Mercurial > repos > yufei-luo > s_mart
view commons/pyRepetUnit/profilesDB/tests/Test_F_CompleteProfilDB.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
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import unittest import os from commons.core.utils.FileUtils import FileUtils class Test_F_CompleteProfilDB(unittest.TestCase): def setUp(self): self._fileProfilesList = "./datas/ListPfamProfilsInRepbase.txt" self._filePfamList = "./datas/ListpfamAccNumber.txt" self._profilesDB = "./datas/profilesDBTest.hmm" self._expectedGetzCmd = "getz -e \'[pfamhmm-Id:\"zf-CCHC*\"] | [pfamhmm-Id:\"InvE*\"] | [pfamhmm-Id:\"Chromo*\"] | [pfamhmm-Id:\"TLV_coat*\"]\'" self._expectedFile(self._expectedGetzCmd) self._outputFileName = "./datas/outputFile" self._expectedGetzCmd2 = "getz -e \'[pfamhmm-AccNumber:\"PF00075\"] | [pfamhmm-AccNumber:\"PF00424\"] | [pfamhmm-AccNumber:\"PF00469\"]\'" def tearDown(self): os.remove(self._outputFileName) os.remove(self._expectedGetzCmdFile) def testCompleteProfilesDBScriptByName(self): Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._fileProfilesList + " -o " + self._outputFileName + "\n" os.system (Cmd) self.assertTrue (FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile)) def testCompleteProfilesDBScriptByAccession(self): self._expectedFile(self._expectedGetzCmd2) Cmd = "completeProfilesDBFromAFileWithProfilesList_script.py -d " + self._profilesDB + " -l " + self._filePfamList + " -o " + self._outputFileName + " -n\n" os.system(Cmd) self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileName, self._expectedGetzCmdFile)) def _expectedFile(self, expectedGetzCmd): self._expectedGetzCmdFile = "./datas/expectedCmdFile" f = open(self._expectedGetzCmdFile, 'w') f.write(expectedGetzCmd) f.close if __name__ == "__main__": unittest.main()