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6
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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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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()
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