Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/fastaTranslation/allFrames/tests/Test_TranslateInAllFramesAndReplaceStopByX.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 os | |
| 2 import unittest | |
| 3 from commons.pyRepetUnit.fastaTranslation.allFrames.TranslateInAllFramesAndReplaceStopByX import TranslateInAllFramesAndReplaceStopByX | |
| 4 from commons.core.seq.Bioseq import Bioseq | |
| 5 from commons.core.utils.FileUtils import FileUtils | |
| 6 | |
| 7 class Test_TranslateInAllFramesAndReplaceStopByX(unittest.TestCase): | |
| 8 | |
| 9 def setUp(self): | |
| 10 self.bioseq = Bioseq() | |
| 11 self.preProcess = TranslateInAllFramesAndReplaceStopByX() | |
| 12 self._inputFile = "./datas/dummy.fa" | |
| 13 self._outputFile = "./datas/dummyoutput.fa" | |
| 14 | |
| 15 | |
| 16 def testRun(self): | |
| 17 self.preProcess.setInputFile(self._inputFile) | |
| 18 self.preProcess.setOutputFile(self._outputFile) | |
| 19 # real fasta file | |
| 20 f = open(self._inputFile, "w") | |
| 21 f.write(">header1 description\n") | |
| 22 f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTC\n") | |
| 23 f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA\n") | |
| 24 f.write(">header2\n") | |
| 25 f.write("TGTGGCTTCTAGTTGATCAGTTTATGATCACAATGATTTCACGTAGGTGTCTCGTGGCTA\n") | |
| 26 f.write("CGACTAATCAACAATATAATGCGAGTAGAGCTTGA") | |
| 27 f.close() | |
| 28 # expected fasta translated file | |
| 29 f = open("./datas/expectedTranslated.fa", "w") | |
| 30 f.write(">header1_1 description\n") | |
| 31 f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n") | |
| 32 f.write(">header1_2 description\n") | |
| 33 f.write("VASSXSVYDHNDFTXVSRGSDXSTIXCEXSL\n") | |
| 34 f.write(">header1_3 description\n") | |
| 35 f.write("WLLVDQFMITMISRRCLVAPTNQQYNASRAX\n") | |
| 36 f.write(">header1_4 description\n") | |
| 37 f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n") | |
| 38 f.write(">header1_5 description\n") | |
| 39 f.write("QALLALYCXLVGATRHLREIIVIINXSTRSH\n") | |
| 40 f.write(">header1_6 description\n") | |
| 41 f.write("KLYSHYIVDXSEPRDTYVKSLXSXTDQLEAT\n") | |
| 42 f.write(">header2_1\n") | |
| 43 f.write("CGFXLISLXSQXFHVGVSWLRLINNIMRVEL\n") | |
| 44 f.write(">header2_2\n") | |
| 45 f.write("VASSXSVYDHNDFTXVSRGYDXSTIXCEXSL\n") | |
| 46 f.write(">header2_3\n") | |
| 47 f.write("WLLVDQFMITMISRRCLVATTNQQYNASRAX\n") | |
| 48 f.write(">header2_4\n") | |
| 49 f.write("SSSTRIILLISRSHETPTXNHCDHKLINXKP\n") | |
| 50 f.write(">header2_5\n") | |
| 51 f.write("QALLALYCXLVVATRHLREIIVIINXSTRSH\n") | |
| 52 f.write(">header2_6\n") | |
| 53 f.write("KLYSHYIVDXSXPRDTYVKSLXSXTDQLEAT\n") | |
| 54 f.close() | |
| 55 self.preProcess.run() | |
| 56 self.assertTrue(FileUtils.are2FilesIdentical("./datas/expectedTranslated.fa", self._outputFile)) | |
| 57 os.system("rm " + self._inputFile) | |
| 58 os.system("rm " + self._outputFile) | |
| 59 os.system("rm ./datas/expectedTranslated.fa") | |
| 60 # empty fasta file | |
| 61 #self.preProcess.translateAfastaFileInAllFrame() | |
| 62 #self.assertFalse(FileUtils.isRessourceExists(self._outputFile)) | |
| 63 | |
| 64 if __name__ == "__main__": | |
| 65 unittest.main() |