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1 import unittest
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2 import os
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3 import time
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4 from commons.core.utils.FileUtils import FileUtils
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5 from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample_NonOrder
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6 from SMART.Java.Python.ncList.FindOverlaps_naif import FindOverlaps_naif
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7 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
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8
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9 class Test_F_FindOverlaps_randomExample(unittest.TestCase):
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10
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11 def setUp(self):
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12 self._output_optim = 'output_optim.gff3'
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13
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14 def test_FindOverlaps_NonOrder(self):
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15 inputRefGff3FileName = 'refMOverlaps.gff3'
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16 inputQueryGff3FileName = 'queryMOverlaps.gff3'
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17 outputDataName = 'timeResult.dat'
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18 fTime = open(outputDataName, 'w')
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19 fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n')
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20 numberOfRefReads = 10
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21 chromSize = 100000
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22 numberOfQReads = 10
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23 print 'ref size = %d, query size = %d' %(numberOfRefReads, numberOfQReads)
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24 iMFOR_ref = MockFindOverlaps_randomExample_NonOrder(inputRefGff3FileName, 'ref', numberOfRefReads, chromSize)
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25 iMFOR_ref.write()
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26 iMFOR_query = MockFindOverlaps_randomExample_NonOrder(inputQueryGff3FileName,'q', numberOfQReads, chromSize)
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27 iMFOR_query.write()
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28 iFOO = FindOverlapsOptim(0)
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29 iFOO.setRefFileName(inputRefGff3FileName, "gff3")
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30 iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
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31 iFOO.setOutputFileName(self._output_optim)
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32 startTime_optim = time.time()
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33 iFOO.run()
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34 iFOO.close()
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35 nbOverlap = iFOO._nbOverlaps
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36 endTime_optim = time.time()
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37 totalTime_optim = endTime_optim - startTime_optim
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38 print 'we take %s second.' % (totalTime_optim)
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39 fTime.write('%d\t%d\t%d\t%.2f\n'%(numberOfRefReads, numberOfQReads, nbOverlap, totalTime_optim))
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40 fTime.close()
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41 os.remove(inputQueryGff3FileName)
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42 os.remove(inputRefGff3FileName)
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43 os.remove(self._output_optim)
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44 os.remove(outputDataName)
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45
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46
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47 if __name__ == "__main__":
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48 unittest.main()
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