Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/RepeatMaskerClusterLauncher.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2
3 ##@file
4 # Launch RepeatMaskerProgramLauncher 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.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher
14
15
16 class RepeatMaskerClusterLauncher( AbstractClusterLauncher ):
17 """
18 Launch RepeatMasker on several files in parallel on a cluster.
19 """
20
21 def __init__( self ):
22 """
23 Constructor.
24 """
25 AbstractClusterLauncher.__init__( self )
26 AbstractClusterLauncher.setAcronym( self, "RM" )
27
28 self._cmdLineSpecificOptions = "s:n:gbl"
29
30 self._exeWrapper = "RepeatMaskerProgramLauncher.py"
31 self._prgLauncher = RepeatMaskerProgramLauncher()
32 self._prgLauncher.setInputFile( GENERIC_IN_FILE )
33 self._prgLauncher.setOutputFile( GENERIC_IN_FILE )
34 self._prgLauncher.setClean()
35 self._prgLauncher.setVerbosityLevel( 1 )
36 self._prgLauncher.setListFilesToKeep()
37 self._prgLauncher.setListFilesToRemove()
38
39
40 def getSpecificHelpAsString( self ):
41 """
42 Return the specific help as a string.
43 """
44 string = ""
45 string += "\nspecific options:"
46 string += "\n -s: name of the subject file (repeats, format='fasta')"
47 string += "\n -n: nb of processors to use in parallel (default=1)"
48 string += "\n -g: calculate the GC content"
49 string += "\n -b: skip bacterial insertion element check"
50 string += "\n -l: mask low-complexity DNA or simple repeats"
51 return string
52
53
54 def getSubjectFile( self ):
55 return self._prgLauncher.getSubjectFile()
56
57
58 def getNbProcessors( self ):
59 return self._prgLauncher.getNbProcessors()
60
61
62 def getCalculateGCcontent( self ):
63 return self._prgLauncher.getCalculateGCcontent()
64
65
66 def getSkipBacterialIsCheck( self ):
67 return self._prgLauncher.getSkipBacterialIsCheck()
68
69
70 def getMaskSsr( self ):
71 return self._prgLauncher.getMaskSsr()
72
73
74 if __name__ == "__main__":
75 i = RepeatMaskerClusterLauncher()
76 i.setAttributesFromCmdLine()
77 i.run()