Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/ncList/test/Test_FindOverlapsWithOneInterval.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 import unittest
2 import struct
3 import os
4 from SMART.Java.Python.structure.Interval import Interval
5 from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval
6 from SMART.Java.Python.ncList.NCListCursor import NCListCursor
7
8 class Test_FindOverlapsWithOneInterval(unittest.TestCase):
9
10 def setUp(self):
11 self._inputGff3FileName = 'sortedFile.gff3'
12 self._writeGFF3File(self._inputGff3FileName)
13 self._obsFileName = "overlap.gff3"
14 self._iFOWOI = FindOverlapsWithOneInterval(0)
15 self._iFOWOI.setFileName(self._inputGff3FileName, "gff3")
16 self._iFOWOI._chromosome = "chr1"
17 self._iFOWOI.prepareIntermediateFiles()
18 self._iFOWOI.createNCList()
19 self._ncList = self._iFOWOI._ncList
20 self._iFOWOI.setOutputFileName(self._obsFileName)
21
22 def tearDown(self):
23 return
24 self._iFOWOI.close()
25 for file in (self._inputGff3FileName, self._obsFileName):
26 if os.path.exists(file):
27 os.remove(file)
28
29 def test_binarySearch_first_element_overlap(self):
30 self._iFOWOI.setInterval("chr1", 500, 850)
31 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 0, 0), 0, 6)
32 expReadPosition = 0
33 self._iFOWOI.dumpWriter()
34 self._iFOWOI.close()
35 self.assertEquals(expReadPosition, obsReadPosition._lIndex)
36
37 def test_binarySearch_second_element_overlap(self):
38 self._iFOWOI.setInterval("chr1", 500, 850)
39 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 2, 0), 2, 6)
40 expReadPosition = 3
41 self._iFOWOI.dumpWriter()
42 self._iFOWOI.close()
43 self.assertEquals(expReadPosition, obsReadPosition._lIndex)
44
45 def test_binarySearch_empty_subList(self):
46 self._iFOWOI.setInterval("chr1", 500, 850)
47 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 5, 0), 5, 5)
48 expReadPosition = None
49 self._iFOWOI.dumpWriter()
50 self._iFOWOI.close()
51 self.assertEquals(expReadPosition, obsReadPosition)
52
53 def test_binarySearch_no_overlap_right(self):
54 self._iFOWOI.setInterval("chr1", 1400, 1500)
55 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 0, 0), 0, 6)
56 expReadPosition = None
57 self._iFOWOI.dumpWriter()
58 self._iFOWOI.close()
59 self.assertEquals(expReadPosition, obsReadPosition)
60
61 def test_binarySearch_no_overlap_left(self):
62 self._iFOWOI.setInterval("chr1", 0, 45)
63 obsReadPosition = self._iFOWOI.binarySearch(NCListCursor(None, self._ncList, 2, 0), 2, 6)
64 expReadPosition = None
65 self._iFOWOI.dumpWriter()
66 self._iFOWOI.close()
67 self.assertEquals(expReadPosition, obsReadPosition)
68
69 def _writeGFF3File(self, fileName):
70 f = open(fileName, "w")
71 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
72 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
73 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
74 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
75 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
76 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
77 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
78 f.close()
79
80 if __name__ == "__main__":
81 unittest.main()