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Changeset 0:2f2c7fd180e1 (2016-03-18)

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diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/._.DS_Store

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diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/._readme.txt

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diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/integrate7_15nodes.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/integrate7_15nodes.py Fri Mar 18 05:53:39 2016 -0400

b'@@ -0,0 +1,227 @@\n+"""\n+@summary: INTEGRATER\n+@version 7\n+\n+"""\n+# INTEGRATER --> 15 files\n+\n+# Input: QTLs_total1.txt\n+# QTLs_total2.txt\n+# QTLs_total3.txt\n+# QTLs_total4.txt\n+# QTLs_total5.txt\n+\n+# Output: QTLs_summary_all.txt\n+\n+import optparse, sys\n+import tempfile\n+\n+def stop_err( msg ):\n+\tsys.stderr.write( "%s\\n" % msg )\n+\tsys.exit()\n+ \n+def __main__():\n+\tparser = optparse.OptionParser()\n+\tparser.add_option("--i1", "--input1", default=None, dest="input1", \n+\t\t\t help="QTLs_total1.txt file")\n+\tparser.add_option("--i2", "--input2", default=None, dest="input2", \n+\t\t\t help="QTLs_total2.txt file")\n+\tparser.add_option("--i3", "--input3", default=None, dest="input3", \n+\t\t\t help="QTLs_total3.txt file")\n+\tparser.add_option("--i4", "--input4", default=None, dest="input4", \n+\t\t\t help="QTLs_total4.txt file")\n+\tparser.add_option("--i5", "--input5", default=None, dest="input5", \n+\t\t\t help="QTLs_total5.txt file")\n+\tparser.add_option("--i6", "--input6", default=None, dest="input6", \n+\t\t\t help="QTLs_total6.txt file")\n+\tparser.add_option("--i7", "--input7", default=None, dest="input7", \n+\t\t\t help="QTLs_total7.txt file")\n+\tparser.add_option("--i8", "--input8", default=None, dest="input8", \n+\t\t\t help="QTLs_total8.txt file")\n+\tparser.add_option("--i9", "--input9", default=None, dest="input9", \n+\t\t\t help="QTLs_total9.txt file")\n+\tparser.add_option("--i10", "--input10", default=None, dest="input10", \n+\t\t\t help="QTLs_total10.txt file")\n+\tparser.add_option("--i11", "--input11", default=None, dest="input11", \n+\t\t\t help="QTLs_total11.txt file")\n+\tparser.add_option("--i12", "--input12", default=None, dest="input12", \n+\t\t\t help="QTLs_total12.txt file")\n+\tparser.add_option("--i13", "--input13", default=None, dest="input13", \n+\t\t\t help="QTLs_total13.txt file")\n+\tparser.add_option("--i14", "--input14", default=None, dest="input14", \n+\t\t\t help="QTLs_total14.txt file")\n+\tparser.add_option("--i15", "--input15", default=None, dest="input15", \n+\t\t\t help="QTLs_total15.txt file")\n+\t\n+\tparser.add_option("-o", "--output1", default=None, dest="output1", \n+\t\t\t help="QTLs_summary_all.txt file")\n+\t(options, args) = parser.parse_args()\n+\t\n+\ttry:\n+\t open(options.input1, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total1.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total1.txt file:\\n" + str(e))\n+ \n+\ttry:\n+\t open(options.input2, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total2.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total2.txt file:\\n" + str(e))\n+\t \n+\ttry:\n+\t open(options.input3, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total3.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total3.txt file:\\n" + str(e))\n+ \n+\ttry:\n+\t open(options.input4, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total4.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total4.txt file:\\n" + str(e))\n+\t \n+\ttry:\n+\t open(options.input5, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total5.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total5.txt file:\\n" + str(e))\n+\t \n+\ttry:\n+\t open(options.input6, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total6.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total6.txt file:\\n" + str(e))\n+ \n+\ttry:\n+\t open(options.input7, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total7.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total7.txt file:\\n" + str(e))\n+\t \n+\ttry:\n+\t open(options.input8, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total8.txt file:\\n" + str'..b'"You need to supply the QTLs_total10.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total10.txt file:\\n" + str(e))\n+\t\n+\ttry:\n+\t open(options.input11, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total11.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total11.txt file:\\n" + str(e))\n+ \n+\ttry:\n+\t open(options.input12, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total12.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total12.txt file:\\n" + str(e))\n+\t \n+\ttry:\n+\t open(options.input13, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total13.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total13.txt file:\\n" + str(e))\n+ \n+\ttry:\n+\t open(options.input14, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total14.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total14.txt file:\\n" + str(e))\n+\t \n+\ttry:\n+\t open(options.input15, "r").close()\n+\texcept TypeError, e:\n+\t stop_err("You need to supply the QTLs_total15.txt file:\\n" + str(e))\n+\texcept IOError, e:\n+\t stop_err("Can not open the QTLs_total15.txt file:\\n" + str(e))\n+\t \n+\t######################################################################\n+\t# submit.py\n+\t######################################################################\n+\t\n+\timport subprocess\n+\timport os\n+\t\n+\t# Create temp direcotry\n+\ttempdir = tempfile.mkdtemp()\n+\t#print tempdir\n+\t#fixdir = "/lustre/galaxy/MeQTL/eQTL_pipeline"\n+\t#os.system("cp %s/parameters.txt %s" %(fixdir,options.output2))\n+\t#os.system("cp %s/qtlcart_partial.z %s" %(fixdir,options.output3))\n+\n+\t# copy INPUT file to the temp directory\n+\ts = "cp %s %s/QTLs_total1.txt" %(options.input1, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total2.txt" %(options.input2, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total3.txt" %(options.input3, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total4.txt" %(options.input4, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total5.txt" %(options.input5, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total6.txt" %(options.input6, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total7.txt" %(options.input7, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total8.txt" %(options.input8, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total9.txt" %(options.input9, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total10.txt" %(options.input10, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total11.txt" %(options.input11, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total12.txt" %(options.input12, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total13.txt" %(options.input13, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total14.txt" %(options.input14, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\ts = "cp %s %s/QTLs_total15.txt" %(options.input15, tempdir)\n+\tsubprocess.call(s, shell=True)\n+\t\n+\tw=open(tempdir+"/eQTL_summary_cat_0","w")\n+\tw.write("trait_name\\ttrait_number\\teQTL_number\\tchr\\tpeak_marker\\tpeak_position\\tpeak_LR\\tpeak_LOD\\tR2\\tTR2\\tS\\tadditive\\tdominance\\tLOD1_L_m\\tLOD1_L_pos\\tLOD1_R_m\\tLOD1_R_pos\\tLOD2_L_m\\tLOD2_L_pos\\tLOD2_R_m\\tLOD2_R_pos\\n")\n+\tw.close()\n+\t\n+\tfor i in range(15):\n+\t\tinstruction="cat %s/eQTL_summary_cat_%s %s/QTLs_total%s.txt > %s/eQTL_summary_cat_%s" %(tempdir,str(i),tempdir,str(i+1),tempdir,str(i+1))\n+\t\tos.system(instruction)\n+\t\t\n+\tos.system("mv %s/eQTL_summary_cat_%s %s" %(tempdir,str(i+1),options.output1))\n+ \n+\t######################################################################\n+\t\n+if __name__=="__main__": \n+ __main__()\n+\n+\n+\t\t\n\\ No newline at end of file\n'

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/integrate7_15nodes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/integrate7_15nodes.xml Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,53 @@
+<tool id="integrate7_15nodes" name="Integrates eQTL results" version="7.0.0">
+ <description> after 15 parallel runs</description>
+ <command interpreter="python">
+     integrate7_15nodes.py --input1 $input1 --input2 $input2 --input3 $input3 --input4 $input4 --input5 $input5 --input6 $input6 --input7 $input7 --input8 $input8 --input9 $input9 --input10 $input10 --input11 $input11 --input12 $input12 --input13 $input13 --input14 $input14 --input15 $input15 --output1 $output1
+        </command>
+        <inputs>
+            <param label="eQTL results file 1" name="input1" type="data" format="tabular" help="A tabular with eQTL results 1"></param>
+     <param label="eQTL results file 2" name="input2" type="data" format="tabular" help="A tabular with eQTL results 2"></param>
+            <param label="eQTL results file 3" name="input3" type="data" format="tabular" help="A tabular with eQTL results 3"></param>
+     <param label="eQTL results file 4" name="input4" type="data" format="tabular" help="A tabular with eQTL results 4"></param>
+            <param label="eQTL results file 5" name="input5" type="data" format="tabular" help="A tabular with eQTL results 5"></param>
+            <param label="eQTL results file 6" name="input6" type="data" format="tabular" help="A tabular with eQTL results 6"></param>
+     <param label="eQTL results file 7" name="input7" type="data" format="tabular" help="A tabular with eQTL results 7"></param>
+            <param label="eQTL results file 8" name="input8" type="data" format="tabular" help="A tabular with eQTL results 8"></param>
+     <param label="eQTL results file 9" name="input9" type="data" format="tabular" help="A tabular with eQTL results 9"></param>
+            <param label="eQTL results file 10" name="input10" type="data" format="tabular" help="A tabular with eQTL results 10"></param>
+            <param label="eQTL results file 11" name="input11" type="data" format="tabular" help="A tabular with eQTL results 11"></param>
+     <param label="eQTL results file 12" name="input12" type="data" format="tabular" help="A tabular with eQTL results 12"></param>
+            <param label="eQTL results file 13" name="input13" type="data" format="tabular" help="A tabular with eQTL results 13"></param>
+     <param label="eQTL results file 14" name="input14" type="data" format="tabular" help="A tabular with eQTL results 14"></param>
+            <param label="eQTL results file 15" name="input15" type="data" format="tabular" help="A tabular with eQTL results 15"></param>
+        </inputs>
+ <outputs>
+                <data format="tabular" name="output1" />
+ </outputs>
+ <requirements>
+ </requirements>
+ <tests>
+          <test>
+          </test>
+ </tests>
+ <help>
+
+**What it does**
+
+Concatenates eQTL result files after parallel runs on the cluster.
+
+
+**Example output file**
+
+eQTL results file, each row correspond to an eQTL (21 columns; only a part of the file is shown)::
+
+ trait_name trait_number eQTL_number chr peak_marker peak_position peak_LR peak_LOD R2 TR2 S additive dominance LOD1_L_m LOD1_L_pos LOD1_R_m LOD1_R_pos LOD2_L_m LOD2_L_pos LOD2_R_m LOD2_R_pos
+ geneA 4 2 3 15 79.31 14.576 3.162992 0.1093 0.1915 5.2649 -0.0602 0 12 0.6318 15 0.8678 11 0.5984 15 0.8941
+ geneB 5 1 6 7 54.41 12.0029 2.6046293 0.0833 0.1621 5.0323 0.0516 0 6 0.4803 7 0.6296 5 0.4237 7 0.6509
+ geneC 6 1 1 12 81.5 13.2053 2.8655501 0.082 0.2517 154.622 -0.0513 0 11 0.7835 12 0.815 10 0.6549 12 0.815
+ geneC 6 2 5 6 33.92 12.4418 2.6998706 0.0881 0.2653 161.127 0.0546 0 4 0.2652 6 0.4058 2 0.1031 7 0.4629
+ geneF 11 1 9 4 11.74 14.4418 3.1338706 0.0937 0.252 72.2489 -0.0562 0 1 0.0014 4 0.1995 1 0.0001 4 0.2035
+ geneH 12 2 1 9 43.66 16.9545 3.6791265 0.092 0.3558 0.1466 0.0544 0 8 0.4159 9 0.5408 5 0.3295 9 0.5987
+ geneJ 13 1 7 11 66.41 15.6251 3.3906467 0.0965 0.2625 8.2335 -0.0558 0 9 0.5515 11 0.7408 9 0.5464 12 0.7631
+
+        </help>
+</tool>

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/readme.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/readme.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,20 @@
+======================================================================
+integrate_15
+======================================================================
+### This is the last tool in the eQTL mapper workflow:
+split_15, qtlmap_15, save_z_15, integrate_15
+
+Link to the workflow (for import): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/15-parallel
+
+Concatenates eQTL result files after 15 parallel runs.
+
+---------------
+Installation
+---------------
+
+The eQTL mapper pipeline is available for:
+* command line usage
+* integration into Galaxy servers
+
+
+Requirements: Python 2.7
\ No newline at end of file

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diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_1.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,10 @@
+A_92_P039116 1 1 6 13 1.5339 15.9210885 3.4548762045 0.1919114 0.3879427 77.2994584 -311.3306014 0.0000000 13 1.4516 15 1.7163 13 1.4181 15 1.7956
+A_92_P039116 1 3 9 6 0.9214 15.3291347 3.3264222299 0.1176972 0.3098947 73.0022134 -249.9855214 0.0000000 5 0.8372 6 0.9652 5 0.7772 6 0.9724
+A_92_P039116 1 4 9 8 1.2052 13.9017110 3.016671287 0.1050450 0.3111284 71.1474755 245.1582644 0.0000000 7 1.2011 9 1.3362 7 1.1768 9 1.3935
+A_92_P038628 2 1 9 1 0.1601 24.5310019 5.3232274123 0.1989293 0.5098951 52.0670152 -701.7675097 0.0000000 1 0.0725 2 0.2239 1 0.0379 2 0.2472
+A_92_P038628 2 2 10 1 0.0201 12.8665772 2.7920472524 0.0951165 0.4914030 48.4981968 -480.0477241 0.0000000 1 0.0001 1 0.1196 1 0.0001 1 0.1444
+A_92_P038150 4 1 6 9 0.7773 13.7094809 2.9749573553 0.1131346 0.5435596 1.1541518 394.9822315 0.0000000 8 0.6819 9 0.8709 6 0.6046 9 0.8844
+A_92_P038150 4 2 9 9 1.2479 13.7334120 2.980150404 0.0784721 0.4919043 1.3007608 351.9779719 0.0000000 7 1.1444 9 1.3206 7 1.0201 9 1.3679
+A_92_P038150 4 3 10 2 0.1503 14.0299522 3.0444996274 0.0845627 0.4961190 1.2914158 342.6938285 0.0000000 1 0.0422 2 0.2273 1 0.0001 2 0.2856
+A_92_P038150 4 4 10 3 0.4058 15.3264104 3.3258310568 0.1320742 0.5272216 1.1053058 -483.3117444 0.0000000 3 0.3449 6 0.797 2 0.32 6 0.8084
+A_92_P038150 4 5 10 5 0.6500 39.1826820 8.502641994 0.3966235 0.5336773 19.1694948 -742.6937805 0.0000000 5 0.5749 5 0.7461 5 0.5467 5 0.7508

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_10.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_10.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,10 @@
+A_92_P027554 1 1 2 13 1.6825 12.7611437 2.7691681829 0.1018072 0.3903601 4.4296057 167.8795132 0.0000000 12 1.5655 13 1.6825 11 1.4988 13 1.6825
+A_92_P027554 1 2 3 13 1.5510 20.3857124 4.4236995908 0.1619413 0.4031766 2.7686481 -211.1740827 0.0000000 12 1.4823 13 1.5956 12 1.4466 14 1.706
+A_92_P027554 1 4 10 4 0.4606 17.5002478 3.7975537726 0.1313607 0.3906483 3.3345446 -188.6856642 0.0000000 3 0.3584 4 0.5233 2 0.3245 5 0.6256
+A_92_P027390 2 1 6 8 0.6528 18.1173076 3.9314557492 0.2563745 0.6640015 0.4052638 47.1173201 0.0000000 6 0.5578 8 0.693 6 0.5159 8 0.7133
+A_92_P027390 2 2 6 12 1.3157 17.7087013 3.8427881821 0.3257878 0.6980663 0.4043924 -51.5935951 0.0000000 12 1.2576 12 1.3818 11 1.2481 12 1.3906
+A_92_P027072 3 2 7 11 1.1032 44.9795778 9.7605683826 0.2969825 0.5035042 4.6985714 1843.6463564 0.0000000 11 1.0867 11 1.1032 11 1.0772 11 1.1032
+A_92_P027072 3 3 9 8 1.2052 14.5812965 3.1641413405 0.0775113 0.5066064 4.4592073 985.5528170 0.0000000 7 1.1257 8 1.2359 7 1.0763 9 1.3895
+A_92_P026747 4 1 3 1 0.0401 24.1515872 5.2408944224 0.3905649 0.6410914 3.8219363 37.8546571 0.0000000 1 0.0081 1 0.1007 1 0.0001 1 0.1048
+A_92_P026747 4 2 3 9 0.8051 13.3190279 2.8902290543 0.1942427 0.5175014 30.0430325 -26.6445313 0.0000000 7 0.7614 9 0.9686 7 0.7247 9 1.0276
+A_92_P026747 4 3 6 5 0.3587 11.9666148 2.5967554116 0.1700650 0.5144391 28.6662391 25.6423152 0.0000000 3 0.2763 5 0.4027 3 0.1899 6 0.5236

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_11.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_11.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,4 @@
+A_92_P025313 1 1 3 13 1.5510 20.6064068 4.4715902756 0.1710257 0.2747041 1109.4668897 -1905.2184858 0.0000000 12 1.5085 13 1.5862 12 1.4679 14 1.7055
+A_92_P024994 2 1 5 2 0.2121 17.4534281 3.7873938977 0.2637088 0.6641010 15.0444221 320.9327481 0.0000000 2 0.0364 3 0.2867 1 0.026 3 0.3122
+A_92_P024836 3 1 4 12 1.2626 14.9192368 3.2374743856 0.1173577 0.3739031 13.0708073 -100.1363730 0.0000000 11 1.143 13 1.3648 11 1.1137 14 1.4605
+A_92_P024836 3 2 8 8 0.9609 16.4094504 3.5608507368 0.1247620 0.3640049 12.1550179 111.8531092 0.0000000 7 0.8899 9 0.9997 7 0.8506 10 1.1185

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_12.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_12.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,7 @@
+A_92_P024516 1 1 1 19 2.0214 20.5892047 4.4678574199 0.1627540 0.2898391 12.5794392 255.4967487 0.0000000 18 1.9865 19 2.1519 18 1.9586 19 2.2042
+A_92_P024516 1 3 1 23 2.7904 11.7412564 2.5478526388 0.1205252 0.3260419 11.5022960 -218.6650149 0.0000000 21 2.6455 23 2.9188 21 2.6407 23 2.9708
+A_92_P023713 2 1 2 1 0.1001 15.0930867 3.2751998139 0.1490762 0.3233012 1.0763490 252.8027941 0.0000000 1 0.0085 2 0.2729 1 0.0001 2 0.3274
+A_92_P023713 2 3 5 16 1.6832 20.6465042 4.4802914114 0.2378846 0.3902667 0.2904053 323.5459459 0.0000000 15 1.6398 16 1.7329 15 1.6326 16 1.7647
+A_92_P023713 2 5 6 3 0.2255 13.1162156 2.8462187852 0.1138979 0.3974125 3.4227484 -218.8805035 0.0000000 1 0.0163 4 0.3178 1 0.0001 4 0.3477
+A_92_P023551 3 1 1 14 1.6098 12.1963674 2.6466117258 0.1372960 0.3800574 4.6993484 133.4043424 0.0000000 14 1.5338 15 1.6972 13 1.4897 15 1.7507
+A_92_P023551 3 2 10 1 0.0601 19.0928858 4.1431562186 0.2468352 0.4758394 0.5013347 175.2143455 0.0000000 1 0.0045 1 0.1223 1 0.0001 1 0.1422

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_13.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_13.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,4 @@
+A_92_P023080 3 1 1 1 0.0601 37.7011957 8.1811594669 0.2848013 0.9322797 1.6358983 104.0142532 0.0000000 1 0.0317 2 0.1189 1 0.0187 2 0.1296
+A_92_P023080 3 3 1 20 2.3609 13.6788863 2.9683183271 0.0553721 0.8882827 3.8493444 -32.3646289 0.0000000 19 2.2733 20 2.4304 19 2.2101 20 2.4852
+A_92_P023080 3 4 7 11 1.1032 31.0287041 6.7332287897 0.1789058 0.8966296 3.4735566 -67.0784555 0.0000000 10 1.0607 11 1.1032 10 1.0104 11 1.1032
+A_92_P023080 3 5 8 5 0.5015 51.6576621 11.2097126757 0.4555327 0.8732000 3.3751192 -96.9461713 0.0000000 4 0.4549 5 0.5372 4 0.4234 5 0.5707

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_14.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_14.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,7 @@
+A_92_P022918 1 1 8 1 0.0401 31.7555607 6.8909566719 0.3030513 0.5086103 5.0865774 -681.3026366 0.0000000 1 0.0111 1 0.0817 1 0.0001 1 0.0967
+A_92_P022755 2 1 3 16 1.9454 12.2519892 2.6586816564 0.1092460 0.4087476 8.3542742 -1752.0761466 0.0000000 15 1.8842 17 2.1202 15 1.8784 17 2.1344
+A_92_P022755 2 4 8 4 0.4274 20.6933638 4.4904599446 0.1369886 0.5115352 6.5683702 1984.0754662 0.0000000 3 0.2923 5 0.5831 3 0.264 5 0.6403
+A_92_P022755 2 6 9 7 0.9782 16.3122115 3.5397498955 0.1202802 0.3841991 7.0636630 -1823.7633241 0.0000000 6 0.9287 7 1.0488 5 0.8089 7 1.0942
+A_92_P022755 2 7 10 11 1.1764 13.8857650 3.013211005 0.1003230 0.3792059 7.0186621 -1705.3060098 0.0000000 10 1.1196 11 1.225 10 1.0773 11 1.2614
+A_92_P022592 3 1 1 13 1.4670 14.1819258 3.0774778986 0.1495470 0.3618150 9.7749401 -73.0555529 0.0000000 13 1.4278 14 1.5786 12 1.4169 14 1.6308
+A_92_P022592 3 2 1 18 2.0143 11.8257352 2.5661845384 0.1011971 0.3249504 7.5422339 52.5612035 0.0000000 18 1.9421 19 2.1435 17 1.8757 19 2.2445

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_15.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_15.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,7 @@
+A_92_P022110 1 1 1 18 2.0143 12.0455951 2.6138941367 0.0928423 0.3268055 0.5377619 140.2867239 0.0000000 17 1.9036 19 2.1396 16 1.8722 19 2.2243
+A_92_P022110 1 2 10 12 1.4054 13.2804218 2.8818515306 0.1419048 0.3733549 0.3170982 -169.0318841 0.0000000 12 1.3123 12 1.4654 11 1.2993 12 1.4654
+A_92_P021792 2 1 1 14 1.6098 13.7867804 2.9917313468 0.1154861 0.4159935 1.5415854 -187.9840206 0.0000000 14 1.526 15 1.7162 13 1.4892 15 1.7577
+A_92_P021792 2 2 1 19 2.0214 21.2959774 4.6212270958 0.1459124 0.3894262 1.6071086 212.4539382 0.0000000 18 1.973 19 2.1178 18 1.9474 19 2.1703
+A_92_P021792 2 3 7 3 0.2061 14.4512266 3.1359161722 0.0953207 0.3877693 1.6159454 -166.6958319 0.0000000 2 0.1497 3 0.2588 2 0.1091 3 0.2887
+A_92_P021792 2 4 10 10 1.0861 19.1017279 4.1450749543 0.1666632 0.4539051 0.0927683 -215.6184203 0.0000000 9 1.0403 10 1.1595 9 1.0153 10 1.1695
+A_92_P021634 3 1 6 16 1.9423 30.9698873 6.7204655441 0.2910527 0.3081694 2.0286370 795.9301198 0.0000000 16 1.9009 16 1.9423 16 1.8746 16 1.9423

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_2.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,12 @@
+A_92_P037834 1 1 4 5 0.5309 24.0416490 5.217037833 0.1788150 0.4904768 20.2186322 -215.1013986 0.0000000 4 0.483 5 0.5471 4 0.4502 5 0.5558
+A_92_P037834 1 2 5 19 1.9955 12.8100275 2.7797759675 0.1007023 0.5007851 24.0032764 -164.1721772 0.0000000 18 1.9338 19 2.0355 16 1.7878 19 2.0355
+A_92_P037834 1 3 7 3 0.2861 28.3465676 6.1512051692 0.2712756 0.5525036 11.0181706 274.5318342 0.0000000 3 0.2457 4 0.3541 3 0.2299 4 0.382
+A_92_P037509 2 1 2 5 0.8205 20.9015193 4.5356296881 0.1920072 0.8228764 0.6300379 50.7070865 0.0000000 4 0.7702 5 0.8741 4 0.7317 5 0.8958
+A_92_P037509 2 2 3 14 1.7522 14.5634804 3.1602752468 0.1395012 0.8505212 0.6992039 43.6613918 0.0000000 14 1.6705 15 1.84 14 1.6376 15 1.8775
+A_92_P037509 2 3 6 15 1.7431 18.4634837 4.0065759629 0.1907638 0.8576937 0.9327344 52.4041957 0.0000000 15 1.6376 16 1.9224 14 1.6228 16 1.9367
+A_92_P037509 2 5 8 5 0.5015 28.4825171 6.1807062107 0.3078012 0.8259992 0.6597413 -63.9160300 0.0000000 4 0.4414 5 0.5539 4 0.419 5 0.5893
+A_92_P037035 3 1 2 8 1.1375 32.8400994 7.1263015698 0.2303759 0.5341618 178.1779135 -434.9303913 0.0000000 7 1.0942 8 1.1598 7 1.0586 8 1.1634
+A_92_P037035 3 2 2 10 1.3263 16.5244802 3.5858122034 0.0980168 0.5049068 100.6701175 284.2624983 0.0000000 9 1.322 10 1.3666 9 1.3177 10 1.4038
+A_92_P037035 3 3 9 7 0.9782 39.2967801 8.5274012817 0.2607592 0.5063220 118.6289643 -382.9703278 0.0000000 6 0.9547 7 1.0159 6 0.9389 7 1.046
+A_92_P036877 4 1 2 7 1.0104 13.6743073 2.9673246841 0.1091632 0.3352177 193.4943050 151.5554180 0.0000000 6 0.934 7 1.0843 5 0.9044 7 1.113
+A_92_P036877 4 2 4 11 1.1329 15.8680278 3.4433620326 0.1814249 0.3996043 198.2704407 -204.6505552 0.0000000 11 1.1138 11 1.1821 10 1.1081 13 1.3664

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_3.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,10 @@
+A_92_P036723 1 1 3 2 0.1176 25.5451801 5.5433040817 0.3367142 0.7495437 0.1420987 30.1380150 0.0000000 1 0.0634 2 0.1606 1 0.0373 2 0.193
+A_92_P036723 1 2 3 5 0.5925 12.4777349 2.7076684733 0.1140458 0.8663131 0.6745923 19.2755898 0.0000000 5 0.5496 5 0.6126 5 0.5279 5 0.6129
+A_92_P036723 1 4 3 18 2.1961 20.6998468 4.4918667556 0.2566942 0.7530538 0.1563160 27.1528712 0.0000000 18 2.1488 18 2.1961 17 2.0507 18 2.1961
+A_92_P036723 1 5 6 14 1.5977 11.7592146 2.5517495682 0.1189907 0.7522249 0.1368680 -18.8320617 0.0000000 13 1.4591 15 1.6792 12 1.3915 15 1.8129
+A_92_P036564 2 1 1 17 1.9125 14.0649598 3.0520962766 0.1257104 0.3385352 8.3880503 178.1987126 0.0000000 16 1.8419 18 2.0148 16 1.8028 18 2.0189
+A_92_P036564 2 3 4 12 1.2426 11.7618881 2.5523297177 0.1027206 0.3215265 9.5874467 -163.3414051 0.0000000 11 1.1355 13 1.361 10 1.0381 13 1.3718
+A_92_P036402 3 1 3 3 0.3960 11.9578142 2.5948456814 0.1717407 0.6684378 37.0007748 33.8745914 0.0000000 2 0.2539 5 0.5279 2 0.2406 5 0.6001
+A_92_P036402 3 2 10 12 1.4654 13.2511287 2.8754949279 0.1735358 0.6527381 31.4598473 31.5911238 0.0000000 12 1.3866 12 1.4654 12 1.327 12 1.4654
+A_92_P036241 4 1 5 17 1.7894 12.4339606 2.6981694502 0.0944238 0.3150629 15.8341283 -207.6782322 0.0000000 16 1.733 17 1.8612 16 1.6728 17 1.8975
+A_92_P036241 4 2 10 1 0.0401 11.8407342 2.5694393214 0.1081500 0.3340395 19.0765856 221.2449803 0.0000000 1 0.0001 1 0.1413 1 0.0001 1 0.1475

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_4.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,6 @@
+A_92_P036076 1 1 6 1 0.0201 12.0508049 2.6150246633 0.0638608 0.7313758 5.7647286 -148.2950721 0.0000000 1 0.0001 3 0.2309 1 0.0001 3 0.288
+A_92_P036076 1 2 8 4 0.3874 63.8836181 13.8627451277 0.5007644 0.7018512 12.7850245 -411.4754368 0.0000000 3 0.3594 4 0.4126 3 0.3341 4 0.4342
+A_92_P035602 2 1 3 7 0.7403 33.6744317 7.3073516789 0.3067255 0.5170118 11.8654223 -88.4458067 0.0000000 6 0.7166 7 0.7641 6 0.6808 7 0.7728
+A_92_P035118 3 1 2 6 0.9061 11.9240992 2.5875295264 0.1226207 0.4624417 11.3460016 -51.7009439 0.0000000 5 0.854 6 0.9836 3 0.6382 6 1.0072
+A_92_P035118 3 2 2 10 1.4063 20.1741062 4.3777810454 0.2324464 0.5069494 0.0863209 84.9271020 0.0000000 10 1.3551 11 1.4363 10 1.3341 11 1.492
+A_92_P035118 3 4 10 8 0.9063 13.5647584 2.9435525728 0.1296273 0.4429836 11.9072611 58.1585016 0.0000000 7 0.8506 8 0.9832 5 0.7509 9 1.0316

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_5.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,6 @@
+A_92_P034794 1 2 10 2 0.1903 13.7851819 2.9913844723 0.1500800 0.4826392 1.3172075 37.9229818 0.0000000 1 0.0205 2 0.2714 1 0.0001 2 0.3136
+A_92_P034308 2 1 1 10 1.0811 21.5408069 4.6743550973 0.2277382 0.7592832 1.5834036 -33.7902103 0.0000000 10 0.994 11 1.2061 10 0.9663 11 1.2428
+A_92_P034308 2 2 3 18 2.1361 37.6966811 8.1801797987 0.4294746 0.7461673 0.5001206 -46.4689965 0.0000000 17 2.0979 18 2.1767 17 2.0704 18 2.1961
+A_92_P034308 2 4 6 15 1.6231 15.0777058 3.2718621586 0.1278544 0.7208327 0.6238438 -25.3129593 0.0000000 14 1.6037 15 1.7696 12 1.3838 15 1.8092
+A_92_P033825 3 1 5 12 1.2112 26.3566078 5.7193838926 0.2959435 0.6404193 5.3064385 75.0605964 0.0000000 12 1.1492 13 1.2967 12 1.124 13 1.3275
+A_92_P033667 4 1 1 10 1.0011 32.5164489 7.0560694113 0.2841753 0.6066141 14.4318293 -402.5391792 0.0000000 9 0.9597 10 1.0702 9 0.9144 10 1.1011

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_6.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_6.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,11 @@
+A_92_P033184 1 1 2 6 0.9061 14.8587743 3.2243540231 0.2333258 0.6091560 22.0542994 -38.6663227 0.0000000 5 0.8719 6 0.9577 5 0.8433 6 0.9883
+A_92_P033019 2 1 4 1 0.0001 18.0264218 3.9117335306 0.2358947 0.7043399 1.1338535 -36.1921190 0.0000000 1 0.0001 1 0.1049 1 0.0001 1 0.1658
+A_92_P033019 2 3 4 14 1.3767 24.4933746 5.3150622882 0.3512706 0.6952266 0.7481420 -44.9542340 0.0000000 13 1.3132 14 1.4571 13 1.291 14 1.4719
+A_92_P033019 2 4 8 9 1.0132 12.4174801 2.6945931817 0.1576451 0.7132070 1.5293308 -31.2505707 0.0000000 8 0.9674 10 1.0946 6 0.8291 10 1.1515
+A_92_P032694 3 1 7 8 0.6320 32.1699934 6.9808885678 0.2420005 0.6003624 24.9291265 344.4116975 0.0000000 7 0.5956 8 0.6784 7 0.5757 8 0.7048
+A_92_P032694 3 2 7 10 0.8764 13.4413200 2.91676644 0.0878881 0.5980498 25.7814583 206.5255165 0.0000000 9 0.7973 10 1.0197 5 0.4516 10 1.0602
+A_92_P032375 4 1 5 16 1.7032 16.9984527 3.6886642359 0.1302289 0.5128756 27.8335593 107.9491425 0.0000000 15 1.5695 16 1.7838 15 1.5206 16 1.7866
+A_92_P032375 4 2 7 7 0.5545 25.7188796 5.5809968732 0.1610310 0.4683558 29.9770539 119.3799447 0.0000000 6 0.5181 7 0.583 6 0.4944 7 0.6026
+A_92_P032375 4 3 8 1 0.1001 19.6244369 4.2585028073 0.1304073 0.4749124 32.9505567 -126.1800898 0.0000000 1 0.0263 2 0.1759 1 0.0001 2 0.2199
+A_92_P032375 4 4 8 5 0.5015 12.1700046 2.6408909982 0.0729679 0.4682935 31.2541491 94.9172785 0.0000000 4 0.4357 5 0.5812 4 0.4057 5 0.6382
+A_92_P032375 4 5 9 8 1.2252 11.9054995 2.5834933915 0.0724122 0.4722985 30.5643015 83.1749874 0.0000000 7 1.1385 9 1.3136 7 1.083 9 1.3852

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_7.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_7.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,3 @@
+A_92_P031891 1 1 3 6 0.7129 12.1291440 2.632024248 0.1463481 0.4572059 3.3024336 22.7464054 0.0000000 6 0.6425 7 0.7575 5 0.6128 9 0.8513
+A_92_P031571 2 1 1 9 0.8188 15.5773107 3.3802764219 0.1576819 0.6595742 4.9462336 30.4289126 0.0000000 8 0.7654 9 0.9028 8 0.7266 9 0.9461
+A_92_P030934 4 1 1 12 1.3484 12.7269818 2.7617550506 0.1554477 0.3181084 11.0051898 1307.8971923 0.0000000 11 1.2068 12 1.4126 10 1.1262 12 1.4225

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_8.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_8.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,5 @@
+A_92_P030772 1 1 1 12 1.2884 14.6017579 3.1685814643 0.1322083 0.3547828 68.3702870 92.1827784 0.0000000 11 1.1967 12 1.3849 11 1.1334 12 1.4137
+A_92_P030772 1 2 2 8 1.1175 12.2942458 2.6678513386 0.0951207 0.3365067 55.8325996 91.5133766 0.0000000 7 1.0195 8 1.1608 6 1.0079 8 1.1701
+A_92_P029488 3 1 1 23 2.7504 12.7423639 2.7650929663 0.0886911 0.3771941 0.6115715 -170.6386723 0.0000000 22 2.6575 23 2.8791 21 2.6432 23 2.9422
+A_92_P029488 3 2 4 14 1.4567 15.7422210 3.416061957 0.1252436 0.3938654 0.8032518 -197.3601638 0.0000000 14 1.3938 15 1.5144 13 1.342 16 1.6101
+A_92_P029164 4 2 2 12 1.5405 22.4499094 4.8716303398 0.3269444 0.5618480 132.0731880 -1222.1310894 0.0000000 11 1.4693 12 1.6362 11 1.4302 12 1.6609

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/input/qtl_out_9.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/input/qtl_out_9.txt Fri Mar 18 05:53:39 2016 -0400

@@ -0,0 +1,5 @@
+A_92_P028842 2 1 2 7 1.0904 28.2461323 6.1294107091 0.3118840 0.5439671 5.6068692 -54.5035913 0.0000000 7 1.0324 8 1.1416 7 1.0179 8 1.1585
+A_92_P028842 2 2 3 12 1.3680 18.5426079 4.0237459143 0.1741882 0.5155299 3.8667059 -33.5409799 0.0000000 11 1.3328 12 1.4349 11 1.3142 12 1.4792
+A_92_P028042 4 1 1 11 1.2671 38.7087949 8.3998084933 0.3305027 0.4144519 2.1621607 120.1256345 0.0000000 11 1.2357 11 1.2675 11 1.2082 11 1.2679
+A_92_P028042 4 2 1 14 1.4898 13.3623833 2.8996371761 0.1034618 0.3996348 4.3479198 -71.0505158 0.0000000 13 1.4431 14 1.547 10 1.123 14 1.5891
+A_92_P028042 4 4 9 10 1.4239 17.8301407 3.8691405319 0.1743896 0.4645963 0.1983911 73.9224765 0.0000000 9 1.3211 10 1.4971 9 1.2873 10 1.5309

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/output/._qtl_out_all.txt

Binary file integrate_15/test-data/output/._qtl_out_all.txt has changed

diff -r 000000000000 -r 2f2c7fd180e1 integrate_15/test-data/output/qtl_out_all.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate_15/test-data/output/qtl_out_all.txt Fri Mar 18 05:53:39 2016 -0400

b'@@ -0,0 +1,108 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