Mercurial > repos > yufei-luo > s_mart

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