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1 import unittest
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2 import os
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3 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
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4 from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
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5
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6 class Test_FindOverlaps_optim(unittest.TestCase):
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7
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8 def setUp(self):
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9 self._inputRefGff3FileName = 'sorted_Ref.gff3'
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10 iMock = MockFindOverlapsWithServeralIntervals_case1()
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11 iMock.write(self._inputRefGff3FileName)
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12 self._inputQueryGff3FileName = 'sorted_Query.gff3'
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13 self._writeQueryGff3File(self._inputQueryGff3FileName)
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14 self._outputGff3FileName = 'overlaps.gff3'
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15 self._iFOO = FindOverlaps_optim(self._inputRefGff3FileName, self._inputQueryGff3FileName)
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16 self._iFOO.prepareIntermediateFiles_sorted()
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17 self._iFOO.setOutputGff3FileName(self._outputGff3FileName)
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18
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19 def tearDown(self):
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20 os.remove(self._inputRefGff3FileName)
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21 os.remove(self._inputQueryGff3FileName)
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22 os.remove(self._outputGff3FileName)
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23 self._iFOO.deletIntermediateFiles()
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24
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25 def test_isOverlapping_true(self):
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26 queryGff3Addr = 116
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27 RefGff3Addr = 231
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28 obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
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29 exp = 0
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30 self.assertEquals(exp, obs)
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31
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32 def test_isOverlapping_false_left(self):
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33 queryGff3Addr = 116
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34 RefGff3Addr = 58
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35 obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
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36 exp = -1
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37 self.assertEquals(exp, obs)
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38
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39 def test_isOverlapping_false_right(self):
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40 queryGff3Addr = 116
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41 RefGff3Addr = 347
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42 obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
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43 exp = 1
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44 self.assertEquals(exp, obs)
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45
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46 def test_getHisFirstChild(self):
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47 firstRefLAddr = 0
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48 obsFirstChildLAddr = self._iFOO.getHisFirstChild(firstRefLAddr)
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49 expFirstChildLAddr = 48
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50 self.assertEquals(expFirstChildLAddr, obsFirstChildLAddr)
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51
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52 def test_isLastElement_true(self):
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53 refLAddr = 96
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54 obsBool = self._iFOO.isLastElement(refLAddr)
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55 expBool = True
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56 self.assertEquals(expBool, obsBool)
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57
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58 def test_isLastElement_false(self):
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59 refLAddr = 72
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60 obsBool = self._iFOO.isLastElement(refLAddr)
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61 expBool = False
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62 self.assertEquals(expBool, obsBool)
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63
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64 def test_isLastElement_highestLevel_true(self):
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65 refLAddr = 24
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66 obsBool = self._iFOO.isLastElement(refLAddr)
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67 expBool = True
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68 self.assertEquals(expBool, obsBool)
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69
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70 def test_isLastElement_highestLevel_false(self):
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71 refLAddr = 0
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72 obsBool = self._iFOO.isLastElement(refLAddr)
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73 expBool = False
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74 self.assertEquals(expBool, obsBool)
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75
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76 def test_findOverlapIter(self):
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77 queryGff3Addr = 175
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78 firstRefLAddr = 0
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79 done = False
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80 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
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81 expFirstOverlapLAddr = 96, True
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82 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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83
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84 def test_not_findOverlapIter(self):
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85 queryGff3Addr = 295
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86 firstRefLAddr = 24
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87 done = False
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88 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
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89 expFirstOverlapLAddr = None, False
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90 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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91
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92 def test_findOverlapIter_not_the_first_RefOverlap(self):
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93 queryGff3Addr = 235
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94 firstRefLAddr = 96
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95 done = True
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96 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
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97 expFirstOverlapLAddr = 24, False
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98 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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99
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100 def test_changeToNewSubEndLAddr(self):
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101 firstChildLAddr = 48
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102 subEndLAddr = 48
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103 expSubEndLAddr = 120
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104 obsSubEndLAddr = self._iFOO.changeToNewSubEndLAddr(firstChildLAddr, subEndLAddr)
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105 self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
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106
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107 def test_defineSubEndLaddr(self):
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108 parentLAddr = -1
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109 expSubEndLAddr = 48
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110 obsSubEndLAddr = self._iFOO.defineSubEndLaddr(parentLAddr)
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111 self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
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112
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113 def test_getNextRefIntervalInCaseNotOverLap(self):
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114 firstRefLAddr = 96
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115 expRefLAddr = 24
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116 obsRefLAddr = self._iFOO.getNext(firstRefLAddr)
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117 self.assertEquals(expRefLAddr, obsRefLAddr)
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118
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119
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120 def test_not_findOverlapIter_between2RefIntervals(self):
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121 inputQueryGff3FileName = 'query2.gff3'
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122 self._writeQueryGff3File2(inputQueryGff3FileName)
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123 self._iFOO.setQueryGff3FileName(inputQueryGff3FileName)
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124 queryGff3Addr = 0
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125 firstRefLAddr = 0
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126 done = False
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127 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
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128 expFirstOverlapLAddr = 24, False
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129 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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130 os.remove(inputQueryGff3FileName)
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131
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132 def _writeQueryGff3File2(self, fileName):
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133 f = open(fileName, 'w')
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134 f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
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135 f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=test1.2;Name=test1.2\n")
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136 f.close()
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137
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138 def _writeQueryGff3File(self, fileName):
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139 f = open(fileName, 'w')
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140 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
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141 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=test1.2;Name=test1.2\n")
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142 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=test1.3;Name=test1.3\n")
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143 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=test1.4;Name=test1.4\n")
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144 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=test1.5;Name=test1.5\n")
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145 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=test1.6;Name=test1.6\n")
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146 f.close()
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147
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148 if __name__ == "__main__":
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149 unittest.main() |
