Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/ncList/test/Test_randExample.py @ 31:0ab839023fe4
Uploaded
author | m-zytnicki |
---|---|
date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
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()