diff commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/tests/TestFunctionalHmmpfamClusterComponent.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,38 @@
+import os
+import sys
+import unittest
+from sets import Set
+import ConfigParser 
+from pyRepet.sql.RepetJobMySQL import *
+from pyRepet.util.file.FileUtils import *
+import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent
+
+CONFIG_FILE = "datas/configTestFunctionalHmmpfamLauncherInparallel.cfg"
+CURRENT_DIR = os.getcwd()
+
+class TestFunctionalHmmpfamClusterComponent(unittest.TestCase):
+    
+    def setUp(self):
+        os.chdir(CURRENT_DIR)
+        self._config = ConfigParser.ConfigParser()
+        self._config.readfp( open(CONFIG_FILE) )
+        self._hmmer = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent()
+
+    def testHmmpfamHasRunInparallel (self):
+        user = self._config.get( "db_config","user" )
+        host = self._config.get( "db_config","host" )
+        passwd = self._config.get( "db_config","passwd" )
+        dbName = self._config.get( "db_config","dbname" )
+        jobDb = RepetJob(user , host , passwd , dbName)
+        self._hmmer.setJobDb(jobDb)
+        self._hmmer.loadConfig(self._config)
+        self._hmmer.run()
+        fileUtils = FileUtils()
+        dirFiles = fileUtils.listDir(self._config.get("hmmer_config", "result_dir"))
+        dirSet = Set(dirFiles)
+        alignFileSet = Set([self._config.get("hmmer_config", "result_dir") + "/" + "batch_1.fa.hmmpfamOut", self._config.get("hmmer_config", "result_dir") + "/" + "batch_2.fa.hmmpfamOut"])
+        self.assertTrue(alignFileSet.issubset(dirSet))
+        self._hmmer.clean()
+        
+if __name__ == "__main__":
+        unittest.main()