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