Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/hmmer/profilsSearchInTEClassifier/tests/Test_ProfilesSearch.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 import unittest
2 import os
3 import ConfigParser
4 import shutil
5 from commons.pyRepetUnit.hmmer.profilsSearchInTEClassifier.ProfilesSearch import ProfilesSearch
6
7 class Test_ProfilesSearch(unittest.TestCase):
8
9
10 def setUp(self):
11 self._section = 'detect_features'
12 self._option1 = 'TE_HMM_profiles'
13 self._option2 = 'TE_HMMER_evalue'
14 self._config = ConfigParser.ConfigParser()
15 self._config.add_section(self._section)
16 self._config.set(self._section, self._option1, './datas/hmmbank_test')
17 self._config.set(self._section, self._option2, '10')
18 self._iProfilesSearch = ProfilesSearch()
19 self._launch1 = 'First Command\n'
20 self._launch2 = '\nSecond Command\n'
21 self._cDir = '.'
22 self._profileBank = self._config.get(self._section, self._option1)
23 self._bank = os.path.basename(self._profileBank)
24 shutil.copy(self._profileBank, self._cDir + "/" + self._bank)
25
26 def tearDown(self):
27 os.remove(self._cDir + "/" + self._bank)
28
29 def test_prepareProfilesBank(self):
30 hmmpressLaunched = False
31 self._iProfilesSearch.prepareProfilesBank( self._launch1, self._launch2, self._config, self._cDir )
32 if ( os.path.exists(self._cDir + "/" + self._bank + ".h3m") \
33 and os.path.exists(self._cDir + "/" + self._bank + ".h3i") \
34 and os.path.exists(self._cDir + "/" + self._bank + ".h3f") \
35 and os.path.exists(self._cDir + "/" + self._bank + ".h3p")) :
36 hmmpressLaunched = True
37 os.remove(self._cDir + "/" + self._bank + ".h3m")
38 os.remove(self._cDir + "/" + self._bank + ".h3i")
39 os.remove(self._cDir + "/" + self._bank + ".h3f")
40 os.remove(self._cDir + "/" + self._bank + ".h3p")
41 self.assertTrue(hmmpressLaunched)
42
43 def test_detectHmmProfiles(self):
44 inputFileName = ' FileName'
45 dirTemp = 'Tempory directory'
46 eValueMax = self._config.get(self._section, self._option2)
47
48 expCommand = self._launch1
49 expCommand += os.environ["REPET_PATH"] + "/bin/translateAfastaFileInAllFrameAndReplaceStopsByX_script.py"
50 expCommand += " -i %s" % ( inputFileName ) + " -o %s_translated" % ( inputFileName )
51 expCommand += self._launch2
52
53 expCommand += self._launch1
54 expCommand += "hmmscan "
55 expCommand += " -o %s_tr.hmmScanOut" % ( inputFileName )
56 expCommand += " --domtblout %s_tr.hmmScanOutTab" % ( inputFileName )
57 expCommand += " --noali "
58 expCommand += "-E " + eValueMax
59 expCommand += " --cpu 1"
60 expCommand += " " + self._cDir + "/" + self._bank + " " + "%s_translated" % ( inputFileName )
61
62 expCommand += self._launch2
63
64 expCommand += "if os.path.exists( \"%s_translated\" ):\n" % ( inputFileName )
65 expCommand += "\tos.remove( \"%s_translated\" )\n" % ( inputFileName )
66
67 expCommand += self._launch1
68 expCommand += os.environ["REPET_PATH"] + "/bin/HmmOutput2alignAndTransformCoordInNtAndFilterScores_script.py"
69 expCommand += " -i %s_tr.hmmScanOutTab" % ( inputFileName )
70 expCommand += " -o %s_profiles_%s.align" % ( inputFileName, self._bank )
71 expCommand += " -T %s" % ( inputFileName )
72 expCommand += " -p hmmscan"
73 expCommand += " -c"
74 expCommand += self._launch2
75
76 expCommand += self._launch1
77 expCommand += os.environ["REPET_PATH"] + "/bin/matcher"
78 expCommand += " -m %s_profiles_%s.align" % ( inputFileName, self._bank )
79 expCommand += " -j"
80 expCommand += " -E 10"
81 expCommand += " -L 0"
82 expCommand += " -v 1"
83 expCommand += self._launch2
84
85 expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.path\" ):\n" % ( self._cDir, inputFileName, self._bank )
86 expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.path %s\" )\n" % ( inputFileName, self._bank, self._cDir )
87 expCommand += "if not os.path.exists( \"%s/%s_profiles_%s.align.clean_match.param\" ):\n" % ( self._cDir, inputFileName, self._bank )
88 expCommand += "\tos.system( \"mv %s_profiles_%s.align.clean_match.param %s\" )\n" % ( inputFileName, self._bank, self._cDir )
89 expCommand += "if os.path.exists( \"%s_profiles_%s.align\" ):\n" % ( inputFileName, self._bank )
90 expCommand += "\tos.remove( \"%s_profiles_%s.align\" )\n" % ( inputFileName, self._bank )
91 expCommand += "if os.path.exists( \"%s_profiles_%s.align.clean_match.map\" ):\n" % ( inputFileName, self._bank )
92 expCommand += "\tos.remove( \"%s_profiles_%s.align.clean_match.map\" )\n" % ( inputFileName, self._bank )
93 expCommand += "if os.path.exists( \"%s_hmmScanOut\" ):\n" % ( inputFileName )
94 expCommand += "\tos.remove( \"%s_hmmScanOut\" )\n" % ( inputFileName )
95
96 if dirTemp != dir:
97 expCommand += "if os.path.exists( \"%s\" ):\n" % ( self._bank )
98 expCommand += "\tos.remove( \"%s\" )\n" % ( self._bank )
99
100 obsCommand = self._iProfilesSearch.detectHmmProfiles( inputFileName, self._launch1, self._launch2, self._cDir, dirTemp, self._config )
101 self.assertEquals(expCommand, obsCommand)
102
103
104
105 if __name__ == "__main__":
106 unittest.main()