Mercurial > repos > yufei-luo > s_mart
view commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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import os import unittest import ConfigParser import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent from pyRepet.sql.RepetJobMySQL import * from pyRepet.util.file.FileUtils import * class TestHmmpfamClusterComponent(unittest.TestCase): def setUp(self): self.component = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent() def testLoadConfig(self): config = open("tmpConfig.cfg", "w") config.write("[profil_search]\n") config.write("ProfilDatabank: /repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms\n") config.write("[hmmer_config]\n") config.write("result_dir: /repet_results\n") config.write("query_dir: /repet_datas/hmmer_in_parallel\n") config.write("tmp_dir: /repet_tmp\n") config.write("[sge_config]\n") config.write("queue: main.q\n") config.write("groupid: fake\n") config.close() config = ConfigParser.ConfigParser() config.readfp( open("tmpConfig.cfg") ) self.component.loadConfig(config) self.assertEquals( "/repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms", self.component.getProfilDatabank() ) self.assertEquals( "/repet_results", self.component.getResultDir() ) self.assertEquals( "/repet_datas/hmmer_in_parallel", self.component.getQueryDir() ) self.assertEquals( "/repet_tmp", self.component.getTmpDir() ) self.assertEquals( "main.q", self.component.getSGEQueue() ) self.assertEquals( "fake", self.component.getSGEGroupId() ) os.system("rm tmpConfig.cfg") def testClean (self): fileUtils = FileUtils() if (fileUtils.isRessourceExists("dummyTmpDir")): os.system("rm -r dummyTmpDir") if (fileUtils.isRessourceExists("dummyResultDir")): os.system("rm -r dummyResultDir") os.mkdir("dummyTmpDir") os.system("touch dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py") os.system("touch dummyTmpDir/srptJob2_fake_HmmpfamJob1_2009-3-11_12394.py") os.system("touch dummyTmpDir/srptJob3_fake_HmmpfamJob1_2009-3-11_12394.py") os.system("touch dummyTmpDir/srptJob4_fake_HmmpfamJob1_2009-3-11_12394.py") os.mkdir("dummyResultDir") os.system("touch dummyResultDir/batch_1.fa.hmmpfamOut") os.system("touch dummyResultDir/batch_2.fa.hmmpfamOut") os.system("touch dummyResultDir/batch_3.fa.hmmpfamOut") os.system("touch dummyResultDir/batch_4.fa.hmmpfamOut") self.component.setTmpDir("dummyTmpDir") self.component.setResultDir("dummyResultDir") self.component.clean() self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py")) self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob2_2009-3-11_12394.py")) self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob3_2009-3-11_12394.py")) self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob4_2009-3-11_12394.py")) self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_1.fa.hmmpfamOut")) self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_2.fa.hmmpfamOut")) self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_3.fa.hmmpfamOut")) self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_4.fa.hmmpfamOut")) os.system("rm -r dummyTmpDir") os.system("rm -r dummyResultDir") if __name__ == "__main__": unittest.main()