Mercurial > repos > yufei-luo > s_mart

import os
import unittest
from commons.pyRepetUnit.align.transformAACoordIntoNtCoord.TransformAACoordIntoNtCoordInAlignFormat import TransformAACoordIntoNtCoordInAlignFormat
from commons.core.utils.FileUtils import FileUtils

class Test_F_TransformAACoordIntoNtCoordAndScoreFiltering (unittest.TestCase):

    def setUp(self):
        self._inputFile = "./datas/OutputHmmpfamTest.align"
        self._consensusFile = "./datas/ConsensusTestFile_nt.fsa"
        self._outputFile = "./datas/alignTransformedToTest.align"
        self._expectedFile = "./datas/PostPostProcessTest.align"
        self._expectedFileFiltered = "./datas/PostPostProcessTestFiltered.align"
        self._alignTransformation = TransformAACoordIntoNtCoordInAlignFormat()

    def testRun_with_no_filter(self):
        self._alignTransformation.setInFileName(self._inputFile)
        self._alignTransformation.setOutFileName(self._outputFile)
        self._alignTransformation.setConsensusFileName(self._consensusFile)
        self._alignTransformation.setIsFiltered(False)
        self._alignTransformation.run()
        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFile, self._outputFile))
        os.remove(self._outputFile)

    def testRun_with_filter(self):
        self._alignTransformation.setInFileName(self._inputFile)
        self._alignTransformation.setOutFileName(self._outputFile)
        self._alignTransformation.setConsensusFileName(self._consensusFile)
        self._alignTransformation.setIsFiltered(True)
        self._alignTransformation.run()
        self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
        self.assertTrue(FileUtils.are2FilesIdentical(self._expectedFileFiltered, self._outputFile))
        os.remove(self._outputFile)


if __name__ == "__main__" :
    unittest.main()
author	m-zytnicki
date	Mon, 29 Apr 2013 03:20:15 -0400
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