|
18
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 ##@file
|
|
|
4 # Launch MapProgramLauncher.py on several files in parallel on a cluster.
|
|
|
5
|
|
|
6
|
|
|
7 import os
|
|
|
8 import sys
|
|
|
9 import getopt
|
|
|
10 import exceptions
|
|
|
11
|
|
|
12 from pyRepet.launcher.AbstractClusterLauncher import *
|
|
|
13 from commons.launcher.MapProgramLauncher import MapProgramLauncher
|
|
|
14
|
|
|
15
|
|
|
16 class MapClusterLauncher( AbstractClusterLauncher ):
|
|
|
17 """
|
|
|
18 Launch Map on several files in parallel on a cluster.
|
|
|
19 """
|
|
|
20
|
|
|
21
|
|
|
22 def __init__( self ):
|
|
|
23 """
|
|
|
24 Constructor.
|
|
|
25 """
|
|
|
26 AbstractClusterLauncher.__init__( self )
|
|
|
27 AbstractClusterLauncher.setAcronym( self, "Map" )
|
|
|
28
|
|
|
29 self._cmdLineSpecificOptions = "s:m:O:e:"
|
|
|
30
|
|
|
31 self._exeWrapper = "MapProgramLauncher.py"
|
|
|
32 self._prgLauncher = None
|
|
|
33 self._prgLauncher = self.getProgramLauncherInstance()
|
|
|
34
|
|
|
35
|
|
|
36 def getSpecificHelpAsString( self ):
|
|
|
37 """
|
|
|
38 Return the specific help as a string.
|
|
|
39 """
|
|
|
40 string = ""
|
|
|
41 string += "\nspecific options:"
|
|
|
42 string += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self.getGapSize() )
|
|
|
43 string += "\n -m: penalty for a mismatch (default='%i')" % ( self.getMismatchPenalty() )
|
|
|
44 string += "\n -O: penalty for a gap openning (default='%i')" % ( self.getGapOpenPenalty() )
|
|
|
45 string += "\n -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() )
|
|
|
46 return string
|
|
|
47
|
|
|
48
|
|
|
49 def getGapSize( self ):
|
|
|
50 return self._prgLauncher.getGapSize()
|
|
|
51
|
|
|
52
|
|
|
53 def getMismatchPenalty( self ):
|
|
|
54 return self._prgLauncher.getMismatchPenalty()
|
|
|
55
|
|
|
56
|
|
|
57 def getGapOpenPenalty( self ):
|
|
|
58 return self._prgLauncher.getGapOpenPenalty()
|
|
|
59
|
|
|
60
|
|
|
61 def getGapExtendPenalty( self ):
|
|
|
62 return self._prgLauncher.getGapExtendPenalty()
|
|
|
63
|
|
|
64
|
|
|
65 def getProgramLauncherInstance( self ):
|
|
|
66 if self._prgLauncher == None:
|
|
|
67 self._prgLauncher = MapProgramLauncher()
|
|
|
68 self._prgLauncher.setInputFile( GENERIC_IN_FILE )
|
|
|
69 self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) )
|
|
|
70 #TESt de SATannot verifier si clean est a vrai
|
|
|
71 #self._prgLauncher.setClean()
|
|
|
72 self._prgLauncher.setVerbosityLevel( 1 )
|
|
|
73 self._prgLauncher.setListFilesToKeep()
|
|
|
74 self._prgLauncher.setListFilesToRemove()
|
|
|
75 return self._prgLauncher
|
|
|
76
|
|
|
77
|
|
|
78 if __name__ == "__main__":
|
|
|
79 i = MapClusterLauncher()
|
|
|
80 i.setAttributesFromCmdLine()
|
|
|
81 i.run()
|
