Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/ncList/test/Test_F_NCList.py @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/ncList/test/Test_F_NCList.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,302 @@ +import os +import unittest +import struct +from SMART.Java.Python.ncList.NCList import NCList +from SMART.Java.Python.misc import Utils +from commons.core.utils.FileUtils import FileUtils +from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import * +from commons.core.parsing.GffParser import GffParser +from SMART.Java.Python.ncList.FileSorter import FileSorter + +class Test_F_NCList(unittest.TestCase): + + def setUp(self): + self._inputGff3FileName = 'sortedFile.gff3' + self._sortedFileName = 'sortedFile.pkl' + self._expHFileName = 'expH.bin' + self._expLFileName = 'expL.bin' + self._obsHFileName = 'H.bin' + self._obsLFileName = 'L.bin' + self._addressFileName = 'address.txt' + self._writeGFF3File(self._inputGff3FileName) + self._ncList = NCList(0) + self._ncList.setChromosome("chr1") + + def tearDown(self): + return + for fileName in (self._inputGff3FileName, self._sortedFileName, self._expHFileName, self._expLFileName, self._obsHFileName, self._obsLFileName, self._addressFileName): + if os.path.exists(fileName): + os.remove(fileName) + + def _sortAndBuild(self): + parser = GffParser(self._inputGff3FileName) + fs = FileSorter(parser, 0) + fs.setOutputFileName(self._sortedFileName) + fs.sort() + self._ncList.setFileName(self._sortedFileName) + self._ncList.setNbElements(parser.getNbTranscripts()) + self._ncList.buildLists() + + def test_run_with_one_elementSubList(self): + iMock = MockFindOverlapsWithOneInterval() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFile_one_elementSubList() + self._writeExpLFile_one_elementSubList() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case1(self): + iMock = MockFindOverlapsWithServeralIntervals_case1() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase1() + self._writeExpLFileCase1() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case2(self): + iMock = MockFindOverlapsWithServeralIntervals_case2() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase2() + self._writeExpLFileCase2() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case3(self): + iMock = MockFindOverlapsWithServeralIntervals_case3() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase3() + self._writeExpLFileCase3() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case4_5(self): + iMock = MockFindOverlapsWithServeralIntervals_case4_5() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase4_5() + self._writeExpLFileCase4_5() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case6_7(self): + iMock = MockFindOverlapsWithServeralIntervals_case6_7() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase6_7() + self._writeExpLFileCase6_7() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case8(self): + iMock = MockFindOverlapsWithServeralIntervals_case8() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase8() + self._writeExpLFileCase8() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case9(self): + iMock = MockFindOverlapsWithServeralIntervals_case9() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase9() + self._writeExpLFileCase9() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case10(self): + iMock = MockFindOverlapsWithServeralIntervals_case10() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase10() + self._writeExpLFileCase10() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case11(self): + iMock = MockFindOverlapsWithServeralIntervals_case11() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase11() + self._writeExpLFileCase11() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + def test_case12(self): + iMock = MockFindOverlapsWithServeralIntervals_case12() + iMock.write(self._inputGff3FileName) + self._sortAndBuild() + self._writeExpHFileCase12() + self._writeExpLFileCase12() + self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) + + 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() + + def _writeBinFile(self, fileName, elements): + handle = open(fileName, "wb") + for element in elements: + handle.write(struct.pack('l', element)) + handle.close() + + def _writeExpHFile(self, HFileName): + list = [0, 2, 48, 3, -1, -1, -1, -1, 120, 1, 144, 1, -1, -1, -1, -1] + H = open(HFileName, 'wb') + + for item in list: + item = struct.pack('l', item) + H.write(item) + H.close() + + def _writeExpHFile_with_empty_SubParentDict(self, HFileName): + list = [0, 1, -1, -1] + H = open(HFileName, 'wb') + + for item in list: + item = struct.pack('l', item) + H.write(item) + H.close() + + def _writeExpHFile_one_elementSubList(self): + elements = [0, 1] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase1(self): + elements = [0, 2, 2, 3, 5, 1, 6, 1] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase2(self): + elements = [0, 2, 2, 1, 3, 1, 4, 1] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase3(self): + elements = [0, 2, 2, 1, 3, 1, 4, 2] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase4_5(self): + elements = [0, 1, 1, 1, 2, 1] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase6_7(self): + elements = [0, 1, 1, 4] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase8(self): + elements = [0, 1, 1, 2] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase9(self): + elements = [0, 2, 2, 1] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase10(self): + elements = [0, 3, 3, 3] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase11(self): + elements = [0, 2, 2, 2, 4, 2] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpHFileCase12(self): + elements = [0, 1, 1, 3, 4, 1] + self._writeBinFile(self._expHFileName, elements) + + def _writeExpLFile_one_elementSubList(self): + elements = [0, 1000, 0, -1, -1] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase1(self): + elements = [ 0, 1000, 0, 1, -1, \ + 1200, 1300, 2345, -1, -1, \ + 50, 350, 391, -1, 0, \ + 100, 600, 781, 2, 0, \ + 700, 950, 1563, 3, 0, \ + 200, 450, 1172, -1, 3, \ + 800, 900, 1954, -1, 4] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase2(self): + elements = [ 0, 500, 0, 1, -1, \ + 900, 1200, 1561, -1, -1, \ + 50, 450, 389, 2, 0, \ + 100, 400, 779, 3, 2, \ + 100, 200, 1170, -1, 3] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase3(self): + elements = [ 0, 500, 0, 1, -1, \ + 800, 1000, 1952, -1, -1, \ + 50, 450, 389, 2, 0, \ + 100, 400, 779, 3, 2, \ + 100, 200, 1170, -1, 3, \ + 300, 400, 1561, -1, 3] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase4_5(self): + elements = [ 0, 1000, 0, 1, -1, \ + 200, 800, 391, 2, 0, \ + 400, 600, 782, -1, 1] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase6_7(self): + elements = [ 0, 1000, 0, 1, -1, \ + 100, 300, 391, -1, 0, \ + 400, 500, 782, -1, 0, \ + 510, 520, 1173, -1, 0, \ + 850, 950, 1563, -1, 0] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase8(self): + elements = [ 0, 1000, 0, 1, -1, \ + 100, 200, 391, -1, 0, \ + 300, 400, 782, -1, 0] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase9(self): + elements = [ 0, 1000, 0, 1, -1, \ + 800, 1200, 782, -1, -1, \ + 600, 700, 391, -1, 0] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase10(self): + elements = [ 0, 1000, 0, 1, -1, \ + 1200, 1300, 1576, -1, -1, \ + 1400, 1500, 1972, -1, -1, \ + 100, 200, 394, -1, 0, \ + 300, 400, 788, -1, 0, \ + 500, 600, 1182, -1, 0] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase11(self): + elements = [ 0, 500, 0, 1, -1, \ + 700, 900, 1180, 2, -1, \ + 100, 200, 392, -1, 0, \ + 300, 400, 786, -1, 0, \ + 710, 720, 1574, -1, 1, \ + 740, 750, 1967, -1, 1] + self._writeBinFile(self._expLFileName, elements) + + def _writeExpLFileCase12(self): + elements = [ 0, 1400, 0, 1, -1, \ + 300, 500, 368, 2, 0, \ + 800, 1100, 1106, -1, 0, \ + 1200, 1300, 1476, -1, 0, \ + 300, 500, 737, -1, 1] + self._writeBinFile(self._expLFileName, elements) + +if __name__ == "__main__": + unittest.main()