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1 import os
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2 import unittest
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3 from pyRepet.launcher.programLauncher import *
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4 from pyRepet.util.file.FileUtils import *
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5 import commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX
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6 import commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing
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7 import ConfigParser
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8
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9 class LaunchPreProcessHmmpfamPostProcessNotInParallel:
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10
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11 def __init__( self ):
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12
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13 #for global analysis
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14 self._configFile = ""
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15 self._inputFile = ""
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16 self._outputFile = ""
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17 self.fileUtils = FileUtils()
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18 self._programLauncherInstance = programLauncher()
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19 #specific to PreProcess
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20 self.bioseq = Bioseq()
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21 self.preProcess = commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX.TranslateInAllFramesAndReplaceStopByX()
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22 self._outputFilePreprocess = ""
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23 #specific to PostProcess
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24 self.hmmpfamOutputProcess = commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing.HmmpfamOutputProcessing()
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25
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26 def _cleanTemporaryFiles(self, outputFilePreProcess, outputFileHmmpfam):
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27 os.remove( outputFilePreProcess )
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28 os.remove( outputFileHmmpfam )
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29
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30 def _launchPostProcess(self, outputFileHmmpfam):
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31 return self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(outputFileHmmpfam, self._outputFile)
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32
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33
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34 def _launchHmmpfam(self, outputFilePreprocess):
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35 config = ConfigParser.ConfigParser()
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36 config.readfp(open(self._configFile))
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37 self._programLauncherInstance.reset(outputFilePreprocess)
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38 outputFileHmmpfam = outputFilePreprocess + ".hmmpfamOut"
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39 self._programLauncherInstance.setOutputFileName(outputFileHmmpfam)
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40 self._programLauncherInstance.launchHmmpfam(evalFilter=config.get("profil_search", "Evalue"), inputFormat=config.get("profil_search", "InputFormat"), profilDatabank=config.get("profil_search", "ProfilDatabank"))
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41 return outputFileHmmpfam
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42
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43
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44 def _launchHmmpfamPreProcess(self):
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45 self.preProcess.setInputFile(self._inputFile)
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46 outputFilePreprocess = self._inputFile + ".translated"
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47 self.preProcess.setOutputFile(outputFilePreprocess)
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48 self.preProcess.run()
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49 return outputFilePreprocess
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50
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51 def setInputFile( self, input ):
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52 self._inputFile = input;
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53
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54 def setOutputFile( self, output ):
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55 self._outputFile = output;
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56
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57 def setConfigFile ( self, configFile ):
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58 self._configFile = configFile
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59
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60 def checkInputFile(self):
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61 return self._checkFileExitsAndNotEmpty( self._inputFile )
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62
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63 def checkConfigFile(self):
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64 return self._checkFileExitsAndNotEmpty( self._configFile )
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65
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66 def _checkFileExitsAndNotEmpty(self, fileName):
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67 fileUtils = FileUtils()
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68 if fileUtils.isRessourceExists(fileName) and not fileUtils.isFileEmpty(fileName):
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69 return 1
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70 return 0
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71
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72 def run(self):
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73
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74 if not self.checkInputFile():
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75 print "Warning : there is no input file : " + self._inputFile + "\n"
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76 return 0
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77 if not self.checkConfigFile():
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78 print "Warning : there is no config file : " + self._configFile + "\n"
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79 return 0
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80 outputFilePreProcess = self._launchHmmpfamPreProcess()
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81 outputFileHmmpfam = self._launchHmmpfam(outputFilePreProcess)
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82 self._launchPostProcess(outputFileHmmpfam)
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83 self._cleanTemporaryFiles(outputFilePreProcess, outputFileHmmpfam)
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84
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85
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86 if __name__ == "__main__":
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87 main()
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121 if __name__ == "__main__":
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122 main() |
