diff commons/tools/tests/Test_getCumulLengthFromTEannot.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/tests/Test_getCumulLengthFromTEannot.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,71 @@
+import unittest
+import os
+import time
+from commons.core.sql.DbMySql import DbMySql
+from commons.tools.getCumulLengthFromTEannot import getCumulLengthFromTEannot
+from commons.core.utils.FileUtils import FileUtils
+
+
+class Test_getCumulLengthFromTEannot( unittest.TestCase ):
+    
+    def setUp( self ):
+        self.fileUtils = FileUtils()
+        self._getCumulLengthFromTEannot = None
+        self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
+        self._configFileName = "dummyConfig_%s" % self._uniqId
+        configFile = open( self._configFileName, "w" )
+        configFile.write("[repet_env]\n")
+        configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
+        configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
+        configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
+        configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
+        configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
+        configFile.close()
+        
+        
+    def tearDown( self ):
+        os.remove( self._configFileName )
+        
+        
+    def test_getAllSubjectsAsMapOfQueries( self ):
+        inFileName = "dummyInFile_%s" % self._uniqId
+        expFileName = "dummyExp_%s" % self._uniqId
+        for f in [inFileName,expFileName]:
+            if os.path.exists(f): os.remove(f)
+        inFile = open( inFileName, "w" )
+        inFile.write( "1\tchr1\t1501\t2500\tTE1\t1\t500\t0.0\t880\t95.7\n" )
+        inFile.write( "2\tchr1\t3401\t4000\tTE3\t101\t700\t0.0\t950\t97.2\n" )
+        inFile.close()
+        inTable = "dummyPathTable_%s" % self._uniqId
+        db = DbMySql(cfgFileName=self._configFileName)
+        db.createTable(inTable, "path", inFileName)
+        expFile = open( expFileName, "w" )
+        expFile.write( "TE1\tchr1\t1501\t2500\n" )
+        expFile.write( "TE3\tchr1\t3401\t4000\n" )
+        expFile.close()
+        self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
+        self._getCumulLengthFromTEannot._tableName = inTable
+        self._getCumulLengthFromTEannot._configFileName = self._configFileName
+        self._getCumulLengthFromTEannot.setAdaptatorToTable()
+        obsFileName = self._getCumulLengthFromTEannot.getAllSubjectsAsMapOfQueries()
+        self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
+        for f in [inFileName,inTable+".map",expFileName]:
+            if os.path.exists(f): os.remove(f)
+        db.dropTable(inTable)
+        db.close()
+        
+        
+    def test_getCumulLength( self ):
+        mergeFileName = "dummyInFile_%s" % self._uniqId
+        mergeFile = open( mergeFileName, "w" )
+        mergeFile.write( "TE1\tchr1\t1501\t2500\n" )
+        mergeFile.write( "TE3\tchr1\t4000\t3401\n" )
+        mergeFile.close()
+        exp = 1000+600
+        self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
+        obs = self._getCumulLengthFromTEannot.getCumulLength( mergeFileName )
+        self.assertEqual( obs, exp )
+        os.remove( mergeFileName )
+
+if __name__ == "__main__":
+        unittest.main()
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