Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/structure/test/Test_Interval.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest |
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2 from SMART.Java.Python.structure.Interval import Interval |
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3 |
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4 class Test_Interval(unittest.TestCase): |
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5 |
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6 def setUp(self): |
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7 self.iInterval = Interval() |
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8 self.iInterval1 = Interval() |
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9 self.iInterval2 = Interval() |
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10 |
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11 def test__init__(self): |
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12 self.iInterval.setChromosome("chromosome") |
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13 self.iInterval.setName("sequence") |
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14 self.iInterval.setStart(0) |
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15 self.iInterval.setEnd(123) |
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16 obsStart = self.iInterval.getStart() |
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17 obsEnd = self.iInterval.getEnd() |
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18 expStart = 0 |
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19 expEnd = 123 |
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20 |
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21 self.assertEqual(expStart, obsStart) |
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22 self.assertEqual(expEnd, obsEnd) |
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23 |
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24 def test_copy(self): |
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25 self.iInterval1.setName("interval1") |
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26 self.iInterval1.setChromosome("chr1") |
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27 self.iInterval1.setStart(100) |
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28 self.iInterval1.setEnd(300) |
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29 self.iInterval1.setDirection("+") |
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30 |
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31 self.iInterval2.copy(self.iInterval1) |
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32 self.assertEqual(self.iInterval2.getName(), "interval1") |
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33 self.assertEqual(self.iInterval2.getChromosome(), "chr1") |
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34 self.assertEqual(self.iInterval2.getStart(), 100) |
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35 self.assertEqual(self.iInterval2.getEnd(), 300) |
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36 self.assertEqual(self.iInterval2.getDirection(), 1) |
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37 |
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38 self.iInterval1.setStart(200) |
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39 self.assertEqual(self.iInterval2.getStart(), 100) |
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40 |
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41 def test_getDirection(self): |
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42 self.iInterval1.setName("interval1") |
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43 self.iInterval1.setChromosome("chr1") |
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44 self.iInterval1.setStart(100) |
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45 self.iInterval1.setEnd(300) |
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46 self.iInterval1.setDirection("+") |
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47 expDirect = 1 |
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48 self.assertEquals(expDirect,self.iInterval1.getDirection()) |
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49 |
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50 #!!!! Warning: two methods getStart() and getEnd() give the information maximum and minimum in interval.!!!!# |
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51 #In case strand = "+", start < end; strand = "-", start > end |
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52 def test_setStartEnd(self): |
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53 self.iInterval1 = Interval() |
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54 self.iInterval1.setName("interval1") |
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55 self.iInterval1.setChromosome("chr1") |
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56 self.iInterval1.setStart(100) |
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57 self.iInterval1.setEnd(300) |
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58 self.iInterval1.setDirection("+") |
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59 |
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60 self.assertEqual(self.iInterval1.getName(), "interval1") |
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61 self.assertEqual(self.iInterval1.getChromosome(), "chr1") |
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62 self.assertEqual(self.iInterval1.getStart(),100) |
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63 self.assertEqual(self.iInterval1.getEnd(), 300) |
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64 self.assertEqual(self.iInterval1.getDirection(), 1) |
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65 |
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66 self.iInterval1.setStart(200) |
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67 self.assertEqual(self.iInterval1.getStart(), 200) |
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68 self.assertEqual(self.iInterval1.getEnd(), 300) |
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69 |
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70 self.iInterval1.setEnd(300) |
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71 self.iInterval1.setStart(100) |
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72 self.assertEqual(self.iInterval1.getStart(), 100) |
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73 self.assertEqual(self.iInterval1.getEnd(), 300) |
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74 |
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75 self.iInterval1.setEnd(1200) |
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76 self.iInterval1.setStart(1000) |
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77 self.assertEqual(self.iInterval1.getStart(), 1000) |
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78 self.assertEqual(self.iInterval1.getEnd(), 1200) |
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79 |
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80 self.iInterval1.reverse() |
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81 self.assertEqual(self.iInterval1.getDirection(), -1) |
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82 self.assertEqual(self.iInterval1.getStart(), 1000) |
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83 self.assertEqual(self.iInterval1.getEnd(), 1200) |
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84 |
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85 self.iInterval1.setStart(1100) |
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86 self.assertEqual(self.iInterval1.getStart(), 1100) |
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87 self.assertEqual(self.iInterval1.getEnd(), 1200) |
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88 |
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89 self.iInterval1.setEnd(2200) |
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90 self.iInterval1.setStart(2000) |
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91 self.assertEqual(self.iInterval1.getStart(), 2000) |
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92 self.assertEqual(self.iInterval1.getEnd(), 2200) |
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93 |
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94 self.iInterval1.setStart(1000) |
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95 self.iInterval1.setEnd(1200) |
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96 self.assertEqual(self.iInterval1.getStart(), 1000) |
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97 self.assertEqual(self.iInterval1.getEnd(), 1200) |
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98 |
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99 def test_reverse(self): |
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100 self.iInterval1 = Interval() |
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101 self.iInterval1.setName("interval1") |
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102 self.iInterval1.setChromosome("chr1") |
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103 self.iInterval1.setStart(100) |
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104 self.iInterval1.setEnd(200) |
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105 self.iInterval1.setDirection("+") |
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106 self.iInterval1.reverse() |
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107 self.assertEqual(self.iInterval1.getStart(), 100) |
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108 self.assertEqual(self.iInterval1.getEnd(), 200) |
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109 self.assertEqual(self.iInterval1.getDirection(), -1) |
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110 |
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111 def test_overlapWith(self): |
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112 self.iInterval1 = Interval() |
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113 self.iInterval1.setName("interval1") |
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114 self.iInterval1.setChromosome("chr1") |
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115 self.iInterval1.setStart(100) |
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116 self.iInterval1.setEnd(200) |
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117 self.iInterval1.setDirection("+") |
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118 |
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119 self.iInterval2 = Interval() |
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120 self.iInterval2.copy(self.iInterval1) |
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121 self.iInterval2.setName("interval2") |
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122 |
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123 self.assertTrue(self.iInterval1.overlapWith(self.iInterval2)) |
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124 |
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125 self.iInterval2.setChromosome("chr2") |
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126 try: |
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127 self.iInterval1.overlapWith(self.iInterval2) |
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128 self.fail() |
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129 except Exception: |
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130 pass |
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131 |
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132 self.iInterval2.setChromosome("chr1") |
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133 self.iInterval2.setEnd(400) |
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134 self.iInterval2.setStart(300) |
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135 self.assertFalse(self.iInterval1.overlapWith(self.iInterval2)) |
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136 |
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137 self.iInterval2.setStart(200) |
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138 self.assertTrue(self.iInterval1.overlapWith(self.iInterval2)) |
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139 |
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140 def test_isIncludeIn(self): |
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141 self.iInterval1 = Interval() |
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142 self.iInterval1.setName("interval1") |
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143 self.iInterval1.setChromosome("chr1") |
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144 self.iInterval1.setStart(100) |
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145 self.iInterval1.setEnd(200) |
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146 self.iInterval1.setDirection("+") |
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147 |
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148 self.iInterval2 = Interval() |
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149 self.iInterval2.setName("interval2") |
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150 self.iInterval2.setChromosome("chr1") |
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151 self.iInterval2.setStart(80) |
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152 self.iInterval2.setEnd(280) |
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153 self.iInterval2.setDirection("+") |
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154 self.assertTrue(self.iInterval1.isIncludeIn(self.iInterval2)) |
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155 |
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156 def test_getDistance(self): |
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157 self.iInterval1 = Interval() |
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158 self.iInterval1.setName("interval1") |
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159 self.iInterval1.setChromosome("chr1") |
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160 self.iInterval1.setStart(100) |
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161 self.iInterval1.setEnd(200) |
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162 self.iInterval1.setDirection("+") |
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163 |
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164 self.iInterval2 = Interval() |
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165 self.iInterval2.copy(self.iInterval1) |
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166 self.iInterval2.setName("interval2") |
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167 |
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168 self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 0) |
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169 self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 0) |
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170 |
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171 self.iInterval2.setChromosome("chr2") |
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172 try: |
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173 self.iInterval1.getDistance(self.iInterval2) |
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174 self.fail() |
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175 except Exception: |
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176 pass |
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177 |
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178 self.iInterval2.setChromosome("chr1") |
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179 self.iInterval2.setEnd(400) |
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180 self.iInterval2.setStart(300) |
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181 self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 100) |
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182 self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 100) |
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183 |
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184 def test_getRelativeDistance(self): |
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185 self.iInterval1 = Interval() |
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186 self.iInterval1.setName("interval1") |
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187 self.iInterval1.setChromosome("chr1") |
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188 self.iInterval1.setStart(100) |
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189 self.iInterval1.setEnd(200) |
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190 self.iInterval1.setDirection("+") |
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191 |
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192 self.iInterval2 = Interval() |
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193 self.iInterval2.copy(self.iInterval1) |
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194 self.iInterval2.setName("interval2") |
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195 |
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196 self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 0) |
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197 self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 0) |
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198 |
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199 self.iInterval2.setChromosome("chr2") |
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200 try: |
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201 self.iInterval1.getDistance(self.iInterval2) |
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202 self.fail() |
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203 except Exception: |
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204 pass |
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205 |
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206 self.iInterval2.setChromosome("chr1") |
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207 self.iInterval2.setEnd(400) |
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208 self.iInterval2.setStart(300) |
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209 self.assertEqual(self.iInterval1.getRelativeDistance(self.iInterval2), 100) |
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210 self.assertEqual(self.iInterval2.getRelativeDistance(self.iInterval1), -100) |
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211 |
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212 def test_merge(self): |
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213 self.iInterval1 = Interval() |
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214 self.iInterval1.setName("interval1") |
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215 self.iInterval1.setChromosome("chr1") |
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216 self.iInterval1.setStart(100) |
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217 self.iInterval1.setEnd(200) |
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218 self.iInterval1.setDirection("+") |
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219 |
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220 self.iInterval2 = Interval() |
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221 self.iInterval2.copy(self.iInterval1) |
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222 self.iInterval2.setName("interval2") |
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223 self.iInterval2.merge(self.iInterval1) |
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224 |
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225 self.assertEqual(self.iInterval1, self.iInterval2) |
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226 |
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227 self.iInterval2.setChromosome("chr2") |
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228 expMessage = "Cannot merge '%s' and '%s' for they are on different chromosomes." % (str(self.iInterval2), str(self.iInterval1)) |
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229 isExceptionRaised = False |
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230 try: |
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231 self.iInterval2.merge(self.iInterval1) |
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232 except Exception, e: |
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233 isExceptionRaised = True |
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234 obsMessage = str(e) |
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235 |
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236 self.assertTrue(isExceptionRaised) |
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237 self.assertEquals(expMessage, obsMessage) |
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238 #Warning! Both two intervals should be on the same chromosome and direction. |
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239 self.iInterval2.setChromosome("chr1") |
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240 self.iInterval2.setStart(300) |
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241 self.iInterval2.setEnd(400) |
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242 self.iInterval2.merge(self.iInterval1) |
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243 self.assertEqual(self.iInterval2.getStart(), 100) |
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244 self.assertEqual(self.iInterval2.getEnd(), 400) |
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245 self.assertEqual(self.iInterval2.getChromosome(), "chr1") |
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246 |
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247 def test_include(self): |
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248 iInterval1 = Interval() |
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249 iInterval1.setName("interval1") |
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250 iInterval1.setChromosome("chr1") |
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251 iInterval1.setStart(100) |
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252 iInterval1.setEnd(200) |
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253 iInterval1.setDirection("+") |
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254 |
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255 iInterval2 = Interval() |
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256 iInterval2.copy(iInterval1) |
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257 iInterval2.setName("interval2") |
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258 self.assertTrue(iInterval1.include(iInterval2)) |
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259 self.assertTrue(iInterval2.include(iInterval1)) |
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260 |
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261 iInterval2.setChromosome("chr2") |
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262 self.assertFalse(iInterval1.include(iInterval2)) |
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263 self.assertFalse(iInterval2.include(iInterval1)) |
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264 |
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265 iInterval2.setChromosome("chr1") |
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266 iInterval1.setStart(1) |
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267 self.assertTrue(iInterval1.include(iInterval2)) |
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268 self.assertFalse(iInterval2.include(iInterval1)) |
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269 |
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270 iInterval1.setStart(100) |
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271 iInterval1.setEnd(300) |
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272 self.assertTrue(iInterval1.include(iInterval2)) |
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273 self.assertFalse(iInterval2.include(iInterval1)) |
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274 |
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275 |
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276 def test_getDifference(self): |
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277 iInterval1 = Interval() |
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278 iInterval1.setName("interval1") |
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279 iInterval1.setChromosome("chr1") |
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280 iInterval1.setStart(100) |
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281 iInterval1.setEnd(400) |
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282 iInterval1.setDirection("+") |
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283 |
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284 iInterval2 = Interval() |
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285 iInterval2.copy(iInterval1) |
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286 iInterval2.setName("interval2") |
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287 self.assertEqual(iInterval1.getDifference(iInterval2), []) |
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288 self.assertEqual(iInterval2.getDifference(iInterval1), []) |
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289 |
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290 iInterval2.setChromosome("chr2") |
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291 results = iInterval1.getDifference(iInterval2) |
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292 self.assertEqual(len(results), 1) |
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293 resultInterval = results[0] |
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294 self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) |
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295 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) |
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296 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) |
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297 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) |
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298 |
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299 iInterval2.setChromosome("chr1") |
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300 iInterval2.setEnd(300) |
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301 results = iInterval1.getDifference(iInterval2) |
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302 self.assertEqual(len(results), 1) |
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303 resultInterval = results[0] |
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304 self.assertEqual(resultInterval.getStart(), 301) |
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305 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) |
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306 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) |
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307 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) |
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308 |
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309 iInterval2.setDirection("-") |
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310 results = iInterval1.getDifference(iInterval2, True) |
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311 self.assertEqual(len(results), 1) |
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312 resultInterval = results[0] |
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313 self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) |
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314 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) |
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315 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) |
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316 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) |
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317 |
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318 iInterval2.setDirection("+") |
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319 iInterval2.setStart(200) |
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320 results = iInterval1.getDifference(iInterval2) |
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321 self.assertEqual(len(results), 2) |
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322 resultInterval1, resultInterval2 = results |
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323 self.assertEqual(resultInterval1.getStart(), iInterval1.getStart()) |
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324 self.assertEqual(resultInterval1.getEnd(), 199) |
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325 self.assertEqual(resultInterval1.getDirection(), iInterval1.getDirection()) |
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326 self.assertEqual(resultInterval1.getChromosome(), iInterval1.getChromosome()) |
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327 self.assertEqual(resultInterval2.getStart(), 301) |
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328 self.assertEqual(resultInterval2.getEnd(), iInterval1.getEnd()) |
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329 self.assertEqual(resultInterval2.getDirection(), iInterval1.getDirection()) |
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330 self.assertEqual(resultInterval2.getChromosome(), iInterval1.getChromosome()) |
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331 |
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332 iInterval2.setEnd(2000) |
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333 iInterval2.setStart(1000) |
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334 results = iInterval1.getDifference(iInterval2) |
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335 self.assertEqual(len(results), 1) |
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336 resultInterval = results[0] |
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337 self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) |
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338 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) |
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339 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) |
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340 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) |
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341 |
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342 def test_mergeWithDifferentStrand(self): |
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343 self.iInterval1 = Interval() |
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344 self.iInterval1.setName("interval1") |
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345 self.iInterval1.setChromosome("chr1") |
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346 self.iInterval1.setStart(100) |
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347 self.iInterval1.setEnd(200) |
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348 self.iInterval1.setDirection("+") |
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349 |
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350 self.iInterval2 = Interval() |
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351 self.iInterval2.setName("interval2") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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352 self.iInterval2.setChromosome("chr1") |
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353 self.iInterval2.setStart(300) |
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354 self.iInterval2.setEnd(400) |
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355 self.iInterval2.setDirection("-") |
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356 |
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357 expMessage = "Cannot merge '%s' and '%s' for they are on different strands." % (str(self.iInterval2), str(self.iInterval1)) |
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358 isExceptionRaised = False |
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359 try: |
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360 self.iInterval2.merge(self.iInterval1) |
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361 except Exception, e: |
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362 isExceptionRaised = True |
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363 obsMessage = str(e) |
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364 |
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365 self.assertTrue(isExceptionRaised) |
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366 self.assertEquals(expMessage, obsMessage) |
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367 |
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368 if __name__ == "__main__": |
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369 unittest.main() |