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1 import unittest
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2 import os
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3 from SMART.Java.Python.misc import Utils
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4 from commons.core.utils.FileUtils import FileUtils
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5 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
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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_FindOverlapsOptim(unittest.TestCase):
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9
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10 def setUp(self):
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11 self._inputRefGff3FileName = 'sorted_Ref.gff3'
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12 self._writeGFF3File(self._inputRefGff3FileName)
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13 self._inputQueryGff3FileName = 'sorted_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
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18 def tearDown(self):
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19 for fileName in (self._inputRefGff3FileName, self._inputQueryGff3FileName, self._outputGff3FileName, self._expOutputFileName):
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20 if os.path.exists(fileName):
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21 os.remove(fileName)
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22
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23 def test_run_general_asScript(self):
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24 cmd = 'python ../FindOverlapsOptim.py -i %s -f gff -j %s -g gff -o %s -v 0' % (self._inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName)
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25 os.system(cmd)
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26 self._writeExpOutFile_general(self._expOutputFileName)
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27 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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28
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29 def test_run_overlap_special_case(self):
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30 inputQueryGff3FileName = 'query2.gff3'
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31 self._writeQueryGff3File2(inputQueryGff3FileName)
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32 iFOO = FindOverlapsOptim(0)
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33 iFOO.setRefFileName(self._inputRefGff3FileName, "gff")
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34 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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35 iFOO.setOutputFileName(self._outputGff3FileName)
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36 iFOO.run()
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37 iFOO.close()
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38 self._writeExpOutFile_special_case(self._expOutputFileName)
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39 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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40 os.remove(inputQueryGff3FileName)
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41
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42 def test_run_overlap_special_case_asScript(self):
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43 inputQueryGff3FileName = 'query2.gff3'
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44 self._writeQueryGff3File2(inputQueryGff3FileName)
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45 cmd = 'python ../FindOverlapsOptim.py -i %s -f gff -j %s -g gff -o %s -v 0' % (inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName)
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46 os.system(cmd)
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47 self._writeExpOutFile_special_case(self._expOutputFileName)
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48 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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49 os.remove(inputQueryGff3FileName)
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50
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51 def test_case_2(self):
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52 inputRefGff3FileName = 'ref_case2.gff3'
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53 iMock = MockFindOverlapsWithServeralIntervals_case2()
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54 iMock.write(inputRefGff3FileName)
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55 inputQueryGff3FileName = 'query_case2.gff3'
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56 self._writeQueryGff3File_case2(inputQueryGff3FileName)
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57 iFOO = FindOverlapsOptim(0)
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58 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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59 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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60 iFOO.setOutputFileName(self._outputGff3FileName)
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61 iFOO.run()
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62 iFOO.close()
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63 self._writeExpOutFile_case2(self._expOutputFileName)
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64 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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65 os.remove(inputQueryGff3FileName)
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66 os.remove(inputRefGff3FileName)
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67
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68 def test_case_3(self):
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69 inputRefGff3FileName = 'ref_case3.gff3'
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70 iMock = MockFindOverlapsWithServeralIntervals_case3()
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71 iMock.write(inputRefGff3FileName)
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72 inputQueryGff3FileName = 'query_case3.gff3'
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73 self._writeQueryGff3File_case3(inputQueryGff3FileName)
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74 iFOO = FindOverlapsOptim(0)
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75 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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76 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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77 iFOO.setOutputFileName(self._outputGff3FileName)
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78 iFOO.run()
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79 iFOO.close()
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80 self._writeExpOutFile_case3(self._expOutputFileName)
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81 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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82 os.remove(inputQueryGff3FileName)
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83 os.remove(inputRefGff3FileName)
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84
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85 def test_case_4(self):
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86 inputRefGff3FileName = 'ref_case4.gff3'
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87 iMock = MockFindOverlapsWithServeralIntervals_case4_5()
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88 iMock.write(inputRefGff3FileName)
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89 inputQueryGff3FileName = 'query_case4.gff3'
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90 self._writeQueryGff3File_case4(inputQueryGff3FileName)
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91 iFOO = FindOverlapsOptim(0)
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92 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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93 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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94 iFOO.setOutputFileName(self._outputGff3FileName)
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95 iFOO.run()
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96 iFOO.close()
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97 self._writeExpOutFile_case4(self._expOutputFileName)
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98 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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99 os.remove(inputQueryGff3FileName)
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100 os.remove(inputRefGff3FileName)
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101
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102 def test_case_5(self):
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103 inputRefGff3FileName = 'ref_case5.gff3'
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104 iMock = MockFindOverlapsWithServeralIntervals_case4_5()
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105 iMock.write(inputRefGff3FileName)
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106 inputQueryGff3FileName = 'query_case5.gff3'
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107 self._writeQueryGff3File_case5(inputQueryGff3FileName)
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108 iFOO = FindOverlapsOptim(0)
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109 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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110 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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111 iFOO.setOutputFileName(self._outputGff3FileName)
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112 iFOO.run()
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113 iFOO.close()
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114 self._writeExpOutFile_case5(self._expOutputFileName)
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115 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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116 os.remove(inputQueryGff3FileName)
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117 os.remove(inputRefGff3FileName)
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118
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119 def test_case_6(self):
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120 inputRefGff3FileName = 'ref_case6.gff3'
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121 iMock = MockFindOverlapsWithServeralIntervals_case6_7()
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122 iMock.write(inputRefGff3FileName)
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123 inputQueryGff3FileName = 'query_case6.gff3'
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124 self._writeQueryGff3File_case6(inputQueryGff3FileName)
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125 iFOO = FindOverlapsOptim(0)
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126 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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127 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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128 iFOO.setOutputFileName(self._outputGff3FileName)
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129 iFOO.run()
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130 iFOO.close()
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131 self._writeExpOutFile_case6(self._expOutputFileName)
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132 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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133 os.remove(inputQueryGff3FileName)
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134 os.remove(inputRefGff3FileName)
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135
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136 def test_case_7(self):
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137 inputRefGff3FileName = 'ref_case7.gff3'
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138 iMock = MockFindOverlapsWithServeralIntervals_case6_7()
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139 iMock.write(inputRefGff3FileName)
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140 inputQueryGff3FileName = 'query_case7.gff3'
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141 self._writeQueryGff3File_case7(inputQueryGff3FileName)
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142 iFOO = FindOverlapsOptim(0)
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143 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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144 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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145 iFOO.setOutputFileName(self._outputGff3FileName)
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146 iFOO.run()
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147 iFOO.close()
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148 self._writeExpOutFile_case7(self._expOutputFileName)
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149 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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150 os.remove(inputQueryGff3FileName)
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151 os.remove(inputRefGff3FileName)
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152
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153 def test_case_8(self):
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154 inputRefGff3FileName = 'ref_case8.gff3'
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155 iMock = MockFindOverlapsWithServeralIntervals_case8()
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156 iMock.write(inputRefGff3FileName)
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157 inputQueryGff3FileName = 'query_case8.gff3'
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158 self._writeQueryGff3File_case8(inputQueryGff3FileName)
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159 iFOO = FindOverlapsOptim(0)
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160 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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161 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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162 iFOO.setOutputFileName(self._outputGff3FileName)
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163 iFOO.run()
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164 iFOO.close()
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165 self._writeExpOutFile_case8(self._expOutputFileName)
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166 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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167 os.remove(inputQueryGff3FileName)
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168 os.remove(inputRefGff3FileName)
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169
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170 def test_case_9(self):
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171 inputRefGff3FileName = 'ref_case9.gff3'
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172 iMock = MockFindOverlapsWithServeralIntervals_case9()
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173 iMock.write(inputRefGff3FileName)
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174 inputQueryGff3FileName = 'query_case9.gff3'
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175 self._writeQueryGff3File_case9(inputQueryGff3FileName)
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176 iFOO = FindOverlapsOptim(0)
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177 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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178 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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179 iFOO.setOutputFileName(self._outputGff3FileName)
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180 iFOO.run()
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181 iFOO.close()
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182 self._writeExpOutFile_case9(self._expOutputFileName)
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183 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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184 os.remove(inputQueryGff3FileName)
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185 os.remove(inputRefGff3FileName)
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186
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187 def test_case_10(self):
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188 inputRefGff3FileName = 'ref_case10.gff3'
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189 iMock = MockFindOverlapsWithServeralIntervals_case10()
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190 iMock.write(inputRefGff3FileName)
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191 inputQueryGff3FileName = 'query_case10.gff3'
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192 self._writeQueryGff3File_case10(inputQueryGff3FileName)
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193 iFOO = FindOverlapsOptim(0)
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194 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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195 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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196 iFOO.setOutputFileName(self._outputGff3FileName)
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197 iFOO.run()
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198 iFOO.close()
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199 self._writeExpOutFile_case10(self._expOutputFileName)
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200 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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201 os.remove(inputQueryGff3FileName)
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202 os.remove(inputRefGff3FileName)
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203
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204 def test_case_11(self):
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205 inputRefGff3FileName = 'ref_case11.gff3'
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206 iMock = MockFindOverlapsWithServeralIntervals_case11()
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207 iMock.write(inputRefGff3FileName)
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208 inputQueryGff3FileName = 'query_case11.gff3'
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209 self._writeQueryGff3File_case11(inputQueryGff3FileName)
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210 iFOO = FindOverlapsOptim(0)
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211 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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212 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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213 iFOO.setOutputFileName(self._outputGff3FileName)
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214 iFOO.run()
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215 iFOO.close()
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216 self._writeExpOutFile_case11(self._expOutputFileName)
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217 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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218 os.remove(inputQueryGff3FileName)
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219 os.remove(inputRefGff3FileName)
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220
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221 def test_case_12(self):
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222 inputRefGff3FileName = 'ref_case12.gff3'
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223 iMock = MockFindOverlapsWithServeralIntervals_case12()
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224 iMock.write(inputRefGff3FileName)
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225 inputQueryGff3FileName = 'query_case12.gff3'
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226 self._writeQueryGff3File_case12(inputQueryGff3FileName)
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227 iFOO = FindOverlapsOptim(0)
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228 iFOO.setRefFileName(inputRefGff3FileName, "gff")
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229 iFOO.setQueryFileName(inputQueryGff3FileName, "gff")
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230 iFOO.setOutputFileName(self._outputGff3FileName)
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231 iFOO.run()
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232 iFOO.close()
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233 self._writeExpOutFile_case12(self._expOutputFileName)
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234 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName))
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235 os.remove(inputQueryGff3FileName)
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236 os.remove(inputRefGff3FileName)
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237
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238 def _writeExpOutFile_special_case(self, fileName):
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239 f = open(fileName, 'w')
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240 f.write("chr1\tS-MART\ttest2\t1250\t1300\t781\t+\t.\tnbOverlaps=1;overlapsWith=test2.7;ID=query_2;Name=test1.2\n")
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241 f.close()
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242
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243 def _writeExpOutFile_general(self, fileName):
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244 f = open(fileName, 'w')
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245 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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246 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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247 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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248 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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249 chr1 S-MART test1.5 1201 1210 10 + . nbOverlaps=1;overlapsWith=test2.7;ID=query_5;Name=test1.5
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250 """)
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251 f.close()
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252
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253 def _writeExpOutFile_cas_1(self, fileName):
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254 f = open(fileName, 'w')
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255 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_3;ID=test2.1\n")
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256 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;overlapsWith=query_3;ID=test2.3\n")
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257 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;overlapsWith=query_3;ID=test2.5\n")
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258 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;overlapsWith=query_3;ID=test2.6\n")
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259 f.close()
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260
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261 def _writeExpOutFile_cas_2(self, fileName):
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262 f = open(fileName, 'w')
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263 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_2;score=1001;feature=test2.1;ID=test2.1\n")
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264 f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tName=test2.2;overlapsWith=query_2;score=301;feature=test2.2;ID=test2.2\n")
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265 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;overlapsWith=query_2;score=501;feature=test2.3;ID=test2.3\n")
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266 f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tName=test2.4;overlapsWith=query_2;score=251;feature=test2.4;ID=test2.4\n")
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267 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;overlapsWith=query_2;score=251;feature=test2.5;ID=test2.5\n")
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268 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;overlapsWith=query_2;score=101;feature=test2.6;ID=test2.6\n")
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269 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_3;score=1001;feature=test2.1;ID=test2.1\n")
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270 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;overlapsWith=query_3;score=501;feature=test2.3;ID=test2.3\n")
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271 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;overlapsWith=query_3;score=251;feature=test2.5;ID=test2.5\n")
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272 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;overlapsWith=query_3;score=101;feature=test2.6;ID=test2.6\n")
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273 f.close()
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274
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275 def _writeExpOutFile_all_overlap(self, fileName):
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276 f = open(fileName, 'w')
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277 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_2;score=1001;feature=test2.1;ID=test2.1\n")
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278 f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tName=test2.2;overlapsWith=query_2;score=301;feature=test2.2;ID=test2.2\n")
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279 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;overlapsWith=query_2;score=501;feature=test2.3;ID=test2.3\n")
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280 f.write("chr1\tS-MART\ttest2.4\t200\t450\t251\t+\t.\tName=test2.4;overlapsWith=query_2;score=251;feature=test2.4;ID=test2.4\n")
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281 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;overlapsWith=query_2;score=251;feature=test2.5;ID=test2.5\n")
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282 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;overlapsWith=query_2;score=101;feature=test2.6;ID=test2.6\n")
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|
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283 f.close()
|
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|
284
|
|
|
285 def _writeExpOutFile_overlap_to_children(self, fileName):
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|
286 f = open(fileName, 'w')
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287 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_3;score=1001;feature=test2.1;ID=test2.1\n")
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288 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;overlapsWith=query_3;score=501;feature=test2.3;ID=test2.3\n")
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289 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;overlapsWith=query_3;score=251;feature=test2.5;ID=test2.5\n")
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290 f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;overlapsWith=query_3;score=101;feature=test2.6;ID=test2.6\n")
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291 f.close()
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292
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|
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293 def _writeExpOutFile_not_overlap_to_children(self, fileName):
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294 f = open(fileName, 'w')
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295 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_1;score=1001;feature=test2.1;ID=test2.1\n")
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296 f.write("chr1\tS-MART\ttest2.2\t50\t350\t301\t+\t.\tName=test2.2;overlapsWith=query_1;score=301;feature=test2.2;ID=test2.2\n")
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297 f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;overlapsWith=query_1;score=501;feature=test2.3;ID=test2.3\n")
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298 f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_4;score=1001;feature=test2.1;ID=test2.1\n")
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299 f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;overlapsWith=query_4;score=251;feature=test2.5;ID=test2.5\n")
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300 f.close()
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301
|
|
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302 def _writeExpOutFile_no_overlap_right(self, fileName):
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303 f = open(fileName, 'w')
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304 f.close()
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305
|
|
|
306 def _writeExpOutFile_one_overlap(self, fileName):
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307 f = open(fileName, 'w')
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308 f.write("chr1\tS-MART\ttest2.7\t1200\t1300\t101\t+\t.\tName=test2.7;overlapsWith=query_5;score=101;feature=test2.7;ID=test2.7\n")
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309 f.close()
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310
|
|
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311 def _writeExpOutFile_case2(self, fileName):
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312 f = open(fileName, 'w')
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313 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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314 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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|
|
315 chr1 S-MART test2.3 480 800 321 + . nbOverlaps=1;overlapsWith=test2.1;ID=query_3;Name=test2.3
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|
|
316 chr1 S-MART test2.5 850 1000 151 + . nbOverlaps=1;overlapsWith=test2.5;ID=query_5;Name=test2.5
|
|
|
317 """)
|
|
|
318 f.close()
|
|
|
319
|
|
|
320 def _writeExpOutFile_case3(self, fileName):
|
|
|
321 f = open(fileName, 'w')
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322 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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|
|
323 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
|
|
|
324 chr1 S-MART test3.3 480 520 41 + . nbOverlaps=1;overlapsWith=test3.1;ID=query_3;Name=test3.3
|
|
|
325 chr1 S-MART test3.5 900 950 51 + . nbOverlaps=1;overlapsWith=test3.6;ID=query_5;Name=test3.5
|
|
|
326 """)
|
|
|
327 f.close()
|
|
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328
|
|
|
329 def _writeExpOutFile_case4(self, fileName):
|
|
|
330 f = open(fileName, 'w')
|
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|
331 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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|
|
332 chr1 S-MART test4.2 450 600 151 + . nbOverlaps=3;overlapsWith=test4.1--test4.2--test4.3;ID=query_2;Name=test4.2
|
|
|
333 chr1 S-MART test4.3 700 800 101 + . nbOverlaps=2;overlapsWith=test4.1--test4.2;ID=query_3;Name=test4.3
|
|
|
334 """)
|
|
|
335 f.close()
|
|
|
336
|
|
|
337 def _writeExpOutFile_case5(self, fileName):
|
|
|
338 f = open(fileName, 'w')
|
|
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339 f.write("chr1 S-MART test5.1 850 950 101 + . nbOverlaps=1;overlapsWith=test4.1;ID=query_1;Name=test5.1\n")
|
|
|
340 f.close()
|
|
|
341
|
|
|
342 def _writeExpOutFile_case6(self, fileName):
|
|
|
343 f = open(fileName, 'w')
|
|
|
344 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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345 chr1 S-MART test6.2 800 900 101 + . nbOverlaps=2;overlapsWith=test6.1--test6.5;ID=query_2;Name=test6.2
|
|
|
346 """)
|
|
|
347 f.close()
|
|
|
348
|
|
|
349 def _writeExpOutFile_case7(self, fileName):
|
|
|
350 f = open(fileName, 'w')
|
|
|
351 f.write("""chr1 S-MART test7.1 530 550 21 + . nbOverlaps=1;overlapsWith=test6.1;ID=query_1;Name=test7.1
|
|
|
352 chr1 S-MART test7.2 600 700 101 + . nbOverlaps=1;overlapsWith=test6.1;ID=query_2;Name=test7.2
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|
|
353 chr1 S-MART test7.3 650 900 251 + . nbOverlaps=2;overlapsWith=test6.1--test6.5;ID=query_3;Name=test7.3
|
|
|
354 """)
|
|
|
355 f.close()
|
|
|
356
|
|
|
357 def _writeExpOutFile_case8(self, fileName):
|
|
|
358 f = open(fileName, 'w')
|
|
|
359 f.write("""chr1 S-MART test8.1 500 600 101 + . nbOverlaps=1;overlapsWith=test8.1;ID=query_1;Name=test8.1
|
|
|
360 chr1 S-MART test8.2 700 800 101 + . nbOverlaps=1;overlapsWith=test8.1;ID=query_2;Name=test8.2
|
|
|
361 chr1 S-MART test8.3 900 1100 201 + . nbOverlaps=1;overlapsWith=test8.1;ID=query_3;Name=test8.3
|
|
|
362 """)
|
|
|
363 f.close()
|
|
|
364
|
|
|
365 def _writeExpOutFile_case9(self, fileName):
|
|
|
366 f = open(fileName, 'w')
|
|
|
367 f.write("""chr1 S-MART test9.1 400 500 101 + . nbOverlaps=1;overlapsWith=test9.1;ID=query_1;Name=test9.1
|
|
|
368 chr1 S-MART test9.2 550 650 101 + . nbOverlaps=2;overlapsWith=test9.1--test9.2;ID=query_2;Name=test9.2
|
|
|
369 """)
|
|
|
370 f.close()
|
|
|
371
|
|
|
372 def _writeExpOutFile_case10(self, fileName):
|
|
|
373 f = open(fileName, 'w')
|
|
|
374 f.write("""chr1 S-MART test10.1 700 800 101 + . nbOverlaps=1;overlapsWith=test10.1;ID=query_1;Name=test10.1
|
|
|
375 chr1 S-MART test10.2 900 1000 101 + . nbOverlaps=1;overlapsWith=test10.1;ID=query_2;Name=test10.2
|
|
|
376 chr1 S-MART test10.3 1100 1300 201 + . nbOverlaps=1;overlapsWith=test10.5;ID=query_3;Name=test10.3
|
|
|
377 """)
|
|
|
378 f.close()
|
|
|
379
|
|
|
380 def _writeExpOutFile_case11(self, fileName):
|
|
|
381 f = open(fileName, 'w')
|
|
|
382 f.write("""chr1 S-MART test11.1 420 480 61 + . nbOverlaps=1;overlapsWith=test11.1;ID=query_1;Name=test11.1
|
|
|
383 chr1 S-MART test11.2 450 715 266 + . nbOverlaps=3;overlapsWith=test11.1--test11.4--test11.5;ID=query_2;Name=test11.2
|
|
|
384 """)
|
|
|
385 f.close()
|
|
|
386
|
|
|
387 def _writeExpOutFile_case12(self, fileName):
|
|
|
388 f = open(fileName, 'w')
|
|
|
389 f.write("""chr1 S-MART test12.1 200 400 . + . nbOverlaps=3;overlapsWith=test12.1--test12.2--test12.3;ID=query_1;Name=test12.1
|
|
|
390 chr1 S-MART test12.2 600 900 . + . nbOverlaps=2;overlapsWith=test12.1--test12.4;ID=query_2;Name=test12.2
|
|
|
391 chr1 S-MART test12.3 700 1000 . + . nbOverlaps=2;overlapsWith=test12.1--test12.4;ID=query_3;Name=test12.3
|
|
|
392 """)
|
|
|
393 f.close()
|
|
|
394
|
|
|
395 def _writeQueryGff3File2(self, fileName):
|
|
|
396 f = open(fileName, 'w')
|
|
|
397 f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=query_1;Name=test1.1\n")
|
|
|
398 f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=query_2;Name=test1.2\n")
|
|
|
399 f.close()
|
|
|
400
|
|
|
401 def _writeQueryGff3File(self, fileName):
|
|
|
402 f = open(fileName, 'w')
|
|
|
403 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
|
|
|
404 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=query_2;Name=test1.2\n")
|
|
|
405 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=query_3;Name=test1.3\n")
|
|
|
406 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
|
|
|
407 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
|
|
|
408 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
|
|
|
409 f.close()
|
|
|
410
|
|
|
411 def _writeQueryGff3File_case2(self, fileName):
|
|
|
412 f = open(fileName, 'w')
|
|
|
413 f.write("chr1\tquery\ttest2.1\t150\t300\t151\t+\t.\tID=query_1;Name=test2.1\n")
|
|
|
414 f.write("chr1\tquery\ttest2.2\t300\t450\t781\t+\t.\tID=query_2;Name=test2.2\n")
|
|
|
415 f.write("chr1\tquery\ttest2.3\t480\t800\t321\t+\t.\tID=query_3;Name=test2.3\n")
|
|
|
416 f.write("chr1\tquery\ttest2.4\t560\t800\t241\t+\t.\tID=query_4;Name=test2.4\n")
|
|
|
417 f.write("chr1\tquery\ttest2.5\t850\t1000\t151\t+\t.\tID=query_5;Name=test2.5\n")
|
|
|
418 f.close()
|
|
|
419
|
|
|
420 def _writeQueryGff3File_case3(self, fileName):
|
|
|
421 f = open(fileName, 'w')
|
|
|
422 f.write("chr1\tquery\ttest3.1\t150\t250\t101\t+\t.\tID=query_1;Name=test3.1\n")
|
|
|
423 f.write("chr1\tquery\ttest3.2\t380\t400\t21\t+\t.\tID=query_2;Name=test3.2\n")
|
|
|
424 f.write("chr1\tquery\ttest3.3\t480\t520\t41\t+\t.\tID=query_3;Name=test3.3\n")
|
|
|
425 f.write("chr1\tquery\ttest3.4\t510\t700\t191\t+\t.\tID=query_4;Name=test3.4\n")
|
|
|
426 f.write("chr1\tquery\ttest3.5\t900\t950\t51\t+\t.\tID=query_5;Name=test3.5\n")
|
|
|
427 f.close()
|
|
|
428
|
|
|
429 def _writeQueryGff3File_case4(self, fileName):
|
|
|
430 f = open(fileName, 'w')
|
|
|
431 f.write("chr1\tquery\ttest4.1\t400\t500\t101\t+\t.\tID=query_1;Name=test4.1\n")
|
|
|
432 f.write("chr1\tquery\ttest4.2\t450\t600\t151\t+\t.\tID=query_2;Name=test4.2\n")
|
|
|
433 f.write("chr1\tquery\ttest4.3\t700\t800\t101\t+\t.\tID=query_3;Name=test4.3\n")
|
|
|
434 f.close()
|
|
|
435
|
|
|
436 def _writeQueryGff3File_case5(self, fileName):
|
|
|
437 f = open(fileName, 'w')
|
|
|
438 f.write("chr1\tquery\ttest5.1\t850\t950\t101\t+\t.\tID=query_1;Name=test5.1\n")
|
|
|
439 f.close()
|
|
|
440
|
|
|
441 def _writeQueryGff3File_case6(self, fileName):
|
|
|
442 f = open(fileName, 'w')
|
|
|
443 f.write("chr1\tquery\ttest6.1\t200\t300\t101\t+\t.\tID=query_1;Name=test6.1\n")
|
|
|
444 f.write("chr1\tquery\ttest6.2\t800\t900\t101\t+\t.\tID=query_2;Name=test6.2\n")
|
|
|
445 f.close()
|
|
|
446
|
|
|
447 def _writeQueryGff3File_case7(self, fileName):
|
|
|
448 f = open(fileName, 'w')
|
|
|
449 f.write("chr1\tquery\ttest7.1\t530\t550\t21\t+\t.\tID=query_1;Name=test7.1\n")
|
|
|
450 f.write("chr1\tquery\ttest7.2\t600\t700\t101\t+\t.\tID=query_2;Name=test7.2\n")
|
|
|
451 f.write("chr1\tquery\ttest7.3\t650\t900\t251\t+\t.\tID=query_3;Name=test7.3\n")
|
|
|
452 f.close()
|
|
|
453
|
|
|
454 def _writeQueryGff3File_case8(self, fileName):
|
|
|
455 f = open(fileName, 'w')
|
|
|
456 f.write("chr1\tquery\ttest8.1\t500\t600\t101\t+\t.\tID=query_1;Name=test8.1\n")
|
|
|
457 f.write("chr1\tquery\ttest8.2\t700\t800\t101\t+\t.\tID=query_2;Name=test8.2\n")
|
|
|
458 f.write("chr1\tquery\ttest8.3\t900\t1100\t201\t+\t.\tID=query_3;Name=test8.3\n")
|
|
|
459 f.write("chr1\tquery\ttest8.4\t1200\t1300\t101\t+\t.\tID=query_4;Name=test8.4\n")
|
|
|
460 f.close()
|
|
|
461
|
|
|
462 def _writeQueryGff3File_case9(self, fileName):
|
|
|
463 f = open(fileName, 'w')
|
|
|
464 f.write("chr1\tquery\ttest9.1\t400\t500\t101\t+\t.\tID=query_1;Name=test9.1\n")
|
|
|
465 f.write("chr1\tquery\ttest9.2\t550\t650\t101\t+\t.\tID=query_2;Name=test9.2\n")
|
|
|
466 f.close()
|
|
|
467
|
|
|
468 def _writeQueryGff3File_case10(self, fileName):
|
|
|
469 f = open(fileName, 'w')
|
|
|
470 f.write("chr1\tquery\ttest10.1\t700\t800\t101\t+\t.\tID=query_1;Name=test10.1\n")
|
|
|
471 f.write("chr1\tquery\ttest10.2\t900\t1000\t101\t+\t.\tID=query_2;Name=test10.2\n")
|
|
|
472 f.write("chr1\tquery\ttest10.3\t1100\t1300\t201\t+\t.\tID=query_3;Name=test10.3\n")
|
|
|
473 f.close()
|
|
|
474
|
|
|
475 def _writeQueryGff3File_case11(self, fileName):
|
|
|
476 f = open(fileName, 'w')
|
|
|
477 f.write("chr1\tquery\ttest11.1\t420\t480\t61\t+\t.\tID=query_1;Name=test11.1\n")
|
|
|
478 f.write("chr1\tquery\ttest11.2\t450\t715\t266\t+\t.\tID=query_2;Name=test11.2\n")
|
|
|
479 f.close()
|
|
|
480
|
|
|
481 def _writeQueryGff3File_case12(self, fileName):
|
|
|
482 f = open(fileName, 'w')
|
|
|
483 f.write("chr1\tquery\ttest12.1\t200\t400\t.\t+\t.\tID=query_1;Name=test12.1\n")
|
|
|
484 f.write("chr1\tquery\ttest12.2\t600\t900\t.\t+\t.\tID=query_2;Name=test12.2\n")
|
|
|
485 f.write("chr1\tquery\ttest12.3\t700\t1000\t.\t+\t.\tID=query_3;Name=test12.3\n")
|
|
|
486 f.close()
|
|
|
487
|
|
|
488 def _writeGFF3File(self, fileName):
|
|
|
489 f = open(fileName, "w")
|
|
|
490 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
|
|
|
491 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
|
|
|
492 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
|
|
|
493 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
|
|
|
494 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
|
|
|
495 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
|
|
|
496 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
|
|
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497 f.close()
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498
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499 if __name__ == "__main__":
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500 unittest.main()
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