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1 import unittest
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2 import os
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3 from commons.launcher.LaunchBlastclust import LaunchBlastclust
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6 class Test_F_LaunchBlastclust(unittest.TestCase):
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7
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8 def setUp(self):
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9 self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa"
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10 os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
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11 self._outputFileName = "%s_Blastclust.fa" % self._inputFileName
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12 self._outBlastclustFileName = "%s_blastclust.txt" % self._inputFileName
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13
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14 def tearDown(self):
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15 if os.path.exists(self._outputFileName):
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16 os.remove(self._outputFileName)
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17 if os.path.exists(self._outBlastclustFileName):
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18 os.remove(self._outBlastclustFileName)
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19 os.remove(self._inputFileName)
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20
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21 def test_run(self):
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22 iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
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23 iLaunchBlastclust.run()
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24 expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
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25 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
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26
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27 def test_run_with_tweaked_params(self):
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28 iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
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29 iLaunchBlastclust.setBothSequences("F")
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30 iLaunchBlastclust.setIdentityThreshold(0)
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31 iLaunchBlastclust.setIsBlastToMap()
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32 iLaunchBlastclust.run()
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33
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34 faExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.fa" % os.environ["REPET_DATA"]
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35 mapExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.map" % os.environ["REPET_DATA"]
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36
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37 self.assertTrue(FileUtils.are2FilesIdentical(faExpFileName, self._outputFileName))
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38 self.assertTrue(FileUtils.are2FilesIdentical(mapExpFileName, "%s.map" % os.path.splitext(self._outputFileName)[0]))
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39
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40 os.remove("%s.map" % os.path.splitext(self._outputFileName)[0])
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41
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42 def test_run_with_header_options(self):
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43 inFileName = "dummyHeaderForTEdenovo.fa"
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44 expFileName = "expDummyHeaderForTEdenovo.fa"
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45 self._writeInputFile_header_options(inFileName)
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46 self._writeExpFile_header_options(expFileName)
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47 obsFileName = "%s_Blastclust.fa" % inFileName
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48
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49 iLaunchBlastclust = LaunchBlastclust(inFileName, clean = True)
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50 iLaunchBlastclust.setIsHeaderForTEdenovo(True)
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51 iLaunchBlastclust.run()
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52
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53 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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54
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55 os.remove(inFileName)
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56 os.remove(expFileName)
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57 os.remove(obsFileName)
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58 os.remove("%s_blastclust.txt" % inFileName)
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59
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60 def test_run_as_script(self):
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61 cmd = "LaunchBlastclust.py -i %s" % self._inputFileName
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62 os.system(cmd)
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63 expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
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64 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
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65
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66 def _writeInputFile_header_options(self, inFileName):
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67 f = open(inFileName,"w")
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68 f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n")
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69 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
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70 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
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71 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
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72 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
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73 f.write(">DTX-incomp_DmelChr4-B-R10-Map3_reversed\n")
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74 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
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75 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
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76 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
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77 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
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78 f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
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79 f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
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80 f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
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81 f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
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82 f.close()
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83
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84 def _writeExpFile_header_options(self, expFileName):
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85 f = open(expFileName,"w")
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86 f.write(">DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\n")
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87 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
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88 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
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89 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
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90 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
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91 f.write(">DTX-incomp_Blc1_DmelChr4-B-R10-Map3_reversed\n")
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92 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
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93 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
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94 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
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95 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
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96 f.write(">PotentialHostGene-chim_Blc2_DmelChr4-B-R4-Map5_reversed\n")
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97 f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
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98 f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
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99 f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
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100 f.close()
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101
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102 if __name__ == "__main__":
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103 unittest.main() |
