diff SMART/Java/Python/ncList/test/Test_FindOverlaps_randomExample.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/test/Test_FindOverlaps_randomExample.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,99 @@
+import unittest
+import os
+import time
+from SMART.Java.Python.misc import Utils
+from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import *
+from SMART.Java.Python.ncList.FindOverlaps_naif import FindOverlaps_naif
+from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
+
+class Test_FindOverlaps_randomExample(unittest.TestCase):
+
+    def setUp(self):
+        self._output_naif = 'output_naif.gff3'
+        self._outputOptim = 'outputOptim.gff3'
+
+        
+    def tearDown(self):
+        return
+        os.remove(self._output_naif)
+        os.remove(self._outputOptim)
+        
+    def test_run_smallSize(self):
+        inputRefGff3FileName = 'ref_small.gff3'
+        numberOfReads = 10
+        chromSize = 1000
+        iMFO_rand = MockFindOverlaps_randomExample(inputRefGff3FileName, 'reference', numberOfReads, chromSize)
+        iMFO_rand.write()
+
+        inputQueryGff3FileName = 'query_small.gff3'
+        iMFO_rand = MockFindOverlaps_randomExample(inputQueryGff3FileName,'query', 10, 1000)
+        iMFO_rand.write()
+        
+        iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
+        iFON.setOutputGff3FileName(self._output_naif)
+        iFOO = FindOverlapsOptim(0)
+        iFOO.setRefFileName(inputRefGff3FileName, "gff3")
+        iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
+        iFOO.setOutputFileName(self._outputOptim)
+        iFOO.prepareIntermediateFiles()
+        iFOO.createNCLists()
+        
+        startTime_naif = time.time()
+        iFON.run()
+        iFON.close()
+        endTime_naif = time.time()
+        totalTime_naif = endTime_naif - startTime_naif
+        print 'for naive algo, we take %e second' % (totalTime_naif)
+        
+        startTimeOptim = time.time()
+        iFOO.compare()
+        endTimeOptim = time.time()
+        totalTimeOptim = endTimeOptim - startTimeOptim
+        print 'for optim algo, we take %e second' % (totalTimeOptim)
+        iFOO.close()
+        
+        self.assertTrue(Utils.diff(self._output_naif, self._outputOptim)) 
+        
+        os.remove(inputRefGff3FileName)
+        os.remove(inputQueryGff3FileName)
+      
+
+    def test_creatRandomExampleWithMOverlaps_smallSize(self):
+        inputRefGff3FileName = 'refMOverlaps_small.gff3'
+        inputQueryGff3FileName = 'queryMOverlaps_small.gff3'       
+        numberOfReads = 10
+        chromSize = 1000 
+        iRMSS = MockFindOverlaps_randomExample_MOverlaps(inputRefGff3FileName, inputQueryGff3FileName, 7, numberOfReads, chromSize)
+        iRMSS.createRandomExample()
+  
+  
+        iFON = FindOverlaps_naif(inputRefGff3FileName, inputQueryGff3FileName)
+        iFON.setOutputGff3FileName(self._output_naif)
+        iFOO = FindOverlapsOptim(0)
+        iFOO.setRefFileName(inputRefGff3FileName, "gff3")
+        iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
+        iFOO.setOutputFileName(self._outputOptim)
+        iFOO.prepareIntermediateFiles()
+        iFOO.createNCLists()
+        
+        startTime_naif = time.time()
+        iFON.run()
+        endTime_naif = time.time()
+        totalTime_naif = endTime_naif - startTime_naif
+        print 'for naive algo, we take %e second' % (totalTime_naif)
+        iFON.close()
+        
+        startTimeOptim = time.time()
+        iFOO.compare()
+        endTimeOptim = time.time()
+        totalTimeOptim = endTimeOptim - startTimeOptim
+        print 'for optim algo, we take %e second' % (totalTimeOptim)
+        iFOO.close()        
+        
+        self.assertTrue(Utils.diff(self._output_naif, self._outputOptim)) 
+        
+        os.remove(inputRefGff3FileName)
+        os.remove(inputQueryGff3FileName)        
+        
+if __name__ == "__main__":
+    unittest.main()