Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/ncList/test/Test_F_NCList.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 769e306b7933 |
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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()