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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/test/Test_randExample.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,51 @@
+import unittest
+import time
+from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import *
+from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
+
+class Test_F_FindOverlaps_randomExample(unittest.TestCase):
+
+    def setUp(self):
+        self._output_optim = 'output_optim.gff3'
+        
+    def test_creatRandomExampleWithMOverlaps(self):
+        inputRefGff3FileName = 'refMOverlaps.gff3'
+        inputQueryGff3FileName = 'queryMOverlaps.gff3'
+        outputDataName = 'timeResult.dat'  
+        fTime = open(outputDataName, 'w')  
+        fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n')   
+        numberOfRefReads = 1000
+        chromSize = 100000
+        while numberOfRefReads <= 1000:
+            numberOfQReads = 1000
+            while numberOfQReads <= 1000:
+                print 'ref size = %d,  query size = %d' %(numberOfRefReads, numberOfQReads)
+                iMFOR_ref = MockFindOverlaps_randomExample(inputRefGff3FileName, 'ref', numberOfRefReads, chromSize)
+                iMFOR_ref.write()
+                iMFOR_query = MockFindOverlaps_randomExample(inputQueryGff3FileName,'q', numberOfQReads, chromSize)
+                iMFOR_query.write()
+                iFOO = FindOverlapsOptim(0)
+                iFOO.setRefFileName(inputRefGff3FileName, "gff3")
+                iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
+                iFOO.setOutputFileName(self._output_optim)
+                iFOO.prepareIntermediateFiles()
+                iFOO.createNCLists()
+                
+                startTime_optim = time.time()
+                iFOO.compare()
+                endTime_optim = time.time()
+                totalTime_optim = endTime_optim - startTime_optim
+                print 'we took %s second.' % (totalTime_optim)
+                nbOverlap = iFOO._nbOverlaps
+                iFOO.close()  
+                fTime.write('%d\t%d\t%d\t%.2f\n' % (numberOfRefReads, numberOfQReads, nbOverlap, totalTime_optim))
+                numberOfQReads *= 10
+            numberOfRefReads *= 10
+        fTime.close()
+        os.remove(inputQueryGff3FileName)
+        os.remove(inputRefGff3FileName)
+        os.remove(self._output_optim)
+        
+        
+if __name__ == "__main__":
+    unittest.main()