Mercurial > repos > yufei-luo > s_mart
view commons/pyRepetUnit/profilesDB/tests/TestCompleteProfilesDBFromProfilesNameListOrAccNumber.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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''' Created on 18 mai 2009 @author: choede ''' import unittest import commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber class TestCompleteProfilesDBFromProfilesNameListOrAccNumber(unittest.TestCase): def setUp(self): self._fileProfilesList = "./datas/ListPfamProfilsInRepbase.txt" self._filePfamList = "./datas/ListpfamAccNumber.txt" self._profilesDB = "./datas/profilesDBTest.hmm" self.CompleteProfilesDB = commons.pyRepetUnit.profilesDB.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber.CompleteAProfilesDBFromAFileWithProfilesNamesOrAccNumber() self.CompleteProfilesDB.setProfilesDBFile ( self._profilesDB ) self._expectedList = ["zf-CCHC", "InvE", "Chromo", "TLV_coat"] self._expectedList2 = ["PF00075", "PF00424", "PF00469"] self._expectedGetzCmd = "getz -e \'[pfamhmm-Id:\"zf-CCHC*\"] | [pfamhmm-Id:\"InvE*\"] | [pfamhmm-Id:\"Chromo*\"] | [pfamhmm-Id:\"TLV_coat*\"]\'" self._expectedGetzCmd2 = "getz -e \'[pfamhmm-AccNumber:\"PF00075\"] | [pfamhmm-AccNumber:\"PF00424\"] | [pfamhmm-AccNumber:\"PF00469\"]\'" def tearDown(self): pass def testListNotExistingProfiles(self): #with name self.CompleteProfilesDB.setProfilesToAdd ( self._fileProfilesList ) profilesNotInDBList = self.CompleteProfilesDB.generateNotExistingProfilesList( ) i = 0 if profilesNotInDBList != []: for profil in profilesNotInDBList: self.assertEquals(profil, self._expectedList[i]) i = i + 1 #with pfam accession number self.CompleteProfilesDB.setProfilesToAdd ( self._filePfamList ) self.CompleteProfilesDB.setPfamAccNumberKeys () profilesNotInDBList = self.CompleteProfilesDB.generateNotExistingProfilesList( ) i = 0 if profilesNotInDBList != []: for profil in profilesNotInDBList: self.assertEquals(profil, self._expectedList2[i]) i = i + 1 def testCreateGetzCommand(self): getzCmd = self.CompleteProfilesDB.generateGetzCmdProfilesList( self._expectedList ) # pour le moment je cherche dans les fs ou les ls si je ne veux que les fs specifier type = fs ce sera surement le cas a terme self.assertEqual (getzCmd, self._expectedGetzCmd) def testCmdToCompleteProfileDBFromList(self): #names list self.CompleteProfilesDB.setProfilesToAdd ( self._fileProfilesList ) getzCmd = self.CompleteProfilesDB.CmdToCompleteProfileDB() self.assertEqual (getzCmd, self._expectedGetzCmd) #pfam accession Number list self.CompleteProfilesDB.setPfamAccNumberKeys () self.CompleteProfilesDB.setProfilesToAdd ( self._filePfamList ) getzCmd = self.CompleteProfilesDB.CmdToCompleteProfileDB() self.assertEqual (getzCmd, self._expectedGetzCmd2) if __name__ == "__main__": unittest.main()