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1 import unittest
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4
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5
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6 class Test_CorrelateTEageWithGCcontent( unittest.TestCase ):
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7
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8 def test_zLaunchAsScript( self ):
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9 cDir = os.getcwd()
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10
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11 coordFile = "dummyPathFile"
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12 coordFileHandler = open( coordFile, "w" )
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13 coordFileHandler.write( "1\tchr1\t1\t5\tTE1\t1\t5\t0.0\t100\t98.7\n" )
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14 coordFileHandler.write( "1\tchr1\t11\t20\tTE1\t6\t15\t0.0\t100\t98.7\n" )
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15 coordFileHandler.write( "2\tchr1\t26\t30\tTE1\t1\t5\t0.0\t100\t96.7\n" )
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16 coordFileHandler.write( "3\tchr2\t1\t10\tTE2\t1\t10\t0.0\t100\t98.7\n" )
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17 coordFileHandler.close()
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18
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19 genomeFile = "dummyGenomeFile"
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20 genomeFileHandler = open( genomeFile, "w" )
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21 genomeFileHandler.write( ">chr1\n" )
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22 genomeFileHandler.write( "AGCTGTTTTTAGCAGACGCATTTTTGGAGGTTTT\n" )
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23 genomeFileHandler.write( ">chr2\n" )
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24 genomeFileHandler.write( "ATATATATGGTTTTTTTTTT\n" )
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25 genomeFileHandler.close()
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26
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27 refseqFile = "dummyRefseqFile"
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28 refseqFileHandler = open( refseqFile, "w" )
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29 refseqFileHandler.write( ">TE1\nAGCAGCGACGACGACGACGACTTTT\n" )
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30 refseqFileHandler.write( ">TE2\nAGCAGCGACGACGACGACGACTTTT\n" )
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31 refseqFileHandler.write( ">TE3\nAGCAGCGACGACGACGACGACTTTT\n" )
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32 refseqFileHandler.close()
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33
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34 expFile = "dummyExpFile"
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35 expFileHandler = open( expFile, "w" )
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36 expFileHandler.write( "copy\tTE\tchr\tlength\tid\tGC\tlengthPerc\n" )
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37 expFileHandler.write( "1\tTE1\tchr1\t15\t98.70\t%.2f\t%.2f\n" % ( 100 * 9 / 15.0, 100 * 15 / 25.0 ) )
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38 expFileHandler.write( "2\tTE1\tchr1\t5\t96.70\t%.2f\t%.2f\n" % ( 100 * 4 / 5.0, 100 * 5 / 25.0 ) )
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39 expFileHandler.write( "3\tTE2\tchr2\t10\t98.70\t%.2f\t%.2f\n" % ( 100 * 2 / 10.0, 100 * 10 / 25.0 ) )
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40 expFileHandler.close()
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41
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42 obsFile = "dummyObsFile"
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43
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44 cmd = "CorrelateTEageWithGCcontent.py"
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45 cmd += " -i %s" % ( coordFile )
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46 cmd += " -g %s" % ( genomeFile )
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47 cmd += " -r %s" % ( refseqFile )
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48 cmd += " -o %s" % ( obsFile )
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49 cmd += " -v %i" % ( 0 )
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50 returnStatus = os.system( cmd )
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51
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52 self.assertTrue( returnStatus == 0 )
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53 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
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54
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55 for f in [ coordFile, genomeFile, refseqFile, expFile, obsFile ]:
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56 os.remove( f )
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57 os.chdir( cDir )
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58
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59 if __name__ == "__main__":
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60 unittest.main() |
