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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 BlatProgramLauncher 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.launcher.BlatProgramLauncher import BlatProgramLauncher
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9 from commons.core.coord.AlignUtils import AlignUtils
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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 BlatClusterLauncher( AbstractClusterLauncher ):
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14 """
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15 Launch Blat 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, "Blat" )
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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 = "BlatProgramLauncher.py"
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28 self._prgLauncher = BlatProgramLauncher()
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29 self._prgLauncher.setInputFile( GENERIC_IN_FILE )
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30 self._prgLauncher.setClean()
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31 self._prgLauncher.setVerbosityLevel( 1 )
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32 self._prgLauncher.setListFilesToKeep()
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33 self._prgLauncher.setListFilesToRemove()
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34
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35
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36 def getSpecificHelpAsString( self ):
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37 """
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38 Return the specific help as a string.
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39 """
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40 string = ""
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41 string += "\nspecific options:"
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42 string += "\n -s: name of the subject file (format='fasta')"
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43 string += "\n -p: parameters for '%s'" % ( self._prgLauncher.getProgramName() )
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44 string += "\n -Z: concatenate output files"
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45 string += "\n -A: same sequences (all-by-all)"
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46 return string
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47
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48
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49 def getSubjectFile( self ):
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50 return self._prgLauncher.getSubjectFile()
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51
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52
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53 def getProgramParameters( self ):
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54 return self._prgLauncher.getProgramParameters()
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55
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56
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57 def processOutputFile( self, tmpFile, outFile ):
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58 sortFile = "%s.sort" % ( tmpFile )
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59 AlignUtils.sortAlignFile( tmpFile, sortFile )
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60 if self._prgLauncher.getAllByAll():
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61 srptBlasterMatcher.filterRedundantMatches( sortFile,
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62 outFile )
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63 os.remove( sortFile )
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64 else:
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65 os.rename( sortFile, outFile )
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66
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67 def setASpecificAttributeFromCmdLine( self, o, a="" ):
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68 if o =="-s":
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69 self._prgLauncher.setSubjectFile( a )
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70
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71 if __name__ == "__main__":
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72 i = BlatClusterLauncher()
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73 i.setAttributesFromCmdLine()
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74 i.run()
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