| Next changeset 1:7842cff08f56 (2016-03-18) |
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added:
save_z_15/._.DS_Store save_z_15/._readme.txt save_z_15/readme.txt save_z_15/save_z7_15nodes.py save_z_15/save_z7_15nodes.xml save_z_15/test-data/._.DS_Store save_z_15/test-data/input/._.DS_Store save_z_15/test-data/input/._parameters.txt save_z_15/test-data/input/._qtlcart1.inp save_z_15/test-data/input/._qtlcart_original.map.txt save_z_15/test-data/input/parameters.txt save_z_15/test-data/input/qtlcart1.inp save_z_15/test-data/input/qtlcart_original.map.txt save_z_15/test-data/output/._partial_z.txt save_z_15/test-data/output/partial_z.txt |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/readme.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/save_z_15/readme.txt Fri Mar 18 05:49:55 2016 -0400 |
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| @@ -0,0 +1,23 @@ +====================================================================== +save_z_15 +====================================================================== +### This is the third 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 + +QTL Cartographer is employed for eQTL mapping. + +A partial z file is saved; this is an input file for the eQTL backend pipeline. + +--------------- +Installation +--------------- + +The eQTL mapper pipeline is available for: +* command line usage +* integration into Galaxy servers + + +Requirements: Python 2.7 + QTL Cartographer 1.17 \ No newline at end of file |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/save_z7_15nodes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/save_z_15/save_z7_15nodes.py Fri Mar 18 05:49:55 2016 -0400 |
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| @@ -0,0 +1,137 @@ +""" +@summary: Save partial z file +@version 7 + +""" +# MAPPER --> save z file + +# Input: qtlcart.inp +# qtlcart.map +# parameters.txt + +# Output: z_partial.txt + +import optparse, sys +import tempfile +import re + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def __main__(): + parser = optparse.OptionParser() + parser.add_option("-i", "--input1", default=None, dest="input1", + help="qtlcart.inp file") + parser.add_option("-j", "--input2", default=None, dest="input2", + help="qtlcart.map file") + parser.add_option("-k", "--input3", default=None, dest="input3", + help="parameters.txt file") + + parser.add_option("-p", "--output1", default=None, dest="output1", + help="qtlcart_partial.z file") + (options, args) = parser.parse_args() + + try: + open(options.input1, "r").close() + except TypeError, e: + stop_err("You need to supply the qtlcart.inp file:\n" + str(e)) + except IOError, e: + stop_err("Can not open the qtlcart.inp file:\n" + str(e)) + + try: + open(options.input2, "r").close() + except TypeError, e: + stop_err("You need to supply the qtlcart.map file:\n" + str(e)) + except IOError, e: + stop_err("Can not open the qtlcart.map file:\n" + str(e)) + + try: + open(options.input3, "r").close() + except TypeError, e: + stop_err("You need to supply the parameters.txt file:\n" + str(e)) + except IOError, e: + stop_err("Can not open the parameters.txt file:\n" + str(e)) + + ###################################################################### + # submit.py + ###################################################################### + + import subprocess + import os + + # Create temp direcotry + tempdir = tempfile.mkdtemp() + #print tempdir + + s = "cp %s %s/parameters.txt" %(options.input3, tempdir) + subprocess.call(s, shell=True) + paramters_file = open(tempdir+"/parameters.txt", "r") + parvalues = [] + for line in paramters_file: + l = line.strip().split("\t") + if l[0] == "SRmodel": + SRmodel = l[1] + if l[0] == "Zmodel": + Zmodel = l[1] + if l[0] == "threshold": + threshold = l[1] + if l[0] == "walking_speed": + walking_speed = l[1] + if l[0] == "window_size": + window_size = l[1] + if l[0] == "minimum_cM_between_QTL": + minimum_cM_between_QTL = l[1] + paramters_file.close() + + # copy INPUT file to the temp directory + s = "cp %s %s/qtlcart.inp" %(options.input1, tempdir) + subprocess.call(s, shell=True) + s = "cp %s %s/qtlcart.map" %(options.input2, tempdir) + subprocess.call(s, shell=True) + + f=open(tempdir+"/qtlcart.inp", "r") + ln=f.readlines() + f.close() + count = 0 + + if ln[0] == "NA": + f1=open(tempdir+"/QTLs_total_parsed_LOD.txt", "w") + f1.write("") + f1.close() + os.system("mv %s/QTLs_total_parsed_LOD.txt %s" %(tempdir,options.output1)) + #os.system("mv %s/qtlcart.rc %s" %(tempdir,options.output2)) + else: + count += 1 + if count == 1: + instruction = "/cluster1/bin/Rcross -i %s/qtlcart.inp -o %s/qtlcart.cro -A -V" %(tempdir, tempdir) + os.system(instruction) + + instruction = "/cluster1/bin/SRmapqtl -i %s/qtlcart.cro -e %s/SRqtlcart.log -o %s/qtlcart.sr -m %s/qtlcart.map -M %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(SRmodel)) + os.system(instruction) + + instruction = "/cluster1/bin/Zmapqtl -i %s/qtlcart.cro -o %s/qtlcart.z -m %s/qtlcart.map -S %s/qtlcart.sr -M %s -d %s -w %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(Zmodel), str(walking_speed), str(window_size)) + os.system(instruction) + + ##################### + # Save partial z file + ##################### + + zfile=open(tempdir+"/qtlcart_partial.z", "w") + f=open(tempdir+"/qtlcart.z", "r") + done = "no" + for l in f: + if (done != "yes") and (not l.startswith("-e")): + zfile.write(l.strip()+"\n") + else: + done = "yes" + f.close() + zfile.write("-e\n") + zfile.close() + + os.system("mv %s/qtlcart_partial.z %s" %(tempdir,options.output1)) + +if __name__=="__main__": + __main__() + + |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/save_z7_15nodes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/save_z_15/save_z7_15nodes.xml Fri Mar 18 05:49:55 2016 -0400 |
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| @@ -0,0 +1,27 @@ +<tool id="savez7_15nodes" name="Run QTL Cartographer" version="7.0.0"> + <description> and save partial z file</description> + <command interpreter="python"> + save_z7_15nodes.py --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1 + </command> + <inputs> + <param label="Phenotype-genotype (.inp) file" name="input1" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param> + <param label="QTL Cartographer map file" name="input2" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param> + <param label="Parameters file" name="input3" type="data" format="txt" help="Parameters file with the values of all the parameters for QTL mapping"></param> + </inputs> + <outputs> + <data format="text" name="output1" /> + </outputs> + <requirements> + </requirements> + <tests> + <test> + </test> + </tests> + <help> + +**What it does** + +Runs QTL Cartographer for QTL/eQTL mapping. Parse the results. Save a partial z file. + + </help> +</tool> |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/test-data/input/._qtlcart1.inp |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/test-data/input/._qtlcart_original.map.txt |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/test-data/input/parameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/save_z_15/test-data/input/parameters.txt Fri Mar 18 05:49:55 2016 -0400 |
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| @@ -0,0 +1,6 @@ +SRmodel 2 +Zmodel 6 +threshold 11.5 +walking_speed 2.0 +window_size 10.0 +minimum_cM_between_QTL 20.0 |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/test-data/input/qtlcart1.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/save_z_15/test-data/input/qtlcart1.inp Fri Mar 18 05:49:55 2016 -0400 |
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| b'@@ -0,0 +1,692 @@\n+#bycross\n+-SampleSize 100\n+-Cross Ri1\n+-traits 4\n+-otraits 0\n+-missingtrait .\n+-case yes\n+-TranslationTable\n+AA\t2\tA\n+Aa\t1\t*1\n+aa\t0\tB\n+A-\t12\t*2\n+a-\t10\t*3\n+--\t-1\t-\n+-start markers\n+phi056 A A B B A B B A A A B A B A A A A A A A A A B A \n+B B A B - B B A B B - - A B A B A - - A B A A A A B A A A - B A B B - \n+A - B B B B A B A B A B - - A B A B A - B A A A A B A A B A B A A B A \n+B A B A A B \n+bnl5.62 A A - B A B B A B A B A B B A A A A A A A A B A \n+B A - B - A A A B A - A A B A B A B A A B A A A - B A A A B B A B B - \n+A A B B B B A B A B A A A - A B A B B A B A A - A B A A B A B B A B A \n+B A B A A B \n+umc1041 A A B B A A B A B B A B B A - A B A A A A B B A \n+A A B B - A A A B A B B B B B A - B A A B A A A - A A B - - B A B B B \n+A A B A B A A B A B A A A B A B A B A A B A - A A B A A B A B A A A A \n+B A B B A B \n+umc157a A A B A B A B A A B B - B A A A B - B A A A A A \n+A B B B - A A A B A A A B B A A B B B A A - B A A B A B A A B A A B B \n+A A B A B A A B B A A A A B A B B A B A A A A B A A B A B A B B A B A \n+B A B B B B \n+bnlg1178 A A A A B A B A A B B - B B A A B B B A A B A A \n+A B B B B A A A B A A A B B A A B B B A A - B A B - A B - A A - A B - \n+A A B A A A A B A A A A B B A - A A B B A A A B A A B - B - B B A B A \n+B A B B B B \n+bnlg1429 A A A A B A B A A B B B B B A A B - B A A B A A \n+A B B B B A A A B A A A B B A A B A B A A - B A B B A B - - A A B B - \n+B A B A A A A B A A A A A B A - A A B A A A A B A A B A B A A B A B A \n+B A B B B B \n+bnlg1627 A A A A B B A A B B A B B A A A B B B A A B A A \n+A B - B B A A A B A A A B B A A B A B A A - B A B B A B B - - A B B - \n+A A B A A A A B A B A A A B A B A A B A A A A B A A B A A A A B A B A \n+A A B B B B \n+umc11a A A - A B B B A B B A A B A A B B B B A A A - B \n+A B B B A B A A B B B A B B B A B A B A A B B A B - B B A B A B A B B \n+A A B B A A A B - B A A A B A B B A B A B - A B A A B B A B B - A B A \n+B A B B B B \n+bnlg439 A A A A B B A A B B A A - A A B B B B A A A B B \n+A B A B A A A A B B B A B B B B A A B A A B A B B - - B A B A B A B B \n+A B B A A A A B - B B A B B A - B B B B A A A B A - B A B B B - B - A \n+A A B B B B \n+bnlg2238 A A A - B B A A B B A B A A A B B A A A A A A B \n+A B A B A A A A B B B A A B B A A A - A A B A B B A A B A B A B - B B \n+A B B B A A A B B B B A A B A B B B B A A - A A A A A A A A A A B A A \n+A A - B B B \n+Bnlg1811_U A A A B B A A B B B B B A A A A B A A A A A A B \n+A B A B B B A A B B A A A B B A B A A A B B B B A A B B A B A B A B B \n+A B B B A A A B B B B A A B A B B B B A A A A B - B A B B B A A B A A \n+A A B B A B \n+bnlg2086 A B A A A A A A B B B B A A B - B A A B A A A B \n+A B A B B B A A B A B A A B B B B A A B B - A B B A B B A B B B A B B \n+B B B B A A A B B B A A A B B B - B B A - A A B B A A B B B A A B A A \n+A A A B A B \n+csu61b B B - A B A A A B B B B A B A - B B B B - B A B \n+B A A B B A A A B A B A A B B B B A - B A A - B - B B B A B B B A B B \n+A B B A A A A B B B A B A B A B - B B A - - A B A A - B B B A - B - A \n+A A B B A B \n+bnlg1057 B B A A A A B A B B B B A B A - B B A B B B B B \n+A B A B B A A A - A B A A B B B A A - A A A - B A - B B A - B B A B B \n+A B - A A A A - B A A B A B A B A B B A - B A B A A - B B B A - B - A \n+A A B B A B \n+umc1122 A B A A B A B A B B A B B B A A A B A B A B B A \n+B B A B B B A A B A B A A B B B A A B A A A B B A B B A A A B A A B A \n+A B A A A A B A B A B B A B A B A B B A A A B B A B B B B B B B B B B \n+A A B A A B \n+Bnlg615_U A A B A B B A A B A A B A B A B A B A A A B B B \n+B A A A B A A B B B B A A B B B A A B A A B B B A B B A A - B - A B A \n+A A B A B A B B B A B B A B - B A B B A A A B A A B B B A B B B B B B \n+A A B A A B \n+umc1128 A B B A B B B B B B B A A B A B A B A B A B B A \n+A A B A B A A B B B B A A B B B A A B A A B B B '..b' B A A A A A A A A A A A A A - B A A A A \n+B B B A A A \n+umc182 B B A B A B B A A B B B B B A A B A A B B A A B \n+A A B A B A B A B B B B B A B A A B A B A - A A B A B A B A B A A - B \n+A B B A A B A B B A A A A A A B A B A A A B A A A A A B A B B B A A A \n+B B B A B A \n+bnlg236 B A A B A B A A A B B A B B A A A A A B B A A B \n+A A B A B B B A B B B B B A B A A B A B A A A B B A B A B B B A A A B \n+A B B A A A A B B A A A A A A B A B A A A B A B A - A B A B B A A A A \n+A B B A B A \n+bnl7.49a B A - B B A A - A A A - A B A A A A A B B A A B \n+A - B A B B - A A B B B - B B A A A A A A - A B B A B A B B B A A - B \n+B A A A A B A A B A B A A A A B A B A A B - A - A B - B - B B - A A A \n+A B B A B A \n+bnlg1450 A A A B A B A A A B - A A B A B A A A B A A A B \n+A B B - A B B A A B B B B B B A A B A A A - A A B A B A B A B A B - B \n+B B A B A B A A - A B A B A B B A B A B B A A B A A A B A B B A B A A \n+A B A A B A \n+umc1038 A A A B B B A B B B B A B A A B A A A B A B A B \n+A B B B A A A A B A B B B - A A - A - B A B B A B B B A B A B A B - B \n+B B B B A B A B A A B A - A B B B B A B A A B B A A A B - B A B B B A \n+A B A A B - \n+-stop markers\n+-start traits\n+A_92_P039116\t2281.96\t1818.56\t1371.65\t2512.19\t2454.61\t1407.59\t1601.49\t1688.41\t2206.74\t2710.41\t2129.76\t2525.04\t2379.98\t1993.47\t2531.15\t3692.6\t1855.2\t2459.9\t2050.98\t2753.6\t2665.4\t2895.98\t2573.6\t1828.64\t1740.54\t2093.74\t1916.84\t3316.19\t2008.14\t2396.59\t1789.22\t2469.46\t906.54\t2526.57\t2144.33\t2659.07\t1789.72\t2934.56\t2263.96\t1306.36\t1937.21\t1767.7\t1487.56\t1166.91\t5466.83\t4310.64\t1818.28\t2994.05\t1849.14\t2347.48\t2321.16\t2094.86\t1721.59\t1882.73\t2867.4\t2612.62\t2253.14\t1592.96\t2083.23\t2692.6\t2509.63\t2066.2\t2424.42\t1686.29\t362.32\t293.06\t.\t.\t2100.05\t2681.62\t1858.03\t2697.57\t2166.74\t1724.63\t2481.74\t1603.17\t3067.99\t2798.53\t2281.45\t1871.57\t1618.35\t1379.8\t1643.28\t1789.6\t1980.56\t2379.44\t2321.6\t2101.61\t1933.41\t2038.66\t2756.87\t3021.04\t2094.74\t2145.76\t1747.23\t2507.51\t1532.46\t1668.45\t2678.49\t2078.72\n+A_92_P038628\t421.16\t298.69\t.\t.\t279.28\t1327.26\t3411.8\t3224.54\t621.31\t1887.82\t287.36\t3940.29\t588.77\t2902.94\t882.19\t637.98\t2242.22\t1183.81\t998.47\t997.04\t852.56\t1272.68\t4073.05\t2538.43\t1975.92\t5554.46\t.\t.\t1730.01\t6312.13\t1895.92\t814.38\t.\t.\t645.11\t692.87\t485.94\t126.03\t170.31\t5073.95\t888.36\t5632.5\t336.63\t2834.07\t1172.51\t3994.7\t473.55\t1989.15\t1510.88\t1119.3\t1059.12\t1574.78\t1375.97\t1795.12\t1317.67\t2094.03\t224.05\t1287.88\t1596.29\t1164.15\t601.26\t1294.09\t.\t.\t185.45\t406.28\t.\t.\t5631.89\t1364.25\t4809.46\t833.64\t1115.37\t1086.36\t1500.51\t2170.72\t496.47\t2060.46\t610.86\t2295.13\t169.09\t1562.86\t290.23\t392.46\t805.77\t3461.2\t869.16\t2311.38\t684.56\t301.57\t1995.32\t3611.68\t2927.37\t1746.3\t7127.65\t389.05\t2011.95\t1356.47\t173.13\t2358.56\n+A_92_P038470\t.\t.\t306.12\t271.93\t.\t.\t236.98\t143.72\t170.3\t312.76\t229.45\t298.21\t227.65\t344.05\t.\t.\t328.8\t380.16\t220.48\t287.71\t460.6\t249.8\t227.21\t268.76\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t178.3\t200.95\t276.16\t217.85\t257.85\t229.89\t245.1\t271.68\t.\t.\t398.31\t271.7\t280.94\t189.82\t.\t.\t.\t.\t278.69\t264.84\t.\t.\t255.73\t178.79\t226.85\t236.66\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t424.18\t213.14\t221.17\t255.55\t140.43\t320.81\t337.44\t191.48\t121.84\t216.32\t.\t.\t.\t.\t.\t.\t217.32\t318.08\t132.52\t269.73\t.\t.\t289.95\t337.03\t.\t.\t214.3\t218.2\n+A_92_P038150\t1254.65\t3027.86\t3568.67\t2328.25\t2658.09\t5904.38\t508.89\t562.91\t2571.63\t1687.29\t1827.08\t683.54\t667.26\t1353.95\t1055.86\t1055.8\t1033.17\t1931.23\t3021.96\t1281.73\t2985.33\t2001.71\t1462.14\t3161.77\t1434.97\t1061.68\t1534.86\t1072.1\t1960.25\t3187.95\t1199.39\t2364.05\t.\t.\t1213.63\t3932.68\t4928.96\t868.78\t2066.84\t1094.89\t1069.9\t4829.58\t1051.42\t1586.8\t2425.9\t5025.65\t1591.74\t1862.72\t1952.75\t1794.9\t1290.89\t1546.34\t4237.36\t1519.65\t1501.43\t2884.71\t1344.15\t971.17\t2066.89\t1053.45\t2659.44\t341.27\t921.43\t4391.73\t490.26\t204.39\t.\t.\t1760.11\t1148.13\t1088.95\t1601.91\t2523.37\t614.03\t1032.29\t937.61\t2873.81\t2882.65\t972.04\t1106.16\t1709.07\t1124.55\t1061.09\t1005.36\t1218.5\t1621.98\t1149.98\t2845.99\t959.91\t896.54\t2579.32\t971.96\t2406.24\t2631.56\t969.18\t2102.81\t2803.89\t621.2\t2052.85\t607.76\n+-stop traits\n+-quit\n+-end\n' |
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| diff -r 000000000000 -r ae6f616e7637 save_z_15/test-data/input/qtlcart_original.map.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/save_z_15/test-data/input/qtlcart_original.map.txt Fri Mar 18 05:49:55 2016 -0400 |
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| b'@@ -0,0 +1,251 @@\n+# 671562676 -filetype Rmap.out \n+#\n+#\tQTL Cartographer v. 1.17e, 27 August 2003\n+#\tThis output file (\\\\Trin.bi.up.ac.za\\duncan\\GLS_project\\Pipe_line\\MeQTL\\NewMcd01.map) was created by RMap...\n+#\n+#\tIt is 12:22:33 on Tuesday, 24 July 2012\n+#\n+#\n+#\n+# Here is the Map of Markers...\n+-s\n+-f 2 Map function [1,8]: Haldane is 1\n+-p 0.0000 Extra parameter for map functions [4-8]\n+-u c The units of measurement is centiMorgans.\n+#\n+# Markermap parameters\n+#\n+-c 10 Number of chromosomes.\n+-i 167 Total number of markers.\n+-m 16 Mean, and...\n+-vm 4.9001 ...standard deviation for Markers/Chromosome.\n+-d 11.8571 Mean, and...\n+-vd 6.0265 ...standard deviation for the intermarker distance.\n+-t -1.#IND Mean length of material outside the flanking markers.\n+#\n+ | Chromosome---->\n+--------------------------------------------------------------------------------------------\n+Marker | 1 2 3 4 5 6 7 8 9 10\n+--------------------------------------------------------------------------------------------\n+-l 0 | 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000\n+-l 1 | 7.5300 13.2700 11.7500 19.0000 3.2000 5.6200 9.0300 10.7400 17.9400 15.0200\n+-l 2 | 11.2400 26.0000 13.8400 10.5900 22.8200 8.9200 11.5700 14.7000 9.5600 17.5500\n+-l 3 | 19.9400 25.6300 16.5400 6.3400 7.5600 14.4900 10.2300 13.2900 18.4400 13.4800\n+-l 4 | 5.9100 17.1400 9.1100 17.1500 6.6500 6.8300 10.2300 11.4100 19.1100 6.9400\n+-l 5 | 4.1100 8.5600 10.0400 3.0800 9.6900 5.7300 4.1400 17.3300 27.0800 22.1800\n+-l 6 | 4.4800 10.4300 10.7400 14.0900 11.8600 19.4000 10.2400 15.8400 5.6800 6.3800\n+-l 7 | 16.7600 10.7100 6.1200 4.6300 15.4300 4.2800 7.7500 12.7700 22.7000 9.0700\n+-l 8 | 11.9000 5.3500 2.3600 17.3300 9.4900 6.4500 13.1400 3.2300 4.2700 8.0500\n+-l 9 | 14.2300 15.5300 22.9100 6.1700 7.7200 17.1500 11.3000 3.5800 15.6000 5.9300\n+-l 10 | 16.6000 8.8600 26.3700 12.9000 5.2800 26.9500 18.6800 15.3100 18.4000 13.0300\n+-l 11 | 14.1300 8.5600 7.0100 8.9700 11.4100 9.7400 4.8500 9.6600 0.0000 12.9000\n+-l 12 | 15.8600 16.2000 18.3000 7.6500 13.8900 13.8200 0.0000 3.1300 16.9500\n+-l 13 | 6.2800 2.8700 6.1200 9.7600 8.3200 20.3800 10.3200 0.0000\n+-l 14 | 15.3100 0.0000 16.3500 9.6600 7.7900 2.5400 0.0000 \n+-l 15 | 14.8400 10.9700 4.2500 23.2000 19.9200 \n+-l 16 | 8.1200 10.6200 17.0500 14.6200 13.6300 \n+-l 17 | 6.1800 14.4500 5.5800 11.9000 0.0000 \n+-l 18 | 8.7100 7.6900 9.1900 6.7100 \n+-l 19 | 33.9500 0.0000 4.9800 6.2800 \n+-l 20 | 19.7800 0.0000 0.0000 \n+-l 21 | 8.9400 \n+-l 22 | 10.2300 \n+-l 23 | 22.0600 \n+-l 24 | 3.1000 \n+-l 25 | 14.8400 \n+-l 26 | 9.3700 \n+-l 27 | 0.0000 \n+--------------------------------------------------------------------------------------------\n+-Number | 27 14 19 20 20 17 12 14 11 13\n+\n+\n+\n+Names and positions of the markers'..b' 2 bnl5.62\n+ 1 3 umc1041\n+ 1 4 umc157a\n+ 1 5 bnlg1178\n+ 1 6 bnlg1429\n+ 1 7 bnlg1627\n+ 1 8 umc11a\n+ 1 9 bnlg439\n+ 1 10 bnlg2238\n+ 1 11 Bnlg1811_U\n+ 1 12 bnlg2086\n+ 1 13 csu61b\n+ 1 14 bnlg1057\n+ 1 15 umc1122\n+ 1 16 Bnlg615_U\n+ 1 17 umc1128\n+ 1 18 umc166b\n+ 1 19 dupssr12\n+ 1 20 phi011\n+ 1 21 bnlg1720\n+ 1 22 umc106a\n+ 1 23 umc147b\n+ 1 24 umc1111_P\n+ 1 25 bnlg2331\n+ 1 26 bnlg2123\n+ 1 27 bnl6.32\n+ 2 1 phi402893\n+ 2 2 bnlg1297\n+ 2 3 bnlg2042\n+ 2 4 umc44b\n+ 2 5 csu40\n+ 2 6 umc135\n+ 2 7 csu54a\n+ 2 8 umc55a\n+ 2 9 umc14b\n+ 2 10 csu154a\n+ 2 11 umc150b\n+ 2 12 umc1551\n+ 2 13 umc36a\n+ 2 14 csu109a\n+ 3 1 umc32a\n+ 3 2 phi104127\n+ 3 3 bnlg1325\n+ 3 4 bnlg1447\n+ 3 5 umc92a\n+ 3 6 bnlg1019a\n+ 3 7 phi053\n+ 3 8 bnlg420\n+ 3 9 umc1307\n+ 3 10 Phi073_U\n+ 3 11 Bnlg1449_U\n+ 3 12 bnl10.24a\n+ 3 13 unknown1\n+ 3 14 umc3b\n+ 3 15 umc16a\n+ 3 16 bnlg1108_P\n+ 3 17 umc63a\n+ 3 18 bnlg1182\n+ 3 19 bnlg1754\n+ 4 1 umc1017\n+ 4 2 umc1294\n+ 4 3 phi021\n+ 4 4 umc1550\n+ 4 5 umc1652\n+ 4 6 bnlg490\n+ 4 7 csu100\n+ 4 8 umc156a\n+ 4 9 bnlg2291\n+ 4 10 umc19\n+ 4 11 mmc0341\n+ 4 12 umc133a\n+ 4 13 umc15a\n+ 4 14 csu11b\n+ 4 15 npi593a\n+ 4 16 bnlg589\n+ 4 17 umc1720_P\n+ 4 18 bnlg1337\n+ 4 19 phi019\n+ 4 20 phi006\n+ 5 1 bnl8.33\n+ 5 2 npi409\n+ 5 3 umc147a\n+ 5 4 umc90\n+ 5 5 umc107b\n+ 5 6 Bnlg105_U\n+ 5 7 bnlg1046\n+ 5 8 umc166a\n+ 5 9 bnl6.22\n+ 5 10 csu36b\n+ 5 11 DupSSR10_U\n+ 5 12 bnl5.71a\n+ 5 13 umc1155_P\n+ 5 14 npi237\n+ 5 15 umc54\n+ 5 16 bnlg1346\n+ 5 17 bnlg118\n+ 5 18 umc1225\n+ 5 19 umc104b\n+ 5 20 bnlg1885\n+ 6 1 umc85a\n+ 6 2 bnlg426\n+ 6 3 umc36c\n+ 6 4 umc1572_P\n+ 6 5 Bnlg2191_U\n+ 6 6 bnlg2151\n+ 6 7 umc1887\n+ 6 8 umc65a\n+ 6 9 umc1014\n+ 6 10 bnlg1922\n+ 6 11 umc1413_P\n+ 6 12 mmc0241\n+ 6 13 umc1424_P\n+ 6 14 umc36\n+ 6 15 umc39\n+ 6 16 bnlg1740\n+ 6 17 umc2059\n+ 7 1 csu13\n+ 7 2 bnlg1094\n+ 7 3 umc1393\n+ 7 4 bnlg1808\n+ 7 5 bnl15.21\n+ 7 6 bnlg339\n+ 7 7 bnlg155\n+ 7 8 bnlg1805\n+ 7 9 bnl14.07\n+ 7 10 umc1125\n+ 7 11 phi082\n+ 7 12 umc1799\n+ 8 1 npi114a\n+ 8 2 umc1327\n+ 8 3 npi110a\n+ 8 4 umc103a\n+ 8 5 bnlg669\n+ 8 6 umc1858\n+ 8 7 umc1562_P\n+ 8 8 umc48a\n+ 8 9 asg52a\n+ 8 10 umc150a\n+ 8 11 umc1384\n+ 8 12 umc7\n+ 8 13 bnlg1056\n+ 8 14 umc39b\n+ 9 1 bnlg1272\n+ 9 2 umc113a\n+ 9 3 umc1170_P\n+ 9 4 umc105a\n+ 9 5 umc81\n+ 9 6 bnl8.17\n+ 9 7 umc1231\n+ 9 8 umc1733\n+ 9 9 bnlg1588\n+ 9 10 bnlg1375\n+ 9 11 umc1137\n+ 10 1 phi118\n+ 10 2 npi285a\n+ 10 3 umc1337_P\n+ 10 4 umc130\n+ 10 5 bnlg1079\n+ 10 6 umc1115\n+ 10 7 npi232a\n+ 10 8 umc44a\n+ 10 9 umc182\n+ 10 10 bnlg236\n+ 10 11 bnl7.49a\n+ 10 12 bnlg1450\n+ 10 13 umc1038\n+-e MarkerNames\n+\n+\n+\n+Names of the Chromosomes\n+\n+-b ChromosomeNames \n+ 1 Ch1\n+ 2 Ch2\n+ 3 Ch3\n+ 4 Ch4\n+ 5 Ch5\n+ 6 Ch6\n+ 7 Ch7\n+ 8 Ch8\n+ 9 Ch9\n+ 10 Ch10\n+-e ChromosomeNames\n' |
| b |
| diff -r 000000000000 -r ae6f616e7637 save_z_15/test-data/output/._partial_z.txt |
| b |
| Binary file save_z_15/test-data/output/._partial_z.txt has changed |
| b |
| diff -r 000000000000 -r ae6f616e7637 save_z_15/test-data/output/partial_z.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/save_z_15/test-data/output/partial_z.txt Fri Mar 18 05:49:55 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1033 @@\n+# 1457949995 -filetype Zmapqtl.out\n+#\n+#\tQTL Cartographer v. 1.17j, 28 January 2005\n+#\tThis output file (/tmp/tmpbHrEeu/qtlcart.z) was created by /cluster1/bin/Zmapqtl...\n+#\n+#\tIt is 12:06:35 on Monday, 14 March 2016\n+#\n+#\n+#The position is from the left telomere on the chromosome\n+-window 10.00 Window size for models 5 and 6\n+-background 5 Background parameters in model 6\n+-Model 6 Model number\n+-trait 1 Analyzed trait [A_92_P039116]\n+-cross Ri1 Cross\n+#\n+# Note that our Likelihood ratio test statistic compares two nested hypotheses\n+# and is two times the negative natural log of the ratio of the likelihoods. For example,\n+# assume that hypothesis H0 is nested within H1 and that they have likelihoods L0 and L1 respectively.\n+# Then, the "Likelihood Ratio Test Statistic" is -2ln(L0/L1).\n+#\n+# Test Site * Like. Ratio Test Statistics * Additive * Dominance * Misc. HT\n+c m position H0:H1 R2(0:1) TR2(0:1) H1:a S1 .... .... .... .... .... .... .... ..... .... ..... ..... .... .....\n+-s\n+1 1 0.0001 0.7434324 0.0053812 0.3164638 52.9717580 80.5066354 0.0000000 0.0000000 0.0000000 0.0000000 315574.7095827 0.0000000 0.0000000 315574.7095827 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 1 0.0201 0.5391025 0.0040625 0.3151451 45.8248296 78.4439339 0.0000000 0.0000000 0.0000000 0.0000000 316183.5415323 0.0000000 0.0000000 316183.5415323 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 1 0.0401 0.3589454 0.0027254 0.3138080 37.4654341 76.3185504 0.0000000 0.0000000 0.0000000 0.0000000 316800.8369872 0.0000000 0.0000000 316800.8369872 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 1 0.0601 0.2128560 0.0015747 0.3126573 28.5030082 74.4251441 0.0000000 0.0000000 0.0000000 0.0000000 317332.0907375 0.0000000 0.0000000 317332.0907375 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 2 0.0754 0.1270715 0.0009030 0.3119855 21.6368959 73.2590881 0.0000000 0.0000000 0.0000000 0.0000000 317642.2341381 0.0000000 0.0000000 317642.2341381 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 2 0.0954 0.0033697 0.0000281 0.3111107 3.7769637 71.4960097 0.0000000 0.0000000 0.0000000 0.0000000 318046.1365628 0.0000000 0.0000000 318046.1365628 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 2 0.1154 0.0775107 0.0007218 0.3118043 -19.0003985 68.8864473 0.0000000 0.0000000 0.0000000 0.0000000 317725.8843760 0.0000000 0.0000000 317725.8843760 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 2 0.1354 0.3885475 0.0036489 0.3147315 -42.5748888 65.8557645 0.0000000 0.0000000 0.0000000 0.0000000 316374.4820178 0.0000000 0.0000000 316374.4820178 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 2 0.1554 0.8846176 0.0076869 0.3187694 -61.8010096 63.0271482 0.0000000 0.0000000 0.0000000 0.0000000 314510.2483504 0.0000000 0.0000000 314510.2483504 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+1 2 0.1754 1.4721665 0.0113584 0.3224410 -75.3468673 60.4054413 0.0000000 0.0000000 0.0000000 0.0000000 312815.1697'..b'0000\n+10 11 1.2164 0.3167660 0.0033658 0.3144484 -40.6531472 80.2527741 0.0000000 0.0000000 0.0000000 0.0000000 316505.1811027 0.0000000 0.0000000 316505.1811027 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 11 1.2364 0.3949879 0.0043498 0.3154324 -46.0139033 81.7721538 0.0000000 0.0000000 0.0000000 0.0000000 316050.8911681 0.0000000 0.0000000 316050.8911681 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 11 1.2564 0.4634624 0.0049692 0.3160518 -49.0916418 82.7119051 0.0000000 0.0000000 0.0000000 0.0000000 315764.9313987 0.0000000 0.0000000 315764.9313987 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 11 1.2764 0.5143897 0.0050739 0.3161564 -49.6423050 82.9180964 0.0000000 0.0000000 0.0000000 0.0000000 315716.6024646 0.0000000 0.0000000 315716.6024646 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 11 1.2964 0.5458202 0.0047317 0.3158143 -48.1030697 82.4928398 0.0000000 0.0000000 0.0000000 0.0000000 315874.5817961 0.0000000 0.0000000 315874.5817961 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.3054 0.5545577 0.0044890 0.3155715 -46.9659170 82.1696029 0.0000000 0.0000000 0.0000000 0.0000000 315986.6401091 0.0000000 0.0000000 315986.6401091 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.3254 0.6350617 0.0057962 0.3168788 -53.0592543 83.7808505 0.0000000 0.0000000 0.0000000 0.0000000 315383.1234852 0.0000000 0.0000000 315383.1234852 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.3454 0.7168215 0.0071575 0.3182401 -58.7439049 85.3958914 0.0000000 0.0000000 0.0000000 0.0000000 314754.6356737 0.0000000 0.0000000 314754.6356737 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.3654 0.7926645 0.0083602 0.3194427 -63.3754529 86.7973234 0.0000000 0.0000000 0.0000000 0.0000000 314199.3919284 0.0000000 0.0000000 314199.3919284 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.3854 0.8547274 0.0091565 0.3202390 -66.3310735 87.7364538 0.0000000 0.0000000 0.0000000 0.0000000 313831.7570546 0.0000000 0.0000000 313831.7570546 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.4054 0.8967564 0.0093622 0.3204448 -67.2053274 88.0236801 0.0000000 0.0000000 0.0000000 0.0000000 313736.7806597 0.0000000 0.0000000 313736.7806597 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.4254 0.9161875 0.0089466 0.3200291 -65.9618352 87.6152236 0.0000000 0.0000000 0.0000000 0.0000000 313928.6619107 0.0000000 0.0000000 313928.6619107 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.4454 0.9147434 0.0080444 0.3191269 -62.9449805 86.6334358 0.0000000 0.0000000 0.0000000 0.0000000 314345.1922612 0.0000000 0.0000000 314345.1922612 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+10 12 1.4654 0.8972373 0.0068762 0.3179587 -58.7218641 85.2997460 0.0000000 0.0000000 0.0000000 0.0000000 314884.5208489 0.0000000 0.0000000 314884.5208489 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000\n+-e\n' |