Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_CorrelateTEageWithGCcontent.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os
3 from commons.core.utils.FileUtils import FileUtils
4
5
6 class Test_CorrelateTEageWithGCcontent( unittest.TestCase ):
7
8 def test_zLaunchAsScript( self ):
9 cDir = os.getcwd()
10
11 coordFile = "dummyPathFile"
12 coordFileHandler = open( coordFile, "w" )
13 coordFileHandler.write( "1\tchr1\t1\t5\tTE1\t1\t5\t0.0\t100\t98.7\n" )
14 coordFileHandler.write( "1\tchr1\t11\t20\tTE1\t6\t15\t0.0\t100\t98.7\n" )
15 coordFileHandler.write( "2\tchr1\t26\t30\tTE1\t1\t5\t0.0\t100\t96.7\n" )
16 coordFileHandler.write( "3\tchr2\t1\t10\tTE2\t1\t10\t0.0\t100\t98.7\n" )
17 coordFileHandler.close()
18
19 genomeFile = "dummyGenomeFile"
20 genomeFileHandler = open( genomeFile, "w" )
21 genomeFileHandler.write( ">chr1\n" )
22 genomeFileHandler.write( "AGCTGTTTTTAGCAGACGCATTTTTGGAGGTTTT\n" )
23 genomeFileHandler.write( ">chr2\n" )
24 genomeFileHandler.write( "ATATATATGGTTTTTTTTTT\n" )
25 genomeFileHandler.close()
26
27 refseqFile = "dummyRefseqFile"
28 refseqFileHandler = open( refseqFile, "w" )
29 refseqFileHandler.write( ">TE1\nAGCAGCGACGACGACGACGACTTTT\n" )
30 refseqFileHandler.write( ">TE2\nAGCAGCGACGACGACGACGACTTTT\n" )
31 refseqFileHandler.write( ">TE3\nAGCAGCGACGACGACGACGACTTTT\n" )
32 refseqFileHandler.close()
33
34 expFile = "dummyExpFile"
35 expFileHandler = open( expFile, "w" )
36 expFileHandler.write( "copy\tTE\tchr\tlength\tid\tGC\tlengthPerc\n" )
37 expFileHandler.write( "1\tTE1\tchr1\t15\t98.70\t%.2f\t%.2f\n" % ( 100 * 9 / 15.0, 100 * 15 / 25.0 ) )
38 expFileHandler.write( "2\tTE1\tchr1\t5\t96.70\t%.2f\t%.2f\n" % ( 100 * 4 / 5.0, 100 * 5 / 25.0 ) )
39 expFileHandler.write( "3\tTE2\tchr2\t10\t98.70\t%.2f\t%.2f\n" % ( 100 * 2 / 10.0, 100 * 10 / 25.0 ) )
40 expFileHandler.close()
41
42 obsFile = "dummyObsFile"
43
44 cmd = "CorrelateTEageWithGCcontent.py"
45 cmd += " -i %s" % ( coordFile )
46 cmd += " -g %s" % ( genomeFile )
47 cmd += " -r %s" % ( refseqFile )
48 cmd += " -o %s" % ( obsFile )
49 cmd += " -v %i" % ( 0 )
50 returnStatus = os.system( cmd )
51
52 self.assertTrue( returnStatus == 0 )
53 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
54
55 for f in [ coordFile, genomeFile, refseqFile, expFile, obsFile ]:
56 os.remove( f )
57 os.chdir( cDir )
58
59 if __name__ == "__main__":
60 unittest.main()