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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 from SMART.Java.Python.structure.Transcript import Transcript
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4
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5 class Test_Transcript(unittest.TestCase):
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6
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7 def test_getSize(self):
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8 transcript1 = Transcript()
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9 transcript1.setDirection("+")
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10 transcript1.setStart(2000)
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11 transcript1.setEnd(3000)
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12 transcript1.setChromosome("arm_X")
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13
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14 self.assertEqual(transcript1.getSize(), 1001)
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15
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16 transcript2 = Transcript()
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17 transcript2.copy(transcript1)
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18 self.assertEqual(transcript1.getSize(), 1001)
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19
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20 transcript3 = Transcript()
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21 transcript3.setDirection("+")
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22 transcript3.setChromosome("arm_X")
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23
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24 exon1 = Interval()
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25 exon1.setDirection("+")
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26 exon1.setChromosome("arm_X")
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27 exon1.setStart(100)
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28 exon1.setEnd(200)
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29 transcript3.addExon(exon1)
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30
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31 exon2 = Interval()
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32 exon2.setDirection("+")
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33 exon2.setChromosome("arm_X")
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34 exon2.setStart(300)
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35 exon2.setEnd(400)
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36 transcript3.addExon(exon2)
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37
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38 self.assertEqual(transcript3.getSize(), 203)
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39
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40
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41 def test_overlapWithExons(self):
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42 exon1_1 = Interval()
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43 exon1_1.setChromosome("chr1")
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44 exon1_1.setStart(100)
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45 exon1_1.setEnd(200)
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46 exon1_1.setDirection("+")
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47
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48 exon1_2 = Interval()
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49 exon1_2.setChromosome("chr1")
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50 exon1_2.setStart(500)
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51 exon1_2.setEnd(600)
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52 exon1_2.setDirection("+")
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53
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54 transcript1 = Transcript()
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55 transcript1.setChromosome("chr1")
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56 transcript1.setStart(100)
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57 transcript1.setEnd(600)
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58 transcript1.setDirection("+")
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59 transcript1.addExon(exon1_1)
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60 transcript1.addExon(exon1_2)
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61
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62 exon2_1 = Interval()
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63 exon2_1.copy(exon1_1)
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64
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65 transcript2 = Transcript()
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66 transcript2.setChromosome("chr1")
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67 transcript2.setStart(100)
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68 transcript2.setEnd(200)
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69 transcript2.setDirection("+")
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70 transcript2.addExon(exon2_1)
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71
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72 self.assertTrue(transcript1.overlapWithExon(transcript2))
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73
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74 transcript2.reverse()
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75 try:
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76 self.assertFalse(transcript1.overlapWithExon(transcript2))
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77 except Exception:
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78 pass
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79
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80 transcript2.reverse()
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81 transcript2.setChromosome("chr2")
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82 self.assertFalse(transcript1.overlapWithExon(transcript2))
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83
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84 exon3_1 = Interval()
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85 exon3_1.copy(exon1_1)
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86 exon3_1.setEnd(400)
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87 exon3_1.setStart(300)
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88
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89 transcript3 = Transcript()
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90 transcript3.setChromosome("chr1")
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91 transcript3.setStart(300)
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92 transcript3.setEnd(400)
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93 transcript3.setDirection("+")
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94 transcript3.addExon(exon3_1)
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95 self.assertFalse(transcript1.overlapWithExon(transcript3))
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96
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97
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98 def test_merge(self):
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99 exon1_1 = Interval()
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100 exon1_1.setChromosome("chr1")
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101 exon1_1.setStart(100)
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102 exon1_1.setEnd(200)
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103 exon1_1.setDirection("+")
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104
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105 exon1_2 = Interval()
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106 exon1_2.setChromosome("chr1")
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107 exon1_2.setStart(500)
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108 exon1_2.setEnd(600)
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109 exon1_2.setDirection("+")
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110
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111 transcript1 = Transcript()
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112 transcript1.setChromosome("chr1")
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113 transcript1.setEnd(600)
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114 transcript1.setStart(100)
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115 transcript1.setDirection("+")
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116 transcript1.addExon(exon1_1)
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117 transcript1.addExon(exon1_2)
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118
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119 exon2_1 = Interval()
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120 exon2_1.copy(exon1_1)
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121
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122 transcript2 = Transcript()
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123 transcript2.setChromosome("chr1")
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124 transcript2.setEnd(200)
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125 transcript2.setStart(100)
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126 transcript2.setDirection("+")
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127 transcript2.addExon(exon2_1)
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128
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129 transcript1.merge(transcript2)
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130 transcript1.sortExonsIncreasing()
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131 exons = transcript1.getExons()
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132 self.assertEqual(len(exons), 2)
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133 exon1, exon2 = exons
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134 self.assertEqual(exon1.getStart(), 100)
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135 self.assertEqual(exon1.getEnd(), 200)
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136 self.assertEqual(exon2.getStart(), 500)
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137 self.assertEqual(exon2.getEnd(), 600)
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138
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139 transcript2.setChromosome("chr2")
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140 try:
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141 transcript1.merge(transcript2)
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142 self.fail()
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143 except Exception:
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144 pass
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145
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146 exon3_1 = Interval()
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147 exon3_1.copy(exon1_1)
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148 exon3_1.setEnd(650)
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149 exon3_1.setStart(550)
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150
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151 transcript3 = Transcript()
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152 transcript3.setChromosome("chr1")
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153 transcript3.setEnd(650)
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154 transcript3.setStart(550)
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155 transcript3.setDirection("+")
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156 transcript3.addExon(exon3_1)
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157
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158 transcript1.merge(transcript3)
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159 self.assertEqual(transcript1.getStart(), 100)
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160 self.assertEqual(transcript1.getEnd(), 650)
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161 exons = transcript1.getExons()
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162 self.assertEqual(len(exons), 2)
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163 exon1, exon2 = exons
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164 self.assertEqual(exon1.getStart(), 100)
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165 self.assertEqual(exon1.getEnd(), 200)
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166 self.assertEqual(exon2.getStart(), 500)
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167 self.assertEqual(exon2.getEnd(), 650)
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168
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169 exon4_1 = Interval()
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170 exon4_1.copy(exon1_1)
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171 exon4_1.setEnd(400)
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172 exon4_1.setStart(300)
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173
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174 transcript4 = Transcript()
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175 transcript4.setChromosome("chr1")
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176 transcript4.setStart(300)
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177 transcript4.setEnd(400)
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178 transcript4.setDirection("+")
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179 transcript4.addExon(exon4_1)
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180
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181 transcript1.merge(transcript4)
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182 self.assertEqual(transcript1.getStart(), 100)
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183 self.assertEqual(transcript1.getEnd(), 650)
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184 transcript1.sortExonsIncreasing()
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185 exons = transcript1.getExons()
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186 self.assertEqual(len(exons), 3)
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187 exon1, exon2, exon3 = exons
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188 self.assertEqual(exon1.getStart(), 100)
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189 self.assertEqual(exon1.getEnd(), 200)
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190 self.assertEqual(exon2.getStart(), 300)
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191 self.assertEqual(exon2.getEnd(), 400)
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192 self.assertEqual(exon3.getStart(), 500)
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193 self.assertEqual(exon3.getEnd(), 650)
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194
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195
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196 def test_extendStart(self):
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197 transcript1 = Transcript()
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198 transcript1.setStart(2000)
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199 transcript1.setEnd(3000)
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200 transcript1.setDirection("+")
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201 transcript1.setChromosome("arm_X")
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202
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203 transcript2 = Transcript()
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204 transcript2.copy(transcript1)
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205 transcript2.setDirection("-")
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206
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207 transcript1.extendStart(1000)
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208 transcript2.extendStart(1000)
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209
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210
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211 self.assertEqual(transcript1.getDirection(), 1)
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212 self.assertEqual(transcript1.getStart(), 1000)
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213 self.assertEqual(transcript1.getEnd(), 3000)
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214 self.assertEqual(transcript1.getChromosome(), "arm_X")
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215
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216 self.assertEqual(transcript2.getDirection(), -1)
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217 self.assertEqual(transcript2.getStart(), 2000)
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218 self.assertEqual(transcript2.getEnd(), 4000)
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219 self.assertEqual(transcript2.getChromosome(), "arm_X")
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220
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221
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222 def test_restrictStart(self):
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223 exon1_1 = Interval()
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224 exon1_1.setChromosome("chr1")
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225 exon1_1.setStart(100)
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226 exon1_1.setEnd(200)
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227 exon1_1.setDirection("+")
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228
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229 exon1_2 = Interval()
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230 exon1_2.setChromosome("chr1")
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231 exon1_2.setStart(300)
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232 exon1_2.setEnd(500)
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233 exon1_2.setDirection("+")
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234
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235 transcript1 = Transcript()
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236 transcript1.setChromosome("chr1")
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237 transcript1.setStart(100)
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238 transcript1.setEnd(500)
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239 transcript1.setDirection("+")
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240 transcript1.addExon(exon1_1)
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241 transcript1.addExon(exon1_2)
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242
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243 transcript1.restrictStart(301)
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244 exons = transcript1.getExons()
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245 self.assertEqual(len(exons), 2)
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246 exon1, exon2 = exons
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247 self.assertEqual(exon1.getStart(), 100)
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248 self.assertEqual(exon1.getEnd(), 200)
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249 self.assertEqual(exon2.getStart(), 300)
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250 self.assertEqual(exon2.getEnd(), 400)
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251
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252
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253 def test__include(self):
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254 iTranscript1 = Transcript()
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255 iTranscript1.setName("transcript1")
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256 iTranscript1.setChromosome("chr1")
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257 iTranscript1.setStart(100)
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258 iTranscript1.setEnd(200)
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259 iTranscript1.setDirection("+")
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260
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261 iTranscript2 = Transcript()
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262 iTranscript2.copy(iTranscript1)
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263 iTranscript2.setName("transcript2")
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264 self.assertTrue(iTranscript1.include(iTranscript2))
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265 self.assertTrue(iTranscript2.include(iTranscript1))
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266
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267 iTranscript2.setChromosome("chr2")
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268 self.assertFalse(iTranscript1.include(iTranscript2))
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269 self.assertFalse(iTranscript2.include(iTranscript1))
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270
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271 iTranscript2.setChromosome("chr1")
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272 exon = Interval()
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273 exon.setChromosome("chr1")
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274 exon.setDirection("+")
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275 exon.setStart(300)
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276 exon.setEnd(400)
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277 iTranscript1.addExon(exon)
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278 self.assertTrue(iTranscript1.include(iTranscript2))
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279 self.assertFalse(iTranscript2.include(iTranscript1))
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280
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281 exon = Interval()
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282 exon.setChromosome("chr1")
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283 exon.setDirection("+")
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284 exon.setStart(500)
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285 exon.setEnd(600)
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286 iTranscript2.addExon(exon)
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287 self.assertFalse(iTranscript1.include(iTranscript2))
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288 self.assertFalse(iTranscript2.include(iTranscript1))
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289
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290
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291 def test__getDifference(self):
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292 iTranscript1 = Transcript()
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293 iTranscript1.setName("transcript1")
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294 iTranscript1.setChromosome("chr1")
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295 iTranscript1.setStart(100)
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296 iTranscript1.setEnd(400)
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297 iTranscript1.setDirection("+")
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298
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299 iTranscript2 = Transcript()
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300 iTranscript2.setName("transcript1")
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301 iTranscript2.setChromosome("chr1")
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302 iTranscript2.setStart(200)
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303 iTranscript2.setEnd(400)
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304 iTranscript2.setDirection("+")
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305
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306 newTranscript = iTranscript1.getDifference(iTranscript2)
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307 self.assertTrue(newTranscript.getStart(), 100)
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308 self.assertTrue(newTranscript.getEnd(), 199)
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309 exons = newTranscript.getExons()
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310 self.assertTrue(len(exons), 1)
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311 exon1 = exons[0]
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312 self.assertTrue(exon1.getStart(), 100)
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313 self.assertTrue(exon1.getEnd(), 199)
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314
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315 iTranscript2 = Transcript()
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316 iTranscript2.setName("transcript1")
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317 iTranscript2.setChromosome("chr1")
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318 iTranscript2.setStart(100)
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319 iTranscript2.setEnd(200)
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320 iTranscript2.setDirection("+")
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321
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322 newTranscript = iTranscript1.getDifference(iTranscript2)
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323 self.assertTrue(newTranscript.getStart(), 201)
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324 self.assertTrue(newTranscript.getEnd(), 400)
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325 exons = newTranscript.getExons()
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326 self.assertTrue(len(exons), 1)
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327 exon1 = exons[0]
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328 self.assertTrue(exon1.getStart(), 201)
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329 self.assertTrue(exon1.getEnd(), 400)
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330
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331 iTranscript2 = Transcript()
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332 iTranscript2.setName("transcript1")
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333 iTranscript2.setChromosome("chr1")
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334 iTranscript2.setStart(200)
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335 iTranscript2.setEnd(300)
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336 iTranscript2.setDirection("+")
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337
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338 newTranscript = iTranscript1.getDifference(iTranscript2)
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339 self.assertTrue(newTranscript.getStart(), 100)
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340 self.assertTrue(newTranscript.getEnd(), 400)
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341 exons = newTranscript.getExons()
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342 self.assertTrue(len(exons), 2)
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343 exon1, exon2 = exons
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344 self.assertTrue(exon1.getStart(), 100)
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345 self.assertTrue(exon1.getEnd(), 199)
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346 self.assertTrue(exon2.getStart(), 301)
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347 self.assertTrue(exon2.getEnd(), 400)
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348
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349
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350 if __name__ == '__main__':
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351 unittest.main()
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