Mercurial > repos > yufei-luo > s_mart
comparison commons/launcher/tests/Test_F_LaunchRefalign.py @ 31:0ab839023fe4
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 14:33:21 -0400 |
| parents | 94ab73e8a190 |
| children |
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| 30:5677346472b5 | 31:0ab839023fe4 |
|---|---|
| 1 import unittest | |
| 2 import os | |
| 3 from commons.core.utils.FileUtils import FileUtils | |
| 4 from commons.launcher.LaunchRefAlign import LaunchRefAlign | |
| 5 from shutil import rmtree | |
| 6 | |
| 7 | |
| 8 class Test_F_LaunchRefAlign(unittest.TestCase): | |
| 9 | |
| 10 def setUp(self): | |
| 11 self._curTestDir = os.getcwd() | |
| 12 self._testPrefix = 'test_LRA' | |
| 13 try: | |
| 14 os.makedirs(self._testPrefix) | |
| 15 except:pass | |
| 16 os.chdir(self._testPrefix) | |
| 17 | |
| 18 | |
| 19 self._inputFastaFileName = "%s_input.fa" % self._testPrefix | |
| 20 self._obsOutputFileName = self._inputFastaFileName +'.fa_aln' | |
| 21 self._expOutputFileName = "%s_exp.fa_aln" % self._testPrefix | |
| 22 self._writeInputFile() | |
| 23 | |
| 24 def tearDown(self): | |
| 25 os.chdir(self._curTestDir) | |
| 26 try: | |
| 27 rmtree(self._testPrefix) | |
| 28 except:pass | |
| 29 | |
| 30 def test_run(self): | |
| 31 self._writeExpOutputFile_wo_refseq() | |
| 32 ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5) | |
| 33 ilauncher.run() | |
| 34 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) | |
| 35 | |
| 36 def test_run_KeepRefSeq(self): | |
| 37 self._writeExpOutputFile_with_refseq() | |
| 38 ilauncher = LaunchRefAlign(self._inputFastaFileName,verbosity=5, keepRefseq=True) | |
| 39 ilauncher.run() | |
| 40 | |
| 41 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) | |
| 42 | |
| 43 def test_run_as_script(self): | |
| 44 self._writeExpOutputFile_wo_refseq() | |
| 45 cmd = 'LaunchRefAlign.py -i %s -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName) | |
| 46 os.system(cmd) | |
| 47 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) | |
| 48 | |
| 49 def test_run_as_script_KeepRefSeq(self): | |
| 50 self._writeExpOutputFile_with_refseq() | |
| 51 cmd = 'LaunchRefAlign.py -i %s -r -o %s -v 5' % (self._inputFastaFileName, self._obsOutputFileName) | |
| 52 os.system(cmd) | |
| 53 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutputFileName, self._obsOutputFileName)) | |
| 54 | |
| 55 def _writeInputFile(self): | |
| 56 InputFile = open(self._inputFastaFileName, 'w') | |
| 57 InputFile.write('>sequence\n') | |
| 58 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n') | |
| 59 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n') | |
| 60 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n') | |
| 61 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n') | |
| 62 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n') | |
| 63 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n') | |
| 64 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n') | |
| 65 InputFile.write('>sequence2\n') | |
| 66 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n') | |
| 67 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n') | |
| 68 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n') | |
| 69 InputFile.close() | |
| 70 | |
| 71 def _writeExpOutputFile_wo_refseq(self): | |
| 72 with open(self._expOutputFileName,'w') as expOutputFile: | |
| 73 expOutputFile.write(""">sequence2 | |
| 74 GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC | |
| 75 GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT | |
| 76 GCCTGTGTCTCTTCTCTC------------------------------------------ | |
| 77 ------------------------------------------------------------ | |
| 78 ----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------ | |
| 79 ------------------------------------------------------------ | |
| 80 ----------- | |
| 81 """) | |
| 82 | |
| 83 def _writeExpOutputFile_with_refseq(self): | |
| 84 with open(self._expOutputFileName,'w') as expOutputFile: | |
| 85 expOutputFile.write(""">sequence | |
| 86 GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC | |
| 87 GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT | |
| 88 GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA | |
| 89 TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA | |
| 90 TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC | |
| 91 CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCAAGCGGTAGAAAGTGAG | |
| 92 TGAGTGAGTGA | |
| 93 >sequence2 | |
| 94 GGGCAGC-CGGTGGTGCGGT--TTAGCGCTGTTGGCCCAGGGCGTGATGGACCCGGGATC | |
| 95 GATCCCACATCGGG--------------CTCCCTGCATGGAGCCTGC---TTCTCCCTCT | |
| 96 GCCTGTGTCTCTTCTCTC------------------------------------------ | |
| 97 ------------------------------------------------------------ | |
| 98 ----------TCTCTCTGTGTCTCTCATGA-ATAAA------------------------ | |
| 99 ------------------------------------------------------------ | |
| 100 ----------- | |
| 101 """) | |
| 102 | |
| 103 if __name__ == "__main__": | |
| 104 unittest.main() |