Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/test/Test_PalsToAlign.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/test/Test_PalsToAlign.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,43 @@ +import unittest +from commons.core.utils.FileUtils import FileUtils +import os +from commons.core.parsing.PalsToAlign import PalsToAlign + +class Test_PalsToAlign(unittest.TestCase): + + def setUp(self): + self._palsFileName = "input.gff" + self._expAlignFileName = "file.align" + self._obsAlignFileName = "output.align" + + def tearDown(self): + os.remove(self._palsFileName) + os.remove(self._expAlignFileName) + os.remove(self._obsAlignFileName) + + def testRun(self): + self._writePalsFile(self._palsFileName) + self._writeExpAlignFile(self._expAlignFileName) + + iPalsToAlign = PalsToAlign(self._palsFileName,self._obsAlignFileName) + iPalsToAlign.run() + + self.assertTrue(FileUtils.are2FilesIdentical(self._expAlignFileName, self._obsAlignFileName)) + + + def _writePalsFile(self, fileName): + f = open(fileName, "w") + f.write("chunk01\tpals\thit\t32290\t32583\t252\t+\t.\tTarget chunk02 28975 29268; maxe 0.035\n") + f.write("chunk01\tpals\thit\t28975\t29268\t252\t+\t.\tTarget chunk02 32290 32583; maxe 0.035\n") + f.write("chunk01\tpals\thit\t65932\t66032\t68\t+\t.\tTarget chunk02 59293 59395; maxe 0.085\n") + f.close() + + def _writeExpAlignFile(self, fileName): + f = open(fileName, "w") + f.write("chunk01\t28975\t29268\tchunk02\t32290\t32583\t0.0\t252\t96.5\n") + f.write("chunk01\t32290\t32583\tchunk02\t28975\t29268\t0.0\t252\t96.5\n") + f.write("chunk01\t65932\t66032\tchunk02\t59293\t59395\t0.0\t68\t91.5\n") + f.close() + +if __name__ == "__main__": + unittest.main() \ No newline at end of file