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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.NCListCursor import NCListCursor
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5 from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
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6
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7 REFERENCE = 0
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8 QUERY = 1
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9
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10 class Test_FindOverlapsOptim(unittest.TestCase):
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11
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12 def setUp(self):
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13 self._inputRefGff3FileName = 'sorted_Ref.gff3'
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14 self._inputQueryGff3FileName = 'sorted_Query.gff3'
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15 self._writeQueryGff3File(self._inputQueryGff3FileName)
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16 self._outputGff3FileName = 'overlaps.gff3'
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17 iMock = MockFindOverlapsWithServeralIntervals_case1()
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18 iMock.write(self._inputRefGff3FileName)
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19 self._iFOO = FindOverlapsOptim(0)
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20 self._iFOO.setRefFileName(self._inputRefGff3FileName, "gff3")
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21 self._iFOO.setQueryFileName(self._inputQueryGff3FileName, "gff3")
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22 self._iFOO.setOutputFileName(self._outputGff3FileName)
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23 self._iFOO.prepareIntermediateFiles()
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24 self._iFOO.createNCLists()
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25 self._queryNcList = self._iFOO._ncLists[QUERY]["chr1"]
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26 self._refNcList = self._iFOO._ncLists[REFERENCE]["chr1"]
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27
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28 def tearDown(self):
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29 os.remove(self._inputRefGff3FileName)
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30 os.remove(self._inputQueryGff3FileName)
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31 os.remove(self._outputGff3FileName)
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32
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33 def test_isOverlapping_true(self):
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34 queryCursor = NCListCursor(None, self._queryNcList, 5, 0)
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35 refCursor = NCListCursor(None, self._refNcList, 4, 0)
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36 obs = self._iFOO.isOverlapping(queryCursor, refCursor)
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37 exp = 0
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38 self.assertEquals(exp, obs)
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39
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40 def test_isOverlapping_false_left(self):
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41 queryCursor = NCListCursor(None, self._queryNcList, 5, 0)
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42 refCursor = NCListCursor(None, self._refNcList, 2, 0)
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43 obs = self._iFOO.isOverlapping(queryCursor, refCursor)
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44 exp = -1
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45 self.assertEquals(exp, obs)
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46
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47 def test_isOverlapping_false_right(self):
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48 queryCursor = NCListCursor(None, self._queryNcList, 5, 0)
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49 refCursor = NCListCursor(None, self._refNcList, 1, 0)
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50 obs = self._iFOO.isOverlapping(queryCursor, refCursor)
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51 exp = 1
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52 self.assertEquals(exp, obs)
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53
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54 def test_isLastElement_true(self):
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55 refCursor = NCListCursor(None, self._refNcList, 4, 0)
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56 obsBool = refCursor.isLast()
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57 expBool = True
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58 self.assertEquals(expBool, obsBool)
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59
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60 def test_isLastElement_false(self):
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61 refCursor = NCListCursor(None, self._refNcList, 3, 0)
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62 obsBool = refCursor.isLast()
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63 expBool = False
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64 self.assertEquals(expBool, obsBool)
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65
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66 def test_isLastElement_highestLevel_true(self):
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67 refCursor = NCListCursor(None, self._refNcList, 1, 0)
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68 obsBool = refCursor.isLast()
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69 expBool = True
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70 self.assertEquals(expBool, obsBool)
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71
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72 def test_isLastElement_highestLevel_false(self):
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73 refCursor = NCListCursor(None, self._refNcList, 0, 0)
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74 obsBool = refCursor.isLast()
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75 expBool = False
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76 self.assertEquals(expBool, obsBool)
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77
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78 def test_findOverlapIter(self):
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79 queryCursor = NCListCursor(None, self._queryNcList, 2, 0)
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80 refCursor = NCListCursor(None, self._refNcList, 0, 0)
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81 queryTranscript = queryCursor.getTranscript()
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82 done = False
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83 (cursor, done, empty) = self._iFOO.findOverlapIter(queryTranscript, refCursor, done)
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84 obsFirstOverlapLAddr = (cursor._lIndex, done, empty)
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85 expFirstOverlapLAddr = 4, True, False
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86 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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87
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88 def test_not_findOverlapIter(self):
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89 queryCursor = NCListCursor(None, self._queryNcList, 4, 0)
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90 refCursor = NCListCursor(None, self._refNcList, 1, 0)
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91 queryTranscript = queryCursor.getTranscript()
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92 done = False
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93 (cursor, done, empty) = self._iFOO.findOverlapIter(queryTranscript, refCursor, done)
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94 obsFirstOverlapLAddr = (cursor._lIndex, done, empty)
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95 expFirstOverlapLAddr = -1, False, True
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96 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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97
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98 def test_findOverlapIter_not_the_first_RefOverlap(self):
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99 queryCursor = NCListCursor(None, self._queryNcList, 3, 0)
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100 refCursor = NCListCursor(None, self._refNcList, 4, 0)
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101 queryTranscript = queryCursor.getTranscript()
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102 done = True
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103 (cursor, done, empty) = self._iFOO.findOverlapIter(queryTranscript, refCursor, done)
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104 obsFirstOverlapLAddr = (cursor._lIndex, done, empty)
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105 expFirstOverlapLAddr = 1, True, False
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106 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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107
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108 def test_moveDown(self):
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109 refCursor = NCListCursor(None, self._refNcList, 0, 0)
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110 refCursor.moveDown()
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111 expFirstChildLAddr = 2
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112 self.assertEquals(expFirstChildLAddr, refCursor._lIndex)
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113
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114 def test_moveUp(self):
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115 refCursor = NCListCursor(None, self._refNcList, 4, 0)
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116 refCursor.moveUp()
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117 expFirstChildLAddr = 0
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118 self.assertEquals(expFirstChildLAddr, refCursor._lIndex)
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119
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120 def test_moveRight(self):
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121 refCursor = NCListCursor(None, self._refNcList, 3, 0)
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122 refCursor.moveRight()
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123 expFirstChildLAddr = 4
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124 self.assertEquals(expFirstChildLAddr, refCursor._lIndex)
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125
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126 def test_moveNext(self):
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127 refCursor = NCListCursor(None, self._refNcList, 6, 0)
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128 refCursor.moveNext()
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129 expFirstChildLAddr = 1
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130 self.assertEquals(expFirstChildLAddr, refCursor._lIndex)
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131
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132 def test_not_findOverlapIter_between2RefIntervals(self):
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133 inputQueryGff3FileName = 'query2.gff3'
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134 self._writeQueryGff3File2(inputQueryGff3FileName)
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135 self._outputGff3FileName = 'overlaps.gff3'
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136 iMock = MockFindOverlapsWithServeralIntervals_case1()
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137 iMock.write(self._inputRefGff3FileName)
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138 _iFOO = FindOverlapsOptim(0)
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139 _iFOO.setRefFileName(self._inputRefGff3FileName, "gff3")
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140 _iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
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141 _iFOO.setOutputFileName(self._outputGff3FileName)
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142 _iFOO.prepareIntermediateFiles()
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143 _iFOO.createNCLists()
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144 _queryNcList = _iFOO._ncLists[QUERY]["chr1"]
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145 _refNcList = _iFOO._ncLists[REFERENCE]["chr1"]
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146 queryCursor = NCListCursor(None, _queryNcList, 0, 0)
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147 refCursor = NCListCursor(None, _refNcList, 0, 0)
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148 queryTranscript = queryCursor.getTranscript()
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149 done = True
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150 (cursor, done, empty) = _iFOO.findOverlapIter(queryTranscript, refCursor, done)
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151 lIndex = cursor._lIndex
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152 obsFirstOverlapLAddr = (lIndex, done, empty)
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153 expFirstOverlapLAddr = 1, False, True
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154 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
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155 os.remove(inputQueryGff3FileName)
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156
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157 def _writeQueryGff3File2(self, fileName):
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158 f = open(fileName, 'w')
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159 f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
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160 f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=test1.2;Name=test1.2\n")
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161 f.close()
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162
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163 def _writeQueryGff3File(self, fileName):
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164 f = open(fileName, 'w')
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165 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
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166 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=test1.2;Name=test1.2\n")
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167 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=test1.3;Name=test1.3\n")
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168 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=test1.4;Name=test1.4\n")
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169 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=test1.5;Name=test1.5\n")
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170 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=test1.6;Name=test1.6\n")
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171 f.close()
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172
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173 if __name__ == "__main__":
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174 unittest.main()
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