Mercurial > repos > yufei-luo > s_mart
view commons/core/writer/test/Test_MapWriter.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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from SMART.Java.Python.structure.Transcript import Transcript from SMART.Java.Python.structure.Interval import Interval import unittest import os from SMART.Java.Python.misc import Utils from commons.core.writer.MapWriter import MapWriter from commons.core.utils.FileUtils import FileUtils class Test_MapWriter(unittest.TestCase): def setUp(self): self.expFileName = "expMapWriter.map" self.obsFileName = "testMapWriter1.map" def tearDown(self): os.remove(self.expFileName) os.remove(self.obsFileName) def test_writer(self): self.write_ExpMapFileName() writer = MapWriter(self.obsFileName) transcript = Transcript() transcript.setName("test1.1") transcript.setChromosome("arm_X") transcript.setStart(1000) transcript.setEnd(4000) transcript.setDirection("+") transcript.setTagValue("ID", "test1.1-1") transcript.setTagValue("occurrence", 1) transcript.setTagValue("nbOccurrences", 2) exon1 = Interval() exon1.setChromosome("arm_X") exon1.setStart(1000) exon1.setEnd(2000) exon1.setDirection("+") exon2 = Interval() exon2.setChromosome("arm_X") exon2.setStart(3000) exon2.setEnd(4000) exon2.setDirection("+") transcript.addExon(exon1) transcript.addExon(exon2) writer.addTranscript(transcript) writer.write() writer.close() self.assertTrue(FileUtils.are2FilesIdentical(self.expFileName, self.obsFileName)) def write_ExpMapFileName(self): f = open(self.expFileName, "w") f.write("test1.1\tarm_X\t1000\t4001\n") f.close() if __name__ == '__main__': unittest.main()