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1 import unittest
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2 import os
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3 import ConfigParser
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4 import shutil
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5 from commons.pyRepetUnit.hmmer.profilsSearchInTEClassifier.ProfilesSearch import ProfilesSearch
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6
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7 class Test_ProfilesSearch(unittest.TestCase):
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8
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9
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10 def setUp(self):
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11 self._section = 'detect_features'
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12 self._option1 = 'TE_HMM_profiles'
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13 self._option2 = 'TE_HMMER_evalue'
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14 self._config = ConfigParser.ConfigParser()
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15 self._config.add_section(self._section)
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16 self._config.set(self._section, self._option1, './datas/hmmbank_test')
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17 self._config.set(self._section, self._option2, '10')
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18 self._iProfilesSearch = ProfilesSearch()
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19 self._launch1 = 'First Command\n'
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20 self._launch2 = '\nSecond Command\n'
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21 self._cDir = '.'
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22 self._profileBank = self._config.get(self._section, self._option1)
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23 self._bank = os.path.basename(self._profileBank)
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24 shutil.copy(self._profileBank, self._cDir + "/" + self._bank)
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25
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26 def tearDown(self):
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27 os.remove(self._cDir + "/" + self._bank)
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28
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29 def test_prepareProfilesBank(self):
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30 hmmpressLaunched = False
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31 self._iProfilesSearch.prepareProfilesBank( self._launch1, self._launch2, self._config, self._cDir )
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32 if ( os.path.exists(self._cDir + "/" + self._bank + ".h3m") \
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33 and os.path.exists(self._cDir + "/" + self._bank + ".h3i") \
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34 and os.path.exists(self._cDir + "/" + self._bank + ".h3f") \
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35 and os.path.exists(self._cDir + "/" + self._bank + ".h3p")) :
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36 hmmpressLaunched = True
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37 os.remove(self._cDir + "/" + self._bank + ".h3m")
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38 os.remove(self._cDir + "/" + self._bank + ".h3i")
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39 os.remove(self._cDir + "/" + self._bank + ".h3f")
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40 os.remove(self._cDir + "/" + self._bank + ".h3p")
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41 self.assertTrue(hmmpressLaunched)
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42
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43 def test_detectHmmProfiles(self):
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44 inputFileName = ' FileName'
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45 dirTemp = 'Tempory directory'
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46 eValueMax = self._config.get(self._section, self._option2)
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47
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48 expCommand = self._launch1
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49 expCommand += os.environ["REPET_PATH"] + "/bin/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
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50 expCommand += " -i %s" % ( inputFileName ) + " -o %s_translated" % ( inputFileName )
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51 expCommand += self._launch2
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52
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53 expCommand += self._launch1
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54 expCommand += "hmmscan "
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55 expCommand += " -o %s_tr.hmmScanOut" % ( inputFileName )
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56 expCommand += " --domtblout %s_tr.hmmScanOutTab" % ( inputFileName )
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57 expCommand += " --noali "
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58 expCommand += "-E " + eValueMax
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59 expCommand += " --cpu 1"
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60 expCommand += " " + self._cDir + "/" + self._bank + " " + "%s_translated" % ( inputFileName )
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61
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62 expCommand += self._launch2
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63
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64 expCommand += "if os.path.exists( \"%s_translated\" ):\n" % ( inputFileName )
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65 expCommand += "\tos.remove( \"%s_translated\" )\n" % ( inputFileName )
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66
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67 expCommand += self._launch1
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68 expCommand += os.environ["REPET_PATH"] + "/bin/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py"
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69 expCommand += " -i %s_tr.hmmScanOutTab" % ( inputFileName )
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70 expCommand += " -o %s_profiles_%s.align" % ( inputFileName, self._bank )
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71 expCommand += " -T %s" % ( inputFileName )
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72 expCommand += " -p hmmscan"
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73 expCommand += " -c"
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74 expCommand += self._launch2
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75
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76 expCommand += self._launch1
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77 expCommand += os.environ["REPET_PATH"] + "/bin/matcher"
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78 expCommand += " -m %s_profiles_%s.align" % ( inputFileName, self._bank )
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79 expCommand += " -j"
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80 expCommand += " -E 10"
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81 expCommand += " -L 0"
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82 expCommand += " -v 1"
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83 expCommand += self._launch2
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84
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85 expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.path\" ):\n" % ( self._cDir, inputFileName, self._bank )
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86 expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.path %s\" )\n" % ( inputFileName, self._bank, self._cDir )
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87 expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.param\" ):\n" % ( self._cDir, inputFileName, self._bank )
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88 expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.param %s\" )\n" % ( inputFileName, self._bank, self._cDir )
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89 expCommand += "if os.path.exists( \"%s_profiles_%s.align\" ):\n" % ( inputFileName, self._bank )
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90 expCommand += "\tos.remove( \"%s_profiles_%s.align\" )\n" % ( inputFileName, self._bank )
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91 expCommand += "if os.path.exists( \"%s_profiles_%s.align.clean_match.map\" ):\n" % ( inputFileName, self._bank )
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92 expCommand += "\tos.remove( \"%s_profiles_%s.align.clean_match.map\" )\n" % ( inputFileName, self._bank )
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93 expCommand += "if os.path.exists( \"%s_hmmScanOut\" ):\n" % ( inputFileName )
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94 expCommand += "\tos.remove( \"%s_hmmScanOut\" )\n" % ( inputFileName )
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95
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96 if dirTemp != dir:
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97 expCommand += "if os.path.exists( \"%s\" ):\n" % ( self._bank )
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98 expCommand += "\tos.remove( \"%s\" )\n" % ( self._bank )
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99
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100 obsCommand = self._iProfilesSearch.detectHmmProfiles( inputFileName, self._launch1, self._launch2, self._cDir, dirTemp, self._config )
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101 self.assertEquals(expCommand, obsCommand)
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102
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103
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104
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105 if __name__ == "__main__":
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106 unittest.main() |
