view commons/tools/tests/Test_SpliceTEsFromGenome.py @ 31:0ab839023fe4

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import unittest
import os
from commons.core.utils.FileUtils import FileUtils
from commons.tools.SpliceTEsFromGenome import SpliceTEsFromGenome


class Test_SpliceTEsFromGenome( unittest.TestCase ):
    
    def setUp( self ):
        self._i = SpliceTEsFromGenome()
        
        
    def test_zLaunchAsScript( self ):
        cDir = os.getcwd()
        
        coordFile = "dummyCoordFile"
        coordFileHandler = open( coordFile, "w" )
        coordFileHandler.write( "TE1\tchr1\t2\t5\n" )
        coordFileHandler.write( "TE2\tchr1\t11\t15\n" )
        coordFileHandler.write( "TE3\tchr1\t12\t14\n" )
        coordFileHandler.close()
        
        genomeFile = "dummyGenomeFile"
        genomeFileHandler = open( genomeFile, "w" )
        genomeFileHandler.write( ">chr1\n" )
        genomeFileHandler.write( "AGGGGAAAAACCCCCAAAAA\n" )
        genomeFileHandler.write( ">chr2\n" )
        genomeFileHandler.write( "TTTTTTTTTT\n" )
        genomeFileHandler.close()
        
        expFile = "dummyExpFile"
        expFileHandler = open( expFile, "w" )
        expFileHandler.write( ">chr1\n" )
        expFileHandler.write( "AAAAAAAAAAA\n" )
        expFileHandler.write( ">chr2\n" )
        expFileHandler.write( "TTTTTTTTTT\n" )
        expFileHandler.close()
        
        obsFile = "dummyObsFile"
        
        cmd = "SpliceTEsFromGenome.py"
        cmd += " -i %s" % ( coordFile )
        cmd += " -f %s" % ( "map" )
        cmd += " -g %s" % ( genomeFile )
        cmd += " -o %s" % ( obsFile )
        cmd += " -v %i" % ( 0 )
        returnStatus = os.system( cmd )
        
        self.assertTrue( returnStatus == 0 )
        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
        
        for f in [ coordFile, genomeFile, expFile, obsFile ]:
            os.remove( f )
        os.chdir( cDir )
        
if __name__ == "__main__":
        unittest.main()