Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/ncList/test/Test_F_FindOverlaps_randomExample.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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-1:000000000000 | 0:e0f8dcca02ed |
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1 import unittest | |
2 import os | |
3 import time | |
4 from commons.core.utils.FileUtils import FileUtils | |
5 from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample_NonOrder | |
6 from SMART.Java.Python.ncList.FindOverlaps_naif import FindOverlaps_naif | |
7 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim | |
8 | |
9 class Test_F_FindOverlaps_randomExample(unittest.TestCase): | |
10 | |
11 def setUp(self): | |
12 self._output_optim = 'output_optim.gff3' | |
13 | |
14 def test_FindOverlaps_NonOrder(self): | |
15 inputRefGff3FileName = 'refMOverlaps.gff3' | |
16 inputQueryGff3FileName = 'queryMOverlaps.gff3' | |
17 outputDataName = 'timeResult.dat' | |
18 fTime = open(outputDataName, 'w') | |
19 fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n') | |
20 numberOfRefReads = 10 | |
21 chromSize = 100000 | |
22 numberOfQReads = 10 | |
23 print 'ref size = %d, query size = %d' %(numberOfRefReads, numberOfQReads) | |
24 iMFOR_ref = MockFindOverlaps_randomExample_NonOrder(inputRefGff3FileName, 'ref', numberOfRefReads, chromSize) | |
25 iMFOR_ref.write() | |
26 iMFOR_query = MockFindOverlaps_randomExample_NonOrder(inputQueryGff3FileName,'q', numberOfQReads, chromSize) | |
27 iMFOR_query.write() | |
28 iFOO = FindOverlapsOptim(0) | |
29 iFOO.setRefFileName(inputRefGff3FileName, "gff3") | |
30 iFOO.setQueryFileName(inputQueryGff3FileName, "gff3") | |
31 iFOO.setOutputFileName(self._output_optim) | |
32 startTime_optim = time.time() | |
33 iFOO.run() | |
34 iFOO.close() | |
35 nbOverlap = iFOO._nbOverlaps | |
36 endTime_optim = time.time() | |
37 totalTime_optim = endTime_optim - startTime_optim | |
38 print 'we take %s second.' % (totalTime_optim) | |
39 fTime.write('%d\t%d\t%d\t%.2f\n'%(numberOfRefReads, numberOfQReads, nbOverlap, totalTime_optim)) | |
40 fTime.close() | |
41 os.remove(inputQueryGff3FileName) | |
42 os.remove(inputRefGff3FileName) | |
43 os.remove(self._output_optim) | |
44 os.remove(outputDataName) | |
45 | |
46 | |
47 if __name__ == "__main__": | |
48 unittest.main() |