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comparison SMART/Java/Python/ncList/test/Test_randExample.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 import unittest
2 import time
3 from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import *
4 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
5
6 class Test_F_FindOverlaps_randomExample(unittest.TestCase):
7
8 def setUp(self):
9 self._output_optim = 'output_optim.gff3'
10
11 def test_creatRandomExampleWithMOverlaps(self):
12 inputRefGff3FileName = 'refMOverlaps.gff3'
13 inputQueryGff3FileName = 'queryMOverlaps.gff3'
14 outputDataName = 'timeResult.dat'
15 fTime = open(outputDataName, 'w')
16 fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n')
17 numberOfRefReads = 1000
18 chromSize = 100000
19 while numberOfRefReads <= 1000:
20 numberOfQReads = 1000
21 while numberOfQReads <= 1000:
22 print 'ref size = %d, query size = %d' %(numberOfRefReads, numberOfQReads)
23 iMFOR_ref = MockFindOverlaps_randomExample(inputRefGff3FileName, 'ref', numberOfRefReads, chromSize)
24 iMFOR_ref.write()
25 iMFOR_query = MockFindOverlaps_randomExample(inputQueryGff3FileName,'q', numberOfQReads, chromSize)
26 iMFOR_query.write()
27 iFOO = FindOverlapsOptim(0)
28 iFOO.setRefFileName(inputRefGff3FileName, "gff3")
29 iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
30 iFOO.setOutputFileName(self._output_optim)
31 iFOO.prepareIntermediateFiles()
32 iFOO.createNCLists()
33
34 startTime_optim = time.time()
35 iFOO.compare()
36 endTime_optim = time.time()
37 totalTime_optim = endTime_optim - startTime_optim
38 print 'we took %s second.' % (totalTime_optim)
39 nbOverlap = iFOO._nbOverlaps
40 iFOO.close()
41 fTime.write('%d\t%d\t%d\t%.2f\n' % (numberOfRefReads, numberOfQReads, nbOverlap, totalTime_optim))
42 numberOfQReads *= 10
43 numberOfRefReads *= 10
44 fTime.close()
45 os.remove(inputQueryGff3FileName)
46 os.remove(inputRefGff3FileName)
47 os.remove(self._output_optim)
48
49
50 if __name__ == "__main__":
51 unittest.main()