Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/test/Test_CoordsParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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0
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 |