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1 from commons.core.writer.Gff3Writer import Gff3Writer
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2 from SMART.Java.Python.structure.Transcript import Transcript
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3 from SMART.Java.Python.structure.Interval import Interval
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4 import unittest
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5 import os
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6 from SMART.Java.Python.misc import Utils
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7
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8 class Test_Gff3Writer(unittest.TestCase):
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9
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10 def test_writer(self):
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11 obsFileName = "testGffWriter1.gff3"
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12 writer = Gff3Writer(obsFileName)
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13
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14 transcript = Transcript()
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15 transcript.setName("test1.1")
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16 transcript.setChromosome("arm_X")
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17 transcript.setStart(1000)
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18 transcript.setEnd(4000)
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19 transcript.setDirection("+")
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20 transcript.setTagValue("ID", "test1.1-1")
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21 transcript.setTagValue("occurrence", 1)
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22 transcript.setTagValue("nbOccurrences", 2)
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23
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24 exon1 = Interval()
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25 exon1.setChromosome("arm_X")
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26 exon1.setStart(1000)
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27 exon1.setEnd(2000)
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28 exon1.setDirection("+")
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29
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30 exon2 = Interval()
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31 exon2.setChromosome("arm_X")
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32 exon2.setStart(3000)
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33 exon2.setEnd(4000)
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34 exon2.setDirection("+")
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35
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36 transcript.addExon(exon1)
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37 transcript.addExon(exon2)
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38
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39 writer.addTranscript(transcript)
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40 writer.write()
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41 writer.close()
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42
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43 expFileName = "expFile.gff3"
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44 f = open(expFileName, "w")
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45 f.write("arm_X\tS-MART\ttranscript\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n")
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46 f.write("arm_X\tS-MART\texon\t1000\t2000\t.\t+\t.\tID=test1.1-1-exon1;Name=test1.1-exon1;Parent=test1.1-1\n")
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47 f.write("arm_X\tS-MART\texon\t3000\t4000\t.\t+\t.\tID=test1.1-1-exon2;Name=test1.1-exon2;Parent=test1.1-1\n")
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48 f.close()
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49
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50 self.assertTrue(Utils.diff(expFileName, obsFileName))
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51
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52 os.remove(expFileName)
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53 os.remove(obsFileName)
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54
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55 def test_writerAltNames(self):
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56 obsFileName = "testGffWriter1.gff3"
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57 writer = Gff3Writer(obsFileName,title="ALTSOURCE", feature="Match", featurePart="Match-Part")
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58
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59 transcript = Transcript()
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60 transcript.setName("test1.1")
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61 transcript.setChromosome("arm_X")
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62 transcript.setStart(1000)
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63 transcript.setEnd(4000)
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64 transcript.setDirection("+")
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65 transcript.setTagValue("ID", "test1.1-1")
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66 transcript.setTagValue("occurrence", 1)
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67 transcript.setTagValue("nbOccurrences", 2)
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68
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69 exon1 = Interval()
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70 exon1.setChromosome("arm_X")
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71 exon1.setStart(1000)
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72 exon1.setEnd(2000)
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73 exon1.setDirection("+")
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74
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75 exon2 = Interval()
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76 exon2.setChromosome("arm_X")
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77 exon2.setStart(3000)
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78 exon2.setEnd(4000)
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79 exon2.setDirection("+")
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80
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81 transcript.addExon(exon1)
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82 transcript.addExon(exon2)
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83
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84 writer.addTranscript(transcript)
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85 writer.write()
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86 writer.close()
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87
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88 expFileName = "expFile.gff3"
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89 f = open(expFileName, "w")
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90 f.write("arm_X\tALTSOURCE\tMatch\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n")
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91 f.write("arm_X\tALTSOURCE\tMatch-Part\t1000\t2000\t.\t+\t.\tID=test1.1-1-Match-Part1;Name=test1.1-Match-Part1;Parent=test1.1-1\n")
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92 f.write("arm_X\tALTSOURCE\tMatch-Part\t3000\t4000\t.\t+\t.\tID=test1.1-1-Match-Part2;Name=test1.1-Match-Part2;Parent=test1.1-1\n")
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93 f.close()
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94
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95 self.assertTrue(Utils.diff(expFileName, obsFileName))
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96
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97 os.remove(expFileName)
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98 os.remove(obsFileName)
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99
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100 if __name__ == '__main__':
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101 unittest.main()
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