changeset 0:1cbba720061a draft

Uploaded
author nanettec
date Fri, 18 Mar 2016 05:48:30 -0400
parents
children 063d8e1efa70
files split_15/._.DS_Store split_15/._readme.txt split_15/readme.txt split_15/split7_15nodes.py split_15/split7_15nodes.xml split_15/test-data/._.DS_Store split_15/test-data/input/._.DS_Store split_15/test-data/input/._otraits.txt split_15/test-data/input/._phenotypeGenotype_etraits.inp.txt split_15/test-data/input/MeQTL_raw_data_55.txt split_15/test-data/input/otraits.txt split_15/test-data/input/phenotypeGenotype_etraits.inp.txt split_15/test-data/output/._parameters.txt split_15/test-data/output/._qtlcart1.inp split_15/test-data/output/._qtlcart10.inp split_15/test-data/output/._qtlcart11.inp split_15/test-data/output/._qtlcart12.inp split_15/test-data/output/._qtlcart13.inp split_15/test-data/output/._qtlcart14.inp split_15/test-data/output/._qtlcart15.inp split_15/test-data/output/._qtlcart2.inp split_15/test-data/output/._qtlcart3.inp split_15/test-data/output/._qtlcart4.inp split_15/test-data/output/._qtlcart5.inp split_15/test-data/output/._qtlcart6.inp split_15/test-data/output/._qtlcart7.inp split_15/test-data/output/._qtlcart8.inp split_15/test-data/output/._qtlcart9.inp split_15/test-data/output/parameters.txt split_15/test-data/output/qtlcart1.inp split_15/test-data/output/qtlcart10.inp split_15/test-data/output/qtlcart11.inp split_15/test-data/output/qtlcart12.inp split_15/test-data/output/qtlcart13.inp split_15/test-data/output/qtlcart14.inp split_15/test-data/output/qtlcart15.inp split_15/test-data/output/qtlcart2.inp split_15/test-data/output/qtlcart3.inp split_15/test-data/output/qtlcart4.inp split_15/test-data/output/qtlcart5.inp split_15/test-data/output/qtlcart6.inp split_15/test-data/output/qtlcart7.inp split_15/test-data/output/qtlcart8.inp split_15/test-data/output/qtlcart9.inp
diffstat 44 files changed, 11555 insertions(+), 0 deletions(-) [+]
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Binary file split_15/._.DS_Store has changed
Binary file split_15/._readme.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/readme.txt	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,22 @@
+======================================================================
+split_15
+======================================================================
+### This is the first 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
+
+The input e-trait data are split into 15 .inp files (each containing the same number of e-traits).
+
+This makes 15 parallel runs possible, to reduce the running time of large eQTL datasets. 
+
+---------------
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/split7_15nodes.py	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,329 @@
+"""
+@summary: SPLITTER
+@version 7
+
+"""
+# SPLITTER --> into 15 files
+
+# Input: etraits.txt
+#	 otraits.txt
+#        phenotypeGenotype.inp
+
+# Output: parameters.txt
+#	  qtlcart1.inp
+#         qtlcart2.inp
+#         qtlcart3.inp
+#         qtlcart4.inp
+#         qtlcart5.inp
+
+import optparse, sys
+import tempfile
+
+def stop_err( msg ):
+	sys.stderr.write( "%s\n" % msg )
+	sys.exit()
+    
+def __main__():
+	parser = optparse.OptionParser()
+	# input files: 
+	parser.add_option("-i", "--input1", default=None, dest="input1", 
+			  help="expression traits (etraits.txt) file")
+	parser.add_option("-d", "--input2", default=None, dest="input2", 
+			  help="other traits (otraits.txt) file")
+	parser.add_option("-j", "--input3", default=None, dest="input3", 
+			  help="phenotypeGenotype.inp file")
+
+	# parameters: 
+	parser.add_option("-k", "--SRmodel", default=2, dest="SRmodel", 
+                      help="Select the stepwise regression model to search for QTLs: 0=SF, 1=EB, 2=FB (default)")
+	parser.add_option("-l", "--Zmodel", default=6, dest="Zmodel", 
+                      help="Select interval mapping (3) or composite interval mapping (6, default)")
+	parser.add_option("-b", "--threshold", type="float", default=11.5, dest="threshold", 
+	              help="Select a LR threshold (default=11.5)")
+	parser.add_option("-c", "--walking_speed", type="float", default=2.0, dest="walking_speed", 
+	              help="Select a walking speed in cM (default=2.0)")
+	parser.add_option("-f", "--window_size", type="float", default=10.0, dest="window_size", 
+	              help="Select a window size in cM (default=10)")
+	parser.add_option("-g", "--minimum_cM_between_QTL", type="float", default=20.0, dest="minimum_cM_between_QTL", 
+	              help="Select a minimum cM between QTLs (default=20)")
+	
+	# output files: 
+	parser.add_option("--oa", "--output1", default=None, dest="output1", 
+			  help="qtlcart1.inp file")
+	parser.add_option("--ob", "--output2", default=None, dest="output2", 
+			  help="qtlcart2.inp file")
+	parser.add_option("--oc", "--output3", default=None, dest="output3", 
+			  help="qtlcart3.inp file")
+	parser.add_option("--od", "--output4", default=None, dest="output4", 
+			  help="qtlcart4.inp file")
+	parser.add_option("--oe", "--output5", default=None, dest="output5", 
+			  help="qtlcart5.inp file")
+	parser.add_option("--of", "--output6", default=None, dest="output6", 
+			  help="qtlcart6.inp file")
+	parser.add_option("--og", "--output7", default=None, dest="output7", 
+			  help="qtlcart7.inp file")
+	parser.add_option("--oh", "--output8", default=None, dest="output8", 
+			  help="qtlcart8.inp file")
+	parser.add_option("--oi", "--output9", default=None, dest="output9", 
+			  help="qtlcart9.inp file")
+	parser.add_option("--oj", "--output10", default=None, dest="output10", 
+			  help="qtlcart10.inp file")	
+	parser.add_option("--ok", "--output11", default=None, dest="output11", 
+			  help="qtlcart11.inp file")
+	parser.add_option("--ol", "--output12", default=None, dest="output12", 
+			  help="qtlcart12.inp file")
+	parser.add_option("--om", "--output13", default=None, dest="output13", 
+			  help="qtlcart13.inp file")
+	parser.add_option("--on", "--output14", default=None, dest="output14", 
+			  help="qtlcart14.inp file")
+	parser.add_option("--oo", "--output15", default=None, dest="output15", 
+			  help="qtlcart15.inp file")
+	
+	parser.add_option("--op", "--output16", default=None, dest="output16", 
+			  help="parameters.txt file")
+	(options, args) = parser.parse_args()
+	
+	# input files
+	try:
+	    open(options.input1, "r").close()
+	except TypeError, e:
+	    stop_err("You need to supply the expression traits (etraits.txt) file:\n" + str(e))
+	except IOError, e:
+	    stop_err("Can not open the expression traits (etraits.txt) file:\n" + str(e))
+
+	try:
+	    open(options.input2, "r").close()
+	except TypeError, e:
+	    stop_err("You need to supply the other traits (otraits.txt) file:\n" + str(e))
+	except IOError, e:
+	    stop_err("Can not open the other traits (otraits.txt) file:\n" + str(e))
+	    
+	try:
+	    open(options.input3, "r").close()
+	except TypeError, e:
+	    stop_err("You need to supply the phenotypeGenotype.inp file:\n" + str(e))
+	except IOError, e:
+	    stop_err("Can not open the phenotypeGenotype.inp file:\n" + str(e))
+
+	# parameters
+	try:
+	    options.SRmodel = int(options.SRmodel)
+        except TypeError, e:
+            stop_err("Not an integer, 0, 1 or 2 can be selected (0=SF, 1=EB, 2=FB):\n" + str(e))
+        
+	try:
+	    options.Zmodel = int(options.Zmodel)
+        except TypeError, e:
+            stop_err("Not an integer, 3 or 6 can be selected (3=IM, 6=CIM):\n" + str(e))
+	
+	try:
+            options.threshold = float(options.threshold)
+        except TypeError, e:
+            stop_err("Not a float, provide a LR threshold:\n" + str(e))
+	
+	try:
+            options.walking_speed = float(options.walking_speed)
+        except TypeError, e:
+            stop_err("Not a float, provide a walking speed in cM:\n" + str(e))
+	
+	try:
+            options.threshold = float(options.threshold)
+        except TypeError, e:
+            stop_err("Not a float, provide a LR threshold:\n" + str(e))
+	
+	try:
+            options.window_size = float(options.window_size)
+        except TypeError, e:
+            stop_err("Not a float, provide a window size in cM:\n" + str(e))
+	    
+	try:
+            options.minimum_cM_between_QTL = float(options.minimum_cM_between_QTL)
+        except TypeError, e:
+            stop_err("Not a float, select a minimum cM between QTLs:\n" + str(e))
+
+	######################################################################
+	# phenotype_evaluation.py
+	######################################################################
+	
+	import subprocess
+	import os
+	
+	# Create temp direcotry
+	tempdir = tempfile.mkdtemp()
+	#print tempdir
+	
+	# copy INPUT file to the temp directory
+	s = "cp %s %s/etraits.txt" %(options.input1, tempdir)
+	subprocess.call(s, shell=True)
+	s = "cp %s %s/otraits.txt" %(options.input2, tempdir)
+	subprocess.call(s, shell=True)
+	s = "cp %s %s/phenotypeGenotype.inp" %(options.input3, tempdir)
+	subprocess.call(s, shell=True)
+	
+	
+	sr = options.SRmodel
+	z = options.Zmodel
+	thr = options.threshold
+	ws = options.walking_speed
+	win_size = options.window_size
+	dist_QTL = options.minimum_cM_between_QTL
+	
+	############################
+        # count number of traits in etraits.txt
+        ############################
+        
+	nodes = 15 # change only this
+	
+        etraits = open(tempdir+"/etraits.txt","r")	
+        traits_dict = {}
+        traits_names = []
+        tot_traits = 0
+        for line in etraits:
+            l = line.strip().split("\t")
+            tot_traits += 1
+            if tot_traits == 1:
+                samplesize = len(l)-1
+            traits_dict[l[0]]=line.strip()
+            traits_names.append(l[0])
+        etraits.close()
+        
+        # make list with numbers per node
+        num_traits_per_node = []
+        
+        if tot_traits < nodes:
+            empty = nodes-tot_traits
+            non_empty = nodes-empty
+            base = 1
+            for i in range(non_empty):
+                num_traits_per_node.append(base)
+            for j in range(empty):
+                num_traits_per_node.append(0)
+        else:
+            base = tot_traits/nodes
+            remaining = tot_traits%nodes
+            for i in range(nodes):
+                num_traits_per_node.append(base)
+            for j in range(remaining):
+                num_traits_per_node[j] = num_traits_per_node[j]+1
+	
+	############################
+        # count number of traits in otraits.txt
+        ############################
+
+        otraits = open(tempdir+"/otraits.txt","r")	
+        otraits_dict = {}
+        otraits_names = []
+        tot_otraits = 0
+        for line in otraits:
+            l = line.strip().split("\t")
+            tot_otraits += 1
+            if tot_otraits == 1:
+                samplesize_otraits = len(l)-1
+            otraits_dict[l[0]]=line.strip()
+            otraits_names.append(l[0])
+        etraits.close()
+        #print "otraits samplesize = "+str(samplesize_otraits)
+	#print "etraits samplesize = "+str(samplesize)   
+	
+	if (tot_otraits != 0) and (samplesize_otraits == samplesize):
+		add_otraits = "yes"
+	else:
+		add_otraits = "no"
+		tot_otraits = 0
+	#print "add_otraits "+str(add_otraits)	
+	#print "tot_otraits "+str(tot_otraits)
+	
+        ############################
+        # create header and footer files
+        ############################
+        
+        f = open(tempdir+"/phenotypeGenotype.inp","r")	
+        line=f.readline()
+        
+	hdr = []
+        hold="NULL"
+        # retrieve header of cross.inp
+        while hold !="TRUE":
+            # switch status adjustment
+            if line[0:13]=="-start traits":
+                hold="TRUE"
+            hdr.append(line)
+	    if line[0:13] !="-start traits":
+                line=f.readline()
+	
+        foot = []
+	foot.append("-stop traits\n")
+	foot.append("-quit\n")
+	foot.append("-end\n") 
+                
+	foot = []
+	if (add_otraits == "yes"):
+		foot.append("-stop traits\n")
+		foot.append("-start otraits\n")
+		for k in otraits_dict.keys():
+			otraits_dict[k]
+			foot.append("+"+otraits_dict[k]+"\n")
+		foot.append("-stop otraits\n")
+		foot.append("-quit\n")
+		foot.append("-end\n")
+	else:
+		foot.append("-stop traits\n")
+		foot.append("-quit\n")
+		foot.append("-end\n")
+	#print foot
+	
+        ############################
+        # create output files
+        ############################
+                
+        done = 0
+        c = -1
+        for i in range(nodes):
+            c += 1
+	    for j in range(10):
+		if hdr[j].split(" ")[0] == "-SampleSize":
+		    hdr[j]=hdr[j][0:12]+str(samplesize)+"\n"
+		if hdr[j].split(" ")[0] == "-traits":	
+		    hdr[j]=hdr[j][0:8]+str(num_traits_per_node[c])+"\n"
+		if hdr[j].split(" ")[0] == "-otraits":		
+		    hdr[j]=hdr[j][0:9]+str(tot_otraits)+"\n"
+		    
+            f=open(tempdir+"/qtlcart"+str(c)+".inp","w")
+            for i in hdr:
+                f.write(i)
+            for j in range(num_traits_per_node[c]):
+                j += done
+                f.write(traits_dict[traits_names[j]]+"\n")
+            done += num_traits_per_node[c]
+            for k in foot:
+                f.write(k)
+        f.close()
+	
+	paramters_file=open(tempdir+"/parameters.txt", "w")
+	paramters_file.write("SRmodel\t"+str(sr)+"\nZmodel\t"+str(z)+"\nthreshold\t"+str(thr)+"\nwalking_speed\t"+str(ws)+"\nwindow_size\t"+str(win_size)+"\nminimum_cM_between_QTL\t"+str(dist_QTL)+"\n")
+	paramters_file.close()
+	
+	os.system("mv %s/qtlcart0.inp %s" %(tempdir,options.output1))
+	os.system("mv %s/qtlcart1.inp %s" %(tempdir,options.output2))
+	os.system("mv %s/qtlcart2.inp %s" %(tempdir,options.output3))
+	os.system("mv %s/qtlcart3.inp %s" %(tempdir,options.output4))
+	os.system("mv %s/qtlcart4.inp %s" %(tempdir,options.output5))
+	os.system("mv %s/qtlcart5.inp %s" %(tempdir,options.output6))
+	os.system("mv %s/qtlcart6.inp %s" %(tempdir,options.output7))
+	os.system("mv %s/qtlcart7.inp %s" %(tempdir,options.output8))
+	os.system("mv %s/qtlcart8.inp %s" %(tempdir,options.output9))
+	os.system("mv %s/qtlcart9.inp %s" %(tempdir,options.output10))
+	os.system("mv %s/qtlcart10.inp %s" %(tempdir,options.output11))
+	os.system("mv %s/qtlcart11.inp %s" %(tempdir,options.output12))
+	os.system("mv %s/qtlcart12.inp %s" %(tempdir,options.output13))
+	os.system("mv %s/qtlcart13.inp %s" %(tempdir,options.output14))
+	os.system("mv %s/qtlcart14.inp %s" %(tempdir,options.output15))
+	
+	os.system("mv %s/parameters.txt %s" %(tempdir,options.output16))
+	
+	######################################################################
+	
+if __name__=="__main__": 
+    __main__()
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/split7_15nodes.xml	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,68 @@
+<tool id="split7_15nodes" name="Split e-traits" version="7.0.0">
+	<description> into 15 sub-files</description>
+	<command interpreter="python">
+            split7_15nodes.py --input1 $input1 --input2 $input2 --input3 $input3 --SRmodel $SRmodel --Zmodel $Zmodel --threshold $threshold --walking_speed $walking_speed --window_size $window_size --minimum_cM_between_QTL $minimum_cM_between_QTL --output1 $output1 --output2 $output2 --output3 $output3 --output4 $output4 --output5 $output5 --output6 $output6 --output7 $output7 --output8 $output8 --output9 $output9 --output10 $output10 --output11 $output11 --output12 $output12 --output13 $output13 --output14 $output14 --output15 $output15 --output16 $output16
+	</command>
+        <inputs>
+            <param label="Expression traits (etraits) file" name="input1" type="data" format="tabular" help="A tabular file with the phenotype information"></param>
+	    <param label="Other traits (otraits) file" name="input2" type="data" format="tabular" help="A tabular file with the other trait information"></param>
+	    <param label="Phenotype-genotype (.inp) file" name="input3" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param>
+	    <param name="SRmodel" label="Stepwise regression model: 0=SF, 1=EB, 2=FB (default)" value="2" type="integer" help="Select the stepwise regression model to search for QTLs: 0=SF, 1=EB, 2=FB (default)">
+		<validator type="in_range" message="Number can be 0, 1 or 2" min="0" max="2"/>
+		<validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
+	    </param>
+	    <param name="Zmodel" label="Model for interval mapping: 3=IM or 6=CIM (default)" value="6" type="integer" help="Select interval mapping (3) or composite interval mapping (6, default)">
+		<validator type="in_range" message="Number can be 3 or 6" min="3" max="6"/>
+		<validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
+	    </param>
+	    <param name="threshold" label="LR threshold" value="11.5" type="float" help="Select a LR threshold (default=11.5)">
+		<validator type="in_range" message="Float can be between 0 and 100" min="0" max="100"/>
+		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
+	    </param>
+	    <param name="walking_speed" label="Walking speed in cM" value="2.0" type="float" help="Select a walking speed in cM (default=2.0)">
+		<validator type="in_range" message="Float can be between 0 and 10" min="0" max="10"/>
+		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
+	    </param>
+	    <param name="window_size" label="Window size in cM" value="10.0" type="float" help="Select a window size in cM (default=10.0)">
+		<validator type="in_range" message="Float can be between 0 and 50" min="0" max="50"/>
+		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
+	    </param>
+	    <param name="minimum_cM_between_QTL" label="Minimum cM between QTL" value="20.0" type="float" help="Select a minimum cM between QTL (default=20.0)">
+		<validator type="in_range" message="Float can be between 0 and 50" min="0" max="50"/>
+		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
+	    </param>
+        </inputs>
+	<outputs>
+                <data format="txt" name="output1" />
+		<data format="txt" name="output2" />
+		<data format="txt" name="output3" />
+		<data format="txt" name="output4" />
+		<data format="txt" name="output5" />
+                <data format="txt" name="output6" />
+                <data format="txt" name="output7" />
+		<data format="txt" name="output8" />
+		<data format="txt" name="output9" />
+		<data format="txt" name="output10" />
+                <data format="txt" name="output11" />
+		<data format="txt" name="output12" />
+		<data format="txt" name="output13" />
+		<data format="txt" name="output14" />
+		<data format="txt" name="output15" />
+                <data format="txt" name="output16" />
+	</outputs>
+	<requirements>
+	</requirements>
+	<tests>
+          <test>
+          </test>
+	</tests>
+	<help>
+		
+**What it does**
+
+Splits the input phenotype data into smaller .inp files.
+
+This makes 15 parallel runs on the cluster possible, to reduce the running time of large phenotype datasets (e.g. eQTL data sets). 
+
+        </help>
+</tool>
Binary file split_15/test-data/._.DS_Store has changed
Binary file split_15/test-data/input/._.DS_Store has changed
Binary file split_15/test-data/input/._otraits.txt has changed
Binary file split_15/test-data/input/._phenotypeGenotype_etraits.inp.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/test-data/input/MeQTL_raw_data_55.txt	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,55 @@
+A_92_P039116	2281.96	1818.56	1371.65	2512.19	2454.61	1407.59	1601.49	1688.41	2206.74	2710.41	2129.76	2525.04	2379.98	1993.47	2531.15	3692.6	1855.2	2459.9	2050.98	2753.6	2665.4	2895.98	2573.6	1828.64	1740.54	2093.74	1916.84	3316.19	2008.14	2396.59	1789.22	2469.46	906.54	2526.57	2144.33	2659.07	1789.72	2934.56	2263.96	1306.36	1937.21	1767.7	1487.56	1166.91	5466.83	4310.64	1818.28	2994.05	1849.14	2347.48	2321.16	2094.86	1721.59	1882.73	2867.4	2612.62	2253.14	1592.96	2083.23	2692.6	2509.63	2066.2	2424.42	1686.29	362.32	293.06	.	.	2100.05	2681.62	1858.03	2697.57	2166.74	1724.63	2481.74	1603.17	3067.99	2798.53	2281.45	1871.57	1618.35	1379.8	1643.28	1789.6	1980.56	2379.44	2321.6	2101.61	1933.41	2038.66	2756.87	3021.04	2094.74	2145.76	1747.23	2507.51	1532.46	1668.45	2678.49	2078.72
+A_92_P038628	421.16	298.69	.	.	279.28	1327.26	3411.8	3224.54	621.31	1887.82	287.36	3940.29	588.77	2902.94	882.19	637.98	2242.22	1183.81	998.47	997.04	852.56	1272.68	4073.05	2538.43	1975.92	5554.46	.	.	1730.01	6312.13	1895.92	814.38	.	.	645.11	692.87	485.94	126.03	170.31	5073.95	888.36	5632.5	336.63	2834.07	1172.51	3994.7	473.55	1989.15	1510.88	1119.3	1059.12	1574.78	1375.97	1795.12	1317.67	2094.03	224.05	1287.88	1596.29	1164.15	601.26	1294.09	.	.	185.45	406.28	.	.	5631.89	1364.25	4809.46	833.64	1115.37	1086.36	1500.51	2170.72	496.47	2060.46	610.86	2295.13	169.09	1562.86	290.23	392.46	805.77	3461.2	869.16	2311.38	684.56	301.57	1995.32	3611.68	2927.37	1746.3	7127.65	389.05	2011.95	1356.47	173.13	2358.56
+A_92_P038470	.	.	306.12	271.93	.	.	236.98	143.72	170.3	312.76	229.45	298.21	227.65	344.05	.	.	328.8	380.16	220.48	287.71	460.6	249.8	227.21	268.76	.	.	.	.	.	.	.	.	.	.	178.3	200.95	276.16	217.85	257.85	229.89	245.1	271.68	.	.	398.31	271.7	280.94	189.82	.	.	.	.	278.69	264.84	.	.	255.73	178.79	226.85	236.66	.	.	.	.	.	.	.	.	.	.	.	.	424.18	213.14	221.17	255.55	140.43	320.81	337.44	191.48	121.84	216.32	.	.	.	.	.	.	217.32	318.08	132.52	269.73	.	.	289.95	337.03	.	.	214.3	218.2
+A_92_P038150	1254.65	3027.86	3568.67	2328.25	2658.09	5904.38	508.89	562.91	2571.63	1687.29	1827.08	683.54	667.26	1353.95	1055.86	1055.8	1033.17	1931.23	3021.96	1281.73	2985.33	2001.71	1462.14	3161.77	1434.97	1061.68	1534.86	1072.1	1960.25	3187.95	1199.39	2364.05	.	.	1213.63	3932.68	4928.96	868.78	2066.84	1094.89	1069.9	4829.58	1051.42	1586.8	2425.9	5025.65	1591.74	1862.72	1952.75	1794.9	1290.89	1546.34	4237.36	1519.65	1501.43	2884.71	1344.15	971.17	2066.89	1053.45	2659.44	341.27	921.43	4391.73	490.26	204.39	.	.	1760.11	1148.13	1088.95	1601.91	2523.37	614.03	1032.29	937.61	2873.81	2882.65	972.04	1106.16	1709.07	1124.55	1061.09	1005.36	1218.5	1621.98	1149.98	2845.99	959.91	896.54	2579.32	971.96	2406.24	2631.56	969.18	2102.81	2803.89	621.2	2052.85	607.76
+A_92_P037834	614.76	480	159.36	366.3	294.97	122.92	322.5	168.7	350.87	555.45	228.25	924.42	.	.	733.53	1406.06	471.19	291.21	599.91	1184.39	1811.05	481.8	2288.62	771.68	.	.	776.6	267.51	936.66	335.22	.	.	.	.	407.66	552.37	363.69	640.53	605.49	212.99	322.26	233.7	359.58	180.01	1448.65	1968.31	348.1	1787.13	.	.	252.92	286.18	365.86	299.67	439.85	195.04	251.41	155.69	447.4	922.52	616.42	278.46	469.08	406.14	.	.	.	.	.	.	1544.27	829.77	789.32	314.05	1940.39	573.41	1188.84	1069.96	416.56	850.32	1126.01	136.73	684.91	262.46	1301.09	404.64	.	.	517.48	314.27	439.91	312.15	432.45	857.77	599.45	406.9	.	.	563.83	1052.15
+A_92_P037509	.	.	.	.	157.2	339.31	177.76	216.87	167.97	389.94	.	.	361.74	440.07	.	.	.	.	141.59	193.48	.	.	298.22	98.91	.	.	.	.	.	.	.	.	.	.	.	.	474.05	104.32	.	.	265.64	344.79	.	.	.	.	.	.	.	.	.	.	.	.	.	.	184.48	225.23	.	.	.	.	.	.	.	.	.	.	81.82	324.04	159.19	128.64	326.25	94.29	250.2	86.44	.	.	.	.	.	.	.	.	.	.	.	.	303.92	167.72	.	.	.	.	390.07	124.47	.	.	.	.
+A_92_P037035	1385.12	791.49	375.74	972.44	566.72	1136.6	692.64	395.81	537.73	821.82	643.84	566.22	1071.02	541.94	1680.95	2004.63	383.42	779.75	496.22	1138.04	993.13	586.42	925.9	467.27	419.34	767.3	1325.63	927.63	2382.87	1398.41	731.01	693.42	577.22	1434.44	1709.52	584.7	601.51	1118.4	1566.44	283.84	165.7	612.32	1359.47	319.07	1163.17	4658.47	1019.44	813.34	887.19	1743.35	1648.64	533.28	699.33	447.82	931.22	517.95	665.55	341.87	754.27	1386.56	1235.85	583.05	1174.4	531.88	.	.	.	.	1029.62	612.14	1463.99	701.39	819.65	520.84	1452.92	1772.76	3964.91	817.77	392.82	1805.64	1920.01	384.42	1381.15	1157.34	3067.84	1553.18	537.23	565.3	1209.88	830.18	1898.84	557.04	2182.55	1310.4	548.53	722.11	675.48	468.94	720.57	1335.18
+A_92_P036877	799.28	939.06	727.02	1209.68	1847.99	775.6	288.31	270.58	494.41	889.64	873.03	1321.07	1111.45	1022.83	1545.7	2083.47	746.07	349.71	508.35	1253.53	1584.3	654.29	1093.3	638.98	778.89	883.46	752.2	767.14	1779.18	427.23	.	.	.	.	443.49	1768.67	833.91	437.6	719.94	715.83	574.77	783.37	441.88	305.04	1269.3	2758.96	971.84	1272.12	634.76	358.35	733.71	770.66	508.1	631.74	772.54	328.11	679.57	320.39	472.06	2269	602.58	441.86	1017.69	926.28	.	.	.	.	796.43	1127.55	1314.04	858.73	1064.51	360.01	941.3	772.42	1022.28	1185.29	911.06	759.69	931.43	672.8	917.17	1451.34	724.72	946.06	1320.09	782.91	903.17	755.9	516.06	396.13	457.3	1015.71	465.17	1144.43	281.76	546.66	1273.41	908.38
+A_92_P036723	.	.	.	.	.	.	214.95	159.26	130.76	178.45	265.89	220.27	.	.	.	.	282.1	219.72	204.9	179.84	254.69	300.6	173.81	191.32	.	.	.	.	.	.	.	.	.	.	.	.	.	.	155.74	260.45	251.73	230.09	.	.	.	.	.	.	.	.	.	.	.	.	.	.	214.72	262.26	.	.	.	.	.	.	.	.	.	.	281.56	124.42	.	.	.	.	204.43	185.07	.	.	.	.	.	.	.	.	.	.	.	.	233.71	292.11	.	.	129.64	156.01	217.89	199.59	.	.	.	.
+A_92_P036564	688.45	1036.72	829.29	1023.7	1124.77	1129.93	1344.41	1376.92	706.75	1064.56	805.5	1325.39	1422.2	2347.35	1116.96	544.53	1523.09	1358.2	1527.44	1409.87	1883.67	1993.77	1470.3	2089.67	2467.94	1244.11	619.43	718.9	865.05	2068.72	1815.05	775.96	1264.67	881.18	659.17	1082.76	973.36	344.52	566.44	813.6	2261.25	1590.47	294.79	1053.43	2433.67	1442.05	1269.95	1440.85	.	.	872.73	1821.32	925.74	1584.09	1137.02	1065.68	1498.58	625.33	1371.9	736.02	1291.02	1442.08	1470.73	730.02	243.99	430.01	.	.	1454.86	943.96	1207.53	1469.43	788.14	921.6	470.98	1923.57	301.86	1406.16	1101.23	835.82	476.27	1584.52	683.88	1746.45	541.21	718.65	1902.22	1810.05	935.15	856	589.43	1476.37	614.15	1182.36	886.17	1212.48	659.08	1212.01	1377.43	1264.51
+A_92_P036402	.	.	.	.	205.78	116.83	245.79	129.1	158.94	244.84	175.33	237.51	239.5	256.92	.	.	290.74	194.45	.	.	519.62	189.22	207.99	226.4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	192.59	281.57	.	.	.	.	.	.	231.54	276.58	.	.	.	.	.	.	.	.	.	.	.	.	132.24	236.38	.	.	.	.	.	.	.	.	164.17	104.86	285.28	230.22	220.39	191.88	187.62	276.29	272.61	217.36	.	.	.	.	.	.	.	.	226.03	328.24	126.41	186.82	131.66	286.51	212.36	173.64	.	.	.	.
+A_92_P036241	841.85	2197.26	2085.55	1763.91	2332.38	2291.68	1643.32	1567.36	2470.48	2161.4	2445.94	2515.19	2733.92	2122.02	2787.49	4813.41	1586.2	1618.55	1322.94	2099.28	2883.46	2490.3	1917.43	2032.65	2201.64	2263.6	1850.72	1110.89	2683.28	1840.16	1516.63	2834.64	2844.76	2313.01	2454.84	2552.41	2559.55	1081.76	2493.14	2069.69	1784.29	1532.65	642.74	1132.19	3563.78	3149.46	2412.15	2508.47	1849.12	1565.43	1652.9	1876.16	2263.8	1879.86	2475.94	2020.11	2356.92	2211.49	2102.42	3070.38	2207.57	2421.25	2238.1	2446.2	567.97	512.97	.	.	1773.26	1306.58	2085.71	1684.65	2159.45	1792.38	3104.79	2830.93	1209.97	2582.06	2462.47	2942.99	1360.03	1819.24	1325.41	2527.83	1531.68	3216.05	2065.34	2042.42	1334.74	2473.6	1584.24	2105.07	1698.06	2584.35	1919.43	2187.06	1601.91	1430.88	2272.29	2858.92
+A_92_P036076	337.24	192.57	145.39	1402.89	.	.	964.96	1708.51	304.95	1101.35	320.38	193.12	1451.14	167.94	.	.	96.3	800.87	139.18	136.44	183.73	2461.54	1073.34	178.39	1461.14	1085.66	983.5	342.4	.	.	.	.	.	.	1212.94	139.79	1725.86	347.78	200.02	1789.14	1055.94	1088.89	.	.	.	.	274.79	211.29	.	.	1228.12	238.49	.	.	1175.17	1067.33	948.86	147.82	.	.	1966.57	147.95	.	.	.	.	.	.	.	.	167.19	215.65	844.02	153.81	1247.11	154.19	263.84	1076.07	1221.1	155.34	234.24	234.2	.	.	.	.	.	.	1419.55	875.02	243.07	1164.98	357.29	184.37	1105.99	1185.83	1397.61	1008.11	1261.97	947.65
+A_92_P035602	276.08	399.48	427.32	431.95	481.33	551.25	330.95	433.98	207.05	484.45	454.93	355.93	502.47	230.41	370.61	223.59	359.18	491.33	450.79	298.18	475.73	828.33	343.42	440.98	408.26	456.47	.	.	434.11	429.5	.	.	.	.	250.09	539.26	767.69	216.45	508.12	211.16	250.49	448.41	221.92	273.95	535.28	748.74	840.81	596	413.63	358.58	238.65	317.79	445.08	335.93	278.49	228.52	221.47	537.13	448.46	397.44	194.18	507.01	582	375.24	.	.	.	.	296.56	326.66	470.05	461.32	213.76	257.86	407.43	220.57	474.38	212.31	.	.	289.05	409.87	381.11	613.75	254.07	408.43	.	.	304.34	512.02	443.96	419.09	506.78	393.27	523.28	499.06	492.48	215.27	172.49	560.17
+A_92_P035118	.	.	287.6	331.99	.	.	.	.	326.72	180.28	263.54	318.41	345.53	355.88	317.32	514.08	310.68	192.73	414.15	509.07	509.63	280.86	539.73	217.23	.	.	.	.	.	.	.	.	.	.	294.62	185.25	256.06	447.73	286.17	251.12	158.54	190.12	194.96	106.49	584.87	748.51	722.04	637.92	.	.	247.25	291.1	.	.	.	.	283.81	227.91	.	.	232.89	341.3	.	.	.	.	.	.	208.7	428.69	462.59	253.69	.	.	249.27	471.95	376.23	196.86	196.2	515.09	370.87	252.5	228.52	168.9	682.57	302.11	253.67	283.18	371.2	360.78	269.88	274.96	260.94	534.33	250.4	204.31	.	.	212.19	434.94
+A_92_P034955	855.74	780.62	904.92	896.73	755.68	577.51	861.74	795.06	802.74	1011.2	764.62	719.35	852.4	831.01	.	.	2061.52	1554.96	1461.83	1636.98	3265.39	1909.64	1913.44	1522.54	677.43	800.93	567.19	891.91	521.28	649.47	992.21	881.95	.	.	491.71	756.91	652.6	877.23	1048.87	809.13	906.27	990.88	539.09	841.48	1767.71	2031.15	690.51	975.18	467.13	505.51	465.47	714.89	540.58	656.98	717.77	738.66	528.63	534.43	653.26	661.8	597.78	760.44	550.59	840.06	.	.	.	.	1460.68	1550.99	1340.65	1474.77	676.07	662.09	767.4	747.21	636.01	1079.85	1060.81	755.07	488.41	484.53	573.07	753.02	628.96	781.58	547.29	670.84	503.26	659.41	849.42	896.81	742.25	943.1	815.67	736.61	457.19	467.19	720.08	655.16
+A_92_P034794	272.3	355.1	343.78	429.3	245.13	214.2	240.07	196.07	277.78	286.51	352.24	226.24	376.78	361.17	.	.	209.52	156.03	275.69	238.66	315.01	193.89	222.99	173.06	.	.	280.04	344.1	367.27	392.39	.	.	.	.	198.26	239.79	295.38	309.99	283.58	193.49	342.71	156.23	126.42	176.16	406.6	340.19	296.8	267.07	.	.	426.45	355.73	457.91	181.2	399.16	263.35	164.93	198.17	275.66	338.5	.	.	300.51	456.49	529.29	391.64	.	.	242.23	166.51	259.62	246.07	245.25	247.9	.	.	201.39	372.05	356.35	198.44	361.37	205.86	432.95	427.4	347.36	196.78	368.06	308	609.54	474.31	216.44	284.08	278.13	478.09	455.59	384.76	299.25	238.53	351.81	344.56
+A_92_P034308	188.32	231.11	.	.	287.39	127.43	.	.	184.48	217.8	95.91	303.01	256.13	171.32	.	.	187.66	141.42	165.74	237.05	.	.	169.38	214.18	.	.	.	.	.	.	.	.	.	.	.	.	112.78	187.69	290.05	229.06	.	.	.	.	.	.	353.46	370.46	.	.	.	.	.	.	.	.	140.47	344.61	216.62	286.09	192.19	258.79	.	.	.	.	.	.	.	.	.	.	.	.	197.25	191.65	.	.	.	.	147.3	115.12	.	.	185.4	210.3	251.58	186.42	357.39	181.16	149.78	154.5	.	.	.	.	.	.	.	.
+A_92_P033825	460.01	128.24	.	.	.	.	.	.	385.1	258.97	282.39	281.72	206.93	165.61	.	.	347.97	287.25	486.98	176.54	504.52	231.28	440.25	493.77	.	.	261.87	222.4	.	.	.	.	.	.	229.58	236.71	376.18	703.23	.	.	376.81	367.17	387.15	248.84	.	.	413.74	500.88	.	.	360.97	305.31	.	.	.	.	311.41	246.04	.	.	231.03	351.79	342.72	190.26	.	.	.	.	476.53	604.23	.	.	271.85	215.69	460.8	345.12	195.13	370.41	137.71	343.67	389.96	227.93	372.47	368.99	472.79	241.56	.	.	599.42	193	504.23	121.57	479.63	207.87	.	.	338.52	95.3	373.02	187.95
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/test-data/input/otraits.txt	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,1 @@
+NA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/test-data/input/phenotypeGenotype_etraits.inp.txt	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,699 @@
+#bycross
+-SampleSize 100
+-Cross Ri1
+-traits 1
+-otraits 0
+-missingtrait  .
+-case yes
+-TranslationTable
+AA	2	A
+Aa	1	*1
+aa	0	B
+A-	12	*2
+a-	10	*3
+--	-1	-
+-start markers
+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 
+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 - 
+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 
+B A B A A B 
+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 
+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 - 
+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 
+B A B A A B 
+umc1041               A A B B A A B A B B A B B A - A B A A A A B B A 
+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 
+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 
+B A B B A B 
+umc157a               A A B A B A B A A B B - B A A A B - B A A A A A 
+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 
+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 
+B A B B B B 
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Binary file split_15/test-data/output/._parameters.txt has changed
Binary file split_15/test-data/output/._qtlcart1.inp has changed
Binary file split_15/test-data/output/._qtlcart10.inp has changed
Binary file split_15/test-data/output/._qtlcart11.inp has changed
Binary file split_15/test-data/output/._qtlcart12.inp has changed
Binary file split_15/test-data/output/._qtlcart13.inp has changed
Binary file split_15/test-data/output/._qtlcart14.inp has changed
Binary file split_15/test-data/output/._qtlcart15.inp has changed
Binary file split_15/test-data/output/._qtlcart2.inp has changed
Binary file split_15/test-data/output/._qtlcart3.inp has changed
Binary file split_15/test-data/output/._qtlcart4.inp has changed
Binary file split_15/test-data/output/._qtlcart5.inp has changed
Binary file split_15/test-data/output/._qtlcart6.inp has changed
Binary file split_15/test-data/output/._qtlcart7.inp has changed
Binary file split_15/test-data/output/._qtlcart8.inp has changed
Binary file split_15/test-data/output/._qtlcart9.inp has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/test-data/output/parameters.txt	Fri Mar 18 05:48:30 2016 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/test-data/output/qtlcart1.inp	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,692 @@
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+-stop traits
+-quit
+-end
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/test-data/output/qtlcart10.inp	Fri Mar 18 05:48:30 2016 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+- B B A B B 
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+-stop traits
+-quit
+-end
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_15/test-data/output/qtlcart2.inp	Fri Mar 18 05:48:30 2016 -0400
@@ -0,0 +1,692 @@
+#bycross
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+A_92_P028042	672.2	581.52	734	640.4	477.57	392.32	617.9	783.12	529.08	485.62	731.3	441.44	555.09	645.07	.	.	494.39	982.64	576.33	636.07	1152.67	957.18	1008.05	648.11	.	.	381.61	604.75	250.04	493.76	459.6	525.16	.	.	356.2	633.97	768.08	582.57	512.51	564.81	602.64	849.56	457.76	476.35	545.32	678.45	600.97	614.59	325.89	411.03	393.29	297.9	555.89	505.81	313.05	508.52	561.87	325.16	500.37	495.4	525.84	347.54	378.23	538.49	185.14	255.54	.	.	.	.	611.07	706.2	332.03	375.7	423.68	613.88	372.91	437.45	812.08	549.87	464.13	335.66	405.03	518.77	508.12	607.98	457.45	305.68	442.61	600.65	766.36	457.72	678.98	623.95	679.13	740.87	462.58	417.28	695.19	337.66
+-stop traits
+-quit
+-end