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1 import unittest
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2 from commons.core.parsing.CoordsParser import CoordsParser
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3 from SMART.Java.Python.mappingToCoordinates import MappingToCoordinates
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4
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5
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6 class Test_CoordsParser(unittest.TestCase):
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7
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8
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9 def test_Parser(self):
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10 parser = CoordsParser("data/testCoordsParser.coords")
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11
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12 cpt = 0
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13 for mapping in parser.getIterator():
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14 transcript = mapping.getTranscript()
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15 cpt += 1
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16 if cpt == 1:
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17 self.assertEqual(transcript.getChromosome(), "scaffold_1")
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18 self.assertEqual(transcript.getName(), "gi|240254421:1-30427671")
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19 self.assertEqual(transcript.getStart(), 1)
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20 self.assertEqual(transcript.getEnd(), 6251)
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21 self.assertEqual(transcript.getDirection(), -1)
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22 self.assertEqual(transcript.getNbExons(), 1)
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23 self.assertEqual(transcript.getTagValue("identity"), 89.030000000000001)
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24 exons = transcript.getExons()
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25 self.assertEqual(exons[0].getChromosome(), "scaffold_1")
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26 self.assertEqual(exons[0].getStart(), 1)
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27 self.assertEqual(exons[0].getEnd(), 6251)
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28 self.assertEqual(exons[0].getDirection(), -1)
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29 self.assertEqual(transcript.getSize(), 6251)
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30 elif cpt == 2:
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31 self.assertEqual(transcript.getChromosome(), "scaffold_1")
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32 self.assertEqual(transcript.getName(), "gi|240254421:1-30427671")
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33 self.assertEqual(transcript.getStart(), 9127)
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34 self.assertEqual(transcript.getEnd(), 11947)
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35 self.assertEqual(transcript.getDirection(), -1)
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36 self.assertEqual(transcript.getNbExons(), 1)
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37 self.assertEqual(transcript.getTagValue("identity"), 90.450000000000003)
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38 exons = transcript.getExons()
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39 self.assertEqual(exons[0].getChromosome(), "scaffold_1")
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40 self.assertEqual(exons[0].getStart(), 9127)
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41 self.assertEqual(exons[0].getEnd(), 11947)
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42 self.assertEqual(exons[0].getDirection(), -1)
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43 self.assertEqual(transcript.getSize(), 2821)
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44 if cpt == 3:
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45 self.assertEqual(transcript.getChromosome(), "scaffold_1")
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46 self.assertEqual(transcript.getName(), "gi|240254421:1-30427671")
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47 self.assertEqual(transcript.getStart(), 12201)
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48 self.assertEqual(transcript.getEnd(), 12953)
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49 self.assertEqual(transcript.getDirection(), -1)
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50 self.assertEqual(transcript.getNbExons(), 1)
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51 exons = transcript.getExons()
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52 self.assertEqual(exons[0].getChromosome(), "scaffold_1")
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53 self.assertEqual(exons[0].getStart(), 12201)
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54 self.assertEqual(exons[0].getEnd(), 12953)
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55 self.assertEqual(exons[0].getDirection(), -1)
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56 self.assertEqual(transcript.getSize(), 753)
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57
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58 def test_Parser_showcoord(self):
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59 parser = CoordsParser("data/testCoordsParser_showcoord.coords")
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60 expTranscriptCount = 1
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61 obsTranscriptCount = 0
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62
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63 for mapping in parser.getIterator():
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64 transcript = mapping.getTranscript()
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65 obsTranscriptCount += 1
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66 self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001")
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67 self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003")
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68 self.assertEqual(transcript.getStart(), 296)
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69 self.assertEqual(transcript.getEnd(), 2292)
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70 self.assertEqual(transcript.getDirection(), 1)
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71 self.assertEqual(transcript.getTagValue("identity"), 98.30)
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72 self.assertEqual(transcript.getTagValue("target_pident"), 98.30)
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73 self.assertEqual(transcript.getTagValue("target_pcover"), 3.32)
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74 self.assertEqual(transcript.getTagValue("target_length"), 60273)
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75 self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 1 2001")
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76 self.assertEqual(transcript.getSize(), 1997)
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77
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78 self.assertEquals(expTranscriptCount, obsTranscriptCount)
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79
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80 def test_Parser_showcoord_promer(self):
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81 parser = CoordsParser("data/testCoordsParser_showcoord_promer.coords")
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82 expTranscriptCount = 1
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83 obsTranscriptCount = 0
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84
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85 for mapping in parser.getIterator():
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86 transcript = mapping.getTranscript()
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87 obsTranscriptCount += 1
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88 self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001")
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89 self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003")
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90 self.assertEqual(transcript.getStart(), 291)
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91 self.assertEqual(transcript.getEnd(), 1229)
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92 self.assertEqual(transcript.getDirection(), -1)
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93 self.assertEqual(transcript.getTagValue("identity"), 94.25)
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94 self.assertEqual(transcript.getTagValue("target_pident"), 94.25)
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95 self.assertEqual(transcript.getTagValue("target_pcover"), 1.56)
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96 self.assertEqual(transcript.getTagValue("target_length"), 60273)
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97 self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 939 1")
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98 self.assertEqual(transcript.getSize(), 939)
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99
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100 self.assertEquals(expTranscriptCount, obsTranscriptCount)
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101
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102
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103 if __name__ == '__main__':
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104 unittest.main()
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105
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