Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/ncList/test/Test_FindOverlapsWithSeveralIntervals.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/ncList/test/Test_FindOverlapsWithSeveralIntervals.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,160 @@ +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()