diff smart_toolShed/SMART/Java/Python/ncList/test/Test_F_FindOverlaps_randomExample.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/ncList/test/Test_F_FindOverlaps_randomExample.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,48 @@
+import unittest
+import os
+import time
+from commons.core.utils.FileUtils import FileUtils
+from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample_NonOrder
+from SMART.Java.Python.ncList.FindOverlaps_naif import FindOverlaps_naif
+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_FindOverlaps_NonOrder(self):
+        inputRefGff3FileName = 'refMOverlaps.gff3'
+        inputQueryGff3FileName = 'queryMOverlaps.gff3'
+        outputDataName = 'timeResult.dat'  
+        fTime = open(outputDataName, 'w')  
+        fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n')   
+        numberOfRefReads = 10
+        chromSize = 100000
+        numberOfQReads = 10
+        print 'ref size = %d,  query size = %d' %(numberOfRefReads, numberOfQReads)
+        iMFOR_ref = MockFindOverlaps_randomExample_NonOrder(inputRefGff3FileName, 'ref', numberOfRefReads, chromSize)
+        iMFOR_ref.write()
+        iMFOR_query = MockFindOverlaps_randomExample_NonOrder(inputQueryGff3FileName,'q', numberOfQReads, chromSize)
+        iMFOR_query.write()
+        iFOO = FindOverlapsOptim(0)
+        iFOO.setRefFileName(inputRefGff3FileName, "gff3")
+        iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
+        iFOO.setOutputFileName(self._output_optim)
+        startTime_optim = time.time()
+        iFOO.run()
+        iFOO.close()  
+        nbOverlap = iFOO._nbOverlaps
+        endTime_optim = time.time()    
+        totalTime_optim = endTime_optim - startTime_optim
+        print 'we take %s second.' % (totalTime_optim)
+        fTime.write('%d\t%d\t%d\t%.2f\n'%(numberOfRefReads, numberOfQReads, nbOverlap, totalTime_optim))
+        fTime.close()
+        os.remove(inputQueryGff3FileName)
+        os.remove(inputRefGff3FileName)
+        os.remove(self._output_optim)  
+        os.remove(outputDataName)      
+        
+        
+if __name__ == "__main__":
+    unittest.main()