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1 import os
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2 import unittest
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3 from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6 class TestHmmpfamOutputProcessing(unittest.TestCase):
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7
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8 def setUp(self):
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9 self.fileUtils = FileUtils()
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10 self.hmmpfamOutputProcess = HmmpfamOutputProcessing()
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11 self._inputFile = "./datas/Outputhmmpfam"
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12 self._inputFile2 = "./datas/test_hmmpfam_output"
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13 self._outputFile = "./datas/dummyAlignFile.align"
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14
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15 def testReadHmmOutput(self):
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16 file = open( self._inputFile )
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17 pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file)
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18 self.assertEqual(["7LES_DROME", "437", "522", "fn3", "1", "84", "8.8e-15", "48.3"], pfamOutput.get(0))
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19 self.assertEqual(["7LES_DROME", "825", "914", "fn3", "1", "84", "2.2e-06", "13.4"], pfamOutput.get(1))
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20 self.assertEqual(["7LES_DROME", "1292", "1389", "fn3", "1", "84", "1.2e-06", "15.9"], pfamOutput.get(2))
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21 self.assertEqual(["7LES_DROME", "1799", "1891", "fn3", "1", "84", "2.3e-19", "63.5"], pfamOutput.get(3))
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22 self.assertEqual(["7LES_DROME", "1899", "1978", "fn3", "1", "84", "1.5e-06", "15.2"], pfamOutput.get(4))
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23 self.assertEqual(["7LES_DROME", "1993", "2107", "fn3", "1", "84", "4.3e-07", "20.3"], pfamOutput.get(5))
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24 self.assertEqual(["7LES_DROME", "2209", "2483", "pkinase", "1", "294", "6e-95", "314.6"], pfamOutput.get(6))
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25 self.assertEqual(["7LES_DROME", "2223", "2284", "rrm", "1", "77", "0.72", "-40.4"], pfamOutput.get(7))
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26 file.close()
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27
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28 def test_readHmmOutput_empty_file(self):
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29 file = open( "./datas/OutputhmmpfamEmpty", "w" )
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30 file.close()
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31 file = open( "./datas/OutputhmmpfamEmpty")
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32 pfamOutput = self.hmmpfamOutputProcess.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/OutputhmmpfamEmpty")
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36
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37 def testParseHmmpfamOutput2Align(self):
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38 self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile2, self._outputFile)
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39 self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
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40 self.assertEqual(18, FileUtils.getNbLinesInSingleFile(self._outputFile))
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41 os.system("rm " + self._outputFile)
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42
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43 def test_parseHmmpfamOutput2Align_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.hmmpfamOutputProcess.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_parseHmmpfamOutput2Align_file_not_exists(self):
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53 self._inputFile = "./datas/dummy_hmmpfam_output"
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54 self.hmmpfamOutputProcess.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() |
