|
18
|
1 import unittest
|
|
|
2 import os
|
|
|
3 from commons.core.utils.FileUtils import FileUtils
|
|
|
4 from commons.tools.SpliceTEsFromGenome import SpliceTEsFromGenome
|
|
|
5
|
|
|
6
|
|
|
7 class Test_SpliceTEsFromGenome( unittest.TestCase ):
|
|
|
8
|
|
|
9 def setUp( self ):
|
|
|
10 self._i = SpliceTEsFromGenome()
|
|
|
11
|
|
|
12
|
|
|
13 def test_zLaunchAsScript( self ):
|
|
|
14 cDir = os.getcwd()
|
|
|
15
|
|
|
16 coordFile = "dummyCoordFile"
|
|
|
17 coordFileHandler = open( coordFile, "w" )
|
|
|
18 coordFileHandler.write( "TE1\tchr1\t2\t5\n" )
|
|
|
19 coordFileHandler.write( "TE2\tchr1\t11\t15\n" )
|
|
|
20 coordFileHandler.write( "TE3\tchr1\t12\t14\n" )
|
|
|
21 coordFileHandler.close()
|
|
|
22
|
|
|
23 genomeFile = "dummyGenomeFile"
|
|
|
24 genomeFileHandler = open( genomeFile, "w" )
|
|
|
25 genomeFileHandler.write( ">chr1\n" )
|
|
|
26 genomeFileHandler.write( "AGGGGAAAAACCCCCAAAAA\n" )
|
|
|
27 genomeFileHandler.write( ">chr2\n" )
|
|
|
28 genomeFileHandler.write( "TTTTTTTTTT\n" )
|
|
|
29 genomeFileHandler.close()
|
|
|
30
|
|
|
31 expFile = "dummyExpFile"
|
|
|
32 expFileHandler = open( expFile, "w" )
|
|
|
33 expFileHandler.write( ">chr1\n" )
|
|
|
34 expFileHandler.write( "AAAAAAAAAAA\n" )
|
|
|
35 expFileHandler.write( ">chr2\n" )
|
|
|
36 expFileHandler.write( "TTTTTTTTTT\n" )
|
|
|
37 expFileHandler.close()
|
|
|
38
|
|
|
39 obsFile = "dummyObsFile"
|
|
|
40
|
|
|
41 cmd = "SpliceTEsFromGenome.py"
|
|
|
42 cmd += " -i %s" % ( coordFile )
|
|
|
43 cmd += " -f %s" % ( "map" )
|
|
|
44 cmd += " -g %s" % ( genomeFile )
|
|
|
45 cmd += " -o %s" % ( obsFile )
|
|
|
46 cmd += " -v %i" % ( 0 )
|
|
|
47 returnStatus = os.system( cmd )
|
|
|
48
|
|
|
49 self.assertTrue( returnStatus == 0 )
|
|
|
50 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
|
|
|
51
|
|
|
52 for f in [ coordFile, genomeFile, expFile, obsFile ]:
|
|
|
53 os.remove( f )
|
|
|
54 os.chdir( cDir )
|
|
|
55
|
|
|
56 if __name__ == "__main__":
|
|
|
57 unittest.main() |
