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1 #!/usr/bin/env python
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2
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3 ##@file
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4 # Launch RepeatMaskerProgramLauncher on several files in parallel on a cluster.
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5
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6
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7 import os
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8 import sys
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9 import getopt
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10 import exceptions
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11
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12 from pyRepet.launcher.AbstractClusterLauncher import *
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13 from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher
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14
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15
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16 class RepeatMaskerClusterLauncher( AbstractClusterLauncher ):
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17 """
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18 Launch RepeatMasker on several files in parallel on a cluster.
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19 """
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20
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21 def __init__( self ):
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22 """
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23 Constructor.
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24 """
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25 AbstractClusterLauncher.__init__( self )
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26 AbstractClusterLauncher.setAcronym( self, "RM" )
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27
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28 self._cmdLineSpecificOptions = "s:n:gbl"
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29
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30 self._exeWrapper = "RepeatMaskerProgramLauncher.py"
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31 self._prgLauncher = RepeatMaskerProgramLauncher()
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32 self._prgLauncher.setInputFile( GENERIC_IN_FILE )
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33 self._prgLauncher.setOutputFile( GENERIC_IN_FILE )
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34 self._prgLauncher.setClean()
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35 self._prgLauncher.setVerbosityLevel( 1 )
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36 self._prgLauncher.setListFilesToKeep()
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37 self._prgLauncher.setListFilesToRemove()
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38
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39
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40 def getSpecificHelpAsString( self ):
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41 """
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42 Return the specific help as a string.
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43 """
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44 string = ""
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45 string += "\nspecific options:"
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46 string += "\n -s: name of the subject file (repeats, format='fasta')"
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47 string += "\n -n: nb of processors to use in parallel (default=1)"
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48 string += "\n -g: calculate the GC content"
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49 string += "\n -b: skip bacterial insertion element check"
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50 string += "\n -l: mask low-complexity DNA or simple repeats"
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51 return string
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52
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53
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54 def getSubjectFile( self ):
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55 return self._prgLauncher.getSubjectFile()
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56
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57
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58 def getNbProcessors( self ):
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59 return self._prgLauncher.getNbProcessors()
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60
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61
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62 def getCalculateGCcontent( self ):
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63 return self._prgLauncher.getCalculateGCcontent()
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64
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65
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66 def getSkipBacterialIsCheck( self ):
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67 return self._prgLauncher.getSkipBacterialIsCheck()
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68
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69
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70 def getMaskSsr( self ):
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71 return self._prgLauncher.getMaskSsr()
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72
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73
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74 if __name__ == "__main__":
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75 i = RepeatMaskerClusterLauncher()
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76 i.setAttributesFromCmdLine()
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77 i.run()
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