Mercurial > repos > yufei-luo > s_mart
view commons/core/coord/test/Test_Map.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. import unittest import os from commons.core.coord.Map import Map from commons.core.utils.FileUtils import FileUtils class Test_Map( unittest.TestCase ): def setUp(self): self._map = Map() def test_setFromString(self): line = "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" # test with '\t' separator self._map.setFromString(line) self.assertEqual( self._map.name, "MbQ12Gr2Cl2" ) self.assertEqual( self._map.seqname, "consensus1" ) self.assertEqual( self._map.start, 51 ) self.assertEqual( self._map.end, 1230 ) line = "MbQ12Gr2Cl2;consensus1;51;1230" # test with ';' separator self._map.setFromString(line,";") self.assertEqual( self._map.name, "MbQ12Gr2Cl2" ) self.assertEqual( self._map.seqname, "consensus1" ) self.assertEqual( self._map.start, 51 ) self.assertEqual( self._map.end, 1230 ) def test___eq__(self): self._map.setFromString( "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" ) o = Map() o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" ) self.assertEqual( self._map, o ) # same data o.setFromString( "MbQ12Gr2Cl1\tconsensus1\t51\t1230\n" ) self.assertNotEqual( self._map, o ) # different name o.setFromString( "MbQ12Gr2Cl2\tconsensus2\t51\t1230\n" ) self.assertNotEqual( self._map, o ) # different seqname o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t15\t1230\n" ) self.assertNotEqual( self._map, o ) # different start o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t51\t123000\n" ) self.assertNotEqual( self._map, o ) # different end o.setFromString( "MbQ12Gr2Cl2\tconsensus1\t1230\t51\n" ) self.assertNotEqual( self._map, o ) # same start/end but in different order def test_setFromTuple(self): tuple = ("MbQ12Gr2Cl2", "consensus1","51","1230") self._map.setFromTuple(tuple) expMap = Map("MbQ12Gr2Cl2", "consensus1",51,1230) obsMap = self._map self.assertEquals(expMap, obsMap) def test_read_empty_file(self): fileName = "dummyFile" os.system("touch " + fileName) fileHandle = open(fileName, "r") obsResult = self._map.read(fileHandle) expResult = 0 fileHandle.close() os.remove(fileName) self.assertEquals(expResult, obsResult) def test_read_uncompleted_line( self): uncompletedLine = "MbQ12Gr2Cl2\tconsensus1\t51" fileName = "dummyFile" fileHandle = open(fileName, "w") fileHandle.write(uncompletedLine) fileHandle.close() fileHandle = open(fileName, "r") obsResult = self._map.read(fileHandle) expResult = 0 fileHandle.close() os.remove(fileName) self.assertEquals(obsResult, expResult) def test_read(self): line = "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" fileName = "dummyFile" fileHandle = open(fileName, "w") fileHandle.write(line) fileHandle.close() fileHandle = open(fileName, "r") self._map.read(fileHandle) obsResult = self._map expResult = Map() expResult.setFromString(line) fileHandle.close() os.remove(fileName) self.assertEquals(obsResult, expResult) def test_write(self): line = "MbQ12Gr2Cl2\tconsensus1\t51\t1230\n" expFileName = "expFileName" fileHandle = open(expFileName, "w") fileHandle.write(line) fileHandle.close() obsFileName = "obsFileName" fileHandle = open(obsFileName, "w") self._map.setFromString(line) self._map.write(fileHandle) fileHandle.close() self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) os.remove(obsFileName) os.remove(expFileName) def test_diff1(self): map1 = Map("seq1","DmelChr4", 190000, 390000) map2 = Map("seq2","DmelChr4", 290000, 590000) expMap1 = Map("seq1", "DmelChr4", 190000, 289999) expReturnedMap = Map() obsReturnedMap = map1.diff(map2) obsMap1 = map1 self.assertEquals(expMap1, obsMap1) self.assertEquals(expReturnedMap, obsReturnedMap) def test_diff2(self): map1 = Map("seq1","DmelChr4", 190000, 590000) map2 = Map("seq2","DmelChr4", 290000, 390000) expMap1 = Map("seq1", "DmelChr4", 190000, 289999) expReturnedMap = Map("seq1", "DmelChr4", 390001, 590000) obsReturnedMap = map1.diff(map2) obsMap1 = map1 self.assertEquals(expMap1, obsMap1) self.assertEquals(expReturnedMap, obsReturnedMap) test_suite = unittest.TestSuite() test_suite.addTest( unittest.makeSuite( Test_Map ) ) if __name__ == "__main__": unittest.TextTestRunner(verbosity=2).run( test_suite )