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

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


class Test_F_LaunchRefAlign(unittest.TestCase):
    
    def setUp(self):
        self._curTestDir = os.getcwd()
        self._testPrefix = 'test_LRA'
        try:
            os.makedirs(self._testPrefix)
        except:pass
        os.chdir(self._testPrefix)
        

        self._inputFastaFileName = "%s_input.fa" % self._testPrefix 
        self._obsOutputFileName = self._inputFastaFileName +'.fa_aln'
        self._expOutputFileName = "%s_exp.fa_aln" % self._testPrefix 
        self._writeInputFile()
        
    def tearDown(self):
        os.chdir(self._curTestDir)
        try:
            rmtree(self._testPrefix)
        except:pass

    def test_run(self):
        self._writeExpOutputFile_wo_refseq()
        ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5)
        ilauncher.run()
        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
        
    def test_run_KeepRefSeq(self):
        self._writeExpOutputFile_with_refseq()
        ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5, keepRefseq=True)
        ilauncher.run()
        
        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))
        
    def test_run_as_script(self):
        self._writeExpOutputFile_wo_refseq()
        cmd = 'LaunchRefAlign.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
        os.system(cmd)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))    

    def test_run_as_script_KeepRefSeq(self):
        self._writeExpOutputFile_with_refseq()
        cmd = 'LaunchRefAlign.py -i %s -r -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName)
        os.system(cmd)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName))   
               
    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_wo_refseq(self):
        with open(self._expOutputFileName,'w') as expOutputFile:
            expOutputFile.write(""">sequence2
GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC
GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT
GCCTGTGTCTCTTCTCTC------------------------------------------
------------------------------------------------------------
----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------
------------------------------------------------------------
-----------
""")
            
    def _writeExpOutputFile_with_refseq(self):
        with open(self._expOutputFileName,'w') as expOutputFile:
            expOutputFile.write(""">sequence
GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC
GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT
GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA
TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA
TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC
CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCAAGCGGTAGAAAGTGAG
TGAGTGAGTGA
>sequence2
GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC
GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT
GCCTGTGTCTCTTCTCTC------------------------------------------
------------------------------------------------------------
----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------
------------------------------------------------------------
-----------
""")
                               
if __name__ == "__main__":
    unittest.main()