Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/ncList/test/Test_randExample.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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() |