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1 import unittest
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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()
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