comparison commons/launcher/tests/Test_F_LaunchRefAlign.py @ 18:94ab73e8a190

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18:94ab73e8a190

import unittest
import os
from commons.core.utils.FileUtils import FileUtils
from commons.launcher.LaunchRefAlign import LaunchRefAlign


class Test_F_LaunchRefAlign(unittest.TestCase):
    
    def setUp(self):
        self._inputFastaFileName = "input.fa"
        self._obsOutputFileName = "obs"
        self._expOutputFileName = "exp"
        self._writeInputFile()
        self._writeExpOutputFile()
        
#    def tearDown(self):
#        try:
#            os.remove(self._inputFastaFileName)
#        except:pass
#    
#        try:
#            os.remove(self._expOutputFileName)
#        except:pass
#        try:
#            os.remove(self._obsOutputFileName)
#        except:pass
#        try:
#            os.remove("input.fa.2.3.5.80.10.20.15.dat")
#        except:pass
    
    def test_run(self):
        ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5)
        ilauncher.run()
        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
        
#    def test_run_as_script(self):
#        cmd = 'LaunchTRF.py -i %s -o %s -v 3' % (self._inputFastaFileName, self._obsTRFOutputFileName)
#        os.system(cmd)
#        self.assertTrue(FileUtils.are2FilesIdentical(self._expTRFOutputFileName, self._obsTRFOutputFileName))    

        
    def _writeInputFile(self):        
        InputFile = open(self._inputFastaFileName, 'w')
        InputFile.write('>sequence\n')
        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
        InputFile.write('>sequence2\n')
        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
        InputFile.close()    
        
    def _writeExpOutputFile(self):
        with open(self._expOutputFileName,'w') as expOutputFile:
            expOutputFile.write("""1\t(GTGGT)2\tsequence\t11\t21
2\t(GGT)5\tsequence\t10\t23
3\t(GTGTGA)4\tsequence\t222\t242
4\t(GTCCA)2\tsequence\t282\t292
5\t(AGTG)4\tsequence\t355\t371
6\t(GCCTGTCTCTCCTCT)4\tsequence2\t100\t152
7\t(CTCTGCCTGTGT)3\tsequence2\t112\t151
8\t(TC)23\tsequence2\t107\t152
""")

                       
if __name__ == "__main__":
    unittest.main()