Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/coord/test/Test_Set.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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-1:000000000000 | 0:e0f8dcca02ed |
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1 # Copyright INRA (Institut National de la Recherche Agronomique) | |
2 # http://www.inra.fr | |
3 # http://urgi.versailles.inra.fr | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 | |
31 | |
32 import unittest | |
33 import os | |
34 from commons.core.coord.Set import Set | |
35 from commons.core.coord.Map import Map | |
36 | |
37 | |
38 class Test_Set( unittest.TestCase ): | |
39 | |
40 def test__eq__sets_equals(self): | |
41 set1 = Set( 1, "set1", "seq1", 1, 2 ) | |
42 set2 = Set( 1, "set1", "seq1", 1 ,2 ) | |
43 self.assertEquals( set1, set2 ) | |
44 | |
45 def test__eq__sets_not_equals_ids(self): | |
46 set1 = Set( 1, "set1", "seq1", 1, 2 ) | |
47 set2 = Set( 2, "set1", "seq1", 1 ,2 ) | |
48 self.assertNotEquals( set1, set2 ) | |
49 | |
50 def test__eq__sets_not_equals_name(self): | |
51 set1 = Set( 1, "set1", "seq1", 1, 2 ) | |
52 set2 = Set( 1, "set2", "seq1", 1 ,2 ) | |
53 self.assertNotEquals( set1, set2 ) | |
54 | |
55 def test__eq__on_empty_set(self): | |
56 set1 = Set() | |
57 set2 = Set() | |
58 self.assertEquals( set1, set2 ) | |
59 | |
60 def test_setFromTuple_equals_instances(self): | |
61 tuple = ( 1, "set1", "seq1", 1, 2 ) | |
62 obsSet = Set() | |
63 obsSet.setFromTuple(tuple) | |
64 expSet = Set( 1, "set1", "seq1", 1, 2 ) | |
65 self.assertEquals( expSet, obsSet ) | |
66 | |
67 def test_setFromTuple_not_equals_instances(self): | |
68 tuple = ( 1, "set1", "seq1", 1, 2 ) | |
69 obsSet = Set() | |
70 obsSet.setFromTuple(tuple) | |
71 expSet = Set( 2, "set1", "seq1", 1, 2 ) | |
72 self.assertNotEquals( expSet, obsSet ) | |
73 | |
74 def test_read_empty_line_file(self): | |
75 fileName = "dummyFile" | |
76 | |
77 os.system(" touch " + fileName) | |
78 | |
79 fileHandler = open(fileName, "r") | |
80 | |
81 obsSet = Set() | |
82 | |
83 obsRes = obsSet.read( fileHandler ) | |
84 expRes = 0 | |
85 | |
86 fileHandler.close() | |
87 os.remove(fileName) | |
88 | |
89 self.assertEquals( expRes, obsRes ) | |
90 | |
91 def test_read_one_line_file(self): | |
92 line = ( "1\tset1\tseq1\t1\t2" ) | |
93 fileName = "dummyFile" | |
94 | |
95 fileHandler = open( fileName, "w" ) | |
96 fileHandler.write( line ) | |
97 fileHandler.close() | |
98 | |
99 fileHandler = open( fileName, "r" ) | |
100 | |
101 tuple = line.split("\t") | |
102 expSet = Set() | |
103 expSet.setFromTuple(tuple) | |
104 | |
105 obsSet = Set() | |
106 | |
107 expRes = 1 | |
108 obsRes = obsSet.read(fileHandler) | |
109 | |
110 fileHandler.close() | |
111 os.remove(fileName) | |
112 self.assertEquals( expRes, obsRes ) | |
113 self.assertEquals( expSet, obsSet ) | |
114 | |
115 def test_read_two_line_file(self): | |
116 line1 = ( "1\tset1\tseq1\t1\t2\n" ) | |
117 line2 = ( "2\tset2\tseq2\t3\t4" ) | |
118 fileName = "dummyFile" | |
119 | |
120 fileHandler = open( fileName, "w" ) | |
121 fileHandler.write( line1 ) | |
122 fileHandler.write( line2 ) | |
123 fileHandler.close() | |
124 | |
125 tuple1 = line1.split("\t") | |
126 tuple2 = line2.split("\t") | |
127 | |
128 expSet1 = Set() | |
129 expSet2 = Set() | |
130 | |
131 expSet1.setFromTuple(tuple1) | |
132 expSet2.setFromTuple(tuple2) | |
133 | |
134 expSetList = [ expSet1, expSet2 ] | |
135 expResList = [ 1, 1 ] | |
136 | |
137 fileHandler = open( fileName, "r" ) | |
138 | |
139 obsSet1 = Set() | |
140 obsSet2 = Set() | |
141 | |
142 obsRes1 = obsSet1.read(fileHandler) | |
143 obsRes2 = obsSet2.read(fileHandler) | |
144 | |
145 obsSetList= [ obsSet1, obsSet2 ] | |
146 obsResList = [ obsRes1, obsRes2 ] | |
147 | |
148 fileHandler.close() | |
149 os.remove(fileName) | |
150 | |
151 self.assertEquals( expSetList, obsSetList ) | |
152 self.assertEquals( expResList, obsResList ) | |
153 | |
154 def test_merge_first_id_greater_than_second_id(self): | |
155 firstSet = Set( 2, "set1", "seq1", 10, 40 ) | |
156 secondSet = Set( 1, "set2", "seq1", 20, 60 ) | |
157 | |
158 firstSet.merge( secondSet ) | |
159 | |
160 expSet = Set( 1, "set1", "seq1", 10, 60) | |
161 obsSet = firstSet | |
162 | |
163 self.assertEquals( expSet, obsSet) | |
164 | |
165 def test_merge_first_id_smaller_than_second_id(self): | |
166 firstSet = Set( 1, "set1", "seq1", 10, 40 ) | |
167 secondSet = Set( 2, "set2", "seq1", 20, 60 ) | |
168 | |
169 firstSet.merge( secondSet ) | |
170 | |
171 expSet = Set( 1, "set1", "seq1", 10, 60) | |
172 obsSet = firstSet | |
173 | |
174 self.assertEquals( expSet, obsSet) | |
175 | |
176 def test_merge_first_id_equals_second_id(self): | |
177 firstSet = Set( 1, "set1", "seq1", 10, 40 ) | |
178 secondSet = Set( 1, "set2", "seq1", 20, 60 ) | |
179 | |
180 firstSet.merge( secondSet ) | |
181 | |
182 expSet = Set( 1, "set1", "seq1", 10, 60) | |
183 obsSet = firstSet | |
184 | |
185 self.assertEquals( expSet, obsSet) | |
186 | |
187 def test_merge_different_seqnames(self): | |
188 firstSet = Set( 2, "set1", "seq1", 10, 40 ) | |
189 secondSet = Set( 1, "set1", "seq2", 20, 60 ) | |
190 expSet = Set( 2, "set1", "seq1", 10, 40 ) | |
191 firstSet.merge( secondSet ) | |
192 obsSet = firstSet | |
193 self.assertEquals( expSet, obsSet ) | |
194 | |
195 def test_diff_on_empty_sets(self): | |
196 firstSet = Set() | |
197 firstSet.seqname = "seq1" | |
198 secondSet = Set() | |
199 secondSet.seqname = "seq2" | |
200 | |
201 obsSet = firstSet.diff( secondSet ) | |
202 expSet = Set() | |
203 | |
204 self.assertEquals( expSet, obsSet ) | |
205 | |
206 def test_diff(self): | |
207 firstSet = Set( 2, "set1", "seq1", 10, 80 ) | |
208 secondSet = Set( 1, "set2", "seq1", 20, 60 ) | |
209 | |
210 expSet1 = Set( 2, "set1", "seq1", 10, 19 ) | |
211 expSet2 = Set( 2, "set1", "seq1", 61, 80 ) | |
212 | |
213 obsSet2 = firstSet.diff( secondSet ) | |
214 obsSet1 = firstSet | |
215 | |
216 self.assertEquals( expSet1, obsSet1 ) | |
217 self.assertEquals( expSet2, obsSet2 ) | |
218 | |
219 def test_diff_reverse(self): | |
220 firstSet = Set( 2, "set1", "seq1", 20, 60 ) | |
221 secondSet = Set( 1, "set2", "seq1", 10, 80 ) | |
222 | |
223 expSet1 = Set( 2, "set1", "seq1", 0, 0 ) | |
224 expSet2 = Set( ) | |
225 | |
226 obsSet2 = firstSet.diff( secondSet ) | |
227 obsSet1 = firstSet | |
228 | |
229 self.assertEquals( expSet1, obsSet1 ) | |
230 self.assertEquals( expSet2, obsSet2 ) | |
231 | |
232 def test_diff_list1_overlap_end_list2(self): | |
233 firstSet = Set( 2, "set1", "seq1", 20, 100 ) | |
234 secondSet = Set( 1, "set2", "seq1", 10, 80 ) | |
235 | |
236 expSet1 = Set( 2, "set1", "seq1", 81, 100 ) | |
237 expSet2 = Set( ) | |
238 | |
239 obsSet2 = firstSet.diff( secondSet ) | |
240 obsSet1 = firstSet | |
241 | |
242 self.assertEquals( expSet1, obsSet1 ) | |
243 self.assertEquals( expSet2, obsSet2 ) | |
244 | |
245 def test_diff_with_empty_set1(self): | |
246 set2 = Set( 1, "set1", "seq1", 2, 45 ) | |
247 set1 = Set( ) | |
248 | |
249 expSet1 = Set( ) | |
250 expSet2 = Set( ) | |
251 | |
252 obsSet2 = set1.diff( set2 ) | |
253 obsSet1 = set1 | |
254 | |
255 self.assertEquals( expSet1, obsSet1 ) | |
256 self.assertEquals( expSet2, obsSet2 ) | |
257 | |
258 def test_diff_list2_overlap_end_list1(self): | |
259 firstSet = Set( 2, "set1", "seq1", 10, 70 ) | |
260 secondSet = Set( 1, "set2", "seq1", 40, 100 ) | |
261 | |
262 expSet1 = Set( 2, "set1", "seq1", 10, 39 ) | |
263 expSet2 = Set( ) | |
264 | |
265 obsSet2 = firstSet.diff( secondSet ) | |
266 obsSet1 = firstSet | |
267 | |
268 self.assertEquals( expSet1, obsSet1 ) | |
269 self.assertEquals( expSet2, obsSet2 ) | |
270 | |
271 def test_set2map(self): | |
272 set = Set( 1, "set", "seq", 1, 2 ) | |
273 | |
274 expMap = Map( "set::1", "seq", 1, 2 ) | |
275 obsMap = set.set2map() | |
276 | |
277 self.assertEquals( expMap, obsMap ) | |
278 | |
279 test_suite = unittest.TestSuite() | |
280 test_suite.addTest( unittest.makeSuite( Test_Set ) ) | |
281 if __name__ == "__main__": | |
282 unittest.TextTestRunner(verbosity=2).run( test_suite ) |