.0883366573889214	NA	NA	NA	NA	NA	NA	NA	3R	20315321	20315522	202	+	0	0	0	0	1	0	0	FBtr0084639, FBtr0084640
 FBgn0000039:E010	FBgn0000039	E010	0	NA	NA	NA	NA	NA	NA	NA	3R	20316540	20316875	336	+	0	0	0	0	0	0	0	FBtr0084639, FBtr0084640
 FBgn0000045:E001	FBgn0000045	E001	0	NA	NA	NA	NA	NA	NA	NA	3L	21978310	21978348	39	+	0	0	0	0	0	0	0	FBtr0334090, FBtr0078478
-FBgn0000046:E002	FBgn0000046	E002	0.205235479273134	0.460793423141561	1.25123939241761	0.534929831796245	NA	1.04321764776999	0.051486438340568	-4.34070389748626	3R	9252169	9252304	136	+	0	0	0	0	0	1	0	FBtr0082786
 FBgn0000047:E001	FBgn0000047	E001	0	NA	NA	NA	NA	NA	NA	NA	3R	11265710	11265768	59	+	0	0	0	0	0	0	0	FBtr0083143
 FBgn0000061:E001	FBgn0000061	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	378112	378481	370	+	0	0	0	0	0	0	0	FBtr0078053
 FBgn0000061:E003	FBgn0000061	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	385701	385746	46	+	0	0	0	0	0	0	0	FBtr0078053
-FBgn0000061:E005	FBgn0000061	E005	0.374447732873272	14	0.368028250211317	0.831924052728534	NA	0.634996936298325	2.16261613381655	1.76795607206982	2L	386703	387439	737	+	2	0	0	0	0	0	1	FBtr0078053
 FBgn0000071:E001	FBgn0000071	E001	0	NA	NA	NA	NA	NA	NA	NA	3R	2588315	2588718	404	+	0	0	0	0	0	0	0	FBtr0081618
 FBgn0000075:E001	FBgn0000075	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	19110159	19110350	192	+	0	0	0	0	0	0	0	FBtr0081153
 FBgn0000075:E002	FBgn0000075	E002	0	NA	NA	NA	NA	NA	NA	NA	2L	19110412	19110646	235	+	0	0	0	0	0	0	0	FBtr0081153
@@ -267,41 +281,27 @@
 FBgn0000079:E001	FBgn0000079	E001	84.9770030139345	NA	NA	NA	NA	NA	NA	NA	2R	13006211	13007808	1598	-	44	51	53	78	132	115	99	FBtr0087004
 FBgn0000084:E002	FBgn0000084	E002	0	NA	NA	NA	NA	NA	NA	NA	X	20065962	20065964	3	-	0	0	0	0	0	0	0	FBtr0301931
 FBgn0000099:E001	FBgn0000099	E001	0	NA	NA	NA	NA	NA	NA	NA	2R	1593707	1594728	1022	-	0	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059
-FBgn0000099:E003	FBgn0000099	E003	0.0933261680585749	8.24727293760506	0.167758711123923	0.919542187053798	NA	0.0181896949718858	1.14255481527734	5.97299822130791	2R	1595688	1595884	197	-	1	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
-FBgn0000099:E004	FBgn0000099	E004	0.0883366573889214	8.32831107111954	0.0753073656847008	0.963046402638951	NA	0.674689760173148	0.026887613203348	-4.64921066722288	2R	1596116	1596372	257	-	0	0	0	0	1	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
 FBgn0000099:E005	FBgn0000099	E005	0	NA	NA	NA	NA	NA	NA	NA	2R	1596431	1596604	174	-	0	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
 FBgn0000099:E006	FBgn0000099	E006	0	NA	NA	NA	NA	NA	NA	NA	2R	1596664	1596797	134	-	0	0	0	0	0	0	0	FBtr0086059
-FBgn0000099:E007	FBgn0000099	E007	0.168955759342179	14	0.193694774340941	0.907694521392659	NA	0.0181899442426268	1.4315097812054	6.29825259705369	2R	1604154	1604293	140	-	0	1	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0300504
 FBgn0000099:E008	FBgn0000099	E008	0	NA	NA	NA	NA	NA	NA	NA	2R	1604294	1604554	261	-	0	0	0	0	0	0	0	FBtr0300505
 FBgn0000099:E009	FBgn0000099	E009	0	NA	NA	NA	NA	NA	NA	NA	2R	1604787	1605003	217	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
 FBgn0000099:E010	FBgn0000099	E010	0	NA	NA	NA	NA	NA	NA	NA	2R	1605060	1605268	209	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
 FBgn0000099:E011	FBgn0000099	E011	0	NA	NA	NA	NA	NA	NA	NA	2R	1605269	1605271	3	-	0	0	0	0	0	0	0	FBtr0086058
 FBgn0000099:E012	FBgn0000099	E012	0	NA	NA	NA	NA	NA	NA	NA	2R	1613326	1614335	1010	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
 FBgn0000114:E001	FBgn0000114	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	12175004	12175420	417	+	0	0	0	0	0	0	0	FBtr0331998
-FBgn0000114:E002	FBgn0000114	E002	0.293572136662055	14	0.380904021358191	0.826585424050438	NA	1.52727541848932	0.0127771491956068	-6.90125045939522	2L	12201326	12201771	446	+	0	0	0	0	1	1	0	FBtr0331648
 FBgn0000114:E003	FBgn0000114	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	12205843	12206130	288	+	0	0	0	0	0	0	0	FBtr0331646, FBtr0080344
 FBgn0000114:E004	FBgn0000114	E004	0	NA	NA	NA	NA	NA	NA	NA	2L	12222197	12222337	141	+	0	0	0	0	0	0	0	FBtr0331647, FBtr0331645
-FBgn0000114:E006	FBgn0000114	E006	0.15316821713762	14	0.172605989659559	0.917316247028269	NA	0.0161637136951942	1.00562209278475	5.95918573727722	2L	12270932	12271347	416	+	0	0	1	0	0	0	0	FBtr0331644, FBtr0080345, FBtr0300567
 FBgn0000114:E007	FBgn0000114	E007	0	NA	NA	NA	NA	NA	NA	NA	2L	12271591	12272084	494	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E008	FBgn0000114	E008	0	NA	NA	NA	NA	NA	NA	NA	2L	12278837	12278919	83	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E009	FBgn0000114	E009	0	NA	NA	NA	NA	NA	NA	NA	2L	12282514	12282562	49	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998
-FBgn0000114:E011	FBgn0000114	E011	0.0883366573889214	14	0.0422451536000494	0.979098942398376	NA	0.901165948893395	0.0127751610731135	-6.14037941516088	2L	12288905	12289344	440	+	0	0	0	0	1	0	0	FBtr0080347
-FBgn0000114:E012	FBgn0000114	E012	0.0933261680585749	14	0.0165742552848158	0.991747115940935	NA	0.0161636584595612	0.822669226222095	5.66948679957666	2L	12298568	12298749	182	+	1	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E013	FBgn0000114	E013	0	NA	NA	NA	NA	NA	NA	NA	2L	12298814	12299111	298	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
-FBgn0000114:E014	FBgn0000114	E014	0.0883366573889214	14	0.0422451536000494	0.979098942398376	NA	0.901165948893395	0.0127751610731135	-6.14037941516088	2L	12299188	12299394	207	+	0	0	0	0	1	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
-FBgn0000114:E015	FBgn0000114	E015	0.0883366573889214	14	0.0422451536000494	0.979098942398376	NA	0.901165948893395	0.0127751610731135	-6.14037941516088	2L	12300361	12300396	36	+	0	0	0	0	1	0	0	FBtr0331644
 FBgn0000114:E016	FBgn0000114	E016	0	NA	NA	NA	NA	NA	NA	NA	2L	12300610	12300621	12	+	0	0	0	0	0	0	0	FBtr0331644
 FBgn0000114:E017	FBgn0000114	E017	0	NA	NA	NA	NA	NA	NA	NA	2L	12304446	12304595	150	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E018	FBgn0000114	E018	0	NA	NA	NA	NA	NA	NA	NA	2L	12310682	12311093	412	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
 FBgn0000114:E019	FBgn0000114	E019	0	NA	NA	NA	NA	NA	NA	NA	2L	12311094	12311104	11	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331645, FBtr0080347, FBtr0331998
-FBgn0000116:E002	FBgn0000116	E002	0.0883366573889214	0.649506832951611	0.955102166349974	0.620300597862845	NA	1.06977392668418	0.0168077984590731	-5.99203136858692	3L	9044230	9044817	588	-	0	0	0	0	1	0	0	FBtr0331550, FBtr0076546
-FBgn0000116:E004	FBgn0000116	E004	0.15316821713762	0.43977187338658	0.328021702700227	0.848732811933342	NA	0.0232213523500242	0.90648447279086	5.2867584097007	3L	9046620	9046661	42	-	0	0	1	0	0	0	0	FBtr0331550
-FBgn0000116:E006	FBgn0000116	E006	0.15316821713762	0.43977187338658	0.328021702700227	0.848732811933342	NA	0.0232213523500242	0.90648447279086	5.2867584097007	3L	9055007	9055567	561	-	0	0	1	0	0	0	0	FBtr0076543, FBtr0076544
 FBgn0000116:E007	FBgn0000116	E007	0	NA	NA	NA	NA	NA	NA	NA	3L	9055912	9056048	137	-	0	0	0	0	0	0	0	FBtr0076544
-FBgn0000116:E008	FBgn0000116	E008	0.205235479273134	0.353436872439287	1.98242161309956	0.371127055796381	NA	1.12162424681281	0.0168071427941747	-6.06037114417562	3L	9057564	9057617	54	-	0	0	0	0	0	1	0	FBtr0112791, FBtr0076543
 FBgn0000120:E001	FBgn0000120	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	18078269	18078496	228	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
 FBgn0000120:E002	FBgn0000120	E002	0	NA	NA	NA	NA	NA	NA	NA	2L	18078916	18079723	808	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
 FBgn0000120:E003	FBgn0000120	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	18079957	18080086	130	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
 FBgn0000120:E004	FBgn0000120	E004	0	NA	NA	NA	NA	NA	NA	NA	2L	18080147	18080415	269	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
 FBgn0000137:E001	FBgn0000137	E001	0	NA	NA	NA	NA	NA	NA	NA	X	354533	357209	2677	+	0	0	0	0	0	0	0	FBtr0070075
-FBgn0000139:E001	FBgn0000139	E001	0.187795396756122	0.374758883334333	0.855539171390518	0.651961618776603	NA	0.887149388069345	0.0477444815800361	-4.21577116420462	3R	20475810	20476066	257	+	0	0	0	0	0	0	1	FBtr0084660
diff -r f1c406f9554c -r 6e8b61c54ff3 test-data/dexseq_result_2fact.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dexseq_result_2fact.tabular	Sun Jan 28 04:04:39 2018 -0500
@@ -0,0 +1,307 @@
+FBgn0000042:E005	FBgn0000042	E005	33.8277404051372	0.00974669544746392	12.6851918587988	0.000368562772095343	0.0770296193679266	9.60660113871428	11.248063753255	0.552857243884021	X	5798498	5798821	324	+	119	20	29	45	52	14	8	FBtr0100662, FBtr0070823
+FBgn0000139:E007	FBgn0000139	E007	17.4740062043893	0.0174768174826308	10.9795545088389	0.000921225722996759	0.0962680880531613	8.06219042258468	5.57421805888543	-1.16397691752144	3R	20478032	20478312	281	+	12	5	9	24	28	24	19	FBtr0084660, FBtr0084659, FBtr0306171
+FBgn0000064:E004	FBgn0000064	E004	27.138007646805	0.0443836931820446	9.70272381901728	0.00183995083792701	0.128183241708915	7.41146981322546	10.6361481097095	1.21002224137722	3R	22082196	22082345	150	-	74	30	39	9	25	20	9	FBtr0085000, FBtr0114544
+FBgn0000053:E004	FBgn0000053	E004	6.32535175423168	0.045626142883598	9.02161905056228	0.00266804962459076	0.139405592884867	3.09087219098584	5.79810451815527	1.88622972793307	2L	7018085	7018148	64	-	13	7	15	0	3	3	4	FBtr0100353
+FBgn0000108:E006	FBgn0000108	E006	0.864384408056277	0.0838775850414772	8.17622649197865	0.00424429612727517	0.177411578120102	0.0346924384664682	2.77171489352896	12.6628857089353	X	465164	465166	3	+	4	2	1	0	0	0	0	FBtr0307295, FBtr0307293
+FBgn0000139:E006	FBgn0000139	E006	30.3520375086607	0.0116274168067176	7.51778234858958	0.00610928459168981	0.212806746610528	8.82025966787089	10.4918896523126	0.593446583668732	3R	20477583	20477963	381	+	44	29	34	39	45	15	21	FBtr0084660, FBtr0084659, FBtr0306171
+FBgn0000064:E011	FBgn0000064	E011	121.014747579775	0.0162642807531925	7.07528109396534	0.00781545601050697	0.233347186599423	17.4845079060715	14.7073531946849	-0.740648902697183	3R	22086876	22086879	4	-	154	77	97	210	219	76	86	FBtr0085001
+FBgn0000100:E001	FBgn0000100	E001	6.87698735532182	0.0164557487090339	5.56698102594524	0.0183022903586644	0.455054200649313	4.47698551662587	5.57993111812181	0.668156167650007	3L	22068967	22069026	60	+	16	5	9	9	9	3	3	FBtr0334113
+FBgn0000139:E004	FBgn0000139	E004	6.44700256941908	0.0176034247520841	5.44756371003484	0.0195956354346594	0.455054200649313	4.02487788954067	5.66490257045217	1.03311218729944	3R	20476902	20476973	72	+	14	7	6	3	10	4	5	FBtr0306171
+FBgn0000097:E003	FBgn0000097	E003	558.924889184516	0.00477031371166494	5.18854635674609	0.0227362260928025	0.475187125339572	25.4143298642324	24.7289690820004	-0.161815950506053	2L	2157427	2158405	979	-	725	462	477	524	1052	491	412	FBtr0330658, FBtr0330660, FBtr0077850, FBtr0077851, FBtr0330659
+FBgn0000053:E006	FBgn0000053	E006	247.836023771802	0.00263067838891117	4.96081239277488	0.0259280236472272	0.492632449297317	19.8531147771976	20.6037362803832	0.185238337954743	2L	7018431	7019080	650	-	368	279	279	214	298	171	181	FBtr0079431, FBtr0100353
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+FBgn0000078:E001	FBgn0000078	E001	16.3910327521687	NA	NA	NA	NA	NA	NA	NA	2R	13012267	13013887	1621	+	10	11	11	24	30	16	15	FBtr0086983
+FBgn0000079:E001	FBgn0000079	E001	84.9770030139345	NA	NA	NA	NA	NA	NA	NA	2R	13006211	13007808	1598	-	44	51	53	78	132	115	99	FBtr0087004
+FBgn0000084:E002	FBgn0000084	E002	0	NA	NA	NA	NA	NA	NA	NA	X	20065962	20065964	3	-	0	0	0	0	0	0	0	FBtr0301931
+FBgn0000099:E001	FBgn0000099	E001	0	NA	NA	NA	NA	NA	NA	NA	2R	1593707	1594728	1022	-	0	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059
+FBgn0000099:E005	FBgn0000099	E005	0	NA	NA	NA	NA	NA	NA	NA	2R	1596431	1596604	174	-	0	0	0	0	0	0	0	FBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504
+FBgn0000099:E006	FBgn0000099	E006	0	NA	NA	NA	NA	NA	NA	NA	2R	1596664	1596797	134	-	0	0	0	0	0	0	0	FBtr0086059
+FBgn0000099:E008	FBgn0000099	E008	0	NA	NA	NA	NA	NA	NA	NA	2R	1604294	1604554	261	-	0	0	0	0	0	0	0	FBtr0300505
+FBgn0000099:E009	FBgn0000099	E009	0	NA	NA	NA	NA	NA	NA	NA	2R	1604787	1605003	217	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
+FBgn0000099:E010	FBgn0000099	E010	0	NA	NA	NA	NA	NA	NA	NA	2R	1605060	1605268	209	-	0	0	0	0	0	0	0	FBtr0086058, FBtr0300504
+FBgn0000099:E011	FBgn0000099	E011	0	NA	NA	NA	NA	NA	NA	NA	2R	1605269	1605271	3	-	0	0	0	0	0	0	0	FBtr0086058
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+FBgn0000114:E001	FBgn0000114	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	12175004	12175420	417	+	0	0	0	0	0	0	0	FBtr0331998
+FBgn0000114:E003	FBgn0000114	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	12205843	12206130	288	+	0	0	0	0	0	0	0	FBtr0331646, FBtr0080344
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+FBgn0000114:E007	FBgn0000114	E007	0	NA	NA	NA	NA	NA	NA	NA	2L	12271591	12272084	494	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998
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+FBgn0000114:E013	FBgn0000114	E013	0	NA	NA	NA	NA	NA	NA	NA	2L	12298814	12299111	298	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
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+FBgn0000114:E017	FBgn0000114	E017	0	NA	NA	NA	NA	NA	NA	NA	2L	12304446	12304595	150	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998
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+FBgn0000114:E019	FBgn0000114	E019	0	NA	NA	NA	NA	NA	NA	NA	2L	12311094	12311104	11	+	0	0	0	0	0	0	0	FBtr0300567, FBtr0331648, FBtr0331646, FBtr0331645, FBtr0080347, FBtr0331998
+FBgn0000116:E007	FBgn0000116	E007	0	NA	NA	NA	NA	NA	NA	NA	3L	9055912	9056048	137	-	0	0	0	0	0	0	0	FBtr0076544
+FBgn0000120:E001	FBgn0000120	E001	0	NA	NA	NA	NA	NA	NA	NA	2L	18078269	18078496	228	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
+FBgn0000120:E002	FBgn0000120	E002	0	NA	NA	NA	NA	NA	NA	NA	2L	18078916	18079723	808	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
+FBgn0000120:E003	FBgn0000120	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	18079957	18080086	130	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
+FBgn0000120:E004	FBgn0000120	E004	0	NA	NA	NA	NA	NA	NA	NA	2L	18080147	18080415	269	+	0	0	0	0	0	0	0	FBtr0307350, FBtr0081030
+FBgn0000137:E001	FBgn0000137	E001	0	NA	NA	NA	NA	NA	NA	NA	X	354533	357209	2677	+	0	0	0	0	0	0	0	FBtr0070075
diff -r f1c406f9554c -r 6e8b61c54ff3 test-data/flattened.gtf
--- a/test-data/flattened.gtf	Sun Jan 29 06:59:35 2017 -0500
+++ b/test-data/flattened.gtf	Sun Jan 28 04:04:39 2018 -0500
@@ -1,257 +1,257 @@
 4	dexseq_prepare_annotation.py	aggregate_gene	68336	77667	.	-	.	gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	68336	71088	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "001"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	71142	71239	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "002"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	71240	71306	.	-	.	transcripts "FBtr0306168+FBtr0089178"; exonic_part_number "003"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	71371	71883	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "004"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	71940	72580	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "005"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	72643	73010	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "006"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	76457	76916	.	-	.	transcripts "FBtr0308074+FBtr0089178"; exonic_part_number "007"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	76917	76957	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "008"; gene_id "FBgn0004859"
-4	dexseq_prepare_annotation.py	exonic_part	76958	77667	.	-	.	transcripts "FBtr0306168"; exonic_part_number "009"; gene_id "FBgn0004859"
+4	dexseq_prepare_annotation.py	exonic_part	68336	71088	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "001"
+4	dexseq_prepare_annotation.py	exonic_part	71142	71239	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "002"
+4	dexseq_prepare_annotation.py	exonic_part	71240	71306	.	-	.	transcripts "FBtr0306168+FBtr0089178"; gene_id "FBgn0004859"; exonic_part_number "003"
+4	dexseq_prepare_annotation.py	exonic_part	71371	71883	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "004"
+4	dexseq_prepare_annotation.py	exonic_part	71940	72580	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "005"
+4	dexseq_prepare_annotation.py	exonic_part	72643	73010	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "006"
+4	dexseq_prepare_annotation.py	exonic_part	76457	76916	.	-	.	transcripts "FBtr0308074+FBtr0089178"; gene_id "FBgn0004859"; exonic_part_number "007"
+4	dexseq_prepare_annotation.py	exonic_part	76917	76957	.	-	.	transcripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "008"
+4	dexseq_prepare_annotation.py	exonic_part	76958	77667	.	-	.	transcripts "FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "009"
 4	dexseq_prepare_annotation.py	aggregate_gene	137015	150380	.	-	.	gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	137015	137256	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "001"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	137312	139127	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "002"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	139181	139405	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "003"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	139464	139557	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "004"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	140514	140838	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "005"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	141484	142425	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "006"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	142479	142582	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "007"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	142935	144048	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "008"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	144411	144518	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "009"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	149948	150068	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "010"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	150069	150078	.	-	.	transcripts "FBtr0089173"; exonic_part_number "011"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	150181	150353	.	-	.	transcripts "FBtr0089172"; exonic_part_number "012"; gene_id "FBgn0011747"
-4	dexseq_prepare_annotation.py	exonic_part	150354	150380	.	-	.	transcripts "FBtr0089172+FBtr0089171"; exonic_part_number "013"; gene_id "FBgn0011747"
+4	dexseq_prepare_annotation.py	exonic_part	137015	137256	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "001"
+4	dexseq_prepare_annotation.py	exonic_part	137312	139127	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "002"
+4	dexseq_prepare_annotation.py	exonic_part	139181	139405	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "003"
+4	dexseq_prepare_annotation.py	exonic_part	139464	139557	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "004"
+4	dexseq_prepare_annotation.py	exonic_part	140514	140838	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "005"
+4	dexseq_prepare_annotation.py	exonic_part	141484	142425	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "006"
+4	dexseq_prepare_annotation.py	exonic_part	142479	142582	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "007"
+4	dexseq_prepare_annotation.py	exonic_part	142935	144048	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "008"
+4	dexseq_prepare_annotation.py	exonic_part	144411	144518	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "009"
+4	dexseq_prepare_annotation.py	exonic_part	149948	150068	.	-	.	transcripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "010"
+4	dexseq_prepare_annotation.py	exonic_part	150069	150078	.	-	.	transcripts "FBtr0089173"; gene_id "FBgn0011747"; exonic_part_number "011"
+4	dexseq_prepare_annotation.py	exonic_part	150181	150353	.	-	.	transcripts "FBtr0089172"; gene_id "FBgn0011747"; exonic_part_number "012"
+4	dexseq_prepare_annotation.py	exonic_part	150354	150380	.	-	.	transcripts "FBtr0089172+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "013"
 4	dexseq_prepare_annotation.py	aggregate_gene	522436	560418	.	+	.	gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	522436	522483	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "001"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	524477	524764	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "002"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	536208	536257	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "003"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	542099	543730	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "004"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	544957	545138	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "005"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	545530	547146	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "006"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	550319	551719	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "007"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	551782	551784	.	+	.	transcripts "FBtr0332913+FBtr0089070"; exonic_part_number "008"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	551785	552005	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "009"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	552062	552409	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "010"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	553409	553411	.	+	.	transcripts "FBtr0332913+FBtr0089070"; exonic_part_number "011"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	553412	553552	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "012"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	553609	556506	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "013"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	557592	557701	.	+	.	transcripts "FBtr0332913"; exonic_part_number "014"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	557801	558386	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; exonic_part_number "015"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	558387	558999	.	+	.	transcripts "FBtr0332913"; exonic_part_number "016"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	559164	559230	.	+	.	transcripts "FBtr0089070+FBtr0307167"; exonic_part_number "017"; gene_id "FBgn0004607"
-4	dexseq_prepare_annotation.py	exonic_part	559285	560418	.	+	.	transcripts "FBtr0089070+FBtr0307167"; exonic_part_number "018"; gene_id "FBgn0004607"
+4	dexseq_prepare_annotation.py	exonic_part	522436	522483	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; gene_id "FBgn0004607"; exonic_part_number "001"
+4	dexseq_prepare_annotation.py	exonic_part	524477	524764	.	+	.	transcripts "FBtr0332913+FBtr0089070+FBtr0307167"; gene_id "FBgn0004607"; exonic_part_number "002"
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 4	dexseq_prepare_annotation.py	aggregate_gene	1077991	1084936	.	-	.	gene_id "FBgn0011642"
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 XHet	dexseq_prepare_annotation.py	aggregate_gene	69195	80249	.	+	.	gene_id "FBgn0003559"
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 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	3083	3767	.	+	.	gene_id "FBgn0013675"
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+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	3083	3767	.	+	.	transcripts "FBtr0100863"; gene_id "FBgn0013675"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	3768	3838	.	+	.	gene_id "FBgn0013697"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	3768	3838	.	+	.	transcripts "FBtr0100864"; exonic_part_number "001"; gene_id "FBgn0013697"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	3768	3838	.	+	.	transcripts "FBtr0100864"; gene_id "FBgn0013697"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	3840	3906	.	+	.	gene_id "FBgn0013691"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	3840	3906	.	+	.	transcripts "FBtr0100865"; exonic_part_number "001"; gene_id "FBgn0013691"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	3840	3906	.	+	.	transcripts "FBtr0100865"; gene_id "FBgn0013691"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	5543	5607	.	+	.	gene_id "FBgn0013694"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	5543	5607	.	+	.	transcripts "FBtr0100869"; exonic_part_number "001"; gene_id "FBgn0013694"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	5543	5607	.	+	.	transcripts "FBtr0100869"; gene_id "FBgn0013694"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	5608	5961	.	+	.	gene_id "FBgn0013681"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	5608	5961	.	+	.	transcripts "FBtr0100870"; exonic_part_number "001"; gene_id "FBgn0013681"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	5608	5961	.	+	.	transcripts "FBtr0100870"; gene_id "FBgn0013681"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	5981	6045	.	+	.	gene_id "FBgn0013689"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	5981	6045	.	+	.	transcripts "FBtr0100871"; exonic_part_number "001"; gene_id "FBgn0013689"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	5981	6045	.	+	.	transcripts "FBtr0100871"; gene_id "FBgn0013689"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	6055	6118	.	+	.	gene_id "FBgn0013704"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6055	6118	.	+	.	transcripts "FBtr0100872"; exonic_part_number "001"; gene_id "FBgn0013704"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6055	6118	.	+	.	transcripts "FBtr0100872"; gene_id "FBgn0013704"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	6119	6183	.	+	.	gene_id "FBgn0013701"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6119	6183	.	+	.	transcripts "FBtr0100873"; exonic_part_number "001"; gene_id "FBgn0013701"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6119	6183	.	+	.	transcripts "FBtr0100873"; gene_id "FBgn0013701"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	6184	6251	.	+	.	gene_id "FBgn0013705"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6184	6251	.	+	.	transcripts "FBtr0100874"; exonic_part_number "001"; gene_id "FBgn0013705"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6184	6251	.	+	.	transcripts "FBtr0100874"; gene_id "FBgn0013705"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	6252	6318	.	+	.	gene_id "FBgn0013692"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6252	6318	.	+	.	transcripts "FBtr0100875"; exonic_part_number "001"; gene_id "FBgn0013692"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6252	6318	.	+	.	transcripts "FBtr0100875"; gene_id "FBgn0013692"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	6337	6401	.	-	.	gene_id "FBgn0013693"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6337	6401	.	-	.	transcripts "FBtr0100876"; exonic_part_number "001"; gene_id "FBgn0013693"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6337	6401	.	-	.	transcripts "FBtr0100876"; gene_id "FBgn0013693"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	6402	8124	.	-	.	gene_id "FBgn0013684"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6402	8124	.	-	.	transcripts "FBtr0100877"; exonic_part_number "001"; gene_id "FBgn0013684"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	6402	8124	.	-	.	transcripts "FBtr0100877"; gene_id "FBgn0013684"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	8140	8205	.	-	.	gene_id "FBgn0013695"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	8140	8205	.	-	.	transcripts "FBtr0100878"; exonic_part_number "001"; gene_id "FBgn0013695"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	8140	8205	.	-	.	transcripts "FBtr0100878"; gene_id "FBgn0013695"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	9837	9902	.	+	.	gene_id "FBgn0013707"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	9837	9902	.	+	.	transcripts "FBtr0100881"; exonic_part_number "001"; gene_id "FBgn0013707"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	9837	9902	.	+	.	transcripts "FBtr0100881"; gene_id "FBgn0013707"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	9903	9963	.	-	.	gene_id "FBgn0013702"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	9903	9963	.	-	.	transcripts "FBtr0100882"; exonic_part_number "001"; gene_id "FBgn0013702"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	9903	9963	.	-	.	transcripts "FBtr0100882"; gene_id "FBgn0013702"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	9970	10494	.	+	.	gene_id "FBgn0013685"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	9970	10494	.	+	.	transcripts "FBtr0100883"; exonic_part_number "001"; gene_id "FBgn0013685"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	9970	10494	.	+	.	transcripts "FBtr0100883"; gene_id "FBgn0013685"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	10498	11634	.	+	.	gene_id "FBgn0013678"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	10498	11634	.	+	.	transcripts "FBtr0100884"; exonic_part_number "001"; gene_id "FBgn0013678"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	10498	11634	.	+	.	transcripts "FBtr0100884"; gene_id "FBgn0013678"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	11637	11702	.	+	.	gene_id "FBgn0013706"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	11637	11702	.	+	.	transcripts "FBtr0100885"; exonic_part_number "001"; gene_id "FBgn0013706"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	11637	11702	.	+	.	transcripts "FBtr0100885"; gene_id "FBgn0013706"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	11720	12658	.	-	.	gene_id "FBgn0013679"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	11720	12658	.	-	.	transcripts "FBtr0100886"; exonic_part_number "001"; gene_id "FBgn0013679"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	11720	12658	.	-	.	transcripts "FBtr0100886"; gene_id "FBgn0013679"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	12669	12733	.	-	.	gene_id "FBgn0013698"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	12669	12733	.	-	.	transcripts "FBtr0100887"; exonic_part_number "001"; gene_id "FBgn0013698"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	12669	12733	.	-	.	transcripts "FBtr0100887"; gene_id "FBgn0013698"; exonic_part_number "001"
 dmel_mitochondrion_genome	dexseq_prepare_annotation.py	aggregate_gene	14131	14916	.	-	.	gene_id "FBgn0013688"
-dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	14131	14916	.	-	.	transcripts "FBtr0100890"; exonic_part_number "001"; gene_id "FBgn0013688"
+dmel_mitochondrion_genome	dexseq_prepare_annotation.py	exonic_part	14131	14916	.	-	.	transcripts "FBtr0100890"; gene_id "FBgn0013688"; exonic_part_number "001"