Mercurial > repos > yufei-luo > s_mart
diff commons/core/coord/test/Test_Map.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/commons/core/coord/test/Test_Map.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,183 @@ +# 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 )