Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/Java/Python/ncList/test/Test_randExample.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/Java/Python/ncList/test/Test_randExample.py Thu Jan 17 10:52:14 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()