Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_F_BlatToGff.py @ 18:94ab73e8a190
Uploaded
author | m-zytnicki |
---|---|
date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
import unittest import os from commons.core.utils.FileUtils import FileUtils class Test_F_BlatToGff(unittest.TestCase): def test_run(self): blatInputFileName = '%s/commons/core/parsing/test/inputFile.tab' % os.environ['REPET_PATH'] self._writeBlatInputFile(blatInputFileName) obsOutputFileName = '%s/commons/core/parsing/test/obsOutputFile.tab' % os.environ['REPET_PATH'] cmd = 'python %s/commons/core/parsing/BlatToGff.py -i %s -o %s' % (os.environ['REPET_PATH'], blatInputFileName, obsOutputFileName) os.system(cmd) expOutputFileName = '%s/commons/core/parsing/test/expOutputFile.tab' % os.environ['REPET_PATH'] self._writeExpOutputFile(expOutputFileName) self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName)) os.remove(blatInputFileName) os.remove(obsOutputFileName) os.remove(expOutputFileName) def test_run_with_methodName(self): blatInputFileName = '%s/commons/core/parsing/test/inputFile.tab' % os.environ['REPET_PATH'] self._writeBlatInputFile(blatInputFileName) obsOutputFileName = '%s/commons/core/parsing/test/obsOutputFile.tab' % os.environ['REPET_PATH'] cmd = 'python %s/commons/core/parsing/BlatToGff.py -i %s -o %s -n Test_F' % (os.environ['REPET_PATH'], blatInputFileName, obsOutputFileName) os.system(cmd) expOutputFileName = '%s/commons/core/parsing/test/expOutputFile.tab' % os.environ['REPET_PATH'] self._writeExpOutputFile_with_methodName(expOutputFileName) self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName)) os.remove(blatInputFileName) os.remove(obsOutputFileName) os.remove(expOutputFileName) def _writeBlatInputFile(self, blatInputFileName): file = open(blatInputFileName, 'w') file.write('psLayout version 3\n') file.write('\n') file.write('match mis- rep. N\'s Q gap Q gap T gap T gap strand Q Q Q Q T T T T block blockSizes qStarts tStarts\n') file.write(' match match count bases count bases name size start end name size start end count\n') file.write('---------------------------------------------------------------------------------------------------------------------------------------------------------------\n') file.write('315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,\n') file.write('690\t11\t0\t0\t1\t3\t2\t4\t-\tmachin1\t704\t0\t704\tchr16\t22053297\t21736364\t21737069\t3\t40,647,14,\t0,43,690,\t21736364,21736406,21737055,\n') file.write('554\t26\t0\t0\t1\t16\t1\t17\t-\tMRRE1H032F08FM1\t606\t10\t606\tchr11\t19818926\t3725876\t3726473\t2\t553,27,\t10,579,\t3725876,3726446,\n') file.write('620\t23\t0\t0\t0\t0\t0\t0\t-\tmachin2\t643\t0\t643\tchr11\t19818926\t3794984\t3795627\t1\t643,\t0,\t3794984,\n') file.write('347\t25\t0\t0\t0\t0\t0\t0\t-\tmachin3\t393\t21\t393\tchr18\t29360087\t12067347\t12067719\t1\t372,\t0,\t12067347,\n') file.close() def _writeExpOutputFile(self, expOutputFileName): file = open(expOutputFileName, 'w') file.write('##gff-version 3\n') file.write('chr16\tBlatToGff\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n') file.write('chr16\tBlatToGff\tBES\t21736364\t21737069\t.\t+\t.\tID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n') file.write('chr11\tBlatToGff\tBES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926\n') file.write('chr11\tBlatToGff\tBES\t3794984\t3795627\t.\t+\t.\tID=machin2;Name=machin2;bes_start=3794984;bes_end=3795627;bes_size=19818926\n') file.write('chr18\tBlatToGff\tBES\t12067347\t12067719\t.\t+\t.\tID=machin3;Name=machin3;bes_start=12067347;bes_end=12067719;bes_size=29360087\n') file.close() def _writeExpOutputFile_with_methodName(self, expOutputFileName): file = open(expOutputFileName, 'w') file.write('##gff-version 3\n') file.write('chr16\tBlatToGff\tTest_F:BES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n') file.write('chr16\tBlatToGff\tTest_F:BES\t21736364\t21737069\t.\t+\t.\tID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n') file.write('chr11\tBlatToGff\tTest_F:BES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926\n') file.write('chr11\tBlatToGff\tTest_F:BES\t3794984\t3795627\t.\t+\t.\tID=machin2;Name=machin2;bes_start=3794984;bes_end=3795627;bes_size=19818926\n') file.write('chr18\tBlatToGff\tTest_F:BES\t12067347\t12067719\t.\t+\t.\tID=machin3;Name=machin3;bes_start=12067347;bes_end=12067719;bes_size=29360087\n') file.close() if __name__ == "__main__": unittest.main()