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1 import unittest
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4 from SMART.Java.Python.misc import Utils
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5 from SMART.Java.Python.ncList.FindOverlaps_naif import FindOverlaps_naif
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6 from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
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7
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8 class Test_F_FindOverlaps_naif(unittest.TestCase):
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9
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10 def setUp(self):
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11 self._inputRefGff3FileName = 'ref.gff3'
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12 self._writeGFF3File(self._inputRefGff3FileName)
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13 self._inputQueryGff3FileName = 'query.gff3'
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14 self._writeQueryGff3File(self._inputQueryGff3FileName)
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15 self._outputGff3FileName = 'output.gff3'
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16 self._expOutputFileName = 'expOutGff3.gff3'
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17 self._iFON = FindOverlaps_naif(self._inputRefGff3FileName, self._inputQueryGff3FileName)
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18 self._iFON.setOutputGff3FileName(self._outputGff3FileName)
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19
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20 def tearDown(self):
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21 os.remove(self._inputRefGff3FileName)
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22 os.remove(self._inputQueryGff3FileName)
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23 os.remove(self._outputGff3FileName)
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24 os.remove(self._expOutputFileName)
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25
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26 def test_run_general(self):
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27 self._iFON.run()
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28 self._iFON.close()
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29 self._writeExpOutFile_general(self._expOutputFileName)
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30 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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31
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32 def test_run_general_asScript(self):
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33 cmd = 'python ../FindOverlaps_naif.py -i %s -j %s -o %s' % (self._inputRefGff3FileName, self._inputQueryGff3FileName, self._outputGff3FileName)
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34 os.system(cmd)
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35 self._writeExpOutFile_general(self._expOutputFileName)
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36 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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37
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38 def test_run_overlap_special_case(self):
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39 inputQueryGff3FileName = 'query2.gff3'
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40 self._writeQueryGff3File2(inputQueryGff3FileName)
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41 iFON = FindOverlaps_naif(self._inputRefGff3FileName, inputQueryGff3FileName)
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42 iFON.setOutputGff3FileName(self._outputGff3FileName)
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43 iFON.run()
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44 iFON.close()
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45 self._writeExpOutFile_special_case(self._expOutputFileName)
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46 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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47 os.remove(inputQueryGff3FileName)
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48
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49 def test_run_overlap_special_case_asScript(self):
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50 inputQueryGff3FileName = 'query2.gff3'
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51 self._writeQueryGff3File2(inputQueryGff3FileName)
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52 cmd = 'python ../FindOverlaps_naif.py -i %s -j %s -o %s' % (self._inputRefGff3FileName, inputQueryGff3FileName, self._outputGff3FileName)
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53 os.system(cmd)
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54 self._writeExpOutFile_special_case(self._expOutputFileName)
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55 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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56 os.remove(inputQueryGff3FileName)
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57
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58 def test_case_2(self):
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59 inputRefGff3FileName = 'ref_case2.gff3'
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60 iMock = MockFindOverlapsWithServeralIntervals_case2()
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61 iMock.write(inputRefGff3FileName)
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62 inputQueryGff3FileName = 'query_case2.gff3'
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63 self._writeQueryGff3File_case2(inputQueryGff3FileName)
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64 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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65 iFON.setOutputGff3FileName(self._outputGff3FileName)
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66 iFON.run()
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67 iFON.close()
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68 self._writeExpOutFile_case2(self._expOutputFileName)
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69 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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70 os.remove(inputQueryGff3FileName)
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71 os.remove(inputRefGff3FileName)
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72
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73 def test_case_3(self):
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74 inputRefGff3FileName = 'ref_case3.gff3'
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75 iMock = MockFindOverlapsWithServeralIntervals_case3()
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76 iMock.write(inputRefGff3FileName)
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77 inputQueryGff3FileName = 'query_case3.gff3'
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78 self._writeQueryGff3File_case3(inputQueryGff3FileName)
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79 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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80 iFON.setOutputGff3FileName(self._outputGff3FileName)
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81 iFON.run()
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82 iFON.close()
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83 self._writeExpOutFile_case3(self._expOutputFileName)
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84 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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85 os.remove(inputQueryGff3FileName)
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86 os.remove(inputRefGff3FileName)
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87
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88 def test_case_4(self):
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89 inputRefGff3FileName = 'ref_case4.gff3'
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90 iMock = MockFindOverlapsWithServeralIntervals_case4_5()
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91 iMock.write(inputRefGff3FileName)
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92 inputQueryGff3FileName = 'query_case4.gff3'
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93 self._writeQueryGff3File_case4(inputQueryGff3FileName)
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94 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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95 iFON.setOutputGff3FileName(self._outputGff3FileName)
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96 iFON.run()
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97 iFON.close()
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98 self._writeExpOutFile_case4(self._expOutputFileName)
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99 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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100 os.remove(inputQueryGff3FileName)
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101 os.remove(inputRefGff3FileName)
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102
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103 def test_case_5(self):
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104 inputRefGff3FileName = 'ref_case5.gff3'
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105 iMock = MockFindOverlapsWithServeralIntervals_case4_5()
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106 iMock.write(inputRefGff3FileName)
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107 inputQueryGff3FileName = 'query_case5.gff3'
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108 self._writeQueryGff3File_case5(inputQueryGff3FileName)
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109 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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110 iFON.setOutputGff3FileName(self._outputGff3FileName)
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111 iFON.run()
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112 iFON.close()
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113 self._writeExpOutFile_case5(self._expOutputFileName)
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114 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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115 os.remove(inputQueryGff3FileName)
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116 os.remove(inputRefGff3FileName)
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117
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118 def test_case_6(self):
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119 inputRefGff3FileName = 'ref_case6.gff3'
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120 iMock = MockFindOverlapsWithServeralIntervals_case6_7()
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121 iMock.write(inputRefGff3FileName)
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122 inputQueryGff3FileName = 'query_case6.gff3'
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123 self._writeQueryGff3File_case6(inputQueryGff3FileName)
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124 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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125 iFON.setOutputGff3FileName(self._outputGff3FileName)
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126 iFON.run()
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127 iFON.close()
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128 self._writeExpOutFile_case6(self._expOutputFileName)
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129 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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130 os.remove(inputQueryGff3FileName)
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131 os.remove(inputRefGff3FileName)
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132
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133 def test_case_7(self):
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134 inputRefGff3FileName = 'ref_case7.gff3'
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135 iMock = MockFindOverlapsWithServeralIntervals_case6_7()
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136 iMock.write(inputRefGff3FileName)
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137 inputQueryGff3FileName = 'query_case7.gff3'
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138 self._writeQueryGff3File_case7(inputQueryGff3FileName)
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139 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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140 iFON.setOutputGff3FileName(self._outputGff3FileName)
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141 iFON.run()
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142 iFON.close()
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143 self._writeExpOutFile_case7(self._expOutputFileName)
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144 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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145 os.remove(inputQueryGff3FileName)
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146 os.remove(inputRefGff3FileName)
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147
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148 def test_case_8(self):
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149 inputRefGff3FileName = 'ref_case8.gff3'
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150 iMock = MockFindOverlapsWithServeralIntervals_case8()
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151 iMock.write(inputRefGff3FileName)
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152 inputQueryGff3FileName = 'query_case8.gff3'
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153 self._writeQueryGff3File_case8(inputQueryGff3FileName)
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154 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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155 iFON.setOutputGff3FileName(self._outputGff3FileName)
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156 iFON.run()
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157 iFON.close()
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158 self._writeExpOutFile_case8(self._expOutputFileName)
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159 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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160 os.remove(inputQueryGff3FileName)
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161 os.remove(inputRefGff3FileName)
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162
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163 def test_case_9(self):
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164 inputRefGff3FileName = 'ref_case9.gff3'
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165 iMock = MockFindOverlapsWithServeralIntervals_case9()
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166 iMock.write(inputRefGff3FileName)
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167 inputQueryGff3FileName = 'query_case9.gff3'
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168 self._writeQueryGff3File_case9(inputQueryGff3FileName)
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169 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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170 iFON.setOutputGff3FileName(self._outputGff3FileName)
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171 iFON.run()
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172 iFON.close()
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173 self._writeExpOutFile_case9(self._expOutputFileName)
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174 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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175 os.remove(inputQueryGff3FileName)
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176 os.remove(inputRefGff3FileName)
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177
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178 def test_case_10(self):
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179 inputRefGff3FileName = 'ref_case10.gff3'
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180 iMock = MockFindOverlapsWithServeralIntervals_case10()
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181 iMock.write(inputRefGff3FileName)
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182 inputQueryGff3FileName = 'query_case10.gff3'
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183 self._writeQueryGff3File_case10(inputQueryGff3FileName)
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184 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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185 iFON.setOutputGff3FileName(self._outputGff3FileName)
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186 iFON.run()
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187 iFON.close()
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188 self._writeExpOutFile_case10(self._expOutputFileName)
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189 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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190 os.remove(inputQueryGff3FileName)
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191 os.remove(inputRefGff3FileName)
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192
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193 def test_case_11(self):
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194 inputRefGff3FileName = 'ref_case11.gff3'
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195 iMock = MockFindOverlapsWithServeralIntervals_case11()
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196 iMock.write(inputRefGff3FileName)
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197 inputQueryGff3FileName = 'query_case11.gff3'
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198 self._writeQueryGff3File_case11(inputQueryGff3FileName)
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199 iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
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200 iFON.setOutputGff3FileName(self._outputGff3FileName)
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201 iFON.run()
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202 iFON.close()
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203 self._writeExpOutFile_case11(self._expOutputFileName)
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204 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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205 os.remove(inputQueryGff3FileName)
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206 os.remove(inputRefGff3FileName)
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207
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208 def _writeExpOutFile_special_case(self, fileName):
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209 f = open(fileName, 'w')
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210 f.write("chr1 S-MART test2 1250 1300 781 + . nbOverlaps=1;overlapsWith=test2.7;ID=query_2;Name=test1.2\n")
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211 f.close()
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212
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213 def _writeExpOutFile_general(self, fileName):
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214 f = open(fileName, 'w')
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215 f.write("""chr1 S-MART test1.1 25 150 126 + . nbOverlaps=3;overlapsWith=test2.1--test2.2--test2.3;ID=query_1;Name=test1.1
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216 chr1 S-MART test1.2 70 850 781 + . nbOverlaps=6;overlapsWith=test2.1--test2.2--test2.3--test2.4--test2.5--test2.6;ID=query_2;Name=test1.2
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217 chr1 S-MART test1.3 550 850 201 + . nbOverlaps=4;overlapsWith=test2.1--test2.3--test2.5--test2.6;ID=query_3;Name=test1.3
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218 chr1 S-MART test1.4 925 1025 101 + . nbOverlaps=2;overlapsWith=test2.1--test2.5;ID=query_4;Name=test1.4
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219 chr1 S-MART test1.5 1201 1210 10 + . nbOverlaps=1;overlapsWith=test2.7;ID=query_5;Name=test1.5
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220 """)
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221 f.close()
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222
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223 def _writeExpOutFile_cas_1(self, fileName):
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224 f = open(fileName, 'w')
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225 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tOverlapWith=query_3;ID=test2.1;Name=test2.1\n")
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226 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tOverlapWith=query_3;ID=test2.3;Name=test2.3\n")
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227 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tOverlapWith=query_3;ID=test2.5;Name=test2.5\n")
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228 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tOverlapWith=query_3;ID=test2.6;Name=test2.6\n")
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229 f.close()
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230
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231 def _writeExpOutFile_cas_2(self, fileName):
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232 f = open(fileName, 'w')
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233 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tOverlapWith=query_2;Name=test2.1\n")
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234 f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tOverlapWith=query_2;Name=test2.2\n")
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235 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tOverlapWith=query_2;Name=test2.3\n")
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236 f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tOverlapWith=query_2;Name=test2.4\n")
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237 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tOverlapWith=query_2;Name=test2.5\n")
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238 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tOverlapWith=query_2;Name=test2.6\n")
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239 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tOverlapWith=query_3;Name=test2.1\n")
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240 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tOverlapWith=query_3;Name=test2.3\n")
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241 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tOverlapWith=query_3;Name=test2.5\n")
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242 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tOverlapWith=query_3;Name=test2.6\n")
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243 f.close()
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244
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245 def _writeExpOutFile_all_overlap(self, fileName):
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246 f = open(fileName, 'w')
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247 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tOverlapWith=query_2;ID=test2.1;Name=test2.1\n")
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248 f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tOverlapWith=query_2;D=test2.2;Name=test2.2\n")
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249 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tOverlapWith=query_2;ID=test2.3;Name=test2.3\n")
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250 f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tOverlapWith=query_2;ID=test2.4;Name=test2.4\n")
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251 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tOverlapWith=query_2;ID=test2.5;Name=test2.5\n")
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252 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tOverlapWith=query_2;ID=test2.6;Name=test2.6\n")
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253 f.close()
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254
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255 def _writeExpOutFile_overlap_to_children(self, fileName):
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256 f = open(fileName, 'w')
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257 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tOverlapWith=query_3;ID=test2.1;Name=test2.1\n")
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258 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tOverlapWith=query_3;ID=test2.3;Name=test2.3\n")
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259 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tOverlapWith=query_3;ID=test2.5;Name=test2.5\n")
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260 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tOverlapWith=query_3;ID=test2.6;Name=test2.6\n")
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261 f.close()
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262
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263 def _writeExpOutFile_not_overlap_to_children(self, fileName):
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264 f = open(fileName, 'w')
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265 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tOverlapWith=query_1;ID=test2.1;Name=test2.1\n")
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266 f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tOverlapWith=query_1;ID=test2.2;Name=test2.2\n")
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267 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tOverlapWith=query_1;ID=test2.3;Name=test2.3\n")
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268 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tOverlapWith=query_4;ID=test2.1;Name=test2.1\n")
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269 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tOverlapWith=query_4;ID=test2.5;Name=test2.5\n")
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270 f.close()
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271
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272 def _writeExpOutFile_no_overlap_right(self, fileName):
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273 f = open(fileName, 'w')
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274 f.close()
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275
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276 def _writeExpOutFile_one_overlap(self, fileName):
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277 f = open(fileName, 'w')
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278 f.write("chr1\tS-MART\ttest2.7\t1200\t1300\t101\t+\t.\tOverlapWith=query_5;ID=test2.7;Name=test2.7\n")
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279 f.close()
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280
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281 def _writeExpOutFile_case2(self, fileName):
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282 f = open(fileName, 'w')
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283 f.write("""chr1 S-MART test2.1 150 300 151 + . nbOverlaps=4;overlapsWith=test2.1--test2.2--test2.3--test2.4;ID=query_1;Name=test2.1
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284 chr1 S-MART test2.2 300 450 781 + . nbOverlaps=3;overlapsWith=test2.1--test2.2--test2.3;ID=query_2;Name=test2.2
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285 chr1 S-MART test2.3 480 800 321 + . nbOverlaps=1;overlapsWith=test2.1;ID=query_3;Name=test2.3
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286 chr1 S-MART test2.5 850 1000 151 + . nbOverlaps=1;overlapsWith=test2.5;ID=query_5;Name=test2.5
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287 """)
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288 f.close()
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289
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290 def _writeExpOutFile_case3(self, fileName):
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291 f = open(fileName, 'w')
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292 f.write("""chr1 S-MART test3.1 150 250 101 + . nbOverlaps=4;overlapsWith=test3.1--test3.2--test3.3--test3.4;ID=query_1;Name=test3.1
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293 chr1 S-MART test3.2 380 400 21 + . nbOverlaps=4;overlapsWith=test3.1--test3.2--test3.3--test3.5;ID=query_2;Name=test3.2
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294 chr1 S-MART test3.3 480 520 41 + . nbOverlaps=1;overlapsWith=test3.1;ID=query_3;Name=test3.3
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295 chr1 S-MART test3.5 900 950 51 + . nbOverlaps=1;overlapsWith=test3.6;ID=query_5;Name=test3.5
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296 """)
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297 f.close()
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298
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299 def _writeExpOutFile_case4(self, fileName):
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300 f = open(fileName, 'w')
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301 f.write("""chr1 S-MART test4.1 400 500 101 + . nbOverlaps=3;overlapsWith=test4.1--test4.2--test4.3;ID=query_1;Name=test4.1
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302 chr1 S-MART test4.2 450 600 151 + . nbOverlaps=3;overlapsWith=test4.1--test4.2--test4.3;ID=query_2;Name=test4.2
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303 chr1 S-MART test4.3 700 800 101 + . nbOverlaps=2;overlapsWith=test4.1--test4.2;ID=query_3;Name=test4.3
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304 """)
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305 f.close()
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306
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307 def _writeExpOutFile_case5(self, fileName):
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308 f = open(fileName, 'w')
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309 f.write("chr1 S-MART test5.1 850 950 101 + . nbOverlaps=1;overlapsWith=test4.1;ID=query_1;Name=test5.1\n")
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310 f.close()
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311
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312 def _writeExpOutFile_case6(self, fileName):
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313 f = open(fileName, 'w')
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314 f.write("""chr1 S-MART test6.1 200 300 101 + . nbOverlaps=2;overlapsWith=test6.1--test6.2;ID=query_1;Name=test6.1
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315 chr1 S-MART test6.2 800 900 101 + . nbOverlaps=2;overlapsWith=test6.1--test6.5;ID=query_2;Name=test6.2
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316 """)
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317 f.close()
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318
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319 def _writeExpOutFile_case7(self, fileName):
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320 f = open(fileName, 'w')
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321 f.write("""chr1 S-MART test7.1 530 550 21 + . nbOverlaps=1;overlapsWith=test6.1;ID=query_1;Name=test7.1
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322 chr1 S-MART test7.2 600 700 101 + . nbOverlaps=1;overlapsWith=test6.1;ID=query_2;Name=test7.2
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323 chr1 S-MART test7.3 650 900 251 + . nbOverlaps=2;overlapsWith=test6.1--test6.5;ID=query_3;Name=test7.3
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324 """)
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325 f.close()
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326
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327 def _writeExpOutFile_case8(self, fileName):
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328 f = open(fileName, 'w')
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329 f.write("""chr1 S-MART test8.1 500 600 101 + . nbOverlaps=1;overlapsWith=test8.1;ID=query_1;Name=test8.1
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330 chr1 S-MART test8.2 700 800 101 + . nbOverlaps=1;overlapsWith=test8.1;ID=query_2;Name=test8.2
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331 chr1 S-MART test8.3 900 1100 201 + . nbOverlaps=1;overlapsWith=test8.1;ID=query_3;Name=test8.3
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332 """)
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|
333 f.close()
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334
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335 def _writeExpOutFile_case9(self, fileName):
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336 f = open(fileName, 'w')
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337 f.write("""chr1 S-MART test9.1 400 500 101 + . nbOverlaps=1;overlapsWith=test9.1;ID=query_1;Name=test9.1
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338 chr1 S-MART test9.2 550 650 101 + . nbOverlaps=2;overlapsWith=test9.1--test9.2;ID=query_2;Name=test9.2
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339 """)
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340 f.close()
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341
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342 def _writeExpOutFile_case10(self, fileName):
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343 f = open(fileName, 'w')
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344 f.write("""chr1 S-MART test10.1 700 800 101 + . nbOverlaps=1;overlapsWith=test10.1;ID=query_1;Name=test10.1
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345 chr1 S-MART test10.2 900 1000 101 + . nbOverlaps=1;overlapsWith=test10.1;ID=query_2;Name=test10.2
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346 chr1 S-MART test10.3 1100 1300 201 + . nbOverlaps=1;overlapsWith=test10.5;ID=query_3;Name=test10.3
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347 """)
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|
348 f.close()
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349
|
|
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350 def _writeExpOutFile_case11(self, fileName):
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|
351 f = open(fileName, 'w')
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352 f.write("""chr1 S-MART test11.1 420 480 61 + . nbOverlaps=1;overlapsWith=test11.1;ID=query_1;Name=test11.1
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353 chr1 S-MART test11.2 450 715 266 + . nbOverlaps=3;overlapsWith=test11.1--test11.4--test11.5;ID=query_2;Name=test11.2
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354 """)
|
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355 f.close()
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356
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357 def _writeQueryGff3File2(self, fileName):
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358 f = open(fileName, 'w')
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359 f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=query_1;Name=test1.1\n")
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360 f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=query_2;Name=test1.2\n")
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361 f.close()
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362
|
|
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363 def _writeQueryGff3File(self, fileName):
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|
364 f = open(fileName, 'w')
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365 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
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366 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=query_2;Name=test1.2\n")
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367 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=query_3;Name=test1.3\n")
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368 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
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369 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
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370 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
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|
|
371 f.close()
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|
372
|
|
|
373 def _writeQueryGff3File_case2(self, fileName):
|
|
|
374 f = open(fileName, 'w')
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375 f.write("chr1\tquery\ttest2.1\t150\t300\t151\t+\t.\tID=query_1;Name=test2.1\n")
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376 f.write("chr1\tquery\ttest2.2\t300\t450\t781\t+\t.\tID=query_2;Name=test2.2\n")
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377 f.write("chr1\tquery\ttest2.3\t480\t800\t321\t+\t.\tID=query_3;Name=test2.3\n")
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|
|
378 f.write("chr1\tquery\ttest2.4\t560\t800\t241\t+\t.\tID=query_4;Name=test2.4\n")
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379 f.write("chr1\tquery\ttest2.5\t850\t1000\t151\t+\t.\tID=query_5;Name=test2.5\n")
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|
|
380 f.close()
|
|
|
381
|
|
|
382 def _writeQueryGff3File_case3(self, fileName):
|
|
|
383 f = open(fileName, 'w')
|
|
|
384 f.write("chr1\tquery\ttest3.1\t150\t250\t101\t+\t.\tID=query_1;Name=test3.1\n")
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385 f.write("chr1\tquery\ttest3.2\t380\t400\t21\t+\t.\tID=query_2;Name=test3.2\n")
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386 f.write("chr1\tquery\ttest3.3\t480\t520\t41\t+\t.\tID=query_3;Name=test3.3\n")
|
|
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387 f.write("chr1\tquery\ttest3.4\t510\t700\t191\t+\t.\tID=query_4;Name=test3.4\n")
|
|
|
388 f.write("chr1\tquery\ttest3.5\t900\t950\t51\t+\t.\tID=query_5;Name=test3.5\n")
|
|
|
389 f.close()
|
|
|
390
|
|
|
391 def _writeQueryGff3File_case4(self, fileName):
|
|
|
392 f = open(fileName, 'w')
|
|
|
393 f.write("chr1\tquery\ttest4.1\t400\t500\t101\t+\t.\tID=query_1;Name=test4.1\n")
|
|
|
394 f.write("chr1\tquery\ttest4.2\t450\t600\t151\t+\t.\tID=query_2;Name=test4.2\n")
|
|
|
395 f.write("chr1\tquery\ttest4.3\t700\t800\t101\t+\t.\tID=query_3;Name=test4.3\n")
|
|
|
396 f.close()
|
|
|
397
|
|
|
398 def _writeQueryGff3File_case5(self, fileName):
|
|
|
399 f = open(fileName, 'w')
|
|
|
400 f.write("chr1\tquery\ttest5.1\t850\t950\t101\t+\t.\tID=query_1;Name=test5.1\n")
|
|
|
401 f.close()
|
|
|
402
|
|
|
403 def _writeQueryGff3File_case6(self, fileName):
|
|
|
404 f = open(fileName, 'w')
|
|
|
405 f.write("chr1\tquery\ttest6.1\t200\t300\t101\t+\t.\tID=query_1;Name=test6.1\n")
|
|
|
406 f.write("chr1\tquery\ttest6.2\t800\t900\t101\t+\t.\tID=query_2;Name=test6.2\n")
|
|
|
407 f.close()
|
|
|
408
|
|
|
409 def _writeQueryGff3File_case7(self, fileName):
|
|
|
410 f = open(fileName, 'w')
|
|
|
411 f.write("chr1\tquery\ttest7.1\t530\t550\t21\t+\t.\tID=query_1;Name=test7.1\n")
|
|
|
412 f.write("chr1\tquery\ttest7.2\t600\t700\t101\t+\t.\tID=query_2;Name=test7.2\n")
|
|
|
413 f.write("chr1\tquery\ttest7.3\t650\t900\t251\t+\t.\tID=query_3;Name=test7.3\n")
|
|
|
414 f.close()
|
|
|
415
|
|
|
416 def _writeQueryGff3File_case8(self, fileName):
|
|
|
417 f = open(fileName, 'w')
|
|
|
418 f.write("chr1\tquery\ttest8.1\t500\t600\t101\t+\t.\tID=query_1;Name=test8.1\n")
|
|
|
419 f.write("chr1\tquery\ttest8.2\t700\t800\t101\t+\t.\tID=query_2;Name=test8.2\n")
|
|
|
420 f.write("chr1\tquery\ttest8.3\t900\t1100\t201\t+\t.\tID=query_3;Name=test8.3\n")
|
|
|
421 f.write("chr1\tquery\ttest8.4\t1200\t1300\t101\t+\t.\tID=query_4;Name=test8.4\n")
|
|
|
422 f.close()
|
|
|
423
|
|
|
424 def _writeQueryGff3File_case9(self, fileName):
|
|
|
425 f = open(fileName, 'w')
|
|
|
426 f.write("chr1\tquery\ttest9.1\t400\t500\t101\t+\t.\tID=query_1;Name=test9.1\n")
|
|
|
427 f.write("chr1\tquery\ttest9.2\t550\t650\t101\t+\t.\tID=query_2;Name=test9.2\n")
|
|
|
428 f.close()
|
|
|
429
|
|
|
430 def _writeQueryGff3File_case10(self, fileName):
|
|
|
431 f = open(fileName, 'w')
|
|
|
432 f.write("chr1\tquery\ttest10.1\t700\t800\t101\t+\t.\tID=query_1;Name=test10.1\n")
|
|
|
433 f.write("chr1\tquery\ttest10.2\t900\t1000\t101\t+\t.\tID=query_2;Name=test10.2\n")
|
|
|
434 f.write("chr1\tquery\ttest10.3\t1100\t1300\t201\t+\t.\tID=query_3;Name=test10.3\n")
|
|
|
435 f.close()
|
|
|
436
|
|
|
437 def _writeQueryGff3File_case11(self, fileName):
|
|
|
438 f = open(fileName, 'w')
|
|
|
439 f.write("chr1\tquery\ttest11.1\t420\t480\t61\t+\t.\tID=query_1;Name=test11.1\n")
|
|
|
440 f.write("chr1\tquery\ttest11.2\t450\t715\t266\t+\t.\tID=query_2;Name=test11.2\n")
|
|
|
441 f.close()
|
|
|
442
|
|
|
443 def _writeGFF3File(self, fileName):
|
|
|
444 f = open(fileName, "w")
|
|
|
445 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
|
|
|
446 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
|
|
|
447 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
|
|
|
448 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
|
|
|
449 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
|
|
|
450 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
|
|
|
451 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
|
|
|
452 f.close()
|
|
|
453
|
|
|
454 if __name__ == "__main__":
|
|
|
455 unittest.main()
|
