Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/ncList/test/Test_F_FindOverlaps_randomExample.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
---|---|
date | Fri, 18 Jan 2013 04:54:14 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/ncList/test/Test_F_FindOverlaps_randomExample.py Fri Jan 18 04:54:14 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()