Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/structure/test/Test_Mapping.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
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2 from SMART.Java.Python.structure.Interval import Interval
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3 from SMART.Java.Python.structure.SubMapping import SubMapping
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4 from SMART.Java.Python.structure.Mapping import Mapping
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6 class Test_Mapping(unittest.TestCase):
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8 def test__getTranscript(self):
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9 queryInterval1 = Interval()
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10 queryInterval1.setName("read1_1")
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11 queryInterval1.setStart(1)
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12 queryInterval1.setEnd(10)
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13 queryInterval1.setDirection(1)
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15 targetInterval1 = Interval()
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16 targetInterval1.setChromosome("chr1")
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17 targetInterval1.setStart(100)
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18 targetInterval1.setEnd(110)
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19 targetInterval1.setDirection(1)
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21 subMapping1 = SubMapping()
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22 subMapping1.setQueryInterval(queryInterval1)
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23 subMapping1.setTargetInterval(targetInterval1)
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25 queryInterval2 = Interval()
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26 queryInterval2.setName("read1_2")
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27 queryInterval2.setStart(11)
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28 queryInterval2.setEnd(20)
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29 queryInterval2.setDirection(1)
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31 targetInterval2 = Interval()
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32 targetInterval2.setChromosome("chr1")
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33 targetInterval2.setStart(200)
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34 targetInterval2.setEnd(210)
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35 targetInterval2.setDirection(1)
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36
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37 subMapping2 = SubMapping()
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38 subMapping2.setQueryInterval(queryInterval2)
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39 subMapping2.setTargetInterval(targetInterval2)
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40
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41 mapping = Mapping()
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42 mapping.addSubMapping(subMapping1)
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43 mapping.addSubMapping(subMapping2)
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44
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45 transcript = mapping.getTranscript()
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46 self.assertEqual(transcript.getStart(), 100)
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47 self.assertEqual(transcript.getEnd(), 210)
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48 self.assertEqual(transcript.getChromosome(), "chr1")
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49 exons = transcript.getExons()
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50 self.assertEqual(len(exons), 2)
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51 exon1, exon2 = exons
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52 self.assertEqual(exon1.getStart(), 100)
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53 self.assertEqual(exon1.getEnd(), 110)
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54 self.assertEqual(exon2.getStart(), 200)
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55 self.assertEqual(exon2.getEnd(), 210)
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58 if __name__ == '__main__':
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59 unittest.main()