view commons/tools/tests/Test_OrientSequences.py @ 18:94ab73e8a190

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import unittest
import time
import os
from commons.core.utils.FileUtils import FileUtils
from commons.tools.OrientSequences import OrientSequences


class Test_OrientSequences( unittest.TestCase ):
    
    def setUp( self ):
        self._i = OrientSequences ()
        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
        
        
    def tearDown( self ):
        self._i = None
        self._uniqId = None
        
        
    def test_parseMummerOutput( self ):
        inFileName = "dummyInFile_%s" % ( self._uniqId )
        inF = open( inFileName, "w" )
        inF.write( "> seq1\n" )
        inF.write( "  seq2      20        1        20\n" )
        inF.write( "> seq1 Reverse\n" )
        inF.write( "  seq2      100        1        100\n" )
        inF.write( "  seq2      450      400        50\n" )
        inF.close()
        dExp = { "direct": 1, "reverse": 2 }
        self._i._verbose = 0
        dObs = self._i.parseMummerOutput( inFileName, "seq1", "seq2" )
        self.assertEqual( dObs, dExp )
        os.remove( inFileName )
        
        
    def test_getSequencesToReverseFromMatrix_2seq( self ):
        lNewHeaders = [ "seq1", "seq2" ]
        dMatrix = { "1_vs_2": { "direct": 1, "reverse": 2 } }
        lExp = [ "seq2" ]
        self._i._verbose = 0
        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
        lExp.sort()
        lObs.sort()
        self.assertEqual( lObs, lExp )
        
        
    def test_getSequencesToReverseFromMatrix_3seq( self ):
        lNewHeaders = [ "seq1", "seq2", "seq3" ]
        dMatrix = { "1_vs_2": { "direct": 1, "reverse": 10 },
                   "1_vs_3": { "direct": 10, "reverse": 1 },
                   "2_vs_3": { "direct": 1, "reverse": 10 } }
        lExp = [ "seq2" ]
        self._i._verbose = 0
        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
        lExp.sort()
        lObs.sort()
        self.assertEqual( lExp, lObs )
        
        
    def test_getSequencesToReverseFromMatrix_4seq( self ):
        lNewHeaders = [ "seq1", "seq2", "seq3", "seq4" ]
        dMatrix = { "1_vs_2": { "direct": 10, "reverse": 1 },
                   "1_vs_3": { "direct": 1, "reverse": 10 },
                   "1_vs_4": { "direct": 1, "reverse": 10 },
                   "2_vs_3": { "direct": 1, "reverse": 10 },
                   "2_vs_4": { "direct": 1, "reverse": 10 },
                   "3_vs_4": { "direct": 1, "reverse": 2 } }
        lExp = [ "seq3", "seq4" ]
        self._i._verbose = 0
        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
        lExp.sort()
        lObs.sort()
        self.assertEqual( lExp, lObs )
        
        
    def test_orientInputSequences( self ):
        lSeqToOrient = [ "seq1" ]
        tmpFileName = "dummyInFile_%s" % ( self._uniqId )
        tmpF = open( tmpFileName, "w" )
        tmpF.write( ">seq1\n" )
        tmpF.write( "ATGCGGTGCATG\n" )
        tmpF.write( ">seq2\n" )
        tmpF.write( "GGCGAAGTGAAA\n" )
        tmpF.close()
        expFileName = "dummyExpFile_%s" % ( self._uniqId )
        expF = open( expFileName, "w" )
        expF.write( ">seq1 re-oriented\n" )
        expF.write( "CATGCACCGCAT\n" )
        expF.write( ">seq2\n" )
        expF.write( "GGCGAAGTGAAA\n" )
        expF.close()
        obsFileName = "dummyObsFile_%s" % ( self._uniqId )
        self._i._verbose = 0
        self._i._outFileName = obsFileName
        self._i.orientInputSequences( lSeqToOrient, tmpFileName )
        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
        for f in [ tmpFileName, expFileName, obsFileName ]:
            os.remove( f )
            
if __name__ == "__main__":
        unittest.main()