Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/structure/test/Test_Mapping.py @ 0:e0f8dcca02ed
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 |
| parents | |
| children |
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| -1:000000000000 | 0:e0f8dcca02ed |
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| 1 import unittest | |
| 2 from SMART.Java.Python.structure.Interval import Interval | |
| 3 from SMART.Java.Python.structure.SubMapping import SubMapping | |
| 4 from SMART.Java.Python.structure.Mapping import Mapping | |
| 5 | |
| 6 class Test_Mapping(unittest.TestCase): | |
| 7 | |
| 8 def test__getTranscript(self): | |
| 9 queryInterval1 = Interval() | |
| 10 queryInterval1.setName("read1_1") | |
| 11 queryInterval1.setStart(1) | |
| 12 queryInterval1.setEnd(10) | |
| 13 queryInterval1.setDirection(1) | |
| 14 | |
| 15 targetInterval1 = Interval() | |
| 16 targetInterval1.setChromosome("chr1") | |
| 17 targetInterval1.setStart(100) | |
| 18 targetInterval1.setEnd(110) | |
| 19 targetInterval1.setDirection(1) | |
| 20 | |
| 21 subMapping1 = SubMapping() | |
| 22 subMapping1.setQueryInterval(queryInterval1) | |
| 23 subMapping1.setTargetInterval(targetInterval1) | |
| 24 | |
| 25 queryInterval2 = Interval() | |
| 26 queryInterval2.setName("read1_2") | |
| 27 queryInterval2.setStart(11) | |
| 28 queryInterval2.setEnd(20) | |
| 29 queryInterval2.setDirection(1) | |
| 30 | |
| 31 targetInterval2 = Interval() | |
| 32 targetInterval2.setChromosome("chr1") | |
| 33 targetInterval2.setStart(200) | |
| 34 targetInterval2.setEnd(210) | |
| 35 targetInterval2.setDirection(1) | |
| 36 | |
| 37 subMapping2 = SubMapping() | |
| 38 subMapping2.setQueryInterval(queryInterval2) | |
| 39 subMapping2.setTargetInterval(targetInterval2) | |
| 40 | |
| 41 mapping = Mapping() | |
| 42 mapping.addSubMapping(subMapping1) | |
| 43 mapping.addSubMapping(subMapping2) | |
| 44 | |
| 45 transcript = mapping.getTranscript() | |
| 46 self.assertEqual(transcript.getStart(), 100) | |
| 47 self.assertEqual(transcript.getEnd(), 210) | |
| 48 self.assertEqual(transcript.getChromosome(), "chr1") | |
| 49 exons = transcript.getExons() | |
| 50 self.assertEqual(len(exons), 2) | |
| 51 exon1, exon2 = exons | |
| 52 self.assertEqual(exon1.getStart(), 100) | |
| 53 self.assertEqual(exon1.getEnd(), 110) | |
| 54 self.assertEqual(exon2.getStart(), 200) | |
| 55 self.assertEqual(exon2.getEnd(), 210) | |
| 56 | |
| 57 | |
| 58 if __name__ == '__main__': | |
| 59 unittest.main() |