Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/ncList/test/Test_FindOverlapsWithOneInterval.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 struct import os from SMART.Java.Python.structure.Interval import Interval from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval from SMART.Java.Python.ncList.NCListCursor import NCListCursor class Test_FindOverlapsWithOneInterval(unittest.TestCase): def setUp(self): self._inputGff3FileName = 'sortedFile.gff3' self._writeGFF3File(self._inputGff3FileName) self._obsFileName = "overlap.gff3" self._iFOWOI = FindOverlapsWithOneInterval(0) self._iFOWOI.setFileName(self._inputGff3FileName, "gff3") self._iFOWOI._chromosome = "chr1" self._iFOWOI.prepareIntermediateFiles() self._iFOWOI.createNCList() self._ncList = self._iFOWOI._ncList self._iFOWOI.setOutputFileName(self._obsFileName) def tearDown(self): return self._iFOWOI.close() for file in (self._inputGff3FileName, self._obsFileName): if os.path.exists(file): os.remove(file) def test_binarySearch_first_element_overlap(self): self._iFOWOI.setInterval("chr1", 500, 850) obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 0, 0), 0, 6) expReadPosition = 0 self._iFOWOI.dumpWriter() self._iFOWOI.close() self.assertEquals(expReadPosition, obsReadPosition._lIndex) def test_binarySearch_second_element_overlap(self): self._iFOWOI.setInterval("chr1", 500, 850) obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 2, 0), 2, 6) expReadPosition = 3 self._iFOWOI.dumpWriter() self._iFOWOI.close() self.assertEquals(expReadPosition, obsReadPosition._lIndex) def test_binarySearch_empty_subList(self): self._iFOWOI.setInterval("chr1", 500, 850) obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 5, 0), 5, 5) expReadPosition = None self._iFOWOI.dumpWriter() self._iFOWOI.close() self.assertEquals(expReadPosition, obsReadPosition) def test_binarySearch_no_overlap_right(self): self._iFOWOI.setInterval("chr1", 1400, 1500) obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 0, 0), 0, 6) expReadPosition = None self._iFOWOI.dumpWriter() self._iFOWOI.close() self.assertEquals(expReadPosition, obsReadPosition) def test_binarySearch_no_overlap_left(self): self._iFOWOI.setInterval("chr1", 0, 45) obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 2, 0), 2, 6) expReadPosition = None self._iFOWOI.dumpWriter() self._iFOWOI.close() self.assertEquals(expReadPosition, obsReadPosition) 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()