Mercurial > repos > yufei-luo > s_mart
diff commons/tools/tests/Test_GetSpecificTELibAccordingToAnnotation.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/tools/tests/Test_GetSpecificTELibAccordingToAnnotation.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,64 @@ +import os +import unittest +from commons.core.utils.FileUtils import FileUtils +from commons.core.sql.DbMySql import DbMySql +from commons.tools.GetSpecificTELibAccordingToAnnotation import GetSpecificTELibAccordingToAnnotation + +class Test_GetSpecificTELibAccordingToAnnotation(unittest.TestCase): + + def test_writeFastaFileFromGiveInfoTEAnnot(self): + self._iDb = DbMySql() + fileName = "GiveInfoTEannot.txt" + self._writeGiveInfoTEannotOutput(fileName) + tableName = "projectName_refTEs_chr_seq" + self._createConsensusTable(tableName) + expFileName = "consensusExp.fa" + self._writeExpConsensusFile(expFileName) + obsFileName = "%s.fa" % os.path.splitext(fileName)[0] + iGetTElib = GetSpecificTELibAccordingToAnnotation() + iGetTElib.setTableName(tableName) + iGetTElib.writeFastaFileFromGiveInfoTEAnnot(fileName) + self._iDb.dropTable(tableName) + self._iDb.close() + self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) + os.remove(fileName) + os.remove(expFileName) + os.remove(obsFileName) + + def _writeGiveInfoTEannotOutput(self, fileName): + f = open(fileName, "w") + f.write("TE\tmaxLength\tmeanLength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tsdId\tminId\tq25Id\tmedId\tq75Id\tmaxId\tmeanLgth\tsdLgth\tminLgth\tq25Lgth\tmedLgth\tq75Lgth\tmaxLgth\tmeanLgthPerc\tsdLgthPerc\tminLgthPerc\tq25LgthPerc\tmedLgthPerc\tq75LgthPerc\tmaxLgthPerc\n") + f.write("Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\t2150\t2150\t195657\t158\t49\t152\t52\t84.88\t8.75\t74.29\t77.16\t80.08\t96.40\t97.83\t1287.32\t776.47\t21\t570.00\t1320.50\t2077.00\t2272\t59.88\t36.11\t0.98\t26.51\t61.42\t96.60\t105.67\n") + f.write("Atha_benchs-B-R1047-Map6_classI-LINE-comp\t1653\t1653\t25423\t57\t4\t56\t4\t79.09\t8.21\t64.32\t73.63\t79.21\t83.65\t96.65\t453.98\t488.66\t29\t98.00\t244.00\t634.00\t1650\t27.46\t29.56\t1.75\t5.93\t14.76\t38.35\t99.82\n") + f.write("Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\t1293\t1293\t24416\t48\t4\t47\t4\t80.31\t5.74\t75.14\t77.00\t78.25\t80.89\t99.46\t519.60\t419.01\t37\t171.00\t334.00\t838.00\t1296\t40.19\t32.41\t2.86\t13.23\t25.83\t64.81\t100.23\n") + f.close() + + def _createConsensusTable(self, tableName): + fileName = "consensus.fa" + f = open(fileName, "w") + f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n") + f.write("ATGCTAGCTAGCT\n") + f.write(">Atha_benchs-B-R12-Map5_classII-Helitron-comp\n") + f.write("ATGCTAGCTAGCTATGCTAGCTAGCATGCTAGCTAGCTT\n") + f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n") + f.write("ATGCTAGCTAGCT\n") + f.write(">Atha_benchs-B-G56-Map5_classII-Helitron-comp\n") + f.write("ATGCTAGCTAGCTATGCTAGCTAGCT\n") + f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n") + f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n") + f.close() + self._iDb.createTable(tableName, "seq", fileName, True) + os.remove(fileName) + + def _writeExpConsensusFile(self, fileName): + f = open(fileName, "w") + f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n") + f.write("ATGCTAGCTAGCT\n") + f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n") + f.write("ATGCTAGCTAGCT\n") + f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n") + f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n") + f.close() + +if __name__ == "__main__": + unittest.main() \ No newline at end of file