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1 import unittest
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2 import os
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3 from optparse import OptionParser
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4 from SMART.Java.Python.structure.Transcript import Transcript
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5 from commons.core.parsing.ParserChooser import ParserChooser
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6 from commons.core.parsing.GffParser import GffParser
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7 from commons.core.writer.Gff3Writer import Gff3Writer
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8 from SMART.Java.Python.CombineTags import CombineTags
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9
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10 class Test_F_CombineTags(unittest.TestCase):
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11
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12 def setUp(self):
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13 self._inputFileName = "inputFileTest.gff3"
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14 self._outputFileName = "outputFileTest.gff3"
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15 self._tag1 = "tag1"
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16 self._tag2 = "tag2"
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17 self._outputTag = "outputTag"
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18
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19 def tearDown(self):
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20 os.remove(self._inputFileName)
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21 os.remove(self._outputFileName)
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22
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23 def test_plus(self):
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24 transcript = self._createDummyTranscript()
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25 transcript.setTagValue(self._tag1, 1)
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26 transcript.setTagValue(self._tag2, 2)
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27 self._writeTranscript(transcript)
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28 combiner = CombineTags(0)
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29 combiner.setInputFile(self._inputFileName, "gff3")
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30 combiner.setOutputFile(self._outputFileName)
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31 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
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32 combiner.setOperation("plus")
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33 combiner.run()
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34 self._testOutputTag(3)
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35
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36 def test_minus(self):
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37 transcript = self._createDummyTranscript()
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38 transcript.setTagValue(self._tag1, 2)
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39 transcript.setTagValue(self._tag2, 1)
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40 self._writeTranscript(transcript)
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41 combiner = CombineTags(0)
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42 combiner.setInputFile(self._inputFileName, "gff3")
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43 combiner.setOutputFile(self._outputFileName)
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44 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
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45 combiner.setOperation("minus")
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46 combiner.run()
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47 self._testOutputTag(1)
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48
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49 def test_times(self):
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50 transcript = self._createDummyTranscript()
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51 transcript.setTagValue(self._tag1, 6)
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52 transcript.setTagValue(self._tag2, 3)
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53 self._writeTranscript(transcript)
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54 combiner = CombineTags(0)
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55 combiner.setInputFile(self._inputFileName, "gff3")
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56 combiner.setOutputFile(self._outputFileName)
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57 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
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58 combiner.setOperation("times")
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59 combiner.run()
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60 self._testOutputTag(18)
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61
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62 def test_div(self):
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63 transcript = self._createDummyTranscript()
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64 transcript.setTagValue(self._tag1, 6)
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65 transcript.setTagValue(self._tag2, 3)
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66 self._writeTranscript(transcript)
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67 combiner = CombineTags(0)
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68 combiner.setInputFile(self._inputFileName, "gff3")
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69 combiner.setOutputFile(self._outputFileName)
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70 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
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71 combiner.setOperation("div")
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72 combiner.run()
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73 self._testOutputTag(2)
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74
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75 def test_default(self):
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76 transcript = self._createDummyTranscript()
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77 transcript.setTagValue(self._tag1, 1)
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78 self._writeTranscript(transcript)
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79 combiner = CombineTags(0)
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80 combiner.setInputFile(self._inputFileName, "gff3")
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81 combiner.setOutputFile(self._outputFileName)
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82 combiner.setTags(self._tag1, self._tag2, self._outputTag, 0)
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83 combiner.setOperation("plus")
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84 combiner.run()
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85 self._testOutputTag(0)
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86
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87 def _createDummyTranscript(self):
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88 transcript = Transcript()
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89 transcript.setChromosome("chr1")
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90 transcript.setName("test1")
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91 transcript.setEnd(200)
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92 transcript.setStart(100)
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93 transcript.setDirection("+")
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94 return transcript
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95
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96 def _testOutputTag(self, value):
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97 parser = GffParser(self._outputFileName, 0)
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98 for transcript in parser.getIterator():
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99 self.assertEquals(float(transcript.getTagValue(self._outputTag)), value)
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100 parser.close()
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101
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102 def _writeTranscript(self, transcript):
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103 f = open(self._inputFileName, "w")
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104 f.write(transcript.printGff3("test"))
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105 f.close()
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106
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107
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108 if __name__ == "__main__":
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109 unittest.main()
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