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18
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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 YassProgramLauncher on several files in parallel on a cluster.
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5
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6
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7 from pyRepet.launcher.AbstractClusterLauncher import *
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8 from commons.core.coord.AlignUtils import AlignUtils
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9 from commons.launcher.YassProgramLauncher import YassProgramLauncher
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10 from commons.tools import srptBlasterMatcher
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11
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12
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13 class YassClusterLauncher( AbstractClusterLauncher ):
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14 """
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15 Launch Yass on several files in parallel on a cluster.
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16 """
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17
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18 def __init__( self ):
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19 """
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20 Constructor.
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21 """
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22 AbstractClusterLauncher.__init__( self )
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23 AbstractClusterLauncher.setAcronym( self, "Yass" )
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24
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25 self._cmdLineSpecificOptions = "s:p:A"
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26
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27 self._exeWrapper = "YassProgramLauncher.py"
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28 self._prgLauncher = None
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29 self._prgLauncher = self.getProgramLauncherInstance()
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30
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31
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32 def getSpecificHelpAsString( self ):
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33 """
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34 Return the specific help as a string.
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35 """
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36 string = ""
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37 string += "\nspecific options:"
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38 string += "\n -s: name of the subject file (format='fasta')"
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39 string += "\n -p: parameters for 'yass'"
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40 string += "\n -Z: concatenate output files"
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41 string += "\n -A: same sequences (all-by-all)"
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42 return string
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43
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44
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45 def getSubjectFile( self ):
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46 return self._prgLauncher.getSubjectFile()
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47
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48
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49 def getProgramParameters( self ):
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50 return self._prgLauncher.getProgramParameters()
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51
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52
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53 def getProgramLauncherInstance( self ):
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54 if self._prgLauncher == None:
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55 self._prgLauncher = YassProgramLauncher()
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56 self._prgLauncher.setInputFile( GENERIC_IN_FILE )
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57 self._prgLauncher.setClean()
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58 self._prgLauncher.setVerbosityLevel( 1 )
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59 self._prgLauncher.setListFilesToKeep()
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60 self._prgLauncher.setListFilesToRemove()
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61 return self._prgLauncher
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62
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63
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64 def processOutputFile( self, tmpFile, outFile ):
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65 sortFile = "%s.sort" % ( tmpFile )
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66 AlignUtils.sortAlignFile( tmpFile, sortFile )
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67 if self._prgLauncher.getAllByAll():
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68 srptBlasterMatcher.filterRedundantMatches( sortFile,
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69 outFile )
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70 os.remove( sortFile )
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71 else:
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72 os.rename( sortFile, outFile )
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73
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74
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75 if __name__ == "__main__":
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76 i = YassClusterLauncher()
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77 i.setAttributesFromCmdLine()
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78 i.run()
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