comparison commons/core/coord/test/Test_Map.py @ 6:769e306b7933

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6:769e306b7933

# 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. 
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# that may mean  that it is complicated to manipulate,  and  that  also
# therefore means  that it is reserved for developers  and  experienced
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# same conditions as regards security. 
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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 )