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1 import os
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2 from pyRepet.launcher.Launcher import HmmpfamLauncher
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3
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4
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5 class HmmpfamClusterComponent( object ):
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6
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7 def __init__(self):
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8 self._component = None
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9 self._profilDatabank = ""
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10 self._resultDir = ""
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11 self._queryDir = ""
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12 self._tmpDir = ""
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13 self._jobDb = None
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14 self._SGEQueue = ""
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15 self._SGEGroupId = ""
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16
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17 def loadConfig( self, config ):
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18 self._profilDatabank = config.get( "profil_search","ProfilDatabank" )
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19 self._queryDir = config.get( "hmmer_config","query_dir" )
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20 self._tmpDir = config.get( "hmmer_config", "tmp_dir" )
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21 self._resultDir = config.get( "hmmer_config", "result_dir" )
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22 self._SGEQueue = config.get( "sge_config", "queue" )
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23 self._SGEGroupId = config.get( "sge_config", "groupid" )
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24
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25 def run(self):
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26 params = {"param":"--informat FASTA -E 10",
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27 "profilDB": self._profilDatabank,
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28 "outputDir": self._resultDir,
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29 "query": self._queryDir,
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30 "job_table":"jobs",
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31 "queue" : self._SGEQueue,
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32 "groupid" : self._SGEGroupId,
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33 "tmpDir": self._tmpDir,
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34 "cDir" : "."}
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35 self._component = HmmpfamLauncher(self._jobDb, params)
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36 self._component.run()
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37
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38 def clean (self):
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39 dirToClean = self._tmpDir
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40 os.system("rm " + dirToClean + "/*")
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41 dirToClean = self._resultDir
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42 os.system("rm " + dirToClean + "/*")
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43
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44 def setProfilDatabank (self, profilDatabank):
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45 self._profilDatabank = profilDatabank
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46
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47 def getProfilDatabank(self):
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48 return self._profilDatabank
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49
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50 def setQueryDir(self, input):
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51 self._queryDir = input
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52
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53 def getQueryDir( self ):
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54 return self._queryDir
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55
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56 def setSubjectDir(self, input):
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57 self._subjectDir = input
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58
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59 def getSubjectDir( self ):
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60 return self._subjectDir
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61
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62 def setSGEQueue(self, queue):
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63 self._SGEQueue = queue
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64
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65 def getSGEQueue( self ):
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66 return self._SGEQueue
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67
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68 def setSGEGrouId(self, id):
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69 self._SGEGroupId = id
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70
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71 def getSGEGroupId( self ):
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72 return self._SGEGroupId;
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73
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74 def setTmpDir(self, tmpDir):
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75 self._tmpDir = tmpDir
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76
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77 def getTmpDir( self ):
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78 return self._tmpDir
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79
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80 def setResultDir(self, wkDir):
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81 self._resultDir = wkDir
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82
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83 def getResultDir(self):
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84 return self._resultDir
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85
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86 def setJobDb (self, jobDb):
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87 self._jobDb = jobDb
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88
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89 def getJobDb (self):
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90 return self._jobDb
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91 |
