diff commons/pyRepetUnit/hmmer/tests/TestAcceptanceHmmpfamAndParse2alignInparallel.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/hmmer/tests/TestAcceptanceHmmpfamAndParse2alignInparallel.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,94 @@
+import os
+import sys
+import unittest
+import pyRepet.seq.fastaDB
+from sets import Set
+import ConfigParser 
+from pyRepet.launcher.programLauncher import *
+from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher
+from pyRepet.sql.RepetJobMySQL import *
+from pyRepet.util.file.FileUtils import *
+import commons.pyRepetUnit.dbSplit.LauncherDbSplit
+import commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align
+
+CONFIG_FILE = "datas/configTestAcceptanceHmmpfamAndParse2alignLauncherInparallel.cfg"
+CURRENT_DIR = os.getcwd()
+
+class TestAcceptanceHmmpfamLauncherAndParse2alignInparallel(unittest.TestCase):
+
+    def setUp(self):
+        self._config = ConfigParser.ConfigParser()
+        self._config.readfp( open(CONFIG_FILE) )
+        self._batchFilesList = []
+        self._batchFilesBatchesList = []
+        self._inputFile = self._config.get("dbSplit_config", "input_file")
+        self._programLauncherInstance = programLauncher()   
+        self._outputFileNotInparallel = self._config.get("hmmer_config", "output_file")
+        self._hmmpfamOutput2align = commons.pyRepetUnit.align.hmmOutputParsing.HmmpfamOutput2align.HmmpfamOutput2align()
+        os.chdir(CURRENT_DIR)
+
+    def _launchHmmpfamAndParseNotInParallel(self):
+        self._programLauncherInstance.reset(self._inputFile)
+        self._programLauncherInstance.setOutputFileName(self._outputFileNotInparallel)
+        self._programLauncherInstance.launchHmmpfam(evalFilter=self._config.get("profil_search", "Evalue"), inputFormat=self._config.get("profil_search", "InputFormat"), profilDatabank=self._config.get("profil_search", "ProfilDatabank"))
+        self._hmmpfamOutput2align.setInputFile(self._outputFileNotInparallel)
+        self._outputFileParsingNotInparallel = self._config.get("hmmpfam2align_config", "output_file")
+        self._hmmpfamOutput2align.setOutputFile(self._outputFileParsingNotInparallel)
+        self._hmmpfamOutput2align.run()
+
+
+    def _countNblinesInAllResultsFilesInParallel(self, fileUtils):
+        result_dir = self._config.get("hmmer_config", "result_dir")
+        dirFiles = fileUtils.listFilesInDir(result_dir)
+        listPath = []
+        for file in dirFiles:
+            listPath.append(file)
+        
+        nbLinesInAlignFilesInparallel = fileUtils.countLinesInFiles(listPath)
+        return nbLinesInAlignFilesInparallel
+
+
+    def _launchHmmpfamAndParseInParallel(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)
+        params = {"param": "--informat " + self._config.get("profil_search", "InputFormat") + " -E " + self._config.get("profil_search", "Evalue"), "profilDB": self._config.get("profil_search", "ProfilDatabank"), "outputDir": self._config.get("hmmer_config", "result_dir"), "query": self._config.get("hmmer_config", "query_dir"), "job_table": "jobs", "queue": self._config.get("sge_config", "queue"), "groupid": self._config.get("sge_config", "groupid"), "tmpDir": self._config.get("hmmer_config", "tmp_dir"), "scriptToLaunch": self._config.get("parse_config", "scriptToLaunch"), "cDir" : "."}
+        self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params)
+        self.hmmpfamAndParse2align.run()
+
+
+    def _splitInputFile(self, dbSplit):
+        dbSplit.setInFileName(self._inputFile)
+        dbSplit.setIsNewDir(True)
+        dbSplit.setNbSequences(3)
+        dbSplit.run()
+
+    def testAcceptanceHmmpfamAndParse2alignHasRunInparallel (self):
+        
+        dbSplit = commons.pyRepetUnit.dbSplit.LauncherDbSplit.LauncherDbSplit()
+        self._splitInputFile(dbSplit)         
+        self._launchHmmpfamAndParseInParallel()
+        fileUtils = FileUtils()
+        nbLinesInAlignFilesInparallel = self._countNblinesInAllResultsFilesInParallel(fileUtils)
+        dbSplit.clean()
+        self._launchHmmpfamAndParseNotInParallel()
+        nbLinesInAlignFileNotInparallel = fileUtils.countLinesInAFile(self._outputFileParsingNotInparallel)
+        self.assertEqual(nbLinesInAlignFilesInparallel,nbLinesInAlignFileNotInparallel)
+        self._clean()
+
+    def _clean(self):
+        
+        dirToClean = self._config.get( "hmmer_config", "tmp_dir" )
+        os.system("rm  " + dirToClean + "/*")
+        dirToClean = self._config.get( "hmmer_config", "result_dir" )
+        os.system("rm  " + dirToClean + "/*")
+        os.system("rm  HmmpfamJob*.e*")
+        os.system("rm  HmmpfamJob*.o*")
+        os.remove(self._outputFileNotInparallel)
+        os.remove(self._outputFileParsingNotInparallel)
+
+
+if __name__ == "__main__":
+        unittest.main()