diff commons/pyRepetUnit/profilesDB/tests/TestCompleteProfilesDBFromProfilesNameListOrAccNumber.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/profilesDB/tests/TestCompleteProfilesDBFromProfilesNameListOrAccNumber.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,67 @@
+'''
+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()
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