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1 import unittest
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2 import os
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3 from SMART.Java.Python.getExons import GetExons
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4 from commons.core.parsing.GffParser import GffParser
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5
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6 class Test_F_GetExons(unittest.TestCase):
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7
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8 def setUp(self):
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9 self._inputFileName = "inputFileTest.bed"
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10 self._writeInputFile()
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11 self._outputFileName = "output.gff3"
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12
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13 def tearDown(self):
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14 os.remove(self._inputFileName)
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15 os.remove(self._outputFileName)
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16
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17 def test_run_simple(self):
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18 ge = GetExons(0)
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19 ge.setInputFile(self._inputFileName, "bed")
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20 ge.setOutputFile(self._outputFileName)
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21 ge.run()
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22 parser = GffParser(self._outputFileName, 0)
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23 self.assertEqual(parser.getNbTranscripts(), 5)
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24 for cpt, transcript in enumerate(parser.getIterator()):
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25 self.assertEqual(transcript.getChromosome(), "arm_X")
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26 self.assertEqual(transcript.getDirection(), 1)
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27 self.assertEqual(transcript.getNbExons(), 1)
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28 if cpt == 0:
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29 self.assertEqual(transcript.getStart(), 10000001)
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30 self.assertEqual(transcript.getEnd(), 10000100)
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31 elif cpt == 1:
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32 self.assertEqual(transcript.getStart(), 10000201)
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33 self.assertEqual(transcript.getEnd(), 10000300)
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34 elif cpt == 2:
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35 self.assertEqual(transcript.getStart(), 10000401)
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36 self.assertEqual(transcript.getEnd(), 10000500)
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37 elif cpt == 3:
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38 self.assertEqual(transcript.getStart(), 10000601)
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39 self.assertEqual(transcript.getEnd(), 10000700)
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40 elif cpt == 4:
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41 self.assertEqual(transcript.getStart(), 10000801)
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42 self.assertEqual(transcript.getEnd(), 10000900)
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43
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44 def test_run_firstExon(self):
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45 ge = GetExons(0)
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46 ge.setInputFile(self._inputFileName, "bed")
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47 ge.setOutputFile(self._outputFileName)
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48 ge.setSelection("1")
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49 ge.run()
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50 parser = GffParser(self._outputFileName, 0)
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51 self.assertEqual(parser.getNbTranscripts(), 1)
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52 for cpt, transcript in enumerate(parser.getIterator()):
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53 self.assertEqual(transcript.getChromosome(), "arm_X")
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54 self.assertEqual(transcript.getDirection(), 1)
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55 self.assertEqual(transcript.getNbExons(), 1)
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56 self.assertEqual(transcript.getStart(), 10000001)
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57 self.assertEqual(transcript.getEnd(), 10000100)
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58
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59 def test_run_lastExon(self):
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60 ge = GetExons(0)
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61 ge.setInputFile(self._inputFileName, "bed")
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62 ge.setOutputFile(self._outputFileName)
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63 ge.setSelection("-1")
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64 ge.run()
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65 parser = GffParser(self._outputFileName, 0)
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66 self.assertEqual(parser.getNbTranscripts(), 1)
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67 for cpt, transcript in enumerate(parser.getIterator()):
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68 self.assertEqual(transcript.getChromosome(), "arm_X")
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69 self.assertEqual(transcript.getDirection(), 1)
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70 self.assertEqual(transcript.getNbExons(), 1)
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71 self.assertEqual(transcript.getStart(), 10000801)
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72 self.assertEqual(transcript.getEnd(), 10000900)
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73
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74 def test_run_first_lastExon(self):
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75 ge = GetExons(0)
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76 ge.setInputFile(self._inputFileName, "bed")
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77 ge.setOutputFile(self._outputFileName)
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78 ge.setSelection("1,-1")
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79 ge.run()
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80 parser = GffParser(self._outputFileName, 0)
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81 self.assertEqual(parser.getNbTranscripts(), 2)
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82 for cpt, transcript in enumerate(parser.getIterator()):
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83 self.assertEqual(transcript.getChromosome(), "arm_X")
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84 self.assertEqual(transcript.getDirection(), 1)
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85 self.assertEqual(transcript.getNbExons(), 1)
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86 if cpt == 0:
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87 self.assertEqual(transcript.getStart(), 10000001)
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88 self.assertEqual(transcript.getEnd(), 10000100)
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89 elif cpt == 1:
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90 self.assertEqual(transcript.getStart(), 10000801)
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91 self.assertEqual(transcript.getEnd(), 10000900)
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92
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93 def test_run_interval(self):
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94 ge = GetExons(0)
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95 ge.setInputFile(self._inputFileName, "bed")
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96 ge.setOutputFile(self._outputFileName)
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97 ge.setSelection("2..3")
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98 ge.run()
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99 parser = GffParser(self._outputFileName, 0)
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100 self.assertEqual(parser.getNbTranscripts(), 2)
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101 for cpt, transcript in enumerate(parser.getIterator()):
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102 self.assertEqual(transcript.getChromosome(), "arm_X")
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103 self.assertEqual(transcript.getDirection(), 1)
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104 self.assertEqual(transcript.getNbExons(), 1)
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105 if cpt == 0:
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106 self.assertEqual(transcript.getStart(), 10000201)
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107 self.assertEqual(transcript.getEnd(), 10000300)
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108 elif cpt == 1:
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109 self.assertEqual(transcript.getStart(), 10000401)
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110 self.assertEqual(transcript.getEnd(), 10000500)
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111
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112 def test_run_interval_element(self):
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113 ge = GetExons(0)
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114 ge.setInputFile(self._inputFileName, "bed")
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115 ge.setOutputFile(self._outputFileName)
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116 ge.setSelection("2..3,-1")
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117 ge.run()
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118 parser = GffParser(self._outputFileName, 0)
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119 self.assertEqual(parser.getNbTranscripts(), 3)
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120 for cpt, transcript in enumerate(parser.getIterator()):
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121 self.assertEqual(transcript.getChromosome(), "arm_X")
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122 self.assertEqual(transcript.getDirection(), 1)
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123 self.assertEqual(transcript.getNbExons(), 1)
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124 if cpt == 0:
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125 self.assertEqual(transcript.getStart(), 10000201)
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126 self.assertEqual(transcript.getEnd(), 10000300)
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127 elif cpt == 1:
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128 self.assertEqual(transcript.getStart(), 10000401)
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129 self.assertEqual(transcript.getEnd(), 10000500)
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130 elif cpt == 2:
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131 self.assertEqual(transcript.getStart(), 10000801)
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132 self.assertEqual(transcript.getEnd(), 10000900)
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133
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134
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135
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136 def _writeInputFile(self):
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137 f = open(self._inputFileName, "w")
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138 f.write("arm_X\t10000001\t10000900\ttest1.1\t100\t+\t10000100\t10000200\t0\t5\t100,100,100,100,100,\t0,200,400,600,800,\n")
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139 f.close()
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140
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141
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142
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143 if __name__ == "__main__":
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144 unittest.main()
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145
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