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1 import unittest
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2 import os
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3 import glob
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4 from commons.core.utils.FileUtils import FileUtils
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5 from commons.core.sql.DbFactory import DbFactory
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6 from commons.tools.GameXmlMaker import GameXmlMaker
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7
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8
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9 class Test_F_GameXmlMaker(unittest.TestCase):
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10
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11 def setUp(self):
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12 pass
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13
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14
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15 def tearDown(self):
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16 FileUtils.removeFilesByPattern("*gamexml")
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17
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18
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19 def test_run_as_script_step1(self):
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20 fastaFileName = "input.fa"
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21 self._writeFastaFile(fastaFileName)
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22
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23 cmd = "GameXmlMaker.py -f %s " % fastaFileName
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24 os.system(cmd)
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25
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26 lObsGameXmlNew = glob.glob("*.gamexml")
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27 self._writeStep1ExpectedXmls()
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28 self.assertTrue(len(lObsGameXmlNew) > 0)
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29 for obsGameXmlNew in lObsGameXmlNew:
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30 expGameXmlNew = "exp_%s" % obsGameXmlNew
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31 self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
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32
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33 os.remove(fastaFileName)
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34
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35 def test_run_as_script_step2(self):
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36 self._tableFileName = "annotation_tables.txt"
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37
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38 self._writeStep2InputTableFile()
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39 self._writeStep2InputXmls()
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40 self._writeStep2InputPathFile()
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41 self._writeStep2InputSetFile()
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42 self._writeStep2InputMapFile()
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43 self._createStep2Tables()
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44
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45 lObsGameXmlNew = glob.glob("*.gamexml")
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46
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47 cmd = "GameXmlMaker.py -t %s " % self._tableFileName
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48 os.system(cmd)
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49
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50 self._writeStep2ExpXmls()
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51
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52 self.assertTrue(len(lObsGameXmlNew) > 0)
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53 for obsGameXmlNew in lObsGameXmlNew:
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54 expGameXmlNew = "exp_%s" % obsGameXmlNew
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55 self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
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56
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57 os.remove("Test_F_GameXmlMaker_path.path")
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58 os.remove("Test_F_GameXmlMaker_set.set")
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59 os.remove("Test_F_GameXmlMaker_chk_map.map")
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60
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61 os.remove(self._tableFileName)
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62 os.system("ListAndDropTables.py -d Test_F_GameXmlMaker")
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63
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64 def test_run_step2(self):
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65 self._tableFileName = "annotation_tables.txt"
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66
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67 self._writeStep2InputTableFile()
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68 self._writeStep2InputXmls()
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69 self._writeStep2InputPathFile()
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70 self._writeStep2InputSetFile()
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71 self._writeStep2InputMapFile()
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72 self._createStep2Tables()
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73
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74 lObsGameXmlNew = glob.glob("*.gamexml")
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75
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76 iGameXmlMaker = GameXmlMaker(tablesFileName = self._tableFileName)
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77 iGameXmlMaker.run()
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78 self._writeStep2ExpXmls()
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79 self.assertTrue(len(lObsGameXmlNew) > 0)
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80 for obsGameXmlNew in lObsGameXmlNew:
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81 expGameXmlNew = "exp_%s" % obsGameXmlNew
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82 self.assertTrue(FileUtils.are2FilesIdentical(expGameXmlNew,obsGameXmlNew))
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83
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84 os.remove("Test_F_GameXmlMaker_path.path")
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85 os.remove("Test_F_GameXmlMaker_set.set")
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86 os.remove("Test_F_GameXmlMaker_chk_map.map")
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87
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88 os.remove(self._tableFileName)
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89 os.system("ListAndDropTables.py -d Test_F_GameXmlMaker")
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90
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91 def _writeFastaFile(self, inFileName):
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92 f = open(inFileName,'w')
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93 f.write('>seq1\n')
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94 f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
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95 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
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96 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA\n')
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97 f.write('>seq2\n')
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98 f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
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99 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
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100 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
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101 f.write('>seq3\n')
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102 f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n')
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103 f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n')
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104 f.write('>seq4\n')
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105 f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
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106 f.write('CAGGAATCATGAAGGGTACGACTGTTCG\n')
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107 f.close()
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108
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109 def _writeStep1ExpectedXmls(self):
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110 f = open("exp_seq1.gamexml", 'w')
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111 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
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112 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
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113 f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>')
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114 f.close()
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115 f = open("exp_seq2.gamexml", 'w')
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116 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
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117 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
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118 f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>')
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119 f.close()
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120 f = open("exp_seq3.gamexml", 'w')
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121 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
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122 f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
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123 f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>')
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124 f.close()
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125 f = open("exp_seq4.gamexml", 'w')
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126 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
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127 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
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128 f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>')
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129 f.close()
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130
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131 def _createStep2Tables(self):
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132 iDb = DbFactory.createInstance()
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133 iDb.createTable("Test_F_GameXmlMaker_set", "set", "Test_F_GameXmlMaker_set.set", True)
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134 iDb.createTable("Test_F_GameXmlMaker_chk_map", "map", "Test_F_GameXmlMaker_chk_map.map", True)
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135 iDb.createTable("Test_F_GameXmlMaker_path", "path", "Test_F_GameXmlMaker_path.path", True)
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136 iDb.close()
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137
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138 def _writeStep2InputXmls(self):
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139 f = open("seq1.gamexml", 'w')
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140 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
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141 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
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142 f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position></game>')
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143 f.close()
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144 f = open("seq2.gamexml", 'w')
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145 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
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146 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
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147 f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position></game>')
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148 f.close()
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149 f = open("seq3.gamexml", 'w')
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150 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
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151 f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
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152 f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position></game>')
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153 f.close()
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154 f = open("seq4.gamexml", 'w')
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155 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
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156 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
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157 f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position></game>')
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158 f.close()
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159
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160 def _writeStep2InputPathFile(self):
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161 f = open("Test_F_GameXmlMaker_path.path", 'w')
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162 f.write("1\tseq1\t1\t10\tTE1\t1\t10\t0\t550\t80.7\n")
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163 f.write("2\tseq1\t15\t50\tTE1\t12\t47\t0\t770\t90.8\n")
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164 f.write("2\tseq1\t55\t70\tTE1\t50\t65\t0\t5410\t97.7\n")
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165 f.write("3\tseq1\t75\t80\tTE2\t10\t15\t0\t8710\t60.0\n")
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166 f.write("4\tseq2\t1\t10\tTE2\t20\t30\t0\t5410\t75.7\n")
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167 f.write("5\tseq3\t1\t120\tTE2\t450\t550\t0\t5410\t75.7\n")
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168 f.close()
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169
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170 def _writeStep2InputSetFile(self):
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171 f = open("Test_F_GameXmlMaker_set.set", 'w')
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172 f.write("1\tseq1\tseq1\t1\t10\n")
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173 f.write("2\tseq1\tseq1\t15\t50\n")
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174 f.write("3\tseq1\tseq1\t75\t80\n")
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175 f.write("4\tseq2\tseq2\t1\t10\n")
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176 f.write("5\tseq3\tseq3\t1\t120\n")
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177 f.close()
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178
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179 def _writeStep2InputMapFile(self):
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180 f = open("Test_F_GameXmlMaker_chk_map.map", 'w')
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181 f.write("chunk1\tseq1\t1\t200000\n")
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182 f.write("chunk2\tseq1\t190001\t390000\n")
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183 f.write("chunk3\tseq3\t380001\t580000\n")
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184 f.write("chunk4\tseq4\t570001\t770000\n")
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185 f.write("chunk5\tseq5\t760001\t960000\n")
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186 f.write("chunk6\tseq6\t950001\t1150000\n")
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187 f.write("chunk7\tseq7\t1140001\t1281640\n")
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188 f.close()
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189
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190 def _writeStep2ExpXmls(self):
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191 f = open("exp_seq1.gamexml", 'w')
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192 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq1"><name>seq1</name>')
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193 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACA</residues>')
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194 f.write('</seq><map_position><arm>seq1</arm><span><start>1</start><end>165</end></span></map_position>')
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195 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="1"><name>TE1::1</name>')
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196 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship><seq_relationship seq="TE1::1" type="subject"><span>')
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197 f.write('<start>1</start><end>10</end></span></seq_relationship><score>80.7</score></result_span></result_set><result_set id="2"><name>TE1::2</name><result_span>')
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198 f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship><seq_relationship seq="TE1::2" type="subject"><span><start>12</start>')
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199 f.write('<end>47</end></span></seq_relationship><score>90.8</score></result_span><result_span><seq_relationship seq="seq1" type="query"><span><start>55</start><end>70</end></span></seq_relationship>')
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200 f.write('<seq_relationship seq="TE1::2" type="subject"><span><start>50</start><end>65</end></span></seq_relationship><score>97.7</score></result_span></result_set><result_set id="3"><name>TE2::3</name>')
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201 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship><seq_relationship seq="TE2::3" type="subject"><span><start>10</start><end>15</end></span></seq_relationship>')
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202 f.write('<score>60.0</score></result_span></result_set></computational_analysis>')
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203 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database>')
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204 f.write('<result_set id="1"><name>seq1::1</name><result_span>')
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205 f.write('<seq_relationship seq="seq1" type="query"><span><start>1</start><end>10</end></span></seq_relationship>')
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206 f.write('<seq_relationship seq="seq1::1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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207 f.write('<score>0</score></result_span></result_set>')
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208 f.write('<result_set id="2"><name>seq1::2</name><result_span>')
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209 f.write('<seq_relationship seq="seq1" type="query"><span><start>15</start><end>50</end></span></seq_relationship>')
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210 f.write('<seq_relationship seq="seq1::2" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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211 f.write('<score>0</score></result_span></result_set>')
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212 f.write('<result_set id="3"><name>seq1::3</name><result_span>')
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213 f.write('<seq_relationship seq="seq1" type="query"><span><start>75</start><end>80</end></span></seq_relationship>')
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214 f.write('<seq_relationship seq="seq1::3" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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215 f.write('<score>0</score></result_span></result_set></computational_analysis>')
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216 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
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217 f.write('<result_set id="-1"><name>chunk1::-1</name>')
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218 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>1</start><end>200000</end></span></seq_relationship>')
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219 f.write('<seq_relationship seq="chunk1::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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220 f.write('<score>0</score></result_span></result_set>')
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221 f.write('<result_set id="-1"><name>chunk2::-1</name>')
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222 f.write('<result_span><seq_relationship seq="seq1" type="query"><span><start>190001</start><end>390000</end></span></seq_relationship>')
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223 f.write('<seq_relationship seq="chunk2::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship><score>0</score></result_span></result_set></computational_analysis></game>')
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224 f.close()
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225
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226 f = open("exp_seq2.gamexml", 'w')
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227 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq2"><name>seq2</name>')
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228 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAATCAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT</residues>')
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229 f.write('</seq><map_position><arm>seq2</arm><span><start>1</start><end>180</end></span></map_position>')
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230 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="4"><name>TE2::4</name>')
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231 f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span>')
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232 f.write('</seq_relationship><seq_relationship seq="TE2::4" type="subject"><span><start>20</start><end>30</end></span></seq_relationship>')
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233 f.write('<score>75.7</score></result_span></result_set></computational_analysis>')
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234 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="4"><name>seq2::4</name>')
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235 f.write('<result_span><seq_relationship seq="seq2" type="query"><span><start>1</start><end>10</end></span></seq_relationship>')
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236 f.write('<seq_relationship seq="seq2::4" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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237 f.write('<score>0</score></result_span></result_set></computational_analysis>')
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238 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database></computational_analysis></game>')
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239 f.close()
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240
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241 f = open("exp_seq3.gamexml", 'w')
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242 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq3"><name>seq3</name>')
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243 f.write('<residues>CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAAGGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA</residues>')
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244 f.write('</seq><map_position><arm>seq3</arm><span><start>1</start><end>120</end></span></map_position>')
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245 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database><result_set id="5"><name>TE2::5</name>')
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246 f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span>')
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247 f.write('</seq_relationship><seq_relationship seq="TE2::5" type="subject"><span><start>450</start><end>550</end></span></seq_relationship>')
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248 f.write('<score>75.7</score></result_span></result_set></computational_analysis>')
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249 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database><result_set id="5"><name>seq3::5</name>')
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250 f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>1</start><end>120</end></span></seq_relationship>')
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251 f.write('<seq_relationship seq="seq3::5" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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252 f.write('<score>0</score></result_span></result_set></computational_analysis>')
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253 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
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254 f.write('<result_set id="-1"><name>chunk3::-1</name>')
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255 f.write('<result_span><seq_relationship seq="seq3" type="query"><span><start>380001</start><end>580000</end></span></seq_relationship>')
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256 f.write('<seq_relationship seq="chunk3::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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257 f.write('<score>0</score></result_span></result_set></computational_analysis></game>')
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258 f.close()
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259
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260 f = open("exp_seq4.gamexml", 'w')
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261 f.write('<?xml version="1.0" ?><game><seq focus="true" id="seq4"><name>seq4</name>')
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262 f.write('<residues>TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATGCAGGAATCATGAAGGGTACGACTGTTCG</residues>')
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263 f.write('</seq><map_position><arm>seq4</arm><span><start>1</start><end>88</end></span></map_position>')
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264 f.write('<computational_analysis><program>Test_F_GameXmlMaker_path</program><database>db</database></computational_analysis>')
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265 f.write('<computational_analysis><program>Test_F_GameXmlMaker_set</program><database>db</database></computational_analysis>')
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266 f.write('<computational_analysis><program>Test_F_GameXmlMaker_chk_map</program><database>db</database>')
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267 f.write('<result_set id="-1"><name>chunk4::-1</name>')
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268 f.write('<result_span><seq_relationship seq="seq4" type="query"><span><start>570001</start><end>770000</end></span></seq_relationship>')
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269 f.write('<seq_relationship seq="chunk4::-1" type="subject"><span><start>-1</start><end>-1</end></span></seq_relationship>')
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270 f.write('<score>0</score></result_span></result_set></computational_analysis></game>')
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271 f.close()
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272
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273 def _writeStep2InputTableFile(self):
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274 f = open(self._tableFileName,'w')
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275 f.write("Test_F_GameXmlMaker_path\tpath\tTest_F_GameXmlMaker_path\n")
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276 f.write("Test_F_GameXmlMaker_set\tset\tTest_F_GameXmlMaker_set\n")
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277 f.write("Test_F_GameXmlMaker_chk_map\tmap\tTest_F_GameXmlMaker_chk_map")
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278 f.close()
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279
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280 if __name__ == "__main__":
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281 unittest.main() |
