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comparison commons/core/coord/test/Test_Match.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 # 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 from commons.core.coord.Match import Match
34 from commons.core.coord.Path import Path
35
36
37 class Test_Match( unittest.TestCase ):
38
39 def test_eq_match_equals( self ):
40 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
41 match1 = Match()
42 match1.setFromTuple(tuple1)
43 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
44 match2 = Match()
45 match2.setFromTuple(tuple2)
46 self.assertEquals( match1, match2 )
47
48 def test_eq_match_not_equals_query_name( self ):
49 tuple1 = ("Name", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
50 match1 = Match()
51 match1.setFromTuple(tuple1)
52 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
53 match2 = Match()
54 match2.setFromTuple(tuple2)
55 self.assertNotEquals( match1, match2 )
56
57 def test_eq_match_not_equals_query_start( self ):
58 tuple1 = ("QName", 2, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
59 match1 = Match()
60 match1.setFromTuple(tuple1)
61 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
62 match2 = Match()
63 match2.setFromTuple(tuple2)
64 self.assertNotEquals( match1, match2 )
65
66 def test_eq_match_not_equals_query_end( self ):
67 tuple1 = ("QName", 1, 6, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
68 match1 = Match()
69 match1.setFromTuple(tuple1)
70 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
71 match2 = Match()
72 match2.setFromTuple(tuple2)
73 self.assertNotEquals( match1, match2 )
74
75 def test_eq_match_not_equals_query_length( self ):
76 tuple1 = ("QName", 1, 5, 6, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
77 match1 = Match()
78 match1.setFromTuple(tuple1)
79 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
80 match2 = Match()
81 match2.setFromTuple(tuple2)
82 self.assertNotEquals( match1, match2 )
83
84 def test_eq_match_not_equals_query_length_perc( self ):
85 tuple1 = ("QName", 1, 5, 5, 0.15, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
86 match1 = Match()
87 match1.setFromTuple(tuple1)
88 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
89 match2 = Match()
90 match2.setFromTuple(tuple2)
91 self.assertNotEquals( match1, match2 )
92
93 def test_eq_match_not_equals_match_length_perc( self ):
94 tuple1 = ("QName", 1, 5, 5, 0.1, 0.25, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
95 match1 = Match()
96 match1.setFromTuple(tuple1)
97 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
98 match2 = Match()
99 match2.setFromTuple(tuple2)
100 self.assertNotEquals( match1, match2 )
101
102 def test_eq_match_not_equals_subject_name( self ):
103 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "Name", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
104 match1 = Match()
105 match1.setFromTuple(tuple1)
106 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
107 match2 = Match()
108 match2.setFromTuple(tuple2)
109 self.assertNotEquals( match1, match2 )
110
111 def test_eq_match_not_equals_subject_start( self ):
112 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 6, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
113 match1 = Match()
114 match1.setFromTuple(tuple1)
115 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
116 match2 = Match()
117 match2.setFromTuple(tuple2)
118 self.assertNotEquals( match1, match2 )
119
120 def test_eq_match_not_equals_subject_end( self ):
121 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 26, 20, 0.15, 1e-20, 15, 87.2, 1)
122 match1 = Match()
123 match1.setFromTuple(tuple1)
124 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
125 match2 = Match()
126 match2.setFromTuple(tuple2)
127 self.assertNotEquals( match1, match2 )
128
129 def test_eq_match_not_equals_subject_length( self ):
130 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 21, 0.15, 1e-20, 15, 87.2, 1)
131 match1 = Match()
132 match1.setFromTuple(tuple1)
133 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
134 match2 = Match()
135 match2.setFromTuple(tuple2)
136 self.assertNotEquals( match1, match2 )
137
138 def test_eq_match_not_equals_subject_length_perc( self ):
139 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.16, 1e-20, 15, 87.2, 1)
140 match1 = Match()
141 match1.setFromTuple(tuple1)
142 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
143 match2 = Match()
144 match2.setFromTuple(tuple2)
145 self.assertNotEquals( match1, match2 )
146
147 def test_eq_match_not_equals_subject_e_value( self ):
148 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-21, 15, 87.2, 1)
149 match1 = Match()
150 match1.setFromTuple(tuple1)
151 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
152 match2 = Match()
153 match2.setFromTuple(tuple2)
154 self.assertNotEquals( match1, match2 )
155
156 def test_eq_match_not_equals_subject_score( self ):
157 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 16, 87.2, 1)
158 match1 = Match()
159 match1.setFromTuple(tuple1)
160 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
161 match2 = Match()
162 match2.setFromTuple(tuple2)
163 self.assertNotEquals( match1, match2 )
164
165 def test_eq_match_not_equals_subject_identity( self ):
166 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 85.2, 1)
167 match1 = Match()
168 match1.setFromTuple(tuple1)
169 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
170 match2 = Match()
171 match2.setFromTuple(tuple2)
172 self.assertNotEquals( match1, match2 )
173
174 def test_eq_match_not_equals_subject_id( self ):
175 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 2)
176 match1 = Match()
177 match1.setFromTuple(tuple1)
178 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
179 match2 = Match()
180 match2.setFromTuple(tuple2)
181 self.assertNotEquals( match1, match2 )
182
183 def test_setFromTuple_direct_strand( self ):
184 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
185 obsMatch = Match()
186 obsMatch.setFromTuple(tuple)
187 expMatch = Match()
188 expMatch.range_query.seqname = "QName"
189 expMatch.range_query.start = 1
190 expMatch.range_query.end = 5
191 expMatch.query_length = 5
192 expMatch.query_length_perc = 0.1
193 expMatch.match_length_perc = 0.2
194 expMatch.range_subject.seqname = "SName"
195 expMatch.range_subject.start = 5
196 expMatch.range_subject.end = 25
197 expMatch.subject_length = 20
198 expMatch.subject_length_perc = 0.15
199 expMatch.e_value = 1e-20
200 expMatch.score = 15
201 expMatch.identity = 87.2
202 expMatch.id = 1
203 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
204 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
205 self.assertEquals( expMatch, obsMatch )
206
207 def test_setFromTuple_reverse_strand_on_subject( self ):
208 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 25, 5, 20, 0.15, 1e-20, 15, 87.2, 1)
209 obsMatch = Match()
210 obsMatch.setFromTuple(tuple)
211 expMatch = Match()
212 expMatch.range_query.seqname = "QName"
213 expMatch.range_query.start = 1
214 expMatch.range_query.end = 5
215 expMatch.query_length = 5
216 expMatch.query_length_perc = 0.1
217 expMatch.match_length_perc = 0.2
218 expMatch.range_subject.seqname = "SName"
219 expMatch.range_subject.start = 25
220 expMatch.range_subject.end = 5
221 expMatch.subject_length = 20
222 expMatch.subject_length_perc = 0.15
223 expMatch.e_value = 1e-20
224 expMatch.score = 15
225 expMatch.identity = 87.2
226 expMatch.id = 1
227 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
228 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
229 self.assertEquals( expMatch, obsMatch )
230
231 def test_setFromTuple_reverse_strand_on_query( self ):
232 tuple = ("QName", 5, 1, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
233 obsMatch = Match()
234 obsMatch.setFromTuple(tuple)
235 expMatch = Match()
236 expMatch.range_query.seqname = "QName"
237 expMatch.range_query.start = 1
238 expMatch.range_query.end = 5
239 expMatch.query_length = 5
240 expMatch.query_length_perc = 0.1
241 expMatch.match_length_perc = 0.2
242 expMatch.range_subject.seqname = "SName"
243 expMatch.range_subject.start = 25
244 expMatch.range_subject.end = 5
245 expMatch.subject_length = 20
246 expMatch.subject_length_perc = 0.15
247 expMatch.e_value = 1e-20
248 expMatch.score = 15
249 expMatch.identity = 87.2
250 expMatch.id = 1
251 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
252 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
253 self.assertEquals( expMatch, obsMatch )
254
255 def test_setFromTuple_reverse_strand_on_query_and_subject( self ):
256 tuple = ("QName", 5, 1, 5, 0.1, 0.2, "SName", 25, 5, 20, 0.15, 1e-20, 15, 87.2, 1)
257 obsMatch = Match()
258 obsMatch.setFromTuple(tuple)
259 expMatch = Match()
260 expMatch.range_query.seqname = "QName"
261 expMatch.range_query.start = 1
262 expMatch.range_query.end = 5
263 expMatch.query_length = 5
264 expMatch.query_length_perc = 0.1
265 expMatch.match_length_perc = 0.2
266 expMatch.range_subject.seqname = "SName"
267 expMatch.range_subject.start = 5
268 expMatch.range_subject.end = 25
269 expMatch.subject_length = 20
270 expMatch.subject_length_perc = 0.15
271 expMatch.e_value = 1e-20
272 expMatch.score = 15
273 expMatch.identity = 87.2
274 expMatch.id = 1
275 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
276 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
277 self.assertEquals( expMatch, obsMatch )
278
279 def test_toString( self ):
280 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
281 match = Match()
282 match.setFromTuple(tuple)
283 expString = "QName\t1\t5\t5\t%f\t%f\tSName\t5\t25\t20\t%f\t%g\t15\t%f\t1" % (0.1,0.2,0.15,1e-20, 87.2)
284 obsString = match.toString()
285 self.assertEquals(expString, obsString)
286
287 def test_getPathInstance( self ):
288 tuple = ( "QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1 )
289 match = Match()
290 match.setFromTuple( tuple )
291 tuple = ( 1, "QName", 1, 5, "SName", 5, 25, 1e-20, 15, 87.2 )
292 exp = Path()
293 exp.setFromTuple( tuple )
294 obs = match.getPathInstance()
295 self.assertEqual( exp, obs )
296
297 def test_getQryIsIncluded(self):
298 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
299 match = Match()
300 match.setFromTuple(tuple)
301 expString = "query QName (50 bp: 1-5) is contained in subject SName (133 bp: 5-25): id=87.20 - 0.100 - 0.200 - 0.150"
302 obsString = match.getQryIsIncluded()
303 self.assertEquals(expString, obsString)
304
305 def test_isDoublonWith_Matchs_equals(self):
306 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
307 match1 = Match()
308 match1.setFromTuple(tuple1)
309 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
310 match2 = Match()
311 match2.setFromTuple(tuple2)
312 self.assertTrue(match1.isDoublonWith(match2))
313
314 def test_isDoublonWith_Matchs_unequals_on_MatchNumbers(self):
315 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
316 match1 = Match()
317 match1.setFromTuple(tuple1)
318 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 86.2, 1)
319 match2 = Match()
320 match2.setFromTuple(tuple2)
321 self.assertFalse(match1.isDoublonWith(match2))
322
323 def test_isDoublonWith_Matchs_unequals_on_SeqNames(self):
324 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
325 match1 = Match()
326 match1.setFromTuple(tuple1)
327 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "Name", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
328 match2 = Match()
329 match2.setFromTuple(tuple2)
330 self.assertFalse(match1.isDoublonWith(match2))
331
332 def test_isDoublonWith_Matchs_unequals_on_Coordinates(self):
333 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
334 match1 = Match()
335 match1.setFromTuple(tuple1)
336 tuple2 = ("QName", 1, 6, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
337 match2 = Match()
338 match2.setFromTuple(tuple2)
339 self.assertFalse(match1.isDoublonWith(match2))
340
341 def test_isDoublonWith_Reversed_Matchs_equals(self):
342 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
343 match1 = Match()
344 match1.setFromTuple(tuple1)
345 tuple2 = ("SName", 5, 25, 20, 0.15, 0.2, "QName", 1, 5, 5, 0.1, 1e-20, 15, 87.2, 1)
346 match2 = Match()
347 match2.setFromTuple(tuple2)
348 self.assertTrue(match1.isDoublonWith(match2))
349
350 def test_isDoublonWith_Reversed_Matchs_unequals(self):
351 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
352 match1 = Match()
353 match1.setFromTuple(tuple1)
354 tuple2 = ("SName", 5, 25, 20, 0.15, 0.2, "QName", 1, 6, 5, 0.1, 1e-20, 15, 87.2, 1)
355 match2 = Match()
356 match2.setFromTuple(tuple2)
357 self.assertFalse(match1.isDoublonWith(match2))
358
359
360 test_suite = unittest.TestSuite()
361 test_suite.addTest( unittest.makeSuite( Test_Match ) )
362 if __name__ == "__main__":
363 unittest.TextTestRunner(verbosity=2).run( test_suite )