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1 from commons.core.utils.FileUtils import FileUtils
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2 import unittest
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3 import os
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4 import shutil
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5 from commons.launcher.LaunchMCL import LaunchMCL
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6
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7 class Test_F_LaunchMCL(unittest.TestCase):
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8 # TODO: test query coverage filter
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9
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10 def setUp(self):
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11 self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa"
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12 try:
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13 shutil.rmtree("MCLtmpDirectory")
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14 os.remove(self._inputFileName)
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15 except:
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16 pass
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17 try:
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18 os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
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19 except:
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20 pass
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21 self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0]
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22
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23 def tearDown(self):
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24 try:
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25 os.remove(self._inputFileName)
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26 os.remove(self._outputFileName)
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27 shutil.rmtree("MCLtmpDirectory")
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28 except:
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29 pass
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30 try:
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31 os.remove("DmelChr4_LTRharvest_expected_with_default_params_MCL.map")
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32 except:
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33 pass
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34
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35 def test_run(self):
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36 iLaunchMCL = LaunchMCL(self._inputFileName, doClean = True, verbosity = 1)
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37 iLaunchMCL.run()
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38 expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
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39 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
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40
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41 def test_run_with_map_file(self):
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42 iLaunchMCL = LaunchMCL(self._inputFileName, isCluster2Map = True, doClean = False, verbosity = 1)
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43 # iLaunchMCL.setCoverageThreshold(0.60)
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44 iLaunchMCL.run()
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45 expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
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46 expMapFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.map" % os.environ["REPET_DATA"]
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47 obsMapFileName = "%s.map" % os.path.splitext(self._outputFileName)[0]
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48
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49 self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName))
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50 self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
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51
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52 os.remove(obsMapFileName)
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53
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54 def test_run_clusterConsensus_headers(self):
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55 os.remove(self._inputFileName)
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56 self._inputFileName = "DmelChr4_LTRharvest_MCL_ClusterConsHeaders_input.fa"
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57 os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
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58 iLaunchMCL = LaunchMCL(self._inputFileName, isClusterConsensusHeaders = True, doClean = True, verbosity = 1)
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59 iLaunchMCL.run()
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60 expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_ClusterConsHeaders_expected.fa" % os.environ["REPET_DATA"]
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61 self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0]
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62
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63 self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName))
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64
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65 def test_run_as_script(self):
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66 cmd = "LaunchMCL.py -i %s -j -v 6" % self._inputFileName
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67 os.system(cmd)
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68 expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
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69 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
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70 self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))
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71
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72 def test_run_as_script_allParams(self):
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73 cmd = "LaunchMCL.py -i %s -j -I 1.5 -T 0.0 -m -v 6" % self._inputFileName
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74 os.system(cmd)
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75 expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
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76 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
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77 self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))
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78
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79 def test_run_as_script_without_join(self):
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80 cmd = "LaunchMCL.py -i %s -v 2" % self._inputFileName
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81 os.system(cmd)
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82 expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
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83 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
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84 self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))
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85
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86 if __name__ == "__main__":
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87 unittest.main() |
