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comparison smart_toolShed/commons/core/coord/test/Test_AlignUtils.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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 time
35 import shutil
36 from commons.core.coord.AlignUtils import AlignUtils
37 from commons.core.coord.Align import Align
38 from commons.core.utils.FileUtils import FileUtils
39 from commons.core.coord.Range import Range
40
41
42 class Test_AlignUtils( unittest.TestCase ):
43
44 def setUp( self ):
45 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
46
47
48 def tearDown( self ):
49 self._uniqId = ""
50
51
52 def test_getAlignListFromFile( self ):
53 a1 = Align()
54 a1.setFromTuple( ( "chr1", "1", "100", "seq3", "1", "100", "1e-23", "89", "97.26" ) )
55 a2 = Align()
56 a2.setFromTuple( ( "chr2", "121", "210", "seq5", "21", "110", "1e-32", "95", "98.13" ) )
57
58 inFileName = "dummyFile_%s" % ( self._uniqId )
59 inFileHandler = open( inFileName, "w" )
60 a1.write( inFileHandler )
61 a2.write( inFileHandler )
62 inFileHandler.close()
63
64 lExp = [ a1, a2 ]
65 lObs = AlignUtils.getAlignListFromFile( inFileName )
66
67 self.assertEqual( lExp, lObs )
68
69 if os.path.exists( inFileName ):
70 os.remove( inFileName )
71
72
73 def test_getListOfScores( self ):
74 a1 = Align()
75 a1.setFromTuple( ( "chr1", "1", "100", "seq3", "1", "100", "1e-23", "89", "97.26" ) )
76 a2 = Align()
77 a2.setFromTuple( ( "chr2", "121", "210", "seq5", "21", "110", "1e-32", "95", "98.13" ) )
78 lAligns = [ a1, a2 ]
79
80 lExp = [ 89, 95 ]
81 lObs = AlignUtils.getListOfScores( lAligns )
82
83 self.assertEqual( lExp, lObs )
84
85
86 def test_getScoreListFromFile( self ):
87 alignFile = "dummyAlignFile"
88 alignFileHandler = open( alignFile, "w" )
89 alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.2\n" )
90 alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.9\n" )
91 alignFileHandler.close()
92
93 lExp = [ 133, 235 ]
94 lObs = AlignUtils.getScoreListFromFile( alignFile )
95 self.assertEqual( lExp, lObs )
96
97 os.remove( alignFile )
98
99
100 def test_getScoreListFromFile_empty_file( self ):
101 alignFile = "dummyAlignFile"
102 alignFileHandler = open( alignFile, "w" )
103 alignFileHandler.close()
104
105 lExp = []
106 lObs = AlignUtils.getScoreListFromFile( alignFile )
107
108 self.assertEqual( lExp, lObs )
109
110 os.remove( alignFile )
111
112
113 def test_getScoreListFromFile_with_endline_char( self ):
114 alignFile = "dummyAlignFile"
115 alignFileHandler = open( alignFile, "w" )
116 alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.2\n" )
117 alignFileHandler.write( "\n" )
118 alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.9\n" )
119 alignFileHandler.write( "\n" )
120 alignFileHandler.close()
121
122 lExp = [133, 235]
123 lObs = AlignUtils.getScoreListFromFile( alignFile )
124
125 self.assertEqual( lExp, lObs )
126
127 os.remove( alignFile )
128
129
130 def test_convertAlignFileIntoMapFileWithQueriesAndSubjects( self ):
131 alignFile = "dummyAlignFile_%s" % ( self._uniqId )
132 alignFileHandler = open( alignFile, "w" )
133 alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.2\n" )
134 alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.9\n" )
135 alignFileHandler.close()
136
137 expFile = "dummyExpFile_%s" % ( self._uniqId )
138 expFileHandler = open( expFile, "w" )
139 expFileHandler.write( "repet\tchr3\t1\t100\n" )
140 expFileHandler.write( "repet\tchr5\t11\t110\n" )
141 expFileHandler.write( "repet\tchr7\t1\t200\n" )
142 expFileHandler.write( "repet\tchr2\t11\t210\n" )
143 expFileHandler.close()
144
145 obsFile = "dummyObsFile_%s" % ( self._uniqId )
146
147 AlignUtils.convertAlignFileIntoMapFileWithQueriesAndSubjects( alignFile, obsFile )
148
149 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
150
151 for f in [ alignFile, expFile, obsFile ]:
152 if os.path.exists( f ):
153 os.remove( f )
154
155
156 def test_convertAlignFileIntoMapFileWithSubjectsOnQueries( self ):
157 alignFile = "dummyAlignFile_%s" % ( self._uniqId )
158 alignFileHandler = open( alignFile, "w" )
159 alignFileHandler.write( "chr3\t1\t100\tTE1\t11\t110\t1e-52\t133\t87.2\n" )
160 alignFileHandler.write( "chr7\t1\t200\tTE1\t11\t210\t1e-78\t235\t98.9\n" )
161 alignFileHandler.close()
162
163 expFile = "dummyExpFile_%s" % ( self._uniqId )
164 expFileHandler = open( expFile, "w" )
165 expFileHandler.write( "TE1\tchr3\t1\t100\n" )
166 expFileHandler.write( "TE1\tchr7\t1\t200\n" )
167 expFileHandler.close()
168
169 obsFile = "dummyObsFile_%s" % ( self._uniqId )
170
171 AlignUtils.convertAlignFileIntoMapFileWithSubjectsOnQueries( alignFile, obsFile )
172
173 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
174
175 for f in [ alignFile, expFile, obsFile ]:
176 if os.path.exists( f ):
177 os.remove( f )
178
179
180 def test_getAlignListSortedByDecreasingScoreThenLength( self ):
181 a1 = Align()
182 a1.setFromTuple( ( "chr1", "1", "100", "seq3", "1", "100", "1e-23", "89", "97.26" ) )
183 a2 = Align()
184 a2.setFromTuple( ( "chr7", "121", "200", "seq9", "21", "110", "1e-32", "95", "98.13" ) )
185 a3 = Align()
186 a3.setFromTuple( ( "chr2", "121", "210", "seq5", "21", "110", "1e-32", "95", "98.13" ) )
187 lAligns = [ a1, a2, a3 ]
188
189 lExp = [ a3, a2, a1 ]
190
191 lObs = AlignUtils.getAlignListSortedByDecreasingScoreThenLength( lAligns )
192
193 self.assertEqual( lExp, lObs )
194
195
196 def test_convertAlignFileIntoPathFile( self ):
197 alignFile = "dummyAlignFile_%s" % ( self._uniqId )
198 alignFileHandler = open( alignFile, "w" )
199 alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
200 alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
201 alignFileHandler.close()
202
203 expFile = "dummyExpFile_%s" % ( self._uniqId )
204 expFileHandler = open( expFile, "w" )
205 expFileHandler.write( "1\tchr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
206 expFileHandler.write( "2\tchr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
207 expFileHandler.close()
208
209 obsFile = "dummyObsFile_%s" % ( self._uniqId )
210
211 AlignUtils.convertAlignFileIntoPathFile( alignFile, obsFile )
212
213 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
214
215 for f in [ alignFile, expFile, obsFile ]:
216 if os.path.exists( f ):
217 os.remove( f )
218
219
220 def test_sortAlignFile( self ):
221 alignFile = "dummyAlignFile_%s" % ( self._uniqId )
222 alignFileHandler = open( alignFile, "w" )
223 alignFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
224 alignFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
225 alignFileHandler.write( "chr8\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
226 alignFileHandler.write( "chr8\t1\t100\tchr5\t15\t90\t1e-52\t133\t87.200000\n" )
227 alignFileHandler.write( "chr8\t1\t100\tchr5\t11\t100\t1e-52\t133\t87.200000\n" )
228 alignFileHandler.close()
229
230 expFile = "dummyExpFile_%s" % ( self._uniqId )
231 expFileHandler = open( expFile, "w" )
232 expFileHandler.write( "chr3\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
233 expFileHandler.write( "chr7\t1\t200\tchr2\t11\t210\t1e-78\t235\t98.900000\n" )
234 expFileHandler.write( "chr8\t1\t100\tchr5\t11\t100\t1e-52\t133\t87.200000\n" )
235 expFileHandler.write( "chr8\t1\t100\tchr5\t11\t110\t1e-52\t133\t87.200000\n" )
236 expFileHandler.write( "chr8\t1\t100\tchr5\t15\t90\t1e-52\t133\t87.200000\n" )
237 expFileHandler.close()
238
239 obsFile = "dummyObsFile_%s" % ( self._uniqId )
240
241 AlignUtils.sortAlignFile( alignFile, obsFile )
242
243 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
244
245 for f in [ alignFile, expFile, obsFile ]:
246 if os.path.exists( f ):
247 os.remove( f )
248
249 def test_writeListInFile( self ):
250 line1 = ("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
251 line2 = ("chr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
252 line3 = ("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
253
254 expFileName = "expFileName.align"
255 expFileHandle = open ( expFileName, 'w' )
256 expFileHandle.write(line1)
257 expFileHandle.write(line2)
258 expFileHandle.write(line3)
259 expFileHandle.close()
260
261 iAlign1 = Align()
262 iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
263 iAlign2 = Align()
264 iAlign2.setFromString("chr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
265 iAlign3 = Align()
266 iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
267
268 obsFileName = "obsFileName.align"
269 obsPathList =[iAlign1, iAlign2, iAlign3]
270
271 AlignUtils.writeListInFile( obsPathList, obsFileName )
272
273 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
274
275 os.remove( obsFileName )
276 os.remove( expFileName )
277
278
279 def test_splitAlignListByQueryName_empty_list( self ):
280 lAlign = []
281
282 obsLAlign = AlignUtils.splitAlignListByQueryName( lAlign )
283
284 expLAlign = []
285
286 self.assertEquals( expLAlign, obsLAlign )
287
288
289 def test_splitAlignListByQueryName( self ):
290 iAlign1 = Align()
291 iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
292 iAlign2 = Align()
293 iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
294 iAlign3 = Align()
295 iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
296 lAlign = [ iAlign1, iAlign2, iAlign3 ]
297
298 obsLAlign = AlignUtils.splitAlignListByQueryName( lAlign )
299
300 expLAlign = [ [ iAlign1, iAlign3 ],
301 [ iAlign2 ] ]
302
303 self.assertEquals( expLAlign, obsLAlign )
304
305
306 def test_splitAlignListByQueryName_last_align_alone( self ):
307 iAlign1 = Align()
308 iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
309 iAlign2 = Align()
310 iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
311 iAlign3 = Align()
312 iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
313 iAlign4 = Align()
314 iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
315 iAlign5 = Align()
316 iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
317 iAlign6 = Align()
318 iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
319 iAlign7 = Align()
320 iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
321 iAlign8 = Align()
322 iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
323 iAlign9 = Align()
324 iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
325 lAlign = [ iAlign1, iAlign2, iAlign3, iAlign4, iAlign5, iAlign6, iAlign7, iAlign8, iAlign9 ]
326
327 obsLAlign = AlignUtils.splitAlignListByQueryName( lAlign )
328
329 expLAlign = [ [ iAlign1, iAlign3, iAlign6, iAlign7 ],
330 [ iAlign2, iAlign5, iAlign8 ],
331 [ iAlign4 ],
332 [ iAlign9 ] ]
333
334 self.assertEquals( expLAlign, obsLAlign )
335
336
337 def test_createAlignFiles( self ):
338 expFile1 = "dummyExpAlignFile.align_1"
339 expFile2 = "dummyExpAlignFile.align_2"
340 expFile3 = "dummyExpAlignFile.align_3"
341 expFile4 = "dummyExpAlignFile.align_4"
342
343 f1 = open(expFile1, "w")
344 iAlign1 = Align()
345 iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
346 iAlign1.write(f1)
347 iAlign3 = Align()
348 iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
349 iAlign3.write(f1)
350 iAlign6 = Align()
351 iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
352 iAlign6.write(f1)
353 iAlign7 = Align()
354 iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
355 iAlign7.write(f1)
356 f1.close()
357
358 f2 = open(expFile2, "w")
359 iAlign2 = Align()
360 iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
361 iAlign2.write(f2)
362 iAlign5 = Align()
363 iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
364 iAlign5.write(f2)
365 iAlign8 = Align()
366 iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
367 iAlign8.write(f2)
368 f2.close()
369
370 f3 = open(expFile3, "w")
371 iAlign4 = Align()
372 iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
373 iAlign4.write(f3)
374 f3.close()
375
376 f4 = open(expFile4, "w")
377 iAlign9 = Align()
378 iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
379 iAlign9.write(f4)
380 f4.close()
381
382 lAlignList = [ [ iAlign1, iAlign3, iAlign6, iAlign7 ],
383 [ iAlign2, iAlign5, iAlign8 ],
384 [ iAlign4 ],
385 [ iAlign9 ] ]
386
387 AlignUtils.createAlignFiles( lAlignList, "dummyAlignFile" )
388
389 obsFile1 = "dummyAlignFile_1.align"
390 obsFile2 = "dummyAlignFile_2.align"
391 obsFile3 = "dummyAlignFile_3.align"
392 obsFile4 = "dummyAlignFile_4.align"
393
394 self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
395 self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
396 self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
397 self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
398
399 os.remove(expFile1)
400 os.remove(expFile2)
401 os.remove(expFile3)
402 os.remove(expFile4)
403 os.remove(obsFile1)
404 os.remove(obsFile2)
405 os.remove(obsFile3)
406 os.remove(obsFile4)
407
408
409 def test_createAlignFiles_eleven_output_files( self ):
410 expFile1 = "dummyExpAlignFile.align_01"
411 expFile2 = "dummyExpAlignFile.align_02"
412 expFile3 = "dummyExpAlignFile.align_03"
413 expFile4 = "dummyExpAlignFile.align_04"
414 expFile5 = "dummyExpAlignFile.align_05"
415 expFile6 = "dummyExpAlignFile.align_06"
416 expFile7 = "dummyExpAlignFile.align_07"
417 expFile8 = "dummyExpAlignFile.align_08"
418 expFile9 = "dummyExpAlignFile.align_09"
419 expFile10 = "dummyExpAlignFile.align_10"
420 expFile11 = "dummyExpAlignFile.align_11"
421 lExpFiles = [expFile1, expFile2, expFile3, expFile4, expFile5, expFile6, expFile7, expFile8, expFile9, expFile10, expFile11]
422
423 f1 = open(expFile1, "w")
424 iAlign1 = Align()
425 iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
426 iAlign1.write(f1)
427 f1.close()
428
429 f2 = open(expFile2, "w")
430 iAlign2 = Align()
431 iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
432 iAlign2.write(f2)
433 f2.close()
434
435 f3 = open(expFile3, "w")
436 iAlign3 = Align()
437 iAlign3.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
438 iAlign3.write(f3)
439 f3.close()
440
441 f4 = open(expFile4, "w")
442 iAlign4 = Align()
443 iAlign4.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
444 iAlign4.write(f4)
445 f4.close()
446
447 f = open(expFile5, "w")
448 iAlign5 = Align()
449 iAlign5.setFromString("chr5\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
450 iAlign5.write(f)
451 f.close()
452
453 f = open(expFile6, "w")
454 iAlign6 = Align()
455 iAlign6.setFromString("chr6\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
456 iAlign6.write(f)
457 f.close()
458
459 f = open(expFile7, "w")
460 iAlign7 = Align()
461 iAlign7.setFromString("chr7\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
462 iAlign7.write(f)
463 f.close()
464
465 f = open(expFile8, "w")
466 iAlign8 = Align()
467 iAlign8.setFromString("chr8\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
468 iAlign8.write(f)
469 f.close()
470
471 f = open(expFile9, "w")
472 iAlign9 = Align()
473 iAlign9.setFromString("chr9\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
474 iAlign9.write(f)
475 f.close()
476
477 f = open(expFile10, "w")
478 iAlign10 = Align()
479 iAlign10.setFromString("chr10\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
480 iAlign10.write(f)
481 f.close()
482
483 f = open(expFile11, "w")
484 iAlign11 = Align()
485 iAlign11.setFromString("chr11\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
486 iAlign11.write(f)
487 f.close()
488
489 lAlignList = [[iAlign1], [iAlign2], [iAlign3], [iAlign4], [iAlign5], [iAlign6], [iAlign7], [iAlign8], [iAlign9], [iAlign10], [iAlign11]]
490
491 AlignUtils.createAlignFiles(lAlignList, "dummyAlignFile")
492
493 obsFile1 = "dummyAlignFile_01.align"
494 obsFile2 = "dummyAlignFile_02.align"
495 obsFile3 = "dummyAlignFile_03.align"
496 obsFile4 = "dummyAlignFile_04.align"
497 obsFile5 = "dummyAlignFile_05.align"
498 obsFile6 = "dummyAlignFile_06.align"
499 obsFile7 = "dummyAlignFile_07.align"
500 obsFile8 = "dummyAlignFile_08.align"
501 obsFile9 = "dummyAlignFile_09.align"
502 obsFile10 = "dummyAlignFile_10.align"
503 obsFile11 = "dummyAlignFile_11.align"
504 lObsFiles = [obsFile1, obsFile2, obsFile3, obsFile4, obsFile5, obsFile6, obsFile7, obsFile8, obsFile9, obsFile10, obsFile11]
505
506 self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
507 self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
508 self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
509 self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
510 self.assertTrue( FileUtils.are2FilesIdentical( expFile5, obsFile5 ) )
511 self.assertTrue( FileUtils.are2FilesIdentical( expFile6, obsFile6 ) )
512 self.assertTrue( FileUtils.are2FilesIdentical( expFile7, obsFile7 ) )
513 self.assertTrue( FileUtils.are2FilesIdentical( expFile8, obsFile8 ) )
514 self.assertTrue( FileUtils.are2FilesIdentical( expFile9, obsFile9 ) )
515 self.assertTrue( FileUtils.are2FilesIdentical( expFile10, obsFile10 ) )
516 self.assertTrue( FileUtils.are2FilesIdentical( expFile11, obsFile11 ) )
517
518 for file in lExpFiles:
519 os.remove(file)
520 for file in lObsFiles:
521 os.remove(file)
522
523
524 def test_createAlignFiles_dirName_specified( self ):
525 expFile1 = "dummyExpAlignFile.align_1"
526 expFile2 = "dummyExpAlignFile.align_2"
527 expFile3 = "dummyExpAlignFile.align_3"
528 expFile4 = "dummyExpAlignFile.align_4"
529
530 f1 = open(expFile1, "w")
531 iAlign1 = Align()
532 iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
533 iAlign1.write(f1)
534 iAlign3 = Align()
535 iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
536 iAlign3.write(f1)
537 iAlign6 = Align()
538 iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
539 iAlign6.write(f1)
540 iAlign7 = Align()
541 iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
542 iAlign7.write(f1)
543 f1.close()
544
545 f2 = open(expFile2, "w")
546 iAlign2 = Align()
547 iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
548 iAlign2.write(f2)
549 iAlign5 = Align()
550 iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
551 iAlign5.write(f2)
552 iAlign8 = Align()
553 iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
554 iAlign8.write(f2)
555 f2.close()
556
557 f3 = open(expFile3, "w")
558 iAlign4 = Align()
559 iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
560 iAlign4.write(f3)
561 f3.close()
562
563 f4 = open(expFile4, "w")
564 iAlign9 = Align()
565 iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
566 iAlign9.write(f4)
567 f4.close()
568
569 lAlignList = [[iAlign1, iAlign3, iAlign6, iAlign7], [iAlign2, iAlign5, iAlign8], [iAlign4], [iAlign9]]
570
571 dirName = "dummyAlignDir"
572
573 AlignUtils.createAlignFiles(lAlignList, "dummyAlignFile", dirName)
574
575 obsFile1 = dirName + "/dummyAlignFile_1.align"
576 obsFile2 = dirName + "/dummyAlignFile_2.align"
577 obsFile3 = dirName + "/dummyAlignFile_3.align"
578 obsFile4 = dirName + "/dummyAlignFile_4.align"
579
580 self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
581 self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
582 self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
583 self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
584
585 os.remove(expFile1)
586 os.remove(expFile2)
587 os.remove(expFile3)
588 os.remove(expFile4)
589 shutil.rmtree (dirName)
590
591
592 def test_createAlignFiles_dirName_specified_with_ended_slash( self ):
593 expFile1 = "dummyExpAlignFile.align_1"
594 expFile2 = "dummyExpAlignFile.align_2"
595 expFile3 = "dummyExpAlignFile.align_3"
596 expFile4 = "dummyExpAlignFile.align_4"
597
598 f1 = open(expFile1, "w")
599 iAlign1 = Align()
600 iAlign1.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
601 iAlign1.write(f1)
602 iAlign3 = Align()
603 iAlign3.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
604 iAlign3.write(f1)
605 iAlign6 = Align()
606 iAlign6.setFromString("chr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
607 iAlign6.write(f1)
608 iAlign7 = Align()
609 iAlign7.setFromString("chr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
610 iAlign7.write(f1)
611 f1.close()
612
613 f2 = open(expFile2, "w")
614 iAlign2 = Align()
615 iAlign2.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
616 iAlign2.write(f2)
617 iAlign5 = Align()
618 iAlign5.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
619 iAlign5.write(f2)
620 iAlign8 = Align()
621 iAlign8.setFromString("chr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
622 iAlign8.write(f2)
623 f2.close()
624
625 f3 = open(expFile3, "w")
626 iAlign4 = Align()
627 iAlign4.setFromString("chr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
628 iAlign4.write(f3)
629 f3.close()
630
631 f4 = open(expFile4, "w")
632 iAlign9 = Align()
633 iAlign9.setFromString("chr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
634 iAlign9.write(f4)
635 f4.close()
636
637 lAlignList = [[iAlign1, iAlign3, iAlign6, iAlign7], [iAlign2, iAlign5, iAlign8], [iAlign4], [iAlign9]]
638
639 dirName = "dummyAlignDir/"
640
641 AlignUtils.createAlignFiles(lAlignList, "dummyAlignFile", dirName)
642
643 obsFile1 = dirName + "dummyAlignFile_1.align"
644 obsFile2 = dirName + "dummyAlignFile_2.align"
645 obsFile3 = dirName + "dummyAlignFile_3.align"
646 obsFile4 = dirName + "dummyAlignFile_4.align"
647
648 self.assertTrue( FileUtils.are2FilesIdentical( expFile1, obsFile1 ) )
649 self.assertTrue( FileUtils.are2FilesIdentical( expFile2, obsFile2 ) )
650 self.assertTrue( FileUtils.are2FilesIdentical( expFile3, obsFile3 ) )
651 self.assertTrue( FileUtils.are2FilesIdentical( expFile4, obsFile4 ) )
652
653 os.remove(expFile1)
654 os.remove(expFile2)
655 os.remove(expFile3)
656 os.remove(expFile4)
657 shutil.rmtree (dirName)
658
659
660 def test_sortList( self ):
661 iAlign1 = Align( Range("qry1",3,80), Range("sbj1",3,80), 1e-20, 103, 97.3 ) # higher query start
662 iAlign2 = Align( Range("qry1",1,100), Range("sbj1",1,100), 1e-20, 113, 97.3 ) # higher score
663 iAlign3 = Align( Range("qry2",1,100), Range("sbj1",1,100), 1e-20, 103, 97.3 ) # different query
664 iAlign4 = Align( Range("qry1",1,100), Range("sbj1",1,100), 1e-20, 103, 97.3 ) # canonical
665 iAlign5 = Align( Range("qry1",1,100), Range("sbj2",1,100), 1e-20, 103, 97.3 ) # different subject
666 iAlign6 = Align( Range("qry1",201,300), Range("sbj1",100,1), 1e-20, 103, 97.3 ) # subject on reverse strand
667 iAlign7 = Align( Range("qry1",401,500), Range("sbj1",1,100), 1e-20, 103, 97.3 ) # higher query start
668 lAligns = [ iAlign1, iAlign2, iAlign3, iAlign4, iAlign5, iAlign6, iAlign7 ]
669 lExp = [iAlign4, iAlign2, iAlign1, iAlign6, iAlign7, iAlign5, iAlign3]
670 lObs = AlignUtils.sortList( lAligns )
671 self.assertEquals( lExp, lObs )
672
673
674 def test_isOverlapping( self ):
675 iAlign1 = Align( Range("chr1",1,100), Range("TE1",11,110), 1e-20, 90.2, 30 )
676 iAlign2 = Align( Range("chr1",51,80), Range("TE1",61,90), 1e-20, 90.2, 30 )
677 self.assertTrue( iAlign1.isOverlapping( iAlign2 ) )
678
679 iAlign1 = Align( Range("chr1",1,100), Range("TE1",11,110), 1e-20, 90.2, 30 )
680 iAlign2 = Align( Range("chr1",51,80), Range("TE1",161,190), 1e-20, 90.2, 30 )
681 self.assertFalse( iAlign1.isOverlapping( iAlign2 ) )
682
683
684 def test_mergeList( self ):
685 iAlign1 = Align( Range("chr1",81,120), Range("TE1",91,130), 1e-20, 90.2, 30 )
686 iAlign2 = Align( Range("chr2",51,80), Range("TE1",61,90), 1e-20, 90.2, 30 ) # different query
687 iAlign3 = Align( Range("chr1",1,100), Range("TE1",11,110), 1e-20, 90.2, 30 ) # to be merged with 1st line
688 iAlign4 = Align( Range("chr1",1,200), Range("TE2",11,210), 1e-20, 90.2, 30 ) # different subject
689 iAlign5 = Align( Range("chr1",1,100), Range("TE1",501,600), 1e-20, 90.2, 30 ) # non-overlapping subject
690 lAligns = [ iAlign1, iAlign2, iAlign3, iAlign4, iAlign5 ]
691
692 iAlign6 = Align( Range("chr1",1,120), Range("TE1",11,130), 1e-20, 90.2, 30 )
693 lExp = [ iAlign6, iAlign5, iAlign4, iAlign2 ]
694
695 lObs = AlignUtils.mergeList( lAligns )
696
697 self.assertEquals( lExp, lObs )
698
699
700 def test_mergeFile_empty( self ):
701 inFile = "dummyInFile.align"
702 inF = open( inFile, "w" )
703 inF.close()
704
705 expFile = "dummyExpFile.align"
706 expF = open( expFile, "w" )
707 expF.close()
708
709 obsFile = "dummyObsFile.align"
710 AlignUtils.mergeFile( inFile, obsFile )
711
712 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
713
714 for f in [ inFile, expFile, obsFile ]:
715 os.remove( f )
716
717
718 def test_mergeFile( self ):
719 iAlign = Align()
720
721 inFile = "dummyInFile.align"
722 inF = open( inFile, "w" )
723 iAlign.setFromString( "chr1\t81\t120\tTE1\t91\t130\t1e-20\t30\t90.2\n" )
724 iAlign.write( inF )
725 iAlign.setFromString( "chr2\t51\t80\tTE1\t61\t90\t1e-20\t30\t90.2\n" ) # different query
726 iAlign.write( inF )
727 iAlign.setFromString( "chr1\t1\t100\tTE1\t11\t110\t1e-20\t30\t90.2\n" ) # to be merged with 1st line
728 iAlign.write( inF )
729 iAlign.setFromString( "chr1\t1\t200\tTE2\t11\t210\t1e-20\t30\t90.2\n" ) # different subject
730 iAlign.write( inF )
731 inF.close()
732
733 expFile = "dummyExpFile.align"
734 expF = open( expFile, "w" )
735 iAlign.setFromString( "chr1\t1\t120\tTE1\t11\t130\t1e-20\t30\t90.2\n" )
736 iAlign.write( expF )
737 iAlign.setFromString( "chr1\t1\t200\tTE2\t11\t210\t1e-20\t30\t90.2\n" )
738 iAlign.write( expF )
739 iAlign.setFromString( "chr2\t51\t80\tTE1\t61\t90\t1e-20\t30\t90.2\n" )
740 iAlign.write( expF )
741 expF.close()
742
743 obsFile = "dummyObsFile.align"
744 AlignUtils.mergeFile( inFile, obsFile )
745
746 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
747
748 for f in [ inFile, expFile, obsFile ]:
749 os.remove( f )
750
751
752 def test_updateScoresInFile( self ):
753 iAlign = Align()
754
755 inFile = "dummyInFile.align"
756 inHandler = open( inFile, "w" )
757 iAlign.setFromString( "query1\t1\t100\tsubject1\t1\t95\t1e-180\t230\t90.2\n" )
758 iAlign.write( inHandler )
759 inHandler.close()
760
761 expFile = "dummyExpFile.align"
762 expHandler = open( expFile, "w" )
763 iAlign.setFromString( "query1\t1\t100\tsubject1\t1\t95\t1e-180\t%i\t90.2\n" % ( ( 100 - 1 + 1 ) * 90.2 / 100.0 ) )
764 iAlign.write( expHandler )
765 expHandler.close()
766
767 obsFile = "dummyObsFile.align"
768 AlignUtils.updateScoresInFile( inFile, obsFile )
769
770 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
771
772 for f in [ inFile, expFile, obsFile ]:
773 os.remove( f )
774
775
776 if __name__ == "__main__":
777 unittest.main()