Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/hmmer/HmmpfamClusterComponent.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 import os
2 from pyRepet.launcher.Launcher import HmmpfamLauncher
3
4
5 class HmmpfamClusterComponent( object ):
6
7 def __init__(self):
8 self._component = None
9 self._profilDatabank = ""
10 self._resultDir = ""
11 self._queryDir = ""
12 self._tmpDir = ""
13 self._jobDb = None
14 self._SGEQueue = ""
15 self._SGEGroupId = ""
16
17 def loadConfig( self, config ):
18 self._profilDatabank = config.get( "profil_search","ProfilDatabank" )
19 self._queryDir = config.get( "hmmer_config","query_dir" )
20 self._tmpDir = config.get( "hmmer_config", "tmp_dir" )
21 self._resultDir = config.get( "hmmer_config", "result_dir" )
22 self._SGEQueue = config.get( "sge_config", "queue" )
23 self._SGEGroupId = config.get( "sge_config", "groupid" )
24
25 def run(self):
26 params = {"param":"--informat FASTA -E 10",
27 "profilDB": self._profilDatabank,
28 "outputDir": self._resultDir,
29 "query": self._queryDir,
30 "job_table":"jobs",
31 "queue" : self._SGEQueue,
32 "groupid" : self._SGEGroupId,
33 "tmpDir": self._tmpDir,
34 "cDir" : "."}
35 self._component = HmmpfamLauncher(self._jobDb, params)
36 self._component.run()
37
38 def clean (self):
39 dirToClean = self._tmpDir
40 os.system("rm " + dirToClean + "/*")
41 dirToClean = self._resultDir
42 os.system("rm " + dirToClean + "/*")
43
44 def setProfilDatabank (self, profilDatabank):
45 self._profilDatabank = profilDatabank
46
47 def getProfilDatabank(self):
48 return self._profilDatabank
49
50 def setQueryDir(self, input):
51 self._queryDir = input
52
53 def getQueryDir( self ):
54 return self._queryDir
55
56 def setSubjectDir(self, input):
57 self._subjectDir = input
58
59 def getSubjectDir( self ):
60 return self._subjectDir
61
62 def setSGEQueue(self, queue):
63 self._SGEQueue = queue
64
65 def getSGEQueue( self ):
66 return self._SGEQueue
67
68 def setSGEGrouId(self, id):
69 self._SGEGroupId = id
70
71 def getSGEGroupId( self ):
72 return self._SGEGroupId;
73
74 def setTmpDir(self, tmpDir):
75 self._tmpDir = tmpDir
76
77 def getTmpDir( self ):
78 return self._tmpDir
79
80 def setResultDir(self, wkDir):
81 self._resultDir = wkDir
82
83 def getResultDir(self):
84 return self._resultDir
85
86 def setJobDb (self, jobDb):
87 self._jobDb = jobDb
88
89 def getJobDb (self):
90 return self._jobDb
91