Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/profilesDB/tests/Test_F_CompleteProfilDB.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 class Test_F_CompleteProfilDB(unittest.TestCase):
6
7 def setUp(self):
8 self._fileProfilesList = "./datas/ListPfamProfilsInRepbase.txt"
9 self._filePfamList = "./datas/ListpfamAccNumber.txt"
10 self._profilesDB = "./datas/profilesDBTest.hmm"
11 self._expectedGetzCmd = "getz -e \'[pfamhmm-Id:\"zf-CCHC*\"] | [pfamhmm-Id:\"InvE*\"] | [pfamhmm-Id:\"Chromo*\"] | [pfamhmm-Id:\"TLV_coat*\"]\'"
12 self._expectedFile(self._expectedGetzCmd)
13 self._outputFileName = "./datas/outputFile"
14 self._expectedGetzCmd2 = "getz -e \'[pfamhmm-AccNumber:\"PF00075\"] | [pfamhmm-AccNumber:\"PF00424\"] | [pfamhmm-AccNumber:\"PF00469\"]\'"
15
16 def tearDown(self):
17 os.remove(self._outputFileName)
18 os.remove(self._expectedGetzCmdFile)
19
20 def testCompleteProfilesDBScriptByName(self):
21 Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._fileProfilesList + " -o " + self._outputFileName + "\n"
22 os.system (Cmd)
23 self.assertTrue (FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile))
24
25 def testCompleteProfilesDBScriptByAccession(self):
26 self._expectedFile(self._expectedGetzCmd2)
27 Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._filePfamList + " -o " + self._outputFileName + " -n\n"
28 os.system(Cmd)
29 self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile))
30
31 def _expectedFile(self, expectedGetzCmd):
32 self._expectedGetzCmdFile = "./datas/expectedCmdFile"
33 f = open(self._expectedGetzCmdFile, 'w')
34 f.write(expectedGetzCmd)
35 f.close
36
37
38
39 if __name__ == "__main__":
40 unittest.main()