Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/test/Test_pilerTAToGrouperMap.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_pilerTAToGrouperMap.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,108 @@ +import unittest +import os +from commons.core.parsing.PilerTAToGrouperMap import PilerTAToGrouperMap +from commons.core.utils.FileUtils import FileUtils + +class Test_pilerTAToGrouperMap(unittest.TestCase): + + def setUp(self): + self._inputGffFileName = "input.gff" + self._inputPYRFileName = "input_pyr.gff" + self._inputMOTIFFileName = "input_motif.gff" + + self._obsOutFileName = "output.info" + self._obsGrouperFileName = "input_motif.gff.grp" + self._obsGrpMapFileName = "input_motif.gff.grp.map" + + self._expOutFileName = "exp_output.info" + self._expGrouperFileName = "exp_motif.gff.grp" + self._expGrpMapFileName = "exp_motif.gff.grp.map" + + def tearDown(self): + os.remove(self._inputGffFileName) + os.remove(self._inputPYRFileName) + os.remove(self._inputMOTIFFileName) + + os.remove(self._obsOutFileName) + os.remove(self._obsGrouperFileName) + os.remove(self._obsGrpMapFileName) + + os.remove(self._expOutFileName) + os.remove(self._expGrouperFileName) + os.remove(self._expGrpMapFileName) + + def testRun(self): + self._writePilerTAFilePYR(self._inputPYRFileName) + self._writePilerTAFileMOTIF(self._inputMOTIFFileName) + self._writePilerTAGff(self._inputGffFileName) + + self._writeExpOutputFile(self._expOutFileName) + self._writeExpGrouperFile(self._expGrouperFileName) + self._writeExpGrouperMapFile(self._expGrpMapFileName) + + iPilerTAToGrouperMap = PilerTAToGrouperMap(self._inputGffFileName, self._inputPYRFileName,self._inputMOTIFFileName, self._obsOutFileName) + iPilerTAToGrouperMap.run() + + self.assertTrue(FileUtils.are2FilesIdentical(self._expOutFileName, self._obsOutFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expGrouperFileName, self._obsGrouperFileName)) + self.assertTrue(FileUtils.are2FilesIdentical(self._expGrpMapFileName, self._obsGrpMapFileName)) + + + def _writePilerTAGff(self, fileName): + f = open(fileName, "w") + f.write("chunk21\tpiler\thit\t155146\t156020\t0\t+\t.\tTarget chunk21 150519 151392 ; Pile 510 ; Pyramid 0\n") + f.write("chunk21\tpiler\thit\t154790\t156023\t0\t+\t.\tTarget chunk21 150519 151751 ; Pile 510 ; Pyramid 0\n") + f.write("chunk21\tpiler\thit\t154078\t156023\t0\t+\t.\tTarget chunk21 150519 152463 ; Pile 510 ; Pyramid 0\n") + f.write("chunk21\tpiler\thit\t154256\t156023\t0\t+\t.\tTarget chunk21 150519 152285 ; Pile 510 ; Pyramid 0\n") + f.write("chunk21\tpiler\thit\t154434\t156023\t0\t+\t.\tTarget chunk21 150519 152107 ; Pile 510 ; Pyramid 0\n") + f.close() + + def _writePilerTAFilePYR(self, fileName): + f = open(fileName, "w") + f.write("chunk21\tpiler\tpyramid\t150519\t156023\t0\t.\t.\tPyramidIndex 0\n") + f.write("chunk21\tpiler\tpyramid\t150519\t156023\t0\t.\t.\tPyramidIndex 1\n") + f.write("chunk21\tpiler\tpyramid\t165574\t174424\t0\t.\t.\tPyramidIndex 2\n") + f.write("chunk21\tpiler\tpyramid\t166301\t174424\t0\t.\t.\tPyramidIndex 3\n") + f.write("chunk21\tpiler\tpyramid\t168967\t174424\t0\t.\t.\tPyramidIndex 4\n") + f.write("chunk21\tpiler\tpyramid\t170215\t174424\t0\t.\t.\tPyramidIndex 5\n") + f.close() + + def _writePilerTAFileMOTIF(self, fileName): + f = open(fileName, "w") + f.write("chunk21\tpiler\ttandemmotif\t155843\t156020\t0\t.\t.\tTarget chunk21 151215 151392 ; Pyramid 0\n") + f.write("chunk21\tpiler\ttandemmotif\t151215\t151392\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") + f.write("chunk21\tpiler\ttandemmotif\t151574\t151751\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") + f.write("chunk21\tpiler\ttandemmotif\t152286\t152463\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") + f.write("chunk21\tpiler\ttandemmotif\t152108\t152285\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") + f.close() + + def _writeExpOutputFile(self, fileName): + f = open(fileName, "w") + f.write("Pile 510\tPyramid 0\n") + f.write("\tPyramid 1\n") + f.write("\tPyramid 2\n") + f.write("\tPyramid 3\n") + f.write("\tPyramid 4\n") + f.write("\tPyramid 5\n") + f.close() + + def _writeExpGrouperFile(self, fileName): + f = open(fileName, "w") + f.write("MbS1Gr0Cl510\tchunk21\tpiler\ttandemmotif\t155843\t156020\t0\t.\t.\tTarget chunk21 151215 151392 \tPile 510\tPyramid 0\n") + f.write("MbS2Gr0Cl510\tchunk21\tpiler\ttandemmotif\t151215\t151392\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") + f.write("MbS3Gr0Cl510\tchunk21\tpiler\ttandemmotif\t151574\t151751\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") + f.write("MbS4Gr0Cl510\tchunk21\tpiler\ttandemmotif\t152286\t152463\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") + f.write("MbS5Gr0Cl510\tchunk21\tpiler\ttandemmotif\t152108\t152285\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") + f.close() + + def _writeExpGrouperMapFile(self, fileName): + f = open(fileName, "w") + f.write("MbS1Gr0Cl510\tchunk21\t155843\t156020\n") + f.write("MbS2Gr0Cl510\tchunk21\t151215\t151392\n") + f.write("MbS3Gr0Cl510\tchunk21\t151574\t151751\n") + f.write("MbS4Gr0Cl510\tchunk21\t152286\t152463\n") + f.write("MbS5Gr0Cl510\tchunk21\t152108\t152285\n") + f.close() + +if __name__ == "__main__": + unittest.main() \ No newline at end of file