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1 from SMART.Java.Python.structure.Transcript import Transcript
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2 from SMART.Java.Python.structure.Interval import Interval
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3 import unittest
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4 import os
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5 from SMART.Java.Python.misc import Utils
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6 from commons.core.writer.MapWriter import MapWriter
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7 from commons.core.utils.FileUtils import FileUtils
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8
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9 class Test_MapWriter(unittest.TestCase):
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10
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11 def setUp(self):
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12 self.expFileName = "expMapWriter.map"
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13 self.obsFileName = "testMapWriter1.map"
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14
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15 def tearDown(self):
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16 os.remove(self.expFileName)
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17 os.remove(self.obsFileName)
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18
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19 def test_writer(self):
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20 self.write_ExpMapFileName()
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21 writer = MapWriter(self.obsFileName)
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22
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23 transcript = Transcript()
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24 transcript.setName("test1.1")
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25 transcript.setChromosome("arm_X")
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26 transcript.setStart(1000)
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27 transcript.setEnd(4000)
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28 transcript.setDirection("+")
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29 transcript.setTagValue("ID", "test1.1-1")
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30 transcript.setTagValue("occurrence", 1)
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31 transcript.setTagValue("nbOccurrences", 2)
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32
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33 exon1 = Interval()
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34 exon1.setChromosome("arm_X")
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35 exon1.setStart(1000)
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36 exon1.setEnd(2000)
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37 exon1.setDirection("+")
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38
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39 exon2 = Interval()
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40 exon2.setChromosome("arm_X")
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41 exon2.setStart(3000)
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42 exon2.setEnd(4000)
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43 exon2.setDirection("+")
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44
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45 transcript.addExon(exon1)
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46 transcript.addExon(exon2)
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47
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48 writer.addTranscript(transcript)
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49 writer.write()
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50 writer.close()
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51
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52 self.assertTrue(FileUtils.are2FilesIdentical(self.expFileName, self.obsFileName))
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53
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54
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55 def write_ExpMapFileName(self):
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56 f = open(self.expFileName, "w")
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57 f.write("test1.1\tarm_X\t1000\t4001\n")
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58 f.close()
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59
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60 if __name__ == '__main__':
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61 unittest.main()
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