Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_FindOverlaps_optim.py @ 18:94ab73e8a190

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents
children
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os
3 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
4 from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
5
6 class Test_FindOverlaps_optim(unittest.TestCase):
7
8 def setUp(self):
9 self._inputRefGff3FileName = 'sorted_Ref.gff3'
10 iMock = MockFindOverlapsWithServeralIntervals_case1()
11 iMock.write(self._inputRefGff3FileName)
12 self._inputQueryGff3FileName = 'sorted_Query.gff3'
13 self._writeQueryGff3File(self._inputQueryGff3FileName)
14 self._outputGff3FileName = 'overlaps.gff3'
15 self._iFOO = FindOverlaps_optim(self._inputRefGff3FileName, self._inputQueryGff3FileName)
16 self._iFOO.prepareIntermediateFiles_sorted()
17 self._iFOO.setOutputGff3FileName(self._outputGff3FileName)
18
19 def tearDown(self):
20 os.remove(self._inputRefGff3FileName)
21 os.remove(self._inputQueryGff3FileName)
22 os.remove(self._outputGff3FileName)
23 self._iFOO.deletIntermediateFiles()
24
25 def test_isOverlapping_true(self):
26 queryGff3Addr = 116
27 RefGff3Addr = 231
28 obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
29 exp = 0
30 self.assertEquals(exp, obs)
31
32 def test_isOverlapping_false_left(self):
33 queryGff3Addr = 116
34 RefGff3Addr = 58
35 obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
36 exp = -1
37 self.assertEquals(exp, obs)
38
39 def test_isOverlapping_false_right(self):
40 queryGff3Addr = 116
41 RefGff3Addr = 347
42 obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
43 exp = 1
44 self.assertEquals(exp, obs)
45
46 def test_getHisFirstChild(self):
47 firstRefLAddr = 0
48 obsFirstChildLAddr = self._iFOO.getHisFirstChild(firstRefLAddr)
49 expFirstChildLAddr = 48
50 self.assertEquals(expFirstChildLAddr, obsFirstChildLAddr)
51
52 def test_isLastElement_true(self):
53 refLAddr = 96
54 obsBool = self._iFOO.isLastElement(refLAddr)
55 expBool = True
56 self.assertEquals(expBool, obsBool)
57
58 def test_isLastElement_false(self):
59 refLAddr = 72
60 obsBool = self._iFOO.isLastElement(refLAddr)
61 expBool = False
62 self.assertEquals(expBool, obsBool)
63
64 def test_isLastElement_highestLevel_true(self):
65 refLAddr = 24
66 obsBool = self._iFOO.isLastElement(refLAddr)
67 expBool = True
68 self.assertEquals(expBool, obsBool)
69
70 def test_isLastElement_highestLevel_false(self):
71 refLAddr = 0
72 obsBool = self._iFOO.isLastElement(refLAddr)
73 expBool = False
74 self.assertEquals(expBool, obsBool)
75
76 def test_findOverlapIter(self):
77 queryGff3Addr = 175
78 firstRefLAddr = 0
79 done = False
80 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
81 expFirstOverlapLAddr = 96, True
82 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
83
84 def test_not_findOverlapIter(self):
85 queryGff3Addr = 295
86 firstRefLAddr = 24
87 done = False
88 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
89 expFirstOverlapLAddr = None, False
90 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
91
92 def test_findOverlapIter_not_the_first_RefOverlap(self):
93 queryGff3Addr = 235
94 firstRefLAddr = 96
95 done = True
96 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
97 expFirstOverlapLAddr = 24, False
98 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
99
100 def test_changeToNewSubEndLAddr(self):
101 firstChildLAddr = 48
102 subEndLAddr = 48
103 expSubEndLAddr = 120
104 obsSubEndLAddr = self._iFOO.changeToNewSubEndLAddr(firstChildLAddr, subEndLAddr)
105 self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
106
107 def test_defineSubEndLaddr(self):
108 parentLAddr = -1
109 expSubEndLAddr = 48
110 obsSubEndLAddr = self._iFOO.defineSubEndLaddr(parentLAddr)
111 self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
112
113 def test_getNextRefIntervalInCaseNotOverLap(self):
114 firstRefLAddr = 96
115 expRefLAddr = 24
116 obsRefLAddr = self._iFOO.getNext(firstRefLAddr)
117 self.assertEquals(expRefLAddr, obsRefLAddr)
118
119
120 def test_not_findOverlapIter_between2RefIntervals(self):
121 inputQueryGff3FileName = 'query2.gff3'
122 self._writeQueryGff3File2(inputQueryGff3FileName)
123 self._iFOO.setQueryGff3FileName(inputQueryGff3FileName)
124 queryGff3Addr = 0
125 firstRefLAddr = 0
126 done = False
127 obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
128 expFirstOverlapLAddr = 24, False
129 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
130 os.remove(inputQueryGff3FileName)
131
132 def _writeQueryGff3File2(self, fileName):
133 f = open(fileName, 'w')
134 f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
135 f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=test1.2;Name=test1.2\n")
136 f.close()
137
138 def _writeQueryGff3File(self, fileName):
139 f = open(fileName, 'w')
140 f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
141 f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=test1.2;Name=test1.2\n")
142 f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=test1.3;Name=test1.3\n")
143 f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=test1.4;Name=test1.4\n")
144 f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=test1.5;Name=test1.5\n")
145 f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=test1.6;Name=test1.6\n")
146 f.close()
147
148 if __name__ == "__main__":
149 unittest.main()