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1 #!/usr/bin/env python
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2
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3 """
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4 Author: George Weingart
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5 Description: Prepare parameters to call micropita
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6 """
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7
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8 #####################################################################################
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9 #Copyright (C) <2012>
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10 #
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11 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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12 #this software and associated documentation files (the "Software"), to deal in the
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13 #Software without restriction, including without limitation the rights to use, copy,
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14 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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15 #and to permit persons to whom the Software is furnished to do so, subject to
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16 #the following conditions:
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17 #
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18 #The above copyright notice and this permission notice shall be included in all copies
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19 #or substantial portions of the Software.
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20 #
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21 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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22 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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23 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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24 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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25 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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26 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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27 #####################################################################################
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28
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29 __author__ = "George Weingart"
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30 __copyright__ = "Copyright 2012"
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31 __credits__ = ["George Weingart"]
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32 __license__ = "MIT"
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33 __maintainer__ = "George Weingart"
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34 __email__ = "george.weingart@gmail.com"
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35 __status__ = "Development"
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36
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37 import argparse
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38 from cStringIO import StringIO
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39 import sys,string,time
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40 import os
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41 from time import gmtime, strftime
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42 from pprint import pprint
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43 import subprocess
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44 import blist
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45 import shlex
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46 import tempfile
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47
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48 ##################################################################################
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49 # Modification by George Weingart 5/6/2014 #
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50 # Using subprocess to invoke the calls to Micropita #
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51 # and allocating the temporary file using trmpfile #
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52 ##################################################################################
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53
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54
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55
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56
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57 ##################################################################################
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58 # Decode Parms #
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59 ##################################################################################
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60 def read_params(x):
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61 parser = argparse.ArgumentParser(description='Micropita Annotate Argparser')
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62 parser.add_argument('--input', action="store",dest='inputname')
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63 parser.add_argument('--output', action="store",dest='outputname')
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64 parser.add_argument('-m', action="store",dest='MParameter')
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65 parser.add_argument('-n', action="store",dest='NSamples')
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66 parser.add_argument('--lastmeta', action="store",dest='lastmeta')
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67 parser.add_argument('--stratify_value', action="store",dest='stratify_value')
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68
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69
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70 try:
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71 parser.add_argument('--feature_method', action="store",dest='feature_method')
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72 except:
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73 pass
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74 try:
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75 parser.add_argument('--targets', action="store",dest='targets')
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76 except:
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77 pass
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78 try:
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79 parser.add_argument('--label_value', action="store",dest='label_value')
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80 except:
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81 pass
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82 return parser
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83
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84
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85 ##################################################################################
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86 # Main Program #
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87 ##################################################################################
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88 parser = read_params( sys.argv )
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89 results = parser.parse_args()
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90 #root_dir = os.environ.get('micropita_SCRIPT_PATH')
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91 root_dir = os.path.dirname(os.path.realpath(__file__)) #Find the current directory where the program resides GW 20160810
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92
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93
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94 fname = results.inputname
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95 input_file = open(fname,'rU')
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96 input_lines = input_file.readlines()
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97 input_file.close()
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98 table_lines = []
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99 for x in input_lines:
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100 first_column = x.split('\t')[0]
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101 table_lines.append(first_column)
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102
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103
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104
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105 FileTimeStamp = strftime("%Y%m%d%H%M%S", gmtime())
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106 LastMetaInt = 0
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107 if results.lastmeta and not results.lastmeta == "None":
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108 LastMetaInt = int(results.lastmeta) - 1
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109
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110 StratifyValueInt = 0
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111 if results.stratify_value and not results.stratify_value == "None":
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112 StratifyValueInt = int(results.stratify_value) - 2
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113
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114 LabelValueInt = 0
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115 if results.label_value and not results.label_value == "None":
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116 LabelValueInt = int(results.label_value) - 1
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117
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118 stratify_string = ""
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119 q = '"'
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120 if not results.stratify_value == '1':
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121 stratify_string = " --stratify " + q + table_lines[StratifyValueInt] + q + " "
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122
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123 if results.MParameter == "features":
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124 TBTargets = list()
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125 TableTargets = results.targets.split(',')
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126 for t in TableTargets:
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127 tb_entry = int(t) + LastMetaInt
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128 TBTargets.append(int(tb_entry))
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129
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130
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131 OutTargetsFile = tempfile.NamedTemporaryFile('w', delete=False )
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132 TempTargetsFileName = OutTargetsFile.name
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133 indx = -1
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134 for c in table_lines:
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135 indx+=1
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136 if indx in TBTargets:
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137 OutputString = table_lines[indx] + "\n"
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138 OutTargetsFile.write(OutputString)
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139 OutTargetsFile.close()
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140 os_command = "python " + \
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141 root_dir + \
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142 "/MicroPITA.py "+\
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143 "--lastmeta " + table_lines[LastMetaInt]+ " " +\
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144 "--feature_method " + results.feature_method + " " + \
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145 "--target " + TempTargetsFileName + " " +\
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146 "-m " + results.MParameter + " " + \
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147 "-n " + results.NSamples + " " +\
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148 stratify_string + " " +\
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149 results.inputname + " " +\
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150 results.outputname
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151 #print os_command
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152 os.system(os_command)
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153 argsx = shlex.split(os_command) #Split the command
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154 try:
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155 subprocess.check_call(argsx , shell=False)
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156 except:
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157 print "The call to micropita failed============="
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158 sys.exit(0)
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159
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160
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161
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162 if results.MParameter == "representative"\
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163 or results.MParameter == "diverse"\
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164 or results.MParameter == "extreme":
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165 os_command = "python " + \
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166 root_dir + \
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167 "/MicroPITA.py "+\
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168 "--lastmeta " + table_lines[LastMetaInt]+ " " +\
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169 "-m " + results.MParameter + " " + \
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170 "-n " + results.NSamples + " " +\
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171 stratify_string + " " + \
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172 results.inputname + " " +\
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173 results.outputname
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174 argsx = shlex.split(os_command) #Split the command
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175 try:
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176 ###os.system(os_command)
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177 subprocess.check_call(argsx , shell=False)
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178 except:
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179 print "The call to micropita failed============="
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180 sys.exit(0)
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181
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182
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183
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184
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185 if results.MParameter == "distinct"\
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186 or results.MParameter == "discriminant":
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187 os_command = "python " + \
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188 root_dir + \
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189 "/MicroPITA.py "+\
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190 "--lastmeta " + table_lines[LastMetaInt]+ " " +\
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191 "--label " + table_lines[LastMetaInt]+ " " +\
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192 "-m " + results.MParameter + " " + \
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193 "-n " + results.NSamples + " " +\
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194 stratify_string + " " + \
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195 results.inputname + " " +\
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196 results.outputname
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197 #print os_command
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198 argsx = shlex.split(os_command) #Split the command
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199 try:
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200 subprocess.check_call(argsx , shell=False)
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201 except:
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202 print "The call to micropita failed============="
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203 sys.exit(0)
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