Mercurial > repos > yufei-luo > s_mart
diff commons/launcher/tests/Test_F_LaunchPromer.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/launcher/tests/Test_F_LaunchPromer.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,231 @@ +import unittest +import os +from commons.core.utils.FileUtils import FileUtils +from commons.launcher.LaunchPromer import LaunchPromer + + +class Test_F_LaunchPromer(unittest.TestCase): + + def setUp(self): + self._queryFastaFileName = "query.fa" + self._refFastaFileName = "ref.fa" + self._writeInputFastaFiles() + self._expDeltaFileName = "expPromer.delta" + self._writeExpDeltaFile() + self._obsDeltaFileName = "obsPromer.delta" + self._obsCoordFileName= "obsPromer.coords" + self._expCoordFileName= "expPromer.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 = LaunchPromer(self._refFastaFileName, self._queryFastaFileName,"obsPromer",verbosity=1) + ilauncher.run() + self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) + + def test_run_as_script(self): + cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") + os.system(cmd) + self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) + + def test_run_as_script_gencoords_output(self): + self._writeExpGenCoordsFile() + cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") + 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 = 'LaunchPromer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") + os.system(cmd) + self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName)) + + def test_run_as_script_showcoords_output(self): + self._writeExpShowCoordsFile() + cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer") + 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): + with open(self._expDeltaFileName, 'w') as f: + f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) + f.write('PROMER\n') + f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n') + f.write('1 387 1 369 6 6 10\n') + f.write('115\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('0\n') + f.write('2 388 2 370 6 6 8\n') + f.write('115\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('0\n') + f.write('3 389 3 371 6 6 16\n') + f.write('115\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('0\n') + f.write('388 2 370 2 6 6 6\n') + f.write('10\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('0\n') + f.write('387 1 369 1 6 6 5\n') + f.write('10\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('0\n') + f.write('389 3 371 3 6 6 4\n') + f.write('11\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('1\n') + f.write('0\n') + f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n') + f.write('1 159 1 159 0 0 2\n') + f.write('0\n') + f.write('3 161 3 161 0 0 2\n') + f.write('0\n') + f.write('161 3 161 3 0 0 0\n') + f.write('0\n') + f.write('160 2 160 2 0 0 2\n') + f.write('0\n') + f.write('159 1 159 1 0 0 4\n') + f.write('0\n') + f.write('2 160 2 160 0 0 4\n') + f.write('0\n') + + + + + def _writeExpGenCoordsFile(self): + with open(self._expCoordFileName, 'w') as f: + f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) + f.write('PROMER\n\n') + f.write(' [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] [% SIM] [% STP] | [FRM] [TAGS]\n') + f.write('==============================================================================================================\n') + f.write(' 1 159 | 1 159 | 159 159 | 100.00 100.00 1.89 | 1 1 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write(' 2 160 | 2 160 | 159 159 | 100.00 100.00 3.77 | 2 2 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write(' 3 161 | 3 161 | 159 159 | 100.00 100.00 1.89 | 3 3 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write(' 159 1 | 159 1 | 159 159 | 100.00 100.00 3.77 | -3 -3 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write(' 160 2 | 160 2 | 159 159 | 100.00 100.00 1.89 | -2 -2 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write(' 161 3 | 161 3 | 159 159 | 100.00 100.00 0.00 | -1 -1 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write(' 1 387 | 1 369 | 387 369 | 95.35 95.35 3.88 | 1 1 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write(' 2 388 | 2 370 | 387 369 | 95.35 95.35 3.10 | 2 2 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write(' 3 389 | 3 371 | 387 369 | 95.35 95.35 6.20 | 3 3 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write(' 387 1 | 369 1 | 387 369 | 95.35 95.35 1.94 | -3 -3 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write(' 388 2 | 370 2 | 387 369 | 95.35 95.35 2.33 | -2 -2 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write(' 389 3 | 371 3 | 387 369 | 95.35 95.35 1.55 | -1 -1 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + + + def _writeExpShowCoordsFile(self): + with open(self._expCoordFileName, 'w') as f: + f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName))) + f.write('PROMER\n\n') + f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[% SIM]\t[% STP]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n') + f.write('1\t159\t1\t159\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write('2\t160\t2\t160\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t2\t2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write('3\t161\t3\t161\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t3\t3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write('159\t1\t159\t1\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t-3\t-3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write('160\t2\t160\t2\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t-2\t-2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write('161\t3\t161\t3\t159\t159\t100.00\t100.00\t0.00\t164\t161\t96.95\t98.76\t-1\t-1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n') + f.write('1\t387\t1\t369\t387\t369\t95.35\t95.35\t3.88\t389\t371\t99.49\t99.46\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write('2\t388\t2\t370\t387\t369\t95.35\t95.35\t3.10\t389\t371\t99.49\t99.46\t2\t2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write('3\t389\t3\t371\t387\t369\t95.35\t95.35\t6.20\t389\t371\t99.49\t99.46\t3\t3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write('387\t1\t369\t1\t387\t369\t95.35\t95.35\t1.94\t389\t371\t99.49\t99.46\t-3\t-3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write('388\t2\t370\t2\t387\t369\t95.35\t95.35\t2.33\t389\t371\t99.49\t99.46\t-2\t-2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + f.write('389\t3\t371\t3\t387\t369\t95.35\t95.35\t1.55\t389\t371\t99.49\t99.46\t-1\t-1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n') + +if __name__ == "__main__": + unittest.main() \ No newline at end of file