Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/ncList/test/Test_FindOverlapsWithSeveralIntervals.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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import unittest import os from SMART.Java.Python.ncList.FindOverlapsWithSeveralIntervals import FindOverlapsWithSeveralIntervals class Test_FindOverlapsWithSeveralIntervals(unittest.TestCase): def setUp(self): self._inputRefGff3FileName = 'sortedFile.gff3' self._writeGFF3File(self._inputRefGff3FileName) self._inputQueryGff3FileName = 'sorted_Query.gff3' self._writeQueryGff3File(self._inputQueryGff3FileName) self._outputGff3FileName = 'overlaps.gff3' self._iFOWSI = FindOverlapsWithSeveralIntervals(self._inputRefGff3FileName, self._inputQueryGff3FileName) self._iFOWSI.setOutputGff3FileName(self._outputGff3FileName) def tearDown(self): os.remove(self._inputRefGff3FileName) os.remove(self._inputQueryGff3FileName) os.remove(self._outputGff3FileName) self._iFOWSI.deletIntermediateFiles() def test_isOverlapping_true(self): queryGff3Addr = 116 RefGff3Addr = 231 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr) exp = 0 self.assertEquals(exp, obs) def test_isOverlapping_false_left(self): queryGff3Addr = 116 RefGff3Addr = 58 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr) exp = -1 self.assertEquals(exp, obs) def test_isOverlapping_false_right(self): queryGff3Addr = 116 RefGff3Addr = 347 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr) exp = 1 self.assertEquals(exp, obs) def test_getHisFirstChild(self): firstRefLAddr = 0 obsFirstChildLAddr = self._iFOWSI.getHisFirstChild(firstRefLAddr) expFirstChildLAddr = 48 self.assertEquals(expFirstChildLAddr, obsFirstChildLAddr) def test_isLastElement_true(self): refLAddr = 96 obsBool = self._iFOWSI.isLastElement(refLAddr) expBool = True self.assertEquals(expBool, obsBool) def test_isLastElement_false(self): refLAddr = 72 obsBool = self._iFOWSI.isLastElement(refLAddr) expBool = False self.assertEquals(expBool, obsBool) def test_isLastElement_highestLevel_true(self): refLAddr = 24 obsBool = self._iFOWSI.isLastElement(refLAddr) expBool = True self.assertEquals(expBool, obsBool) def test_isLastElement_highestLevel_false(self): refLAddr = 0 obsBool = self._iFOWSI.isLastElement(refLAddr) expBool = False self.assertEquals(expBool, obsBool) def test_findOverlapIter(self): queryGff3Addr = 175 firstRefLAddr = 0 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) expFirstOverlapLAddr = 0 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) def test_not_findOverlapIter(self): queryGff3Addr = 295 firstRefLAddr = 24 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) expFirstOverlapLAddr = None self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) def test_findOverlapIter_not_the_first_RefOverlap(self): queryGff3Addr = 235 firstRefLAddr = 0 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) expFirstOverlapLAddr = 24 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) def test_changeToNewSubEndLAddr(self): firstChildLAddr = 48 subEndLAddr = 48 expSubEndLAddr = 120 obsSubEndLAddr = self._iFOWSI.changeToNewSubEndLAddr(firstChildLAddr, subEndLAddr) self.assertEquals(expSubEndLAddr, obsSubEndLAddr) def test_defineSubEndLaddr(self): parentLAddr = -1 expSubEndLAddr = 48 obsSubEndLAddr = self._iFOWSI.defineSubEndLaddr(parentLAddr) self.assertEquals(expSubEndLAddr, obsSubEndLAddr) def test_getNextRefIntervalInCaseNotOverLap(self): firstRefLAddr = 96 expRefLAddr = 24 obsRefLAddr = self._iFOWSI.getNextRefIntervalInCaseNotOverLap(firstRefLAddr) self.assertEquals(expRefLAddr, obsRefLAddr) def test_getNextRefIntervalInCaseOverLap(self): firstChildLAddr = -1 firstRefLAddr = 120 subEndLAddr = 144 expRefLAddr, expSubEndLAddr = (96, 144) obsRefLAddr, obsSubEndLAddr = self._iFOWSI.getNextRefIntervalInCaseOverLap(firstChildLAddr, firstRefLAddr, subEndLAddr) self.assertEquals((expRefLAddr, expSubEndLAddr), (obsRefLAddr, obsSubEndLAddr)) def test_not_findOverlapIter_between2RefIntervals(self): inputQueryGff3FileName = 'query2.gff3' self._writeQueryGff3File2(inputQueryGff3FileName) self._iFOWSI.setQueryGff3FileName(inputQueryGff3FileName) queryGff3Addr = 0 firstRefLAddr = 0 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) expFirstOverlapLAddr = 24 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) os.remove(inputQueryGff3FileName) def _writeQueryGff3File2(self, fileName): f = open(fileName, 'w') f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=test1.1;Name=test1.1\n") f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=test1.2;Name=test1.2\n") f.close() def _writeQueryGff3File(self, fileName): f = open(fileName, 'w') f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=test1.1;Name=test1.1\n") f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=test1.2;Name=test1.2\n") f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=test1.3;Name=test1.3\n") f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=test1.4;Name=test1.4\n") f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=test1.5;Name=test1.5\n") f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=test1.6;Name=test1.6\n") f.close() def _writeGFF3File(self, fileName): f = open(fileName, "w") f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n") f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n") f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n") f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n") f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n") f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n") f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n") f.close() if __name__ == "__main__": unittest.main()