Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/test/Test_PalsToAlign.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 from commons.core.utils.FileUtils import FileUtils |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 import os |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 from commons.core.parsing.PalsToAlign import PalsToAlign |
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5 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 class Test_PalsToAlign(unittest.TestCase): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 def setUp(self): |
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9 self._palsFileName = "input.gff" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 self._expAlignFileName = "file.align" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 self._obsAlignFileName = "output.align" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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12 |
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13 def tearDown(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 os.remove(self._palsFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 os.remove(self._expAlignFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 os.remove(self._obsAlignFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 |
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18 def testRun(self): |
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19 self._writePalsFile(self._palsFileName) |
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20 self._writeExpAlignFile(self._expAlignFileName) |
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21 |
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22 iPalsToAlign = PalsToAlign(self._palsFileName,self._obsAlignFileName) |
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23 iPalsToAlign.run() |
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24 |
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25 self.assertTrue(FileUtils.are2FilesIdentical(self._expAlignFileName, self._obsAlignFileName)) |
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26 |
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27 |
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28 def _writePalsFile(self, fileName): |
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29 f = open(fileName, "w") |
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30 f.write("chunk01\tpals\thit\t32290\t32583\t252\t+\t.\tTarget chunk02 28975 29268; maxe 0.035\n") |
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31 f.write("chunk01\tpals\thit\t28975\t29268\t252\t+\t.\tTarget chunk02 32290 32583; maxe 0.035\n") |
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32 f.write("chunk01\tpals\thit\t65932\t66032\t68\t+\t.\tTarget chunk02 59293 59395; maxe 0.085\n") |
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33 f.close() |
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34 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 def _writeExpAlignFile(self, fileName): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 f = open(fileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 f.write("chunk01\t28975\t29268\tchunk02\t32290\t32583\t0.0\t252\t96.5\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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38 f.write("chunk01\t32290\t32583\tchunk02\t28975\t29268\t0.0\t252\t96.5\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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39 f.write("chunk01\t65932\t66032\tchunk02\t59293\t59395\t0.0\t68\t91.5\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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40 f.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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41 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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42 if __name__ == "__main__": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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43 unittest.main() |