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

Uploaded

from commons.core.utils.FileUtils import FileUtils
import unittest
import os
import shutil
from commons.launcher.LaunchMCL import LaunchMCL

class Test_F_LaunchMCL(unittest.TestCase):
# TODO: test query coverage filter

    def setUp(self):
        self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa"
        try:
            shutil.rmtree("MCLtmpDirectory")
            os.remove(self._inputFileName)
        except:
            pass
        try:
            os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
        except:
            pass
        self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0]
        
    def tearDown(self):
        try:
            os.remove(self._inputFileName)
            os.remove(self._outputFileName)
            shutil.rmtree("MCLtmpDirectory")
        except:
            pass
        try:
            os.remove("DmelChr4_LTRharvest_expected_with_default_params_MCL.map")
        except:
            pass    
        
    def test_run(self):
        iLaunchMCL = LaunchMCL(self._inputFileName, doClean = True, verbosity = 1)
        iLaunchMCL.run()
        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))

    def test_run_with_map_file(self):
        iLaunchMCL = LaunchMCL(self._inputFileName, isCluster2Map = True, doClean = False, verbosity = 1)
#        iLaunchMCL.setCoverageThreshold(0.60)
        iLaunchMCL.run()
        expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
        expMapFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.map" % os.environ["REPET_DATA"]
        obsMapFileName = "%s.map" % os.path.splitext(self._outputFileName)[0]
        
        self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName))
        self.assertTrue(FileUtils.are2FilesIdentical(expMapFileName, obsMapFileName))
        
        os.remove(obsMapFileName)

    def test_run_clusterConsensus_headers(self):
        os.remove(self._inputFileName)
        self._inputFileName = "DmelChr4_LTRharvest_MCL_ClusterConsHeaders_input.fa"
        os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
        iLaunchMCL = LaunchMCL(self._inputFileName, isClusterConsensusHeaders = True, doClean = True, verbosity = 1)
        iLaunchMCL.run()
        expFastaFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_ClusterConsHeaders_expected.fa" % os.environ["REPET_DATA"]
        self._outputFileName = "%s_MCL.fa" % os.path.splitext(self._inputFileName)[0]
        
        self.assertTrue(FileUtils.are2FilesIdentical(expFastaFileName, self._outputFileName))
      
    def test_run_as_script(self):
        cmd = "LaunchMCL.py -i %s -j -v 6" % self._inputFileName
        os.system(cmd)
        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
        self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))

    def test_run_as_script_allParams(self):
        cmd = "LaunchMCL.py -i %s -j -I 1.5 -T 0.0 -m -v 6" % self._inputFileName
        os.system(cmd)
        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
        self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))

    def test_run_as_script_without_join(self):
        cmd = "LaunchMCL.py -i %s -v 2" % self._inputFileName
        os.system(cmd)
        expFileName = "%s/Tools/DmelChr4_LTRharvest_MCL_expected.fa" % os.environ["REPET_DATA"]
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
        self.assertTrue(FileUtils.isRessourceExists("MCLtmpDirectory"))
        
if __name__ == "__main__":
    unittest.main()