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

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

class Test_F_LaunchNucmer(unittest.TestCase):
    
    def setUp(self):
        self._queryFastaFileName = "query.fa"
        self._refFastaFileName = "ref.fa"
        self._writeInputFastaFiles()
        self._expDeltaFileName = "expNucmer.delta"
        self._writeExpDeltaFile()
        self._obsDeltaFileName = "obsNucmer.delta"
        self._obsCoordFileName= "obsNucmer.coords"
        self._expCoordFileName= "expNucmer.coords"
        
    def tearDown(self):
        try:
            os.remove(self._queryFastaFileName)
        except:pass
        try:
            os.remove(self._refFastaFileName)
        except:pass
        try:
            os.remove(self._expDeltaFileName)
        except:pass
        try:
            os.remove(self._obsDeltaFileName)
        except:pass
        
    def test_run(self):
        ilauncher = LaunchNucmer(self._refFastaFileName, self._queryFastaFileName,"obsNucmer",verbosity=1)
        ilauncher.run()
        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
        
    def test_run_as_script(self):
        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
        os.system(cmd)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
        
    def test_run_as_script_gencoords_output(self):
        self._writeExpGenCoordsFile()
        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
        os.system(cmd)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
        os.remove(self._obsCoordFileName)
        os.remove(self._expCoordFileName)
    
    def test_run_as_script_with_mincluster(self):
        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
        os.system(cmd)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))      
        
    def test_run_as_script_showcoords_output(self):
        self._writeExpShowCoordsFile()
        cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
        os.system(cmd)
        self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
        os.remove(self._obsCoordFileName)
        os.remove(self._expCoordFileName) 
        
    def _writeInputFastaFiles(self):
        InputFile = open(self._queryFastaFileName, 'w')
        InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
        InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
        InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
        InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
        InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
        InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
        InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
        InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
        InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
        InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
        InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
        InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
        InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
        InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
        InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
        InputFile.write('CCAAAAAAAAA\n')
        InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
        InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
        InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
        InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
        InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
        InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
        InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
        InputFile.write('>SINE_FR2:classI:SINE:?\n')
        InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
        InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
        InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
        InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
        InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
        InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
        InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
        InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
        InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
        InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
        InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
        InputFile.write('AAAAAAA\n')
        InputFile.close()
        
        InputFile = open(self._refFastaFileName, 'w')
        InputFile.write('>SINE_FR2:classI:SINE:?\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('>SINEC1B2_CF:classI:SINE:?\n')
        InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
        InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
        InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
        InputFile.close()
        
    def _writeExpDeltaFile(self):
        f = open(self._expDeltaFileName, 'w')
        f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
        f.write('NUCMER\n')
        f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
        f.write('1 343 1 343 0 0 0\n')
        f.write('0\n')
        f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
        f.write('1 161 1 161 0 0 0\n')
        f.write('0\n')
        f.close()
        
    def _writeExpGenCoordsFile(self):
        f = open(self._expCoordFileName, 'w')
        f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
        f.write('NUCMER\n\n')
        f.write('    [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  | [TAGS]\n')
        f.write('=====================================================================================\n')
        f.write('       1      161  |        1      161  |      161      161  |   100.00  | SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
        f.write('       1      343  |        1      343  |      343      343  |   100.00  | SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
        f.close()
        
    def _writeExpShowCoordsFile(self):
        f = open(self._expCoordFileName, 'w')
        f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
        f.write('NUCMER\n\n')
        f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n')
        f.write('1\t161\t1\t161\t161\t161\t100.00\t164\t161\t98.17\t100.00\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
        f.write('1\t343\t1\t343\t343\t343\t100.00\t389\t371\t88.17\t92.45\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
        f.close()
                       
if __name__ == "__main__":
    unittest.main()