Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/MafftClusterLauncher.py @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 #!/usr/bin/env python
2
3 ##@file
4 # Launch MafftProgramLauncher on several files in parallel on a cluster.
5
6
7 from pyRepet.launcher.AbstractClusterLauncher import *
8 from commons.launcher.MafftProgramLauncher import MafftProgramLauncher
9
10
11 class MafftClusterLauncher( AbstractClusterLauncher ):
12 """
13 Launch Mafft on several files in parallel on a cluster.
14 """
15
16 def __init__( self ):
17 """
18 Constructor.
19 """
20 AbstractClusterLauncher.__init__( self )
21 AbstractClusterLauncher.setAcronym( self, "Mafft" )
22
23 self._cmdLineSpecificOptions = "p:"
24
25 self._exeWrapper = "MafftProgramLauncher.py"
26 self._prgLauncher = None
27 self._prgLauncher = self.getProgramLauncherInstance()
28
29
30 def getSpecificHelpAsString( self ):
31 """
32 Return the specific help as a string.
33 """
34 string = ""
35 string += "\nspecific options:"
36 string += "\n -p: parameters for 'mafft' (default='--auto')"
37 return string
38
39
40 def getProgramParameters( self ):
41 return self._prgLauncher.getProgramParameters()
42
43
44 def getProgramLauncherInstance( self ):
45 if self._prgLauncher == None:
46 self._prgLauncher = MafftProgramLauncher()
47 self._prgLauncher.setInputFile( GENERIC_IN_FILE )
48 self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) )
49 self._prgLauncher.setClean()
50 self._prgLauncher.setVerbosityLevel( 1 )
51 self._prgLauncher.setListFilesToKeep()
52 self._prgLauncher.setListFilesToRemove()
53 return self._prgLauncher
54
55
56 if __name__ == "__main__":
57 i = MafftClusterLauncher()
58 i.setAttributesFromCmdLine()
59 i.run()