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6
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1 from SMART.Java.Python.misc import Utils
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2
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3 class MockFindOverlapsWithOneInterval (object) :
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4 def write(self, inFileName):
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5 Utils.writeFile(inFileName, "chr1\ttest\ttest1.1\t0\t1000\t.\t+\t.\tID=test1.1;Name=test1.1\n")
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6
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7 class MockFindOverlapsWithServeralIntervals_case1 (object) :
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8 def write(self,inFileName):
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9 f = open(inFileName, "w")
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10 f.write("chr1\ttest\ttest1.1\t0\t1000\t1001\t+\t.\tID=test1.1;Name=test1.1\n")
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11 f.write("chr1\ttest\ttest1.2\t50\t350\t301\t+\t.\tID=test1.2;Name=test1.2\n")
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12 f.write("chr1\ttest\ttest1.3\t100\t600\t501\t+\t.\tID=test1.3;Name=test1.3\n")
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13 f.write("chr1\ttest\ttest1.4\t200\t450\t251\t+\t.\tID=test1.4;Name=test1.4\n")
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14 f.write("chr1\ttest\ttest1.5\t700\t950\t251\t+\t.\tID=test1.5;Name=test1.5\n")
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15 f.write("chr1\ttest\ttest1.6\t800\t900\t101\t+\t.\tID=test1.6;Name=test1.6\n")
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16 f.write("chr1\ttest\ttest1.7\t1200\t1300\t101\t+\t.\tID=test1.7;Name=test1.7\n")
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17 f.close()
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18
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19 class MockFindOverlapsWithServeralIntervals_case2 (object) :
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20 def write(self,inFileName):
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21 f = open(inFileName,'w')
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22 f.write("chr1\ttest\ttest2.1\t0\t500\t501\t+\t.\tID=test2.1;Name=test2.1\n")
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23 f.write("chr1\ttest\ttest2.2\t50\t450\t401\t+\t.\tID=test2.2;Name=test2.2\n")
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24 f.write("chr1\ttest\ttest2.3\t100\t400\t301\t+\t.\tID=test2.3;Name=test2.3\n")
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25 f.write("chr1\ttest\ttest2.4\t100\t200\t101\t+\t.\tID=test2.4;Name=test2.4\n")
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26 f.write("chr1\ttest\ttest2.5\t900\t1200\t301\t+\t.\tID=test2.5;Name=test2.5\n")
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27 f.close()
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28
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29 class MockFindOverlapsWithServeralIntervals_case3 (object) :
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30 def write(self,inFileName):
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31 f = open(inFileName,'w')
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32 f.write("chr1\ttest\ttest3.1\t0\t500\t501\t+\t.\tID=test3.1;Name=test3.1\n")
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33 f.write("chr1\ttest\ttest3.2\t50\t450\t401\t+\t.\tID=test3.2;Name=test3.2\n")
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34 f.write("chr1\ttest\ttest3.3\t100\t400\t301\t+\t.\tID=test3.3;Name=test3.3\n")
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35 f.write("chr1\ttest\ttest3.4\t100\t200\t101\t+\t.\tID=test3.4;Name=test3.4\n")
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36 f.write("chr1\ttest\ttest3.5\t300\t400\t101\t+\t.\tID=test3.5;Name=test3.5\n")
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37 f.write("chr1\ttest\ttest3.6\t800\t1000\t201\t+\t.\tID=test3.6;Name=test3.6\n")
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38 f.close()
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39
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40 class MockFindOverlapsWithServeralIntervals_case4_5 (object) :
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41 def write(self,inFileName):
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42 f = open(inFileName,'w')
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43 f.write("chr1\ttest\ttest4.1\t0\t1000\t1001\t+\t.\tID=test4.1;Name=test4.1\n")
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44 f.write("chr1\ttest\ttest4.2\t200\t800\t601\t+\t.\tID=test4.2;Name=test4.2\n")
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45 f.write("chr1\ttest\ttest4.3\t400\t600\t201\t+\t.\tID=test4.3;Name=test4.3\n")
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46 f.close()
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47
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48 class MockFindOverlapsWithServeralIntervals_case6_7 (object) :
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49 def write(self,inFileName):
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50 f = open(inFileName,'w')
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51 f.write("chr1\ttest\ttest6.1\t0\t1000\t1001\t+\t.\tID=test6.1;Name=test6.1\n")
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52 f.write("chr1\ttest\ttest6.2\t100\t300\t201\t+\t.\tID=test6.2;Name=test6.2\n")
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53 f.write("chr1\ttest\ttest6.3\t400\t500\t101\t+\t.\tID=test6.3;Name=test6.3\n")
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54 f.write("chr1\ttest\ttest6.4\t510\t520\t11\t+\t.\tID=test6.4;Name=test6.4\n")
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55 f.write("chr1\ttest\ttest6.5\t850\t950\t001\t+\t.\tID=test6.5;Name=test6.5\n")
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56 f.close()
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57
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58 class MockFindOverlapsWithServeralIntervals_case8 (object) :
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59 def write(self,inFileName):
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60 f = open(inFileName,'w')
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61 f.write("chr1\ttest\ttest8.1\t0\t1000\t1001\t+\t.\tID=test8.1;Name=test8.1\n")
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62 f.write("chr1\ttest\ttest8.2\t100\t200\t101\t+\t.\tID=test8.2;Name=test8.2\n")
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63 f.write("chr1\ttest\ttest8.3\t300\t400\t101\t+\t.\tID=test8.3;Name=test8.3\n")
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64 f.close()
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65
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66 class MockFindOverlapsWithServeralIntervals_case9 (object) :
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67 def write(self,inFileName):
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68 f = open(inFileName,'w')
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69 f.write("chr1\ttest\ttest9.1\t0\t1000\t1001\t+\t.\tID=test9.1;Name=test9.1\n")
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70 f.write("chr1\ttest\ttest9.2\t600\t700\t101\t+\t.\tID=test9.2;Name=test9.2\n")
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71 f.write("chr1\ttest\ttest9.3\t800\t1200\t401\t+\t.\tID=test9.3;Name=test9.3\n")
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72 f.close()
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73
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74 class MockFindOverlapsWithServeralIntervals_case10 (object) :
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75 def write(self,inFileName):
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76 f = open(inFileName,'w')
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77 f.write("chr1\ttest\ttest10.1\t0\t1000\t1001\t+\t.\tID=test10.1;Name=test10.1\n")
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78 f.write("chr1\ttest\ttest10.2\t100\t200\t101\t+\t.\tID=test10.2;Name=test10.2\n")
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79 f.write("chr1\ttest\ttest10.3\t300\t400\t101\t+\t.\tID=test10.3;Name=test10.3\n")
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80 f.write("chr1\ttest\ttest10.4\t500\t600\t101\t+\t.\tID=test10.4;Name=test10.4\n")
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81 f.write("chr1\ttest\ttest10.5\t1200\t1300\t101\t+\t.\tID=test10.5;Name=test10.5\n")
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82 f.write("chr1\ttest\ttest10.6\t1400\t1500\t101\t+\t.\tID=test10.6;Name=test10.6\n")
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83 f.close()
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84
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85 class MockFindOverlapsWithServeralIntervals_case11 (object) :
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86 def write(self,inFileName):
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87 f = open(inFileName,'w')
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88 f.write("chr1\ttest\ttest11.1\t0\t500\t501\t+\t.\tID=test11.1;Name=test11.1\n")
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89 f.write("chr1\ttest\ttest11.2\t100\t200\t101\t+\t.\tID=test11.2;Name=test11.2\n")
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90 f.write("chr1\ttest\ttest11.3\t300\t400\t101\t+\t.\tID=test11.3;Name=test11.3\n")
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91 f.write("chr1\ttest\ttest11.4\t700\t900\t201\t+\t.\tID=test11.4;Name=test11.4\n")
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92 f.write("chr1\ttest\ttest11.5\t710\t720\t11\t+\t.\tID=test11.5;Name=test11.5\n")
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93 f.write("chr1\ttest\ttest11.6\t740\t750\t11\t+\t.\tID=test11.6;Name=test11.6\n")
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94 f.close()
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95
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96 class MockFindOverlapsWithServeralIntervals_case12 (object) :
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97 def write(self,inFileName):
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98 f = open(inFileName,'w')
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99 f.write("chr1\ttest\ttest12.1\t0\t1400\t.\t+\t.\tID=test12.1;Name=test12.1\n")
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100 f.write("chr1\ttest\ttest12.2\t300\t500\t.\t+\t.\tID=test12.2;Name=test12.2\n")
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101 f.write("chr1\ttest\ttest12.3\t300\t500\t.\t+\t.\tID=test12.3;Name=test12.3\n")
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102 f.write("chr1\ttest\ttest12.4\t800\t1100\t.\t+\t.\tID=test12.4;Name=test12.4\n")
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103 f.write("chr1\ttest\ttest12.5\t1200\t1300\t.\t+\t.\tID=test12.5;Name=test12.5\n")
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104 f.close()
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105
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106 class MockFindOverlapsWithServeralIntervals_query_case1 (object):
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107 def write(self, fileName):
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108 f = open(fileName, 'w')
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109 f.write("chr1\tquery\tquery1.1\t25\t150\t126\t+\t.\tID=query_1;Name=query1.1\n")
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110 f.write("chr1\tquery\tquery1.2\t70\t850\t781\t+\t.\tID=query_2;Name=query1.2\n")
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111 f.write("chr1\tquery\tquery1.3\t550\t850\t201\t+\t.\tID=query_3;Name=query1.3\n")
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112 f.write("chr1\tquery\tquery1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=query1.4\n")
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113 f.write("chr1\tquery\tquery1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=query1.5\n")
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114 f.write("chr1\tquery\tquery1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=query1.6\n")
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115 f.close()
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116
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117 class MockFindOverlapsWithServeralIntervals_query_case2 (object):
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118 def write(self, fileName):
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119 f = open(fileName, 'w')
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120 f.write("chr1\tquery\tquery2.1\t150\t300\t151\t+\t.\tID=query_1;Name=query2.1\n")
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121 f.write("chr1\tquery\tquery2.2\t300\t450\t151\t+\t.\tID=query_2;Name=query2.2\n")
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122 f.write("chr1\tquery\tquery2.3\t480\t800\t321\t+\t.\tID=query_3;Name=query2.3\n")
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123 f.write("chr1\tquery\tquery2.4\t560\t800\t241\t+\t.\tID=query_4;Name=query2.4\n")
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124 f.write("chr1\tquery\tquery2.5\t850\t1000\t151\t+\t.\tID=query_5;Name=query2.5\n")
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125 f.close()
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126
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127 class MockFindOverlapsWithServeralIntervals_query_case3 (object):
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128 def write(self, fileName):
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129 f = open(fileName, 'w')
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130 f.write("chr1\tquery\tquery3.1\t150\t250\t101\t+\t.\tID=query_1;Name=query3.1\n")
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131 f.write("chr1\tquery\tquery3.2\t380\t400\t21\t+\t.\tID=query_2;Name=query3.2\n")
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132 f.write("chr1\tquery\tquery3.3\t480\t520\t41\t+\t.\tID=query_3;Name=query3.3\n")
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133 f.write("chr1\tquery\tquery3.4\t510\t700\t191\t+\t.\tID=query_4;Name=query3.4\n")
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134 f.write("chr1\tquery\tquery3.5\t900\t950\t41\t+\t.\tID=query_5;Name=query3.5\n")
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135 f.close()
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136
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137 class MockFindOverlapsWithServeralIntervals_query_case4 (object):
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138 def write(self, fileName):
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139 f = open(fileName, 'w')
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140 f.write("chr1\tquery\tquery4.1\t400\t500\t101\t+\t.\tID=query_1;Name=query4.1\n")
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141 f.write("chr1\tquery\tquery4.2\t450\t600\t151\t+\t.\tID=query_2;Name=query4.2\n")
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142 f.write("chr1\tquery\tquery4.3\t700\t800\t101\t+\t.\tID=query_3;Name=query4.3\n")
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143 f.close()
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144
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145 class MockFindOverlapsWithServeralIntervals_query_case5 (object):
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146 def write(self, fileName):
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147 f = open(fileName, 'w')
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148 f.write("chr1\tquery\tquery5.1\t850\t950\t101\t+\t.\tID=query_1;Name=query5.1\n")
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149 f.close()
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150
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151 class MockFindOverlapsWithServeralIntervals_query_case6 (object):
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152 def write(self, fileName):
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153 f = open(fileName, 'w')
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154 f.write("chr1\tquery\tquery6.1\t200\t300\t101\t+\t.\tID=query_1;Name=query6.1\n")
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155 f.write("chr1\tquery\tquery6.2\t800\t900\t101\t+\t.\tID=query_2;Name=query6.2\n")
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156 f.close()
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157
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158 class MockFindOverlapsWithServeralIntervals_query_case7 (object):
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159 def write(self, fileName):
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160 f = open(fileName, 'w')
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161 f.write("chr1\tquery\tquery6.1\t530\t550\t21\t+\t.\tID=query_1;Name=query6.1\n")
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162 f.write("chr1\tquery\tquery6.2\t600\t700\t101\t+\t.\tID=query_2;Name=query6.2\n")
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163 f.write("chr1\tquery\tquery6.3\t650\t900\t251\t+\t.\tID=query_3;Name=query6.3\n")
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164 f.close()
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165
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166 class MockFindOverlapsWithServeralIntervals_query_case8 (object):
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167 def write(self, fileName):
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168 f = open(fileName, 'w')
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169 f.write("chr1\tquery\tquery7.1\t500\t600\t101\t+\t.\tID=query_1;Name=query7.1\n")
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170 f.write("chr1\tquery\tquery7.2\t700\t800\t101\t+\t.\tID=query_2;Name=query7.2\n")
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171 f.write("chr1\tquery\tquery7.3\t900\t1100\t201\t+\t.\tID=query_3;Name=query7.3\n")
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172 f.write("chr1\tquery\tquery7.4\t1200\t1300\t101\t+\t.\tID=query_4;Name=query7.4\n")
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173 f.close()
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174
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175 class MockFindOverlapsWithServeralIntervals_query_case9 (object):
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176 def write(self, fileName):
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177 f = open(fileName, 'w')
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178 f.write("chr1\tquery\tquery8.1\t400\t400\t101\t+\t.\tID=query_1;Name=query8.1\n")
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179 f.write("chr1\tquery\tquery8.2\t550\t650\t101\t+\t.\tID=query_2;Name=query8.2\n")
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180 f.close()
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181
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182 class MockFindOverlapsWithServeralIntervals_query_case10 (object):
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183 def write(self, fileName):
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184 f = open(fileName, 'w')
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185 f.write("chr1\tquery\tquery10.1\t700\t800\t101\t+\t.\tID=query_1;Name=query10.1\n")
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186 f.write("chr1\tquery\tquery10.2\t900\t1000\t101\t+\t.\tID=query_2;Name=query10.2\n")
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187 f.write("chr1\tquery\tquery10.3\t1100\t1300\t201\t+\t.\tID=query_3;Name=query10.3\n")
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188 f.close()
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189
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190 class MockFindOverlapsWithServeralIntervals_query_case11 (object):
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191 def write(self, fileName):
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192 f = open(fileName, 'w')
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193 f.write("chr1\tquery\tquery11.1\t420\t480\t61\t+\t.\tID=query_1;Name=query11.1\n")
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194 f.write("chr1\tquery\tquery11.2\t450\t715\t266\t+\t.\tID=query_2;Name=query11.2\n")
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195 f.close()
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196
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197
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