view commons/launcher/tests/Test_F_BlatProgramLauncher.py @ 18:94ab73e8a190

Uploaded

import os
import unittest
from commons.core.utils.FileUtils import FileUtils
from devTools.tests.MockFastaSupctg30 import MockFastaSupctg30
from devTools.tests.MockMiniProtBankSupctg30 import MockMiniProtBankSupctg30
from commons.launcher.tests.MockDataBankForBlat import MockDataBankForBlat
from commons.launcher.tests.MockESTBankForBlat import MockESTBankForBlat
from commons.launcher.tests.MockOutputForBlat import MockOutputForBlat
from commons.launcher.BlatProgramLauncher import BlatProgramLauncher

class Test_F_BlatProgramLauncher(unittest.TestCase):

    def test_run_empty_result(self):
        queryFileName = "smallProtBank_supctg30.fa"
        mock = MockMiniProtBankSupctg30()
        mock.write(queryFileName)
        subjectFileName = "subjectBank.fa"
        mock = MockFastaSupctg30()
        mock.write(subjectFileName)
        
        expOutputFileName = "expBlatOutput.blast.align"
        self.writeEmptyExpOutputFile(expOutputFileName)
        
        obsOutputFileName = "obsBlatOutput.blast.align"

        bpl = BlatProgramLauncher()
        bpl.setInputFile(queryFileName)
        bpl.setSubjectFile(subjectFileName)
        bpl.setOutputFile(obsOutputFileName)
        bpl.setProgramParameters("")
        bpl.run()
        
        blastFileName = queryFileName + ".blast"
        
        self.assertTrue(os.path.exists(obsOutputFileName))
        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
        
        os.remove(queryFileName)
        os.remove(subjectFileName)
        os.remove(blastFileName)
        os.remove(expOutputFileName)
        os.remove(obsOutputFileName)

    def test_as_script_empty_result(self):
        queryFileName = "smallProtBank_supctg30.fa"
        mock = MockMiniProtBankSupctg30()
        mock.write(queryFileName)
        subjectFileName = "subjectBank.fa"
        mock = MockFastaSupctg30()
        mock.write(subjectFileName)
        
        expOutputFileName = "expBlatOutput.blast.align"
        self.writeEmptyExpOutputFile(expOutputFileName)
        
        obsOutputFileName = "obsBlatOutput.blast.align"
        
        cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
        
        os.system(cmd2Launch)
        
        blastFileName = queryFileName + ".blast"
                
        self.assertTrue(os.path.exists(obsOutputFileName))
        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
        
        os.remove(queryFileName)
        os.remove(subjectFileName)
        os.remove(blastFileName)
        os.remove(expOutputFileName)
        os.remove(obsOutputFileName)

    def test_run(self):
        queryFileName = "smallESTBank.fa"
        mock = MockESTBankForBlat()
        mock.write(queryFileName)
        subjectFileName = "subjectBank.fa"
        mock = MockDataBankForBlat()
        mock.write(subjectFileName)
        
        expOutputFileName = "expBlatOutput.blast.align"
        mock = MockOutputForBlat()
        mock.write(expOutputFileName)
        
        obsOutputFileName = "obsBlatOutput.blast.align"

        bpl = BlatProgramLauncher()
        bpl.setInputFile(queryFileName)
        bpl.setSubjectFile(subjectFileName)
        bpl.setOutputFile(obsOutputFileName)
        bpl.setProgramParameters("")
        bpl.run()
        
        blastFileName = queryFileName + ".blast"
        
        self.assertTrue(os.path.exists(obsOutputFileName))
        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
        
        os.remove(queryFileName)
        os.remove(subjectFileName)
        os.remove(blastFileName)
        os.remove(expOutputFileName)
        os.remove(obsOutputFileName)

    def test_as_script(self):
        queryFileName = "smallESTBank.fa"
        mock = MockESTBankForBlat()
        mock.write(queryFileName)
        subjectFileName = "subjectBank.fa"
        mock = MockDataBankForBlat()
        mock.write(subjectFileName)
        
        expOutputFileName = "expBlatOutput.blast.align"
        mock = MockOutputForBlat()
        mock.write(expOutputFileName)
        
        obsOutputFileName = "obsBlatOutput.blast.align"
        
        cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
        
        os.system(cmd2Launch)
        
        blastFileName = queryFileName + ".blast"
                
        self.assertTrue(os.path.exists(obsOutputFileName))
        self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
        
        os.remove(queryFileName)
        os.remove(subjectFileName)
        os.remove(blastFileName)
        os.remove(expOutputFileName)
        os.remove(obsOutputFileName)
        
    def writeEmptyExpOutputFile(self, outputFileName):
        f = open(outputFileName, "w")
        f.write("")
        f.close()
        
if __name__ == "__main__":
    unittest.main()