Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/structure/test/Test_Interval.py @ 24:452e051f6562
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:28:24 -0400 |
| parents | 769e306b7933 |
| children |
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import unittest from SMART.Java.Python.structure.Interval import Interval class Test_Interval(unittest.TestCase): def setUp(self): self.iInterval = Interval() self.iInterval1 = Interval() self.iInterval2 = Interval() def test__init__(self): self.iInterval.setChromosome("chromosome") self.iInterval.setName("sequence") self.iInterval.setStart(0) self.iInterval.setEnd(123) obsStart = self.iInterval.getStart() obsEnd = self.iInterval.getEnd() expStart = 0 expEnd = 123 self.assertEqual(expStart, obsStart) self.assertEqual(expEnd, obsEnd) def test_copy(self): self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(300) self.iInterval1.setDirection("+") self.iInterval2.copy(self.iInterval1) self.assertEqual(self.iInterval2.getName(), "interval1") self.assertEqual(self.iInterval2.getChromosome(), "chr1") self.assertEqual(self.iInterval2.getStart(), 100) self.assertEqual(self.iInterval2.getEnd(), 300) self.assertEqual(self.iInterval2.getDirection(), 1) self.iInterval1.setStart(200) self.assertEqual(self.iInterval2.getStart(), 100) def test_getDirection(self): self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(300) self.iInterval1.setDirection("+") expDirect = 1 self.assertEquals(expDirect,self.iInterval1.getDirection()) #!!!! Warning: two methods getStart() and getEnd() give the information maximum and minimum in interval.!!!!# #In case strand = "+", start < end; strand = "-", start > end def test_setStartEnd(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(300) self.iInterval1.setDirection("+") self.assertEqual(self.iInterval1.getName(), "interval1") self.assertEqual(self.iInterval1.getChromosome(), "chr1") self.assertEqual(self.iInterval1.getStart(),100) self.assertEqual(self.iInterval1.getEnd(), 300) self.assertEqual(self.iInterval1.getDirection(), 1) self.iInterval1.setStart(200) self.assertEqual(self.iInterval1.getStart(), 200) self.assertEqual(self.iInterval1.getEnd(), 300) self.iInterval1.setEnd(300) self.iInterval1.setStart(100) self.assertEqual(self.iInterval1.getStart(), 100) self.assertEqual(self.iInterval1.getEnd(), 300) self.iInterval1.setEnd(1200) self.iInterval1.setStart(1000) self.assertEqual(self.iInterval1.getStart(), 1000) self.assertEqual(self.iInterval1.getEnd(), 1200) self.iInterval1.reverse() self.assertEqual(self.iInterval1.getDirection(), -1) self.assertEqual(self.iInterval1.getStart(), 1000) self.assertEqual(self.iInterval1.getEnd(), 1200) self.iInterval1.setStart(1100) self.assertEqual(self.iInterval1.getStart(), 1100) self.assertEqual(self.iInterval1.getEnd(), 1200) self.iInterval1.setEnd(2200) self.iInterval1.setStart(2000) self.assertEqual(self.iInterval1.getStart(), 2000) self.assertEqual(self.iInterval1.getEnd(), 2200) self.iInterval1.setStart(1000) self.iInterval1.setEnd(1200) self.assertEqual(self.iInterval1.getStart(), 1000) self.assertEqual(self.iInterval1.getEnd(), 1200) def test_reverse(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(200) self.iInterval1.setDirection("+") self.iInterval1.reverse() self.assertEqual(self.iInterval1.getStart(), 100) self.assertEqual(self.iInterval1.getEnd(), 200) self.assertEqual(self.iInterval1.getDirection(), -1) def test_overlapWith(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(200) self.iInterval1.setDirection("+") self.iInterval2 = Interval() self.iInterval2.copy(self.iInterval1) self.iInterval2.setName("interval2") self.assertTrue(self.iInterval1.overlapWith(self.iInterval2)) self.iInterval2.setChromosome("chr2") try: self.iInterval1.overlapWith(self.iInterval2) self.fail() except Exception: pass self.iInterval2.setChromosome("chr1") self.iInterval2.setEnd(400) self.iInterval2.setStart(300) self.assertFalse(self.iInterval1.overlapWith(self.iInterval2)) self.iInterval2.setStart(200) self.assertTrue(self.iInterval1.overlapWith(self.iInterval2)) def test_isIncludeIn(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(200) self.iInterval1.setDirection("+") self.iInterval2 = Interval() self.iInterval2.setName("interval2") self.iInterval2.setChromosome("chr1") self.iInterval2.setStart(80) self.iInterval2.setEnd(280) self.iInterval2.setDirection("+") self.assertTrue(self.iInterval1.isIncludeIn(self.iInterval2)) def test_getDistance(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(200) self.iInterval1.setDirection("+") self.iInterval2 = Interval() self.iInterval2.copy(self.iInterval1) self.iInterval2.setName("interval2") self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 0) self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 0) self.iInterval2.setChromosome("chr2") try: self.iInterval1.getDistance(self.iInterval2) self.fail() except Exception: pass self.iInterval2.setChromosome("chr1") self.iInterval2.setEnd(400) self.iInterval2.setStart(300) self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 100) self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 100) def test_getRelativeDistance(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(200) self.iInterval1.setDirection("+") self.iInterval2 = Interval() self.iInterval2.copy(self.iInterval1) self.iInterval2.setName("interval2") self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 0) self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 0) self.iInterval2.setChromosome("chr2") try: self.iInterval1.getDistance(self.iInterval2) self.fail() except Exception: pass self.iInterval2.setChromosome("chr1") self.iInterval2.setEnd(400) self.iInterval2.setStart(300) self.assertEqual(self.iInterval1.getRelativeDistance(self.iInterval2), 100) self.assertEqual(self.iInterval2.getRelativeDistance(self.iInterval1), -100) def test_merge(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(200) self.iInterval1.setDirection("+") self.iInterval2 = Interval() self.iInterval2.copy(self.iInterval1) self.iInterval2.setName("interval2") self.iInterval2.merge(self.iInterval1) self.assertEqual(self.iInterval1, self.iInterval2) self.iInterval2.setChromosome("chr2") expMessage = "Cannot merge '%s' and '%s' for they are on different chromosomes." % (str(self.iInterval2), str(self.iInterval1)) isExceptionRaised = False try: self.iInterval2.merge(self.iInterval1) except Exception, e: isExceptionRaised = True obsMessage = str(e) self.assertTrue(isExceptionRaised) self.assertEquals(expMessage, obsMessage) #Warning! Both two intervals should be on the same chromosome and direction. self.iInterval2.setChromosome("chr1") self.iInterval2.setStart(300) self.iInterval2.setEnd(400) self.iInterval2.merge(self.iInterval1) self.assertEqual(self.iInterval2.getStart(), 100) self.assertEqual(self.iInterval2.getEnd(), 400) self.assertEqual(self.iInterval2.getChromosome(), "chr1") def test_include(self): iInterval1 = Interval() iInterval1.setName("interval1") iInterval1.setChromosome("chr1") iInterval1.setStart(100) iInterval1.setEnd(200) iInterval1.setDirection("+") iInterval2 = Interval() iInterval2.copy(iInterval1) iInterval2.setName("interval2") self.assertTrue(iInterval1.include(iInterval2)) self.assertTrue(iInterval2.include(iInterval1)) iInterval2.setChromosome("chr2") self.assertFalse(iInterval1.include(iInterval2)) self.assertFalse(iInterval2.include(iInterval1)) iInterval2.setChromosome("chr1") iInterval1.setStart(1) self.assertTrue(iInterval1.include(iInterval2)) self.assertFalse(iInterval2.include(iInterval1)) iInterval1.setStart(100) iInterval1.setEnd(300) self.assertTrue(iInterval1.include(iInterval2)) self.assertFalse(iInterval2.include(iInterval1)) def test_getDifference(self): iInterval1 = Interval() iInterval1.setName("interval1") iInterval1.setChromosome("chr1") iInterval1.setStart(100) iInterval1.setEnd(400) iInterval1.setDirection("+") iInterval2 = Interval() iInterval2.copy(iInterval1) iInterval2.setName("interval2") self.assertEqual(iInterval1.getDifference(iInterval2), []) self.assertEqual(iInterval2.getDifference(iInterval1), []) iInterval2.setChromosome("chr2") results = iInterval1.getDifference(iInterval2) self.assertEqual(len(results), 1) resultInterval = results[0] self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) iInterval2.setChromosome("chr1") iInterval2.setEnd(300) results = iInterval1.getDifference(iInterval2) self.assertEqual(len(results), 1) resultInterval = results[0] self.assertEqual(resultInterval.getStart(), 301) self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) iInterval2.setDirection("-") results = iInterval1.getDifference(iInterval2, True) self.assertEqual(len(results), 1) resultInterval = results[0] self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) iInterval2.setDirection("+") iInterval2.setStart(200) results = iInterval1.getDifference(iInterval2) self.assertEqual(len(results), 2) resultInterval1, resultInterval2 = results self.assertEqual(resultInterval1.getStart(), iInterval1.getStart()) self.assertEqual(resultInterval1.getEnd(), 199) self.assertEqual(resultInterval1.getDirection(), iInterval1.getDirection()) self.assertEqual(resultInterval1.getChromosome(), iInterval1.getChromosome()) self.assertEqual(resultInterval2.getStart(), 301) self.assertEqual(resultInterval2.getEnd(), iInterval1.getEnd()) self.assertEqual(resultInterval2.getDirection(), iInterval1.getDirection()) self.assertEqual(resultInterval2.getChromosome(), iInterval1.getChromosome()) iInterval2.setEnd(2000) iInterval2.setStart(1000) results = iInterval1.getDifference(iInterval2) self.assertEqual(len(results), 1) resultInterval = results[0] self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) def test_mergeWithDifferentStrand(self): self.iInterval1 = Interval() self.iInterval1.setName("interval1") self.iInterval1.setChromosome("chr1") self.iInterval1.setStart(100) self.iInterval1.setEnd(200) self.iInterval1.setDirection("+") self.iInterval2 = Interval() self.iInterval2.setName("interval2") self.iInterval2.setChromosome("chr1") self.iInterval2.setStart(300) self.iInterval2.setEnd(400) self.iInterval2.setDirection("-") expMessage = "Cannot merge '%s' and '%s' for they are on different strands." % (str(self.iInterval2), str(self.iInterval1)) isExceptionRaised = False try: self.iInterval2.merge(self.iInterval1) except Exception, e: isExceptionRaised = True obsMessage = str(e) self.assertTrue(isExceptionRaised) self.assertEquals(expMessage, obsMessage) if __name__ == "__main__": unittest.main()