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1 import unittest
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2 import os
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3 from commons.core.parsing.MapParser import MapParser
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4
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5 class Test_MapParser(unittest.TestCase):
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6
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7
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8 def setUp(self):
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9 self.inputMapFileName = "testMapParser.map"
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10 self._writeInputMapFile()
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11
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12 def tearDown(self):
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13 if os.path.exists(self.inputMapFileName):
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14 os.remove(self.inputMapFileName)
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15
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16 def test_Parser(self):
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17 parser = MapParser(self.inputMapFileName)
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18
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19 cpt = 0
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20 for transcript in parser.getIterator():
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21 cpt += 1
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22 if cpt == 1:
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23 self.assertEqual(transcript.getChromosome(), "dmel_chr4")
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24 self.assertEqual(transcript.getName(), "aagatgcgtaacggccatac_17")
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25 self.assertEqual(transcript.getStart(), 4380)
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26 self.assertEqual(transcript.getEnd(), 4400)
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27 self.assertEqual(transcript.getDirection(), 1)
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28 self.assertEqual(transcript.getSize(), 21)
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29 elif cpt == 10:
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30 self.assertEqual(transcript.getChromosome(), "dmel_chr4")
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31 self.assertEqual(transcript.getName(), "aacggccatacattggtttg_12")
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32 self.assertEqual(transcript.getStart(), 4389)
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33 self.assertEqual(transcript.getEnd(), 4409)
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34 self.assertEqual(transcript.getDirection(), 1)
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35 self.assertEqual(transcript.getSize(), 21)
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36
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37
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38 def _writeInputMapFile(self):
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39 inputFile = open(self.inputMapFileName,'w')
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40 inputFile.write("aagatgcgtaacggccatac_17\tdmel_chr4\t4380\t4400\n")
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41 inputFile.write("agatgcgtaacggccataca_16\tdmel_chr4\t4381\t4401\n")
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42 inputFile.write("gatgcgtaacggccatacat_16\tdmel_chr4\t4382\t4402\n")
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43 inputFile.write("atgcgtaacggccatacatt_15\tdmel_chr4\t4383\t4403\n")
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44 inputFile.write("tgcgtaacggccatacattg_15\tdmel_chr4\t4384\t4404\n")
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45 inputFile.write("gcgtaacggccatacattgg_15\tdmel_chr4\t4385\t4405\n")
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46 inputFile.write("cgtaacggccatacattggt_14\tdmel_chr4\t4386\t4406\n")
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47 inputFile.write("gtaacggccatacattggtt_14\tdmel_chr4\t4387\t4407\n")
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48 inputFile.write("taacggccatacattggttt_14\tdmel_chr4\t4388\t4408\n")
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49 inputFile.write("aacggccatacattggtttg_12\tdmel_chr4\t4389\t4409\n")
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50 inputFile.close()
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51
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52 if __name__ == '__main__':
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53 unittest.main() |