Mercurial > repos > yufei-luo > s_mart
diff commons/pyRepetUnit/blastnForClassifierStep1/tests/Test_RepbaseBLRnForClassifierStep1.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/pyRepetUnit/blastnForClassifierStep1/tests/Test_RepbaseBLRnForClassifierStep1.py Tue Apr 30 14:33:21 2013 -0400 @@ -0,0 +1,343 @@ +import unittest +import os +import shutil +import ConfigParser +import sys +from commons.pyRepetUnit.blastnForClassifierStep1.RepbaseBLRnForClassifierStep1 import RepbaseBLRnForClassifierStep1 +from commons.core.utils.FileUtils import FileUtils +from commons.core.sql.DbFactory import DbFactory +from commons.core.sql.TablePathAdaptator import TablePathAdaptator +from commons.core.coord.Path import Path +import pyRepet.launcher.programLauncher + +if not os.environ.has_key( "REPET_PATH" ): + print "*** Error: no environment variable REPET_PATH" + sys.exit(1) +sys.path.append( os.environ["REPET_PATH"] ) + +NB_EXPECTED_LINES_IN_PATH_FILE = 10 +CURRENT_DIR = os.getcwd() + + +class Test_RepbaseBLRnForClassifierStep1( unittest.TestCase ): + + + def setUp( self ): + os.chdir(CURRENT_DIR) + self._inFileName = "dummyFileName" + self._launch_1 = "log = os.system( \"" + self._launch_2 = "\" )\n" + self._launch_2 += "if log != 0:\n" + self._launch_2 += "\tsys.exit(1)\n" + self._cDir = "/home/user/dummy_cdir" + self._tmpDir = "/home/user/dummy_tmpDir" + self._configFileName = "configFile" + self._repbaseName = "dummyRepbase_nt.fa" + f = open(self._configFileName, "w") + f.write("[repet_env]\n") + f.write("repet_host: %s\n" % os.environ["REPET_HOST"]) + f.write("repet_user: %s\n" % os.environ["REPET_USER"]) + f.write("repet_pw: %s\n" % os.environ["REPET_PW"]) + f.write("repet_db: %s\n" % os.environ["REPET_DB"]) + f.write("repet_port: %s\n" % os.environ["REPET_PORT"]) + f.write("[detect_features]\n") + f.write("TE_BLRn: yes\n") + f.write("TE_nucl_bank: %s\n" % self._repbaseName) + f.write("wublast: yes\n") + f.close() + self._verbose = 0 + self._config = ConfigParser.ConfigParser() + self._config.readfp( open(self._configFileName) ) + self._pL = pyRepet.launcher.programLauncher.programLauncher() + self._project = "dummyProject" + self._repbaseBLRn = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project) + self._expFileName = "expFile" + self._bank = self._config.get("detect_features","TE_nucl_bank") + self._db = DbFactory.createInstance() + + + def tearDown( self ): + self._db.dropTable("%s_TE_BLRn_path" % (self._project)) + os.chdir(CURRENT_DIR) + self._repbaseBLRn = None + os.remove(self._configFileName) + if os.path.isfile("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)): + os.remove("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank)) + if os.path.isfile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)): + os.remove("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)) + if os.path.isfile("batch_1.fa_BLRn_%s.*" % (self._bank)): + os.remove("batch_1.fa_BLRn_%s.*" % (self._bank)) + if os.path.isfile("batch_2.fa_BLRn_%s.*" % (self._bank)): + os.remove("batch_2.fa_BLRn_%s.*" % (self._bank)) + if os.path.isfile("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank)): + os.remove("batch_1.fa_BLRn_%s.align.clean_match.path" % (self._bank)) + if os.path.isfile("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank)): + os.remove("batch_2.fa_BLRn_%s.align.clean_match.path" % (self._bank)) + if os.path.isfile(self._repbaseName): + os.remove(self._repbaseName) + os.remove(self._repbaseName + "_cut") + os.remove(self._repbaseName + "_cut.xnd") + os.remove(self._repbaseName + "_cut.xns") + os.remove(self._repbaseName + "_cut.xnt") + os.remove(self._repbaseName + ".Nstretch.map") + os.remove("last_time_stamp.log") + if os.path.isdir( "TE_BLRn" ): + os.chdir( "TE_BLRn" ) + os.chdir(CURRENT_DIR) + shutil.rmtree("TE_BLRn") + if os.path.isfile(self._expFileName): + os.remove(self._expFileName) + + + def test_formatRepbase_ntIfNecessaryWithoutLog( self ): + f = open(self._repbaseName, "w") + f.write(">seq1\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.write(">seq2\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.close() + f = open(self._expFileName, "w") + f.write(">1 seq1 {Cut} 1..180\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.write(">2 seq2 {Cut} 1..180\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.close() + self._repbaseBLRn.formatRepbase_ntIfNecessary() + obsFileName = self._repbaseName + "_cut" + self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) + + + def test_formatRepbase_ntIfNecessary_withLogFile( self ): + f = open(self._repbaseName, "w") + f.write(">seq1\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.write(">seq2\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.close() + f = open(self._expFileName, "w") + f.write(">1 seq1 {Cut} 1..180\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.write(">2 seq2 {Cut} 1..180\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTTTTTTTGCGCGTGGCGTATGCGTGCAT\n") + f.write("ATGCGTGCGTAAATGCGTAATGCGTAAATGCGTAAATTTGCGCGTAAAGTATGCGTGCAT\n") + f.close() + repbaseBLRnWithLog = RepbaseBLRnForClassifierStep1(self._inFileName, self._launch_1, self._launch_2, self._cDir, self._tmpDir, self._configFileName, self._verbose, self._pL, self._project) + repbaseBLRnWithLog.formatRepbase_ntIfNecessary() + obsFileName = self._repbaseName + "_cut" + self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) + + + def test_createCmdToLaunch( self ): + bank = self._config.get("detect_features","TE_nucl_bank") + obsCmd = self._repbaseBLRn.createCmdToLaunch() + expCmd = self._launch_1 + os.environ["REPET_PATH"] + "/bin/blaster" + expCmd += " -q %s" % ( self._inFileName ) + expCmd += " -s %s/%s" % ( self._cDir, bank ) + expCmd += " -B %s_BLRn_%s" % ( self._inFileName, bank ) + expCmd += " -n blastn" + if self._config.get("detect_features","wublast") == "yes": + expCmd += " -W" + expCmd += " -r" + expCmd += " -v 1" + expCmd += self._launch_2 + expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.param\" ):\n" % ( self._cDir, self._inFileName, bank ) + expCmd += "\tos.system( \"mv %s_BLRn_%s.param %s\" )\n" % ( self._inFileName, bank, self._cDir ) + expCmd += "if os.path.exists( \"%s_cut\" ):\n" % ( self._inFileName ) + expCmd += "\tos.system( \"rm -f %s_cut*\" )\n" % ( self._inFileName ) + expCmd += "if os.path.exists( \"%s.Nstretch.map\" ):\n" % ( self._inFileName ) + expCmd += "\tos.remove( \"%s.Nstretch.map\" )\n" % ( self._inFileName ) + expCmd += "if os.path.exists( \"%s_BLRn_%s.raw\" ):\n" % ( self._inFileName, bank ) + expCmd += "\tos.remove( \"%s_BLRn_%s.raw\" )\n" % ( self._inFileName, bank ) + expCmd += "if os.path.exists( \"%s_BLRn_%s.seq_treated\" ):\n" % ( self._inFileName, bank ) + expCmd += "\tos.remove( \"%s_BLRn_%s.seq_treated\" )\n" % ( self._inFileName, bank ) + expCmd += self._launch_1 + expCmd += os.environ["REPET_PATH"] + "/bin/matcher" + expCmd += " -m %s_BLRn_%s.align" % ( self._inFileName, bank ) + expCmd += " -q %s" % ( self._inFileName ) + expCmd += " -s %s/%s" % ( self._cDir, bank ) + expCmd += " -j" + expCmd += " -v 1" + expCmd += self._launch_2 + expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.path\" ):\n" % ( self._cDir, self._inFileName, bank ) + expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.path %s\" )\n" % ( self._inFileName, bank, self._cDir ) + expCmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.param\" ):\n" % ( self._cDir, self._inFileName, bank ) + expCmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.param %s\" )\n" % ( self._inFileName, bank, self._cDir ) + expCmd += "if os.path.exists( \"%s_BLRn_%s.align\" ):\n" % ( self._inFileName, bank ) + expCmd += "\tos.remove( \"%s_BLRn_%s.align\" )\n" % ( self._inFileName, bank ) + expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.fa\" ):\n" % ( self._inFileName, bank ) + expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.fa\" )\n" % ( self._inFileName, bank ) + expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.map\" ):\n" % ( self._inFileName, bank ) + expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.map\" )\n" % ( self._inFileName, bank ) + expCmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.tab\" ):\n" % ( self._inFileName, bank ) + expCmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.tab\" )\n" % ( self._inFileName, bank ) + if self._tmpDir != self._cDir: + expCmd += "if os.path.exists( \"%s\" ):\n" % ( bank ) + expCmd += "\tos.remove( \"%s\" )\n" % ( bank ) + self.assertEquals( expCmd, obsCmd ) + + + def test_concatPathFile( self ): + os.chdir(CURRENT_DIR) + if not FileUtils.isRessourceExists("TE_BLRn"): + os.mkdir( "TE_BLRn" ) + self._createPathFiles(self._bank) + os.chdir( "TE_BLRn" ) + f = open(self._expFileName, "w") + f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.close() + FileUtils.sortFileContent(self._expFileName) + obsFileName = "%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank) + self._repbaseBLRn._concatPathFile(self._bank) + FileUtils.sortFileContent(obsFileName) + self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) + + + def test_adaptIDInPathFile( self ): + f = open("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank), "w") + f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.close() + self._repbaseBLRn._adaptIDInPathFile(self._bank) + f = open(self._expFileName, "w") + f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.close() + obsFileName = "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank) + self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName, obsFileName)) + + + def test_loadPathFileInTable( self ): + os.chdir(CURRENT_DIR) + if not FileUtils.isRessourceExists("TE_BLRn"): + os.mkdir( "TE_BLRn" ) + self._createPathFiles(self._bank) + os.chdir( "TE_BLRn" ) + f = open("%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank), "w") + f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.write("6\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("7\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("8\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("9\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("10\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.close() + self._repbaseBLRn._loadPathFileInTable(self._bank) + resultFromFilePathList = self._readPathResultsFromFileAndFillList() + resultFromTablePathList = self._readPathResultsFromTableAndFillList() + self.assertEquals(resultFromFilePathList, resultFromTablePathList) + + + def test_findAndRemoveUselessFiles( self ): + self._createFile("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank)) + self._createFile("batch_1.fa_BLRn_%s.*" % (self._bank)) + self._createFile("batch_2.fa_BLRn_%s.*" % (self._bank)) + self._repbaseBLRn._findAndRemoveUselessFiles(self._bank) + self.assertFalse(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, self._bank))) + self.assertFalse(FileUtils.isRessourceExists("batch_1.fa_BLRn_%s.*" % (self._bank))) + self.assertFalse(FileUtils.isRessourceExists("batch_2.fa_BLRn_%s.*" % (self._bank))) + + + def test_collectRepbaseBLRn( self ): + os.chdir(CURRENT_DIR) + if not FileUtils.isRessourceExists("TE_BLRn"): + os.mkdir( "TE_BLRn" ) + self._createPathFiles(self._bank) + os.chdir( "TE_BLRn" ) + self._repbaseBLRn.collectRepbaseBLRn() + self.assertTrue(FileUtils.isRessourceExists("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank ))) + self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, FileUtils.getNbLinesInSingleFile("%s_BLRn_%s.align.clean_match.path" % ( self._project, self._bank ))) + self.assertTrue(self._db.doesTableExist("%s_TE_BLRn_path" % (self._project))) + self._db.execute('select * from %s_TE_BLRn_path' % (self._project)) + self.assertEquals(NB_EXPECTED_LINES_IN_PATH_FILE, len(self._db.fetchall())) + self._db.dropTable("%s_TE_BLRn_path" % (self._project)) + + + def _createPathFiles( self, bankFull ): + bank = os.path.split(bankFull)[1] + fileName = "batch_1.fa_BLRn_" + bank + ".align.clean_match.path" + f = open(fileName, "w") + f.write("1\tQueryName1\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName1\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName2\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName3\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName1\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.close() + fileName = "batch_2.fa_BLRn_" + bank + ".align.clean_match.path" + f = open(fileName, "w") + f.write("1\tQueryName4\t2\t250\tsubjectName1\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("2\tQueryName4\t255\t550\tsubjectName2\t5\t255\t0.0002\t32\t78.2\n") + f.write("3\tQueryName5\t1\t150\tsubjectName1\t250\t400\t5.1e-59\t132\t98\n") + f.write("4\tQueryName6\t2\t250\tsubjectName3\t5\t255\t4.1e-39\t132\t88.2\n") + f.write("5\tQueryName7\t300\t450\tsubjectName1\t300\t450\t4.1e-39\t132\t80.2\n") + f.close() + + + def _readPathResultsFromTableAndFillList( self ): + tablePathAdaptatorInstance = TablePathAdaptator (self._db, "%s_TE_BLRn_path" % (self._project)) + pathList = tablePathAdaptatorInstance.getListOfAllPaths() + return pathList + + + def _readPathResultsFromFileAndFillList( self ): + pathInstance = Path() + pathList = [] + f = open( "%s_BLRn_%s.align.clean_match.path" % (self._project, self._bank) , "r") + while pathInstance.read( f ): + pathList.append(pathInstance) + pathInstance = Path() + f.close() + return pathList + + + def _createFile( self, nameFile ): + f = open(nameFile, "w") + f.close() + + +test_suite = unittest.TestSuite() +test_suite.addTest( unittest.makeSuite( Test_RepbaseBLRnForClassifierStep1 ) ) +if __name__ == "__main__": + unittest.TextTestRunner(verbosity=2).run( test_suite )