Mercurial > repos > yufei-luo > s_mart
comparison commons/core/coord/test/Test_MapUtils.py @ 6:769e306b7933
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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 # 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 import sys | |
35 from commons.core.coord.MapUtils import MapUtils | |
36 from commons.core.coord.Map import Map | |
37 from commons.core.coord.Set import Set | |
38 from commons.core.utils.FileUtils import FileUtils | |
39 | |
40 | |
41 class Test_MapUtils( unittest.TestCase ): | |
42 | |
43 def test_getMapListSortedByIncreasingMinThenMax( self ): | |
44 iMap1 = Map("name1", "chr1", 1, 350) | |
45 iMap2 = Map("name2", "chr1", 1, 100) | |
46 iMap3 = Map("name3", "chr1", 50, 350) | |
47 iMap4 = Map("name4", "chr1", 5, 450) | |
48 lMaps = [ iMap1, iMap2, iMap3, iMap4 ] | |
49 | |
50 expLMaps = [ iMap2, iMap1, iMap4, iMap3 ] | |
51 | |
52 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps ) | |
53 | |
54 self.assertEquals( expLMaps, obsLMaps ) | |
55 | |
56 | |
57 def test_getMapListSortedByIncreasingMinThenMax_ordered( self ): | |
58 iMap1 = Map("name1", "chr1", 1, 100) | |
59 iMap2 = Map("name2", "chr1", 1, 350) | |
60 | |
61 lMaps = [ iMap1, iMap2 ] | |
62 expLMaps = [ iMap1, iMap2 ] | |
63 | |
64 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps ) | |
65 | |
66 self.assertEquals( expLMaps, obsLMaps ) | |
67 | |
68 | |
69 def test_getMapListSortedByIncreasingMinThenMax_unordered( self ): | |
70 iMap1 = Map("name1", "chr1", 1, 350) | |
71 iMap2 = Map("name2", "chr1", 1, 100) | |
72 | |
73 lMaps = [ iMap1, iMap2 ] | |
74 expLMaps = [ iMap2, iMap1 ] | |
75 | |
76 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps ) | |
77 | |
78 self.assertEquals( expLMaps, obsLMaps ) | |
79 | |
80 | |
81 def test_getMapListSortedByIncreasingMinThenMax_nonOverlapping( self ): | |
82 iMap1 = Map("name1", "chr1", 1, 350) | |
83 iMap2 = Map("name2", "chr1", 400, 600) | |
84 | |
85 lMaps = [ iMap2, iMap1 ] | |
86 expLMaps = [ iMap1, iMap2 ] | |
87 | |
88 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps ) | |
89 | |
90 self.assertEquals( expLMaps, obsLMaps ) | |
91 | |
92 | |
93 def test_getMapListSortedByIncreasingMinThenMax_sameMinThreeMaps( self ): | |
94 iMap1 = Map("name1", "chr1", 350, 1) | |
95 iMap2 = Map("name2", "chr1", 400, 1) | |
96 iMap3 = Map("name3", "chr1", 500, 1) | |
97 | |
98 lMaps = [ iMap2, iMap1, iMap3 ] | |
99 expLMaps = [ iMap1, iMap2, iMap3 ] | |
100 | |
101 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps ) | |
102 | |
103 self.assertEquals( expLMaps, obsLMaps ) | |
104 | |
105 | |
106 def test_getMapListSortedByIncreasingMinThenMax_included( self ): | |
107 iMap1 = Map("name1", "chr1", 350, 1) | |
108 iMap2 = Map("name2", "chr1", 300, 10) | |
109 | |
110 lMaps = [ iMap2, iMap1 ] | |
111 expLMaps = [ iMap1, iMap2] | |
112 | |
113 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps ) | |
114 | |
115 self.assertEquals( expLMaps, obsLMaps ) | |
116 | |
117 | |
118 def test_getMapListSortedByIncreasingMinThenMax_equal( self ): | |
119 iMap1 = Map("name1", "chr1", 350, 1) | |
120 iMap2 = Map("name2", "chr1", 350, 1) | |
121 | |
122 lMaps = [ iMap2, iMap1 ] | |
123 expLMaps = [ iMap2, iMap1 ] | |
124 notExpLMaps = [ iMap1, iMap2 ] | |
125 | |
126 obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps ) | |
127 | |
128 self.assertEquals( expLMaps, obsLMaps ) | |
129 self.assertNotEquals( notExpLMaps, obsLMaps ) | |
130 | |
131 | |
132 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( self ): | |
133 iMap1 = Map("name1", "chr1", 1, 350) | |
134 iMap2 = Map("name4", "chr2", 5, 450) | |
135 iMap3 = Map("name4", "chr1", 10, 450) | |
136 iMap4 = Map("name4", "chr1", 10, 500) | |
137 iMap5 = Map("name4", "chr1", 5, 450) | |
138 iMap6 = Map("name3", "chr1", 50, 350) | |
139 iMap7 = Map("name2", "chr1", 1, 100) | |
140 | |
141 lMaps = [ iMap1, iMap2, iMap3, iMap4, iMap5, iMap6, iMap7 ] | |
142 | |
143 expLMaps = [ iMap1, iMap7, iMap6, iMap5, iMap3, iMap4, iMap2 ] | |
144 | |
145 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps ) | |
146 | |
147 self.assertEquals( expLMaps, obsLMaps ) | |
148 | |
149 | |
150 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_ordered( self ): | |
151 iMap1 = Map("name1", "chr1", 1, 100) | |
152 iMap2 = Map("name1", "chr2", 1, 350) | |
153 | |
154 lMaps = [ iMap1, iMap2 ] | |
155 expLMaps = [ iMap1, iMap2 ] | |
156 | |
157 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps ) | |
158 | |
159 self.assertEquals( expLMaps, obsLMaps ) | |
160 | |
161 | |
162 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_unordered( self ): | |
163 iMap1 = Map("name1", "chr2", 1, 350) | |
164 iMap2 = Map("name1", "chr1", 1, 100) | |
165 | |
166 lMaps = [ iMap1, iMap2 ] | |
167 expLMaps = [ iMap2, iMap1 ] | |
168 | |
169 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps ) | |
170 | |
171 self.assertEquals( expLMaps, obsLMaps ) | |
172 | |
173 | |
174 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_nonOverlapping( self ): | |
175 iMap1 = Map("name1", "chr1", 1, 350) | |
176 iMap2 = Map("name2", "chr1", 400, 600) | |
177 | |
178 lMaps = [ iMap2, iMap1 ] | |
179 expLMaps = [ iMap1, iMap2 ] | |
180 | |
181 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps ) | |
182 | |
183 self.assertEquals( expLMaps, obsLMaps ) | |
184 | |
185 | |
186 def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_sameMinThreeMaps( self ): | |
187 iMap1 = Map("name2", "chr1", 150, 10) | |
188 iMap2 = Map("name2", "chr1", 1, 100) | |
189 iMap3 = Map("name2", "chr1", 100, 1) | |
190 | |
191 lMaps = [ iMap1, iMap2, iMap3 ] | |
192 expLMaps = [ iMap2, iMap3, iMap1 ] | |
193 | |
194 obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps ) | |
195 | |
196 self.assertEquals( expLMaps, obsLMaps ) | |
197 | |
198 | |
199 def test_getDictPerNameFromMapFile( self ): | |
200 iMap1 = Map( "chunk1", "chromosome1", 1, 100 ) | |
201 iMap2 = Map( "chunk2", "chromosome1", 91, 190 ) | |
202 iMap3 = Map( "chunk3", "chromosome2", 1, 100 ) | |
203 iMap4 = Map( "chunk1", "chromosome1", 1, 100 ) # redundant with iMap1 | |
204 | |
205 mapFile = "dummyFile.map" | |
206 mapFileHandler = open( mapFile, "w" ) | |
207 for iMap in [ iMap1, iMap2, iMap3, iMap4 ]: | |
208 iMap.write( mapFileHandler ) | |
209 mapFileHandler.close() | |
210 | |
211 dExp = { "chunk1": iMap1, "chunk2": iMap2, "chunk3": iMap3 } | |
212 | |
213 dObs = MapUtils.getDictPerNameFromMapFile( mapFile ) | |
214 | |
215 self.assertEquals( dExp, dObs ) | |
216 | |
217 os.remove( mapFile ) | |
218 | |
219 | |
220 def test_mapList2SetList(self): | |
221 map1 = Map( "name1", "desc1", 1, 120 ) | |
222 map2 = Map( "name2", "desc2", 1, 20 ) | |
223 lMap = [ map1, map2 ] | |
224 set1 = Set( 1, "name1", "desc1", 1, 120 ) | |
225 set2 = Set( 2, "name2", "desc2", 1, 20 ) | |
226 explMapSet = [ set1, set2 ] | |
227 obslMapSet = MapUtils.mapList2SetList( lMap ) | |
228 | |
229 self.assertEquals( explMapSet, obslMapSet ) | |
230 | |
231 | |
232 def test_mergeCoordsInFile( self ): | |
233 if sys.modules.has_key( "commons.core.checker.CheckerUtils" ): | |
234 inFile = "dummyInFile" | |
235 inFileHandler = open( inFile, "w" ) | |
236 inFileHandler.write( "TE1\tchr1\t1501\t2500\n" ) | |
237 inFileHandler.write( "TE3\tchr1\t4000\t3401\n" ) | |
238 inFileHandler.write( "TE3\tchr1\t3800\t3601\n" ) | |
239 inFileHandler.close() | |
240 expFile = "dummyExpFile" | |
241 expFileHandler = open( expFile, "w" ) | |
242 expFileHandler.write( "TE1\tchr1\t1501\t2500\n" ) | |
243 expFileHandler.write( "TE3\tchr1\t4000\t3401\n" ) | |
244 expFileHandler.close() | |
245 obsFile = "dummyObsFile" | |
246 MapUtils.mergeCoordsInFile( inFile, obsFile ) | |
247 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) | |
248 for f in [ inFile, expFile, obsFile ]: | |
249 os.remove( f ) | |
250 | |
251 | |
252 def test_getDictPerSeqNameFromMapFile( self ): | |
253 inFile = "dummyInFile" | |
254 inFileHandler = open( inFile, "w" ) | |
255 inFileHandler.write( "TE1\tchr1\t1\t10\n" ) | |
256 inFileHandler.write( "TE2\tchr1\t60\t41\n" ) | |
257 inFileHandler.write( "TE3\tchr2\t5\t36\n" ) | |
258 inFileHandler.close() | |
259 dExp = { "chr1": [ Map( "TE1", "chr1", 1, 10 ), Map( "TE2", "chr1", 60, 41 ) ], | |
260 "chr2": [ Map( "TE3", "chr2", 5, 36 ) ] } | |
261 dObs = MapUtils.getDictPerSeqNameFromMapFile( inFile ) | |
262 self.assertEqual( dExp, dObs ) | |
263 os.remove( inFile ) | |
264 | |
265 def test_convertMapFileIntoSetFile(self): | |
266 mapInputFile = "dummyExpFile" | |
267 mapFileHandler = open( mapInputFile, "w" ) | |
268 mapFileHandler.write( "seq31\tchr1\t151\t250\n" ) | |
269 mapFileHandler.write( "seq27\tchr2\t301\t500\n" ) | |
270 mapFileHandler.write( "seq40\tchr2\t600\t700\n" ) | |
271 mapFileHandler.write( "seq2\tchr3\t301\t500\n" ) | |
272 mapFileHandler.close() | |
273 | |
274 expSetFile = "dummyexpSetFile" | |
275 expSetFileHandler = open( expSetFile, "w" ) | |
276 expSetFileHandler.write( "1\tseq31\tchr1\t151\t250\n" ) | |
277 expSetFileHandler.write( "2\tseq27\tchr2\t301\t500\n" ) | |
278 expSetFileHandler.write( "3\tseq40\tchr2\t600\t700\n" ) | |
279 expSetFileHandler.write( "4\tseq2\tchr3\t301\t500\n" ) | |
280 expSetFileHandler.close() | |
281 | |
282 obsFile = "dummyObsFile" | |
283 | |
284 MapUtils.convertMapFileIntoSetFile( mapInputFile, obsFile ) | |
285 | |
286 self.assertTrue( FileUtils.are2FilesIdentical( expSetFile, obsFile ) ) | |
287 | |
288 for f in [ expSetFile, mapInputFile, obsFile ]: | |
289 os.remove( f ) | |
290 | |
291 def test_convertMapFileIntoSetFile_one_line(self): | |
292 mapInputFile = "dummyExpFile" | |
293 mapFileHandler = open( mapInputFile, "w" ) | |
294 mapFileHandler.write( "seq31\tchr1\t151\t250\n" ) | |
295 mapFileHandler.close() | |
296 | |
297 expSetFile = "dummyexpSetFile" | |
298 expSetFileHandler = open( expSetFile, "w" ) | |
299 expSetFileHandler.write( "1\tseq31\tchr1\t151\t250\n" ) | |
300 expSetFileHandler.close() | |
301 | |
302 obsFile = "dummyObsFile" | |
303 | |
304 MapUtils.convertMapFileIntoSetFile( mapInputFile, obsFile ) | |
305 | |
306 self.assertTrue( FileUtils.are2FilesIdentical( expSetFile, obsFile ) ) | |
307 | |
308 for f in [ expSetFile, mapInputFile, obsFile ]: | |
309 os.remove( f ) | |
310 | |
311 def test_convertMapFileIntoSetFile_empty_file(self): | |
312 mapInputFile = "dummyFile.map" | |
313 mapFileHandler = open( mapInputFile, "w" ) | |
314 mapFileHandler.close() | |
315 | |
316 expFile = "dummyExpFile.map.set" | |
317 expFileHandler = open( expFile, "w" ) | |
318 expFileHandler.close() | |
319 | |
320 obsFile = "dummyFile.map.set" | |
321 | |
322 MapUtils.convertMapFileIntoSetFile( mapInputFile ) | |
323 | |
324 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) | |
325 | |
326 for f in [ expFile, mapInputFile, obsFile ]: | |
327 os.remove( f ) | |
328 | |
329 def test_writeListInFile_empty_list(self): | |
330 lMaps = [ ] | |
331 expFileName = "expFileName" | |
332 fileHandle = open(expFileName, "w") | |
333 fileHandle.close() | |
334 | |
335 obsFileName = "obsFileName" | |
336 fileHandle = open(obsFileName, "w") | |
337 MapUtils.writeListInFile(lMaps, obsFileName, "w") | |
338 fileHandle.close() | |
339 | |
340 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
341 | |
342 os.remove(obsFileName) | |
343 os.remove(expFileName) | |
344 | |
345 def test_writeListInFile_list_one_set(self): | |
346 lMaps = [ Map( "map1", "map1seq", 1, 10 ) ] | |
347 line = "map1\tmap1seq\t1\t10\n" | |
348 | |
349 expFileName = "expFileName" | |
350 | |
351 fileHandle = open(expFileName, "w") | |
352 fileHandle.write(line) | |
353 fileHandle.close() | |
354 | |
355 obsFileName = "obsFileName" | |
356 fileHandle = open(obsFileName, "w") | |
357 MapUtils.writeListInFile(lMaps, obsFileName, "w") | |
358 fileHandle.close() | |
359 | |
360 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
361 | |
362 os.remove(obsFileName) | |
363 os.remove(expFileName) | |
364 | |
365 def test_getMinLengthOfMapFile(self): | |
366 mapFileName = "%s/Gnome_tools/Vein_v4_scaffold_00001.fa.Nstretch.map" % os.environ["REPET_DATA"] | |
367 expMinLengthofMapFile = 20 | |
368 iMap = MapUtils() | |
369 obsMinLengthofMapFile = iMap.getMinLengthOfMapFile(mapFileName) | |
370 self.assertEquals(expMinLengthofMapFile, obsMinLengthofMapFile) | |
371 | |
372 def test_getMaxLengthOfMapFile(self): | |
373 mapFileName = "%s/Gnome_tools/Vein_v4_scaffold_00001.fa.Nstretch.map" % os.environ["REPET_DATA"] | |
374 expMinLengthofMapFile = 6344 | |
375 iMap = MapUtils() | |
376 obsMinLengthofMapFile = iMap.getMaxLengthOfMapFile(mapFileName) | |
377 self.assertEquals(expMinLengthofMapFile, obsMinLengthofMapFile) | |
378 | |
379 | |
380 | |
381 test_suite = unittest.TestSuite() | |
382 test_suite.addTest( unittest.makeSuite( Test_MapUtils ) ) | |
383 if __name__ == "__main__": | |
384 unittest.TextTestRunner(verbosity=2).run( test_suite ) |