Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/ncList/test/Test_F_FindOverlaps_randomExample.py @ 9:1eb55963fe39
Updated CompareOverlappingSmall*.py
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:23:05 -0400 |
parents | 769e306b7933 |
children |
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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()