Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/Java/Python/structure/test/Test_Transcript.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/Java/Python/structure/test/Test_Transcript.py Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,351 @@ +import unittest +from SMART.Java.Python.structure.Interval import Interval +from SMART.Java.Python.structure.Transcript import Transcript + +class Test_Transcript(unittest.TestCase): + + def test_getSize(self): + transcript1 = Transcript() + transcript1.setDirection("+") + transcript1.setStart(2000) + transcript1.setEnd(3000) + transcript1.setChromosome("arm_X") + + self.assertEqual(transcript1.getSize(), 1001) + + transcript2 = Transcript() + transcript2.copy(transcript1) + self.assertEqual(transcript1.getSize(), 1001) + + transcript3 = Transcript() + transcript3.setDirection("+") + transcript3.setChromosome("arm_X") + + exon1 = Interval() + exon1.setDirection("+") + exon1.setChromosome("arm_X") + exon1.setStart(100) + exon1.setEnd(200) + transcript3.addExon(exon1) + + exon2 = Interval() + exon2.setDirection("+") + exon2.setChromosome("arm_X") + exon2.setStart(300) + exon2.setEnd(400) + transcript3.addExon(exon2) + + self.assertEqual(transcript3.getSize(), 203) + + + def test_overlapWithExons(self): + exon1_1 = Interval() + exon1_1.setChromosome("chr1") + exon1_1.setStart(100) + exon1_1.setEnd(200) + exon1_1.setDirection("+") + + exon1_2 = Interval() + exon1_2.setChromosome("chr1") + exon1_2.setStart(500) + exon1_2.setEnd(600) + exon1_2.setDirection("+") + + transcript1 = Transcript() + transcript1.setChromosome("chr1") + transcript1.setStart(100) + transcript1.setEnd(600) + transcript1.setDirection("+") + transcript1.addExon(exon1_1) + transcript1.addExon(exon1_2) + + exon2_1 = Interval() + exon2_1.copy(exon1_1) + + transcript2 = Transcript() + transcript2.setChromosome("chr1") + transcript2.setStart(100) + transcript2.setEnd(200) + transcript2.setDirection("+") + transcript2.addExon(exon2_1) + + self.assertTrue(transcript1.overlapWithExon(transcript2)) + + transcript2.reverse() + try: + self.assertFalse(transcript1.overlapWithExon(transcript2)) + except Exception: + pass + + transcript2.reverse() + transcript2.setChromosome("chr2") + self.assertFalse(transcript1.overlapWithExon(transcript2)) + + exon3_1 = Interval() + exon3_1.copy(exon1_1) + exon3_1.setEnd(400) + exon3_1.setStart(300) + + transcript3 = Transcript() + transcript3.setChromosome("chr1") + transcript3.setStart(300) + transcript3.setEnd(400) + transcript3.setDirection("+") + transcript3.addExon(exon3_1) + self.assertFalse(transcript1.overlapWithExon(transcript3)) + + + def test_merge(self): + exon1_1 = Interval() + exon1_1.setChromosome("chr1") + exon1_1.setStart(100) + exon1_1.setEnd(200) + exon1_1.setDirection("+") + + exon1_2 = Interval() + exon1_2.setChromosome("chr1") + exon1_2.setStart(500) + exon1_2.setEnd(600) + exon1_2.setDirection("+") + + transcript1 = Transcript() + transcript1.setChromosome("chr1") + transcript1.setEnd(600) + transcript1.setStart(100) + transcript1.setDirection("+") + transcript1.addExon(exon1_1) + transcript1.addExon(exon1_2) + + exon2_1 = Interval() + exon2_1.copy(exon1_1) + + transcript2 = Transcript() + transcript2.setChromosome("chr1") + transcript2.setEnd(200) + transcript2.setStart(100) + transcript2.setDirection("+") + transcript2.addExon(exon2_1) + + transcript1.merge(transcript2) + transcript1.sortExonsIncreasing() + exons = transcript1.getExons() + self.assertEqual(len(exons), 2) + exon1, exon2 = exons + self.assertEqual(exon1.getStart(), 100) + self.assertEqual(exon1.getEnd(), 200) + self.assertEqual(exon2.getStart(), 500) + self.assertEqual(exon2.getEnd(), 600) + + transcript2.setChromosome("chr2") + try: + transcript1.merge(transcript2) + self.fail() + except Exception: + pass + + exon3_1 = Interval() + exon3_1.copy(exon1_1) + exon3_1.setEnd(650) + exon3_1.setStart(550) + + transcript3 = Transcript() + transcript3.setChromosome("chr1") + transcript3.setEnd(650) + transcript3.setStart(550) + transcript3.setDirection("+") + transcript3.addExon(exon3_1) + + transcript1.merge(transcript3) + self.assertEqual(transcript1.getStart(), 100) + self.assertEqual(transcript1.getEnd(), 650) + exons = transcript1.getExons() + self.assertEqual(len(exons), 2) + exon1, exon2 = exons + self.assertEqual(exon1.getStart(), 100) + self.assertEqual(exon1.getEnd(), 200) + self.assertEqual(exon2.getStart(), 500) + self.assertEqual(exon2.getEnd(), 650) + + exon4_1 = Interval() + exon4_1.copy(exon1_1) + exon4_1.setEnd(400) + exon4_1.setStart(300) + + transcript4 = Transcript() + transcript4.setChromosome("chr1") + transcript4.setStart(300) + transcript4.setEnd(400) + transcript4.setDirection("+") + transcript4.addExon(exon4_1) + + transcript1.merge(transcript4) + self.assertEqual(transcript1.getStart(), 100) + self.assertEqual(transcript1.getEnd(), 650) + transcript1.sortExonsIncreasing() + exons = transcript1.getExons() + self.assertEqual(len(exons), 3) + exon1, exon2, exon3 = exons + self.assertEqual(exon1.getStart(), 100) + self.assertEqual(exon1.getEnd(), 200) + self.assertEqual(exon2.getStart(), 300) + self.assertEqual(exon2.getEnd(), 400) + self.assertEqual(exon3.getStart(), 500) + self.assertEqual(exon3.getEnd(), 650) + + + def test_extendStart(self): + transcript1 = Transcript() + transcript1.setStart(2000) + transcript1.setEnd(3000) + transcript1.setDirection("+") + transcript1.setChromosome("arm_X") + + transcript2 = Transcript() + transcript2.copy(transcript1) + transcript2.setDirection("-") + + transcript1.extendStart(1000) + transcript2.extendStart(1000) + + + self.assertEqual(transcript1.getDirection(), 1) + self.assertEqual(transcript1.getStart(), 1000) + self.assertEqual(transcript1.getEnd(), 3000) + self.assertEqual(transcript1.getChromosome(), "arm_X") + + self.assertEqual(transcript2.getDirection(), -1) + self.assertEqual(transcript2.getStart(), 2000) + self.assertEqual(transcript2.getEnd(), 4000) + self.assertEqual(transcript2.getChromosome(), "arm_X") + + + def test_restrictStart(self): + exon1_1 = Interval() + exon1_1.setChromosome("chr1") + exon1_1.setStart(100) + exon1_1.setEnd(200) + exon1_1.setDirection("+") + + exon1_2 = Interval() + exon1_2.setChromosome("chr1") + exon1_2.setStart(300) + exon1_2.setEnd(500) + exon1_2.setDirection("+") + + transcript1 = Transcript() + transcript1.setChromosome("chr1") + transcript1.setStart(100) + transcript1.setEnd(500) + transcript1.setDirection("+") + transcript1.addExon(exon1_1) + transcript1.addExon(exon1_2) + + transcript1.restrictStart(301) + exons = transcript1.getExons() + self.assertEqual(len(exons), 2) + exon1, exon2 = exons + self.assertEqual(exon1.getStart(), 100) + self.assertEqual(exon1.getEnd(), 200) + self.assertEqual(exon2.getStart(), 300) + self.assertEqual(exon2.getEnd(), 400) + + + def test__include(self): + iTranscript1 = Transcript() + iTranscript1.setName("transcript1") + iTranscript1.setChromosome("chr1") + iTranscript1.setStart(100) + iTranscript1.setEnd(200) + iTranscript1.setDirection("+") + + iTranscript2 = Transcript() + iTranscript2.copy(iTranscript1) + iTranscript2.setName("transcript2") + self.assertTrue(iTranscript1.include(iTranscript2)) + self.assertTrue(iTranscript2.include(iTranscript1)) + + iTranscript2.setChromosome("chr2") + self.assertFalse(iTranscript1.include(iTranscript2)) + self.assertFalse(iTranscript2.include(iTranscript1)) + + iTranscript2.setChromosome("chr1") + exon = Interval() + exon.setChromosome("chr1") + exon.setDirection("+") + exon.setStart(300) + exon.setEnd(400) + iTranscript1.addExon(exon) + self.assertTrue(iTranscript1.include(iTranscript2)) + self.assertFalse(iTranscript2.include(iTranscript1)) + + exon = Interval() + exon.setChromosome("chr1") + exon.setDirection("+") + exon.setStart(500) + exon.setEnd(600) + iTranscript2.addExon(exon) + self.assertFalse(iTranscript1.include(iTranscript2)) + self.assertFalse(iTranscript2.include(iTranscript1)) + + + def test__getDifference(self): + iTranscript1 = Transcript() + iTranscript1.setName("transcript1") + iTranscript1.setChromosome("chr1") + iTranscript1.setStart(100) + iTranscript1.setEnd(400) + iTranscript1.setDirection("+") + + iTranscript2 = Transcript() + iTranscript2.setName("transcript1") + iTranscript2.setChromosome("chr1") + iTranscript2.setStart(200) + iTranscript2.setEnd(400) + iTranscript2.setDirection("+") + + newTranscript = iTranscript1.getDifference(iTranscript2) + self.assertTrue(newTranscript.getStart(), 100) + self.assertTrue(newTranscript.getEnd(), 199) + exons = newTranscript.getExons() + self.assertTrue(len(exons), 1) + exon1 = exons[0] + self.assertTrue(exon1.getStart(), 100) + self.assertTrue(exon1.getEnd(), 199) + + iTranscript2 = Transcript() + iTranscript2.setName("transcript1") + iTranscript2.setChromosome("chr1") + iTranscript2.setStart(100) + iTranscript2.setEnd(200) + iTranscript2.setDirection("+") + + newTranscript = iTranscript1.getDifference(iTranscript2) + self.assertTrue(newTranscript.getStart(), 201) + self.assertTrue(newTranscript.getEnd(), 400) + exons = newTranscript.getExons() + self.assertTrue(len(exons), 1) + exon1 = exons[0] + self.assertTrue(exon1.getStart(), 201) + self.assertTrue(exon1.getEnd(), 400) + + iTranscript2 = Transcript() + iTranscript2.setName("transcript1") + iTranscript2.setChromosome("chr1") + iTranscript2.setStart(200) + iTranscript2.setEnd(300) + iTranscript2.setDirection("+") + + newTranscript = iTranscript1.getDifference(iTranscript2) + self.assertTrue(newTranscript.getStart(), 100) + self.assertTrue(newTranscript.getEnd(), 400) + exons = newTranscript.getExons() + self.assertTrue(len(exons), 2) + exon1, exon2 = exons + self.assertTrue(exon1.getStart(), 100) + self.assertTrue(exon1.getEnd(), 199) + self.assertTrue(exon2.getStart(), 301) + self.assertTrue(exon2.getEnd(), 400) + + +if __name__ == '__main__': + unittest.main()