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1 import os
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2 import unittest
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3 from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6 class TestHmmscanOutputProcessing(unittest.TestCase):
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7
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8 def setUp(self):
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9 self.hmmscanOutputProcess = HmmscanOutputProcessing()
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10 self._inputFile = "./datas/hmmscanOutputTab.txt"
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11 self._inputFileScan2 = "./datas/hmmscanOutput"
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12 self._outputFileScan2 = "./datas/hmmscanOutput.align"
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13 self._outputFile = "./datas/dummyFile.align"
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14
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15 def tearDown(self):
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16 if os.path.exists(self._outputFile):
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17 os.remove(self._outputFile)
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18
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19 def testReadHmmerscanOutput(self):
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20 file = open( self._inputFile )
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21 pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file)
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22 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2742", "2766", "rve", "50", "78", "2.4e+03", "-3.3"], pfamOutput.get(0))
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23 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2951", "3101", "rve", "4", "168", "6.7e-30", "103.4"], pfamOutput.get(1))
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24 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "3198", "3228", "Chromo", "4", "51", "8.5e-06", "24.7"], pfamOutput.get(2))
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25 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2117", "2125", "GARS_A", "196", "204", "11", "2.5"], pfamOutput.get(3))
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26 file.close()
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27
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28 def test_readHmmerscanOutput_empty_file(self):
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29 file = open( "./datas/OutputhmmscanEmpty", "w" )
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30 file.close()
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31 file = open( "./datas/OutputhmmscanEmpty")
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32 pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file)
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33 file.close()
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34 self.assertEqual(None, pfamOutput)
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35 os.system("rm ./datas/OutputhmmscanEmpty")
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36
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37 def testParseHmmscanOutput2Align(self):
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38 self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFileScan2, self._outputFile)
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39 self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
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40 self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileScan2, self._outputFile))
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41 os.system("rm " + self._outputFile)
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42
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43 def test_parseHmmscanOutput2Align_empty_file(self):
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44 file = open("./datas/dummy_hmmpfam_output", "w")
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45 file.close()
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46 self._inputFile = "./datas/dummy_hmmpfam_output"
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47 self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
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48 self.assertTrue(FileUtils.isEmpty(self._outputFile))
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49 os.system("rm " + self._inputFile)
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50 os.system("rm " + self._outputFile)
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51
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52 def test_parseHmmscanOutput2Align_file_not_exists(self):
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53 self._inputFile = "./datas/dummy_hmmpfam_output"
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54 self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile )
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55 self.assertFalse(FileUtils.isRessourceExists(self._outputFile))
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56
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57 if __name__ == "__main__":
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58 unittest.main() |
