Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_F_LaunchTRF.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 from commons.launcher.LaunchTRF import LaunchTRF
5
6
7 class Test_F_LaunchTRF(unittest.TestCase):
8
9 def setUp(self):
10 self._inputFastaFileName = "input.fa"
11 self._obsTRFOutputFileName = "obsTRF.TRF.set"
12 self._expTRFOutputFileName = "expTRF.TRF.set"
13 self._writeInputFile()
14 self._writeExpTRFOutputFile()
15
16 def tearDown(self):
17 try:
18 os.remove(self._inputFastaFileName)
19 except:pass
20
21 try:
22 os.remove(self._expTRFOutputFileName)
23 except:pass
24 try:
25 os.remove(self._obsTRFOutputFileName)
26 except:pass
27 try:
28 os.remove("input.fa.2.3.5.80.10.20.15.dat")
29 except:pass
30
31 def test_run(self):
32 ilauncher = LaunchTRF(self._inputFastaFileName,self._obsTRFOutputFileName,verbosity=5)
33 ilauncher.run()
34 self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))
35
36 def test_run_as_script(self):
37 cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName)
38 os.system(cmd)
39 self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))
40
41 def test_run_as_scriptNoOutputGiven(self):
42 cmd = 'LaunchTRF.py -i %s -v 3' % (self._inputFastaFileName)
43 os.system(cmd)
44 self._obsTRFOutputFileName = "input.fa.TRF.set"
45 self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))
46
47 def test_run_as_scriptNoOutputGivenDoClean(self):
48 cmd = 'LaunchTRF.py -i %s -c -v 3' % (self._inputFastaFileName)
49 os.system(cmd)
50 self._obsTRFOutputFileName = "input.fa.TRF.set"
51 datFilePath = os.path.join(os.getcwd(),"%s.2.3.5.80.10.20.15.dat" % self._inputFastaFileName)
52 self.assertFalse(os.path.exists(datFilePath))
53
54 def _writeInputFile(self):
55 InputFile = open(self._inputFastaFileName, 'w')
56 InputFile.write('>sequence\n')
57 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
58 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
59 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
60 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
61 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
62 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
63 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
64 InputFile.write('>sequence2\n')
65 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
66 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
67 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
68 InputFile.close()
69
70 def _writeExpTRFOutputFile(self):
71 with open(self._expTRFOutputFileName,'w') as expTRFOutputFile:
72 expTRFOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21
73 2\t(GGT)5\tsequence\t10\t23
74 3\t(GTGTGA)4\tsequence\t222\t242
75 4\t(GTCCA)2\tsequence\t282\t292
76 5\t(AGTG)4\tsequence\t355\t371
77 6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152
78 7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151
79 8\t(TC)23\tsequence2\t107\t152
80 """)
81
82
83 if __name__ == "__main__":
84 unittest.main()