diff commons/pyRepetUnit/hmmer/HmmpfamClusterComponent.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/HmmpfamClusterComponent.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,91 @@
+import os
+from pyRepet.launcher.Launcher import HmmpfamLauncher
+
+
+class HmmpfamClusterComponent( object ):
+    
+    def __init__(self):
+        self._component = None 
+        self._profilDatabank = ""
+        self._resultDir = ""
+        self._queryDir = ""
+        self._tmpDir = ""
+        self._jobDb = None
+        self._SGEQueue = ""
+        self._SGEGroupId = "" 
+        
+    def loadConfig( self, config ):
+        self._profilDatabank = config.get( "profil_search","ProfilDatabank" )
+        self._queryDir = config.get( "hmmer_config","query_dir" )
+        self._tmpDir = config.get( "hmmer_config", "tmp_dir" )
+        self._resultDir = config.get( "hmmer_config", "result_dir" )    
+        self._SGEQueue = config.get( "sge_config", "queue" )
+        self._SGEGroupId = config.get( "sge_config", "groupid" )
+        
+    def run(self):
+        params = {"param":"--informat FASTA -E 10", 
+                  "profilDB": self._profilDatabank, 
+                  "outputDir": self._resultDir,
+                  "query": self._queryDir,
+                  "job_table":"jobs", 
+                  "queue" : self._SGEQueue, 
+                  "groupid" : self._SGEGroupId,
+                  "tmpDir": self._tmpDir,
+                  "cDir" : "."}
+        self._component = HmmpfamLauncher(self._jobDb, params)
+        self._component.run()
+        
+    def clean (self): 
+        dirToClean = self._tmpDir
+        os.system("rm  " + dirToClean + "/*")
+        dirToClean = self._resultDir
+        os.system("rm  " + dirToClean + "/*")
+        
+    def setProfilDatabank (self, profilDatabank):
+        self._profilDatabank = profilDatabank    
+
+    def getProfilDatabank(self):
+        return self._profilDatabank    
+
+    def setQueryDir(self, input):
+        self._queryDir = input
+         
+    def getQueryDir( self ):
+        return self._queryDir
+
+    def setSubjectDir(self, input):
+        self._subjectDir = input
+         
+    def getSubjectDir( self ):
+        return self._subjectDir
+    
+    def setSGEQueue(self, queue):
+        self._SGEQueue = queue
+        
+    def getSGEQueue( self ):
+        return self._SGEQueue
+        
+    def setSGEGrouId(self, id):
+        self._SGEGroupId = id    
+    
+    def getSGEGroupId( self ):
+        return self._SGEGroupId;    
+    
+    def setTmpDir(self, tmpDir):
+        self._tmpDir = tmpDir
+
+    def getTmpDir( self ):
+        return self._tmpDir
+    
+    def setResultDir(self, wkDir):
+        self._resultDir = wkDir
+        
+    def getResultDir(self):
+        return self._resultDir
+    
+    def setJobDb (self, jobDb):
+        self._jobDb = jobDb
+        
+    def getJobDb (self):
+        return self._jobDb
+     
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