Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/ncList/test/Test_FindOverlapsWithOneInterval.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 struct |
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3 import os |
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4 from SMART.Java.Python.structure.Interval import Interval |
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5 from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval |
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6 from SMART.Java.Python.ncList.NCListCursor import NCListCursor |
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7 |
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8 class Test_FindOverlapsWithOneInterval(unittest.TestCase): |
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9 |
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10 def setUp(self): |
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11 self._inputGff3FileName = 'sortedFile.gff3' |
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12 self._writeGFF3File(self._inputGff3FileName) |
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13 self._obsFileName = "overlap.gff3" |
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14 self._iFOWOI = FindOverlapsWithOneInterval(0) |
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15 self._iFOWOI.setFileName(self._inputGff3FileName, "gff3") |
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16 self._iFOWOI._chromosome = "chr1" |
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17 self._iFOWOI.prepareIntermediateFiles() |
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18 self._iFOWOI.createNCList() |
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19 self._ncList = self._iFOWOI._ncList |
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20 self._iFOWOI.setOutputFileName(self._obsFileName) |
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21 |
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22 def tearDown(self): |
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23 return |
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24 self._iFOWOI.close() |
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25 for file in (self._inputGff3FileName, self._obsFileName): |
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26 if os.path.exists(file): |
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27 os.remove(file) |
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28 |
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29 def test_binarySearch_first_element_overlap(self): |
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30 self._iFOWOI.setInterval("chr1", 500, 850) |
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31 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 0, 0), 0, 6) |
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32 expReadPosition = 0 |
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33 self._iFOWOI.dumpWriter() |
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34 self._iFOWOI.close() |
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35 self.assertEquals(expReadPosition, obsReadPosition._lIndex) |
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36 |
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37 def test_binarySearch_second_element_overlap(self): |
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38 self._iFOWOI.setInterval("chr1", 500, 850) |
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39 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 2, 0), 2, 6) |
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40 expReadPosition = 3 |
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41 self._iFOWOI.dumpWriter() |
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42 self._iFOWOI.close() |
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43 self.assertEquals(expReadPosition, obsReadPosition._lIndex) |
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44 |
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45 def test_binarySearch_empty_subList(self): |
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46 self._iFOWOI.setInterval("chr1", 500, 850) |
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47 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 5, 0), 5, 5) |
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48 expReadPosition = None |
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49 self._iFOWOI.dumpWriter() |
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50 self._iFOWOI.close() |
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51 self.assertEquals(expReadPosition, obsReadPosition) |
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52 |
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53 def test_binarySearch_no_overlap_right(self): |
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54 self._iFOWOI.setInterval("chr1", 1400, 1500) |
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55 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 0, 0), 0, 6) |
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56 expReadPosition = None |
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57 self._iFOWOI.dumpWriter() |
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58 self._iFOWOI.close() |
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59 self.assertEquals(expReadPosition, obsReadPosition) |
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60 |
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61 def test_binarySearch_no_overlap_left(self): |
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62 self._iFOWOI.setInterval("chr1", 0, 45) |
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63 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 2, 0), 2, 6) |
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64 expReadPosition = None |
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65 self._iFOWOI.dumpWriter() |
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66 self._iFOWOI.close() |
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67 self.assertEquals(expReadPosition, obsReadPosition) |
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68 |
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69 def _writeGFF3File(self, fileName): |
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70 f = open(fileName, "w") |
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71 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n") |
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72 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n") |
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73 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n") |
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74 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n") |
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75 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n") |
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76 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n") |
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77 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n") |
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78 f.close() |
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79 |
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80 if __name__ == "__main__": |
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81 unittest.main() |