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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/profilesDB/tests/Test_F_CompleteProfilDB.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,40 @@
+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()
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