Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/test/Test_MapParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 |
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52 if __name__ == '__main__': |
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53 unittest.main() |