Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/ncList/test/Test_randExample.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import time
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 class Test_F_FindOverlaps_randomExample(unittest.TestCase):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 def setUp(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 self._output_optim = 'output_optim.gff3'
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 def test_creatRandomExampleWithMOverlaps(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 inputRefGff3FileName = 'refMOverlaps.gff3'
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 inputQueryGff3FileName = 'queryMOverlaps.gff3'
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 outputDataName = 'timeResult.dat'
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 fTime = open(outputDataName, 'w')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n')
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 numberOfRefReads = 1000
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 chromSize = 100000
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 while numberOfRefReads <= 1000:
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20 numberOfQReads = 1000
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 while numberOfQReads <= 1000:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 print 'ref size = %d, query size = %d' %(numberOfRefReads, numberOfQReads)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 iMFOR_ref = MockFindOverlaps_randomExample(inputRefGff3FileName, 'ref', numberOfRefReads, chromSize)
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24 iMFOR_ref.write()
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25 iMFOR_query = MockFindOverlaps_randomExample(inputQueryGff3FileName,'q', numberOfQReads, chromSize)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 iMFOR_query.write()
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27 iFOO = FindOverlapsOptim(0)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 iFOO.setRefFileName(inputRefGff3FileName, "gff3")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 iFOO.setOutputFileName(self._output_optim)
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31 iFOO.prepareIntermediateFiles()
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32 iFOO.createNCLists()
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33
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34 startTime_optim = time.time()
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35 iFOO.compare()
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36 endTime_optim = time.time()
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37 totalTime_optim = endTime_optim - startTime_optim
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 print 'we took %s second.' % (totalTime_optim)
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39 nbOverlap = iFOO._nbOverlaps
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 iFOO.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 fTime.write('%d\t%d\t%d\t%.2f\n' % (numberOfRefReads, numberOfQReads, nbOverlap, totalTime_optim))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 numberOfQReads *= 10
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 numberOfRefReads *= 10
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 fTime.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 os.remove(inputQueryGff3FileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 os.remove(inputRefGff3FileName)
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47 os.remove(self._output_optim)
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 if __name__ == "__main__":
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51 unittest.main()