Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/ncList/test/Test_FindOverlapsWithSeveralIntervals.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 import unittest | |
2 import os | |
3 from SMART.Java.Python.ncList.FindOverlapsWithSeveralIntervals import FindOverlapsWithSeveralIntervals | |
4 | |
5 class Test_FindOverlapsWithSeveralIntervals(unittest.TestCase): | |
6 | |
7 def setUp(self): | |
8 self._inputRefGff3FileName = 'sortedFile.gff3' | |
9 self._writeGFF3File(self._inputRefGff3FileName) | |
10 self._inputQueryGff3FileName = 'sorted_Query.gff3' | |
11 self._writeQueryGff3File(self._inputQueryGff3FileName) | |
12 self._outputGff3FileName = 'overlaps.gff3' | |
13 self._iFOWSI = FindOverlapsWithSeveralIntervals(self._inputRefGff3FileName, self._inputQueryGff3FileName) | |
14 self._iFOWSI.setOutputGff3FileName(self._outputGff3FileName) | |
15 | |
16 def tearDown(self): | |
17 os.remove(self._inputRefGff3FileName) | |
18 os.remove(self._inputQueryGff3FileName) | |
19 os.remove(self._outputGff3FileName) | |
20 self._iFOWSI.deletIntermediateFiles() | |
21 | |
22 def test_isOverlapping_true(self): | |
23 queryGff3Addr = 116 | |
24 RefGff3Addr = 231 | |
25 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr) | |
26 exp = 0 | |
27 self.assertEquals(exp, obs) | |
28 | |
29 def test_isOverlapping_false_left(self): | |
30 queryGff3Addr = 116 | |
31 RefGff3Addr = 58 | |
32 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr) | |
33 exp = -1 | |
34 self.assertEquals(exp, obs) | |
35 | |
36 def test_isOverlapping_false_right(self): | |
37 queryGff3Addr = 116 | |
38 RefGff3Addr = 347 | |
39 obs = self._iFOWSI.isOverlapping(queryGff3Addr, RefGff3Addr) | |
40 exp = 1 | |
41 self.assertEquals(exp, obs) | |
42 | |
43 def test_getHisFirstChild(self): | |
44 firstRefLAddr = 0 | |
45 obsFirstChildLAddr = self._iFOWSI.getHisFirstChild(firstRefLAddr) | |
46 expFirstChildLAddr = 48 | |
47 self.assertEquals(expFirstChildLAddr, obsFirstChildLAddr) | |
48 | |
49 def test_isLastElement_true(self): | |
50 refLAddr = 96 | |
51 obsBool = self._iFOWSI.isLastElement(refLAddr) | |
52 expBool = True | |
53 self.assertEquals(expBool, obsBool) | |
54 | |
55 def test_isLastElement_false(self): | |
56 refLAddr = 72 | |
57 obsBool = self._iFOWSI.isLastElement(refLAddr) | |
58 expBool = False | |
59 self.assertEquals(expBool, obsBool) | |
60 | |
61 def test_isLastElement_highestLevel_true(self): | |
62 refLAddr = 24 | |
63 obsBool = self._iFOWSI.isLastElement(refLAddr) | |
64 expBool = True | |
65 self.assertEquals(expBool, obsBool) | |
66 | |
67 def test_isLastElement_highestLevel_false(self): | |
68 refLAddr = 0 | |
69 obsBool = self._iFOWSI.isLastElement(refLAddr) | |
70 expBool = False | |
71 self.assertEquals(expBool, obsBool) | |
72 | |
73 def test_findOverlapIter(self): | |
74 queryGff3Addr = 175 | |
75 firstRefLAddr = 0 | |
76 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) | |
77 expFirstOverlapLAddr = 0 | |
78 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) | |
79 | |
80 def test_not_findOverlapIter(self): | |
81 queryGff3Addr = 295 | |
82 firstRefLAddr = 24 | |
83 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) | |
84 expFirstOverlapLAddr = None | |
85 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) | |
86 | |
87 def test_findOverlapIter_not_the_first_RefOverlap(self): | |
88 queryGff3Addr = 235 | |
89 firstRefLAddr = 0 | |
90 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) | |
91 expFirstOverlapLAddr = 24 | |
92 self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr) | |
93 | |
94 def test_changeToNewSubEndLAddr(self): | |
95 firstChildLAddr = 48 | |
96 subEndLAddr = 48 | |
97 expSubEndLAddr = 120 | |
98 obsSubEndLAddr = self._iFOWSI.changeToNewSubEndLAddr(firstChildLAddr, subEndLAddr) | |
99 self.assertEquals(expSubEndLAddr, obsSubEndLAddr) | |
100 | |
101 def test_defineSubEndLaddr(self): | |
102 parentLAddr = -1 | |
103 expSubEndLAddr = 48 | |
104 obsSubEndLAddr = self._iFOWSI.defineSubEndLaddr(parentLAddr) | |
105 self.assertEquals(expSubEndLAddr, obsSubEndLAddr) | |
106 | |
107 def test_getNextRefIntervalInCaseNotOverLap(self): | |
108 firstRefLAddr = 96 | |
109 expRefLAddr = 24 | |
110 obsRefLAddr = self._iFOWSI.getNextRefIntervalInCaseNotOverLap(firstRefLAddr) | |
111 self.assertEquals(expRefLAddr, obsRefLAddr) | |
112 | |
113 def test_getNextRefIntervalInCaseOverLap(self): | |
114 firstChildLAddr = -1 | |
115 firstRefLAddr = 120 | |
116 subEndLAddr = 144 | |
117 expRefLAddr, expSubEndLAddr = (96, 144) | |
118 obsRefLAddr, obsSubEndLAddr = self._iFOWSI.getNextRefIntervalInCaseOverLap(firstChildLAddr, firstRefLAddr, subEndLAddr) | |
119 self.assertEquals((expRefLAddr, expSubEndLAddr), (obsRefLAddr, obsSubEndLAddr)) | |
120 | |
121 def test_not_findOverlapIter_between2RefIntervals(self): | |
122 inputQueryGff3FileName = 'query2.gff3' | |
123 self._writeQueryGff3File2(inputQueryGff3FileName) | |
124 self._iFOWSI.setQueryGff3FileName(inputQueryGff3FileName) | |
125 queryGff3Addr = 0 | |
126 firstRefLAddr = 0 | |
127 obsFirstOverlapLAddr = self._iFOWSI.findOverlapIter(queryGff3Addr, firstRefLAddr) | |
128 expFirstOverlapLAddr = 24 | |
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 def _writeGFF3File(self, fileName): | |
149 f = open(fileName, "w") | |
150 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n") | |
151 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n") | |
152 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n") | |
153 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n") | |
154 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n") | |
155 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n") | |
156 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n") | |
157 f.close() | |
158 | |
159 if __name__ == "__main__": | |
160 unittest.main() |