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1 import os
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2 import unittest
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3 from commons.pyRepetUnit.align.AlignList import AlignList
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4 from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils
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5 from commons.core.utils.FileUtils import FileUtils
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6 from commons.core.coord.Range import Range
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7 from commons.core.coord.Align import Align
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8
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9 class Test_AlignListUtils (unittest.TestCase):
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10
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11 def setUp(self):
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12 self.inputFileName = "dummyAlignFile.align"
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13 self.outputFileName = "dummyAlignFile.out"
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14
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15 def testRead(self):
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16 f = open(self.inputFileName, "w")
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17 f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t2.6e-60\t0\t3.2\n")
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18 f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t0\t2.9\n")
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19 f.close()
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20 alignRead = AlignListUtils()
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21 tableauAlignInstance = alignRead.read(self.inputFileName)
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22 self.assertEquals(tableauAlignInstance.get(0).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1")
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23 self.assertEquals(tableauAlignInstance.get(0).range_query.start, 91)
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24 self.assertEquals(tableauAlignInstance.get(0).range_query.end, 108)
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25 self.assertEquals(tableauAlignInstance.get(0).range_subject.seqname, "DUF234")
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26 self.assertEquals(tableauAlignInstance.get(0).range_subject.start, 5)
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27 self.assertEquals(tableauAlignInstance.get(0).range_subject.end, 22)
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28 self.assertEquals(tableauAlignInstance.get(0).e_value, 2.6e-60)
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29 self.assertEquals(tableauAlignInstance.get(0).score, 0)
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30 self.assertEquals(tableauAlignInstance.get(0).identity, 3.2)
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31 self.assertEquals(tableauAlignInstance.get(1).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1")
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32 self.assertEquals(tableauAlignInstance.get(1).range_query.start, 111)
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33 self.assertEquals(tableauAlignInstance.get(1).range_query.end, 119)
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34 self.assertEquals(tableauAlignInstance.get(1).range_subject.seqname, "DUF1414")
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35 self.assertEquals(tableauAlignInstance.get(1).range_subject.start, 1)
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36 self.assertEquals(tableauAlignInstance.get(1).range_subject.end, 9)
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37 self.assertEquals(tableauAlignInstance.get(1).e_value, 6.3)
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38 self.assertEquals(tableauAlignInstance.get(1).score, 0)
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39 self.assertEquals(tableauAlignInstance.get(1).identity, 2.9)
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40 os.system("rm " + self.inputFileName)
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41
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42 def testWrite(self):
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43 f = open("expectedAlignFile.align", "w")
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44 f.write("biduleChouetteQuery\t20\t55\tbiduleChouetteSubject\t2\t15\t0.005\t20\t0.000000\n")
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45 f.write("trucBiduleQuery\t110\t155\ttrucBiduleSubject\t1\t35\t2\t1\t0.000000\n")
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46 f.write("dummyQuery\t1\t65\tdummySubject\t1\t25\t2.6e-60\t50\t0.000000\n")
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47 f.close()
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48 listAlignInstance = AlignList()
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49 align1 = Align()
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50 align1.range_query = Range("biduleChouetteQuery", 20, 55)
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51 align1.range_subject = Range("biduleChouetteSubject", 2, 15)
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52 align1.e_value = 0.005
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53 align1.score = 20
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54 listAlignInstance.append(align1)
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55 align2 = Align()
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56 align2.range_query = Range("trucBiduleQuery", 110, 155)
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57 align2.range_subject = Range("trucBiduleSubject", 1, 35)
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58 align2.e_value = 2
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59 align2.score = 1.5
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60 listAlignInstance.append(align2)
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61 align3 = Align()
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62 align3.range_query = Range("dummyQuery", 1, 65)
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63 align3.range_subject = Range("dummySubject", 1, 25)
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64 align3.e_value = 2.6e-60
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65 align3.score = 50
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66 listAlignInstance.append(align3)
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67 f = open(self.outputFileName, "w")
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68 alignUtils = AlignListUtils()
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69 alignUtils.write(listAlignInstance, self.outputFileName)
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70 self.assertTrue(FileUtils.are2FilesIdentical(self.outputFileName, "expectedAlignFile.align"))
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71 os.system("rm " + self.outputFileName)
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72 os.system("rm expectedAlignFile.align")
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73
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74 def testFilterOnAMinimalScore(self):
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75 listAlignInstance = AlignList()
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76 align1 = Align()
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77 align1.range_query = Range("biduleChouetteQuery", 20, 55)
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78 align1.range_subject = Range("biduleChouetteSubject", 2, 15)
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79 align1.e_value = 5
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80 align1.score = -0.5
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81 listAlignInstance.append(align1)
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82 align2 = Align()
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83 align2.range_query = Range("trucBiduleQuery", 110, 155)
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84 align2.range_subject = Range("trucBiduleSubject", 1, 35)
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85 align2.e_value = 2
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86 align2.score = -2.0
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87 listAlignInstance.append(align2)
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88 align3 = Align()
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89 align3.range_query = Range("dummyQuery", 1, 65)
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90 align3.range_subject = Range("dummySubject", 1, 25)
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91 align3.e_value = 2.6e-60
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92 align3.score = 50
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93 listAlignInstance.append(align3)
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94 expectedAlignInstance = align3
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95 alignUtils = AlignListUtils()
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96 alignUtils.filterOnAMinimalScore(listAlignInstance, 0)
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97 self.assertEquals(listAlignInstance.get(0), expectedAlignInstance)
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98
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99 if __name__ == "__main__" :
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100 unittest.main() |
