Mercurial > repos > yufei-luo > s_mart

comparison commons/core/coord/test/Test_Align.py @ 6:769e306b7933

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
parents
children
comparison
equal deleted inserted replaced
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 import os
34 import time
35 from commons.core.coord.Align import Align
36 from commons.core.coord.Map import Map
37 from commons.core.utils.FileUtils import FileUtils
38 from commons.core.coord.Range import Range
39
40
41 class Test_Align( unittest.TestCase ):
42
43 def setUp(self):
44 self._align = Align()
45 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
46
47 def tearDown(self):
48 self._align = None
49
50 def test_isEmpty_True(self):
51 alignInstance = Align()
52
53 self.assertTrue(alignInstance.isEmpty())
54
55 def test_isEmpty_True_query_is_empty(self):
56 alignInstance = Align()
57 line = "\t-1\t-1\tTE2\t3\t10\t1e-20\t30\t90.2\n"
58 alignInstance.setFromString(line)
59
60 self.assertTrue(alignInstance.isEmpty())
61
62 def test_isEmpty_True_subject_is_empty(self):
63 alignInstance = Align()
64 line = "chr1\t2\t20\t\t-1\t-1\t1e-20\t30\t90.2\n"
65 alignInstance.setFromString(line)
66
67 self.assertTrue(alignInstance.isEmpty())
68
69 def test_isEmpty_False(self):
70 alignInstance = Align()
71 line = "chr1\t2\t20\tTE2\t3\t10\t1e-20\t30\t90.2\n"
72 alignInstance.setFromString(line)
73
74 self.assertFalse(alignInstance.isEmpty())
75
76 def test_read(self):
77 line = "chr2\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n"
78 expReturn = 1
79
80 dummyMockAlignFile = "dummyMockAlignFile"
81 mockAlignFileHandle = open(dummyMockAlignFile, "w")
82 mockAlignFileHandle.write(line)
83 mockAlignFileHandle.close()
84
85 expAlignInstance = Align()
86 expAlignInstance.setFromString(line)
87
88 mockAlignFileHandle = open(dummyMockAlignFile, "r")
89 obsAlignInstance = Align()
90 obsReturn = obsAlignInstance.read(mockAlignFileHandle)
91
92 mockAlignFileHandle.close()
93 os.remove(dummyMockAlignFile)
94
95 self.assertEquals(expAlignInstance, obsAlignInstance)
96 self.assertEquals(expReturn, obsReturn)
97
98 def test_read_empty_file(self):
99 expReturn = 0
100
101 dummyMockAlignFile = "dummyMockAlignFile"
102 mockAlignFileHandle = open(dummyMockAlignFile, "w")
103 mockAlignFileHandle.close()
104
105 mockAlignFileHandle = open(dummyMockAlignFile, "r")
106 obsAlignInstance = Align()
107 obsReturn = obsAlignInstance.read(mockAlignFileHandle)
108 os.remove(dummyMockAlignFile)
109
110 self.assertEquals(expReturn, obsReturn)
111
112 def test_write (self):
113 expAlignFile = "expMockAlignFile"
114 expAlignFileHandle = open(expAlignFile, "w")
115 expLine = "chr1\t1\t10\tTE2\t3\t10\t0\t30\t90.200000\n"
116 expAlignFileHandle.write(expLine)
117 expAlignFileHandle.close()
118
119 obsAlignFile = "obsAlignFile"
120 obsAlignFileHandle = open(obsAlignFile, "w")
121 obsAlignInstance = Align()
122 obsAlignTuple = ("chr1", 1, 10, "TE2", 3, 10, 0.0, 30, 90.2)
123 obsAlignInstance.setFromTuple(obsAlignTuple)
124 obsAlignInstance.write(obsAlignFileHandle)
125 obsAlignFileHandle.close()
126
127 self.assertTrue( FileUtils.are2FilesIdentical( expAlignFile, obsAlignFile ) )
128 os.remove(expAlignFile)
129 os.remove(obsAlignFile)
130
131 def test_merge (self):
132 alignInstanceChr1 = Align()
133 alignInstanceChr2 = Align()
134
135 line1 = "chr1\t1\t10\tTE2\t3\t10\t1e-20\t30\t90.2\n"
136 line2 = "chr2\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n"
137
138 alignInstanceChr1.setFromString(line1)
139 alignInstanceChr2.setFromString(line2)
140
141 expResult = None
142 obsResult = alignInstanceChr1.merge(alignInstanceChr2)
143
144 self.assertEquals(expResult, obsResult)
145
146 line1 = "chr1\t1\t10\tTE2\t3\t10\t1e-20\t30\t90.2\n"
147 line2 = "chr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n"
148
149 alignInstanceTE2 = Align()
150 alignInstanceTE3 = Align()
151
152 alignInstanceTE2.setFromString(line1)
153 alignInstanceTE3.setFromString(line2)
154
155 expResult = None
156 obsResult = alignInstanceTE2.merge(alignInstanceTE3)
157
158 self.assertEquals(expResult, obsResult)
159
160 def test_merge_plus_strand1 (self):
161 alignInstance1 = Align()
162 alignInstance2 = Align()
163
164 line1 = "chr1\t2\t20\tTE2\t3\t10\t1e-20\t30\t90.2\n"
165 line2 = "chr1\t1\t10\tTE2\t1\t9\t1e-20\t30\t90.2\n"
166
167 alignInstance1.setFromString(line1)
168 alignInstance2.setFromString(line2)
169
170 expLine = "chr1\t1\t20\tTE2\t1\t10\t1e-20\t30\t90.2\n"
171 expAlign = Align()
172 expAlign.setFromString(expLine)
173
174 alignInstance1.merge(alignInstance2)
175 obsAlign = alignInstance1
176
177 self.assertEquals(expAlign, obsAlign)
178
179 def test_merge_plus_strand2 (self ):
180 alignInstance1 = Align()
181 alignInstance2 = Align()
182
183 line1 = "chr1\t2\t20\tTE2\t3\t10\t1e-20\t30\t90.2\n"
184 line2 = "chr1\t4\t30\tTE2\t4\t12\t1e-20\t30\t90.2\n"
185
186 alignInstance1.setFromString(line1)
187 alignInstance2.setFromString(line2)
188
189 expLine = "chr1\t2\t30\tTE2\t3\t12\t1e-20\t30\t90.2\n"
190 expAlign = Align()
191 expAlign.setFromString(expLine)
192
193 alignInstance1.merge(alignInstance2)
194 obsAlign = alignInstance1
195
196 self.assertEquals(expAlign, obsAlign)
197
198 def test_merge_plus_strand3 (self ):
199 alignInstance1 = Align()
200 alignInstance2 = Align()
201
202 line1 = "chr1\t2\t10\tTE2\t3\t10\t1e-20\t30\t90.2\n"
203 line2 = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
204
205 alignInstance1.setFromString(line1)
206 alignInstance2.setFromString(line2)
207
208 expLine = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
209 expAlign = Align()
210 expAlign.setFromString(expLine)
211
212 alignInstance1.merge(alignInstance2)
213 obsAlign = alignInstance1
214
215 self.assertEquals(expAlign, obsAlign)
216
217 def test_merge_plus_strand4 (self ):
218 alignInstance1 = Align()
219 alignInstance2 = Align()
220
221 line1 = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
222 line2 = "chr1\t2\t10\tTE2\t2\t10\t1e-20\t30\t90.2\n"
223
224 alignInstance1.setFromString(line1)
225 alignInstance2.setFromString(line2)
226
227 expLine = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
228 expAlign = Align()
229 expAlign.setFromString(expLine)
230
231 alignInstance1.merge(alignInstance2)
232 obsAlign = alignInstance1
233
234 self.assertEquals(expAlign, obsAlign)
235
236 def test_merge__neg_strand1 (self):
237
238 rangeQuery1 = Range("chr1", 20, 2); rangeSubject1 = Range("TE2", 10, 3)
239 rangeQuery2 = Range("chr1", 1, 10); rangeSubject2 = Range("TE2", 1, 9)
240
241 alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
242 alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
243
244 expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 10, 1)
245 expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
246
247 alignInstance1.merge(alignInstance2)
248 obsAlign = alignInstance1
249
250 self.assertEquals(expAlign, obsAlign)
251
252 def test_merge__neg_strand2 (self):
253 rangeQuery1 = Range("chr1", 20, 2); rangeSubject1 = Range("TE2", 10, 3)
254 rangeQuery2 = Range("chr1", 4, 30); rangeSubject2 = Range("TE2", 4, 12)
255
256 alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
257 alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
258
259 expRangeQuery = Range("chr1", 30, 2); expRangeSubject = Range("TE2", 12, 3)
260 expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
261
262 alignInstance1.merge(alignInstance2)
263 obsAlign = alignInstance1
264
265 self.assertEquals(expAlign, obsAlign)
266
267 def test_merge_neg_strand3 (self ):
268 rangeQuery1 = Range("chr1", 10, 2); rangeSubject1 = Range("TE2", 10, 3)
269 rangeQuery2 = Range("chr1", 1, 20); rangeSubject2 = Range("TE2", 1, 12)
270
271 alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
272 alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
273
274 expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 12, 1)
275 expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
276
277 alignInstance1.merge(alignInstance2)
278 obsAlign = alignInstance1
279
280 self.assertEquals(expAlign, obsAlign)
281
282 def test_merge_neg_strand4 (self ):
283 rangeQuery1 = Range("chr1", 20, 1); rangeSubject1 = Range("TE2", 12, 1)
284 rangeQuery2 = Range("chr1", 2, 10); rangeSubject2 = Range("TE2", 2, 10)
285
286 alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
287 alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
288
289 expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 12, 1)
290 expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
291
292 alignInstance1.merge(alignInstance2)
293 obsAlign = alignInstance1
294
295 self.assertEquals(expAlign, obsAlign)
296
297 def test_merge_id_score_identity_eValue (self):
298 rangeQuery1 = Range("chr1", 20, 1); rangeSubject1 = Range("TE2", 12, 1)
299 rangeQuery2 = Range("chr1", 2, 10); rangeSubject2 = Range("TE2", 2, 10)
300
301 alignInstance1 = Align(rangeQuery1, rangeSubject1, 0.05, 20, 90.2)
302 alignInstance1.id = 1
303 alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.3)
304 alignInstance2.id = 2
305
306 expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 12, 1)
307 expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.3)
308 expAlign.id = 1
309
310 alignInstance1.merge(alignInstance2)
311 obsAlign = alignInstance1
312
313 self.assertEquals(expAlign, obsAlign)
314 self.assertEquals(expAlign.id, obsAlign.id)
315
316 def test_setFromTuple_QryRev(self):
317 self._align.setFromTuple( ( "qry1", 100, 1, "sbj1", 201, 300, 0.0, 135, 97.2 ) )
318 self.assertEqual( self._align.range_query.seqname, "qry1" )
319 self.assertEqual( self._align.range_query.start, 1 )
320 self.assertEqual( self._align.range_query.end, 100 )
321 self.assertEqual( self._align.range_subject.seqname, "sbj1" )
322 self.assertEqual( self._align.range_subject.start, 300 )
323 self.assertEqual( self._align.range_subject.end, 201 )
324 self.assertEqual( self._align.e_value, 0.0 )
325 self.assertEqual( self._align.score, 135 )
326 self.assertEquals( self._align.identity, 97.2 )
327
328 def test_setFromTuple_identityAsFloat(self):
329 self._align.setFromTuple( ( "qry1", "301", "600", "sbj1", "1", "300", "0.0", "135", 0.0) )
330 self.assertEqual( self._align.range_query.seqname, "qry1" )
331 self.assertEqual( self._align.range_query.start, 301 )
332 self.assertEqual( self._align.range_query.end, 600 )
333 self.assertEqual( self._align.range_subject.seqname, "sbj1" )
334 self.assertEqual( self._align.range_subject.start, 1 )
335 self.assertEqual( self._align.range_subject.end, 300 )
336 self.assertEqual( self._align.e_value, float("0.0") )
337 self.assertEqual( self._align.score, float("135") )
338 self.assertEquals( self._align.identity, 0.0 )
339
340 def test_setFromString(self):
341 line = "chr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n"
342 self._align.setFromString( line )
343 self.assertEqual( self._align.range_query.seqname, "chr1" )
344 self.assertEqual( self._align.range_query.start, 1 )
345 self.assertEqual( self._align.range_query.end, 10 )
346 self.assertEqual( self._align.range_subject.seqname, "TE2" )
347 self.assertEqual( self._align.range_subject.start, 11 )
348 self.assertEqual( self._align.range_subject.end, 17 )
349 self.assertEqual( self._align.e_value, float("1e-20") )
350 self.assertEqual( self._align.score, float("30") )
351 self.assertEquals( float(self._align.identity), float("90.2") )
352
353 def test__eq__(self):
354 self._align.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
355 o = Align()
356 o.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
357 self.assertEqual( self._align, o )
358 o.setFromString( "chromosome1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
359 self.assertNotEqual( self._align, o )
360 o.setFromString( "chr1\t1\t6\ttranspElem2\t11\t16\t1e-20\t30\t90.2\n" )
361 self.assertNotEqual( self._align, o )
362 o.setFromString( "chr1\t100\t600\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
363 self.assertNotEqual( self._align, o )
364 o.setFromString( "chr1\t1\t6\tTE2\t1100\t1600\t1e-20\t30\t90.2\n" )
365 self.assertNotEqual( self._align, o )
366 o.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30000\t90.2\n" )
367 self.assertNotEqual( self._align, o )
368
369 def test_getSubjectAsMapOfQuery_direct(self):
370 exp = Map( name="TE2", seqname="chr1", start=1, end=6 )
371 self._align.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
372 obs = self._align.getSubjectAsMapOfQuery()
373 self.assertEqual( obs, exp )
374
375 def test_getSubjectAsMapOfQuery_reverse(self):
376 exp = Map( name="TE2", seqname="chr1", start=6, end=1 )
377 self._align.setFromString( "chr1\t1\t6\tTE2\t16\t11\t1e-20\t30\t90.2\n" )
378 obs = self._align.getSubjectAsMapOfQuery()
379 self.assertEqual( obs, exp )
380
381 def test_writeSubjectAsMapOfQuery( self ):
382 self._align.setFromTuple( ( "chr3", "250", "151", "seq5", "1", "100", "1e-32", "147", "87.9" ) )
383 expFile = "dummyExpFile_%s" % ( self._uniqId )
384 expFileHandler = open( expFile, "w" )
385 expFileHandler.write( "seq5\tchr3\t250\t151\n" )
386 expFileHandler.close()
387 obsFile = "dummyObsFile_%s" % ( self._uniqId )
388 obsFileHandler = open( obsFile, "w" )
389 self._align.writeSubjectAsMapOfQuery( obsFileHandler )
390 obsFileHandler.close()
391 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
392 for f in [ expFile, obsFile ]:
393 if os.path.exists( f ):
394 os.remove( f )
395
396 def test_areQrySbjOnOppositeStrands(self):
397 self._align.setFromTuple( ( "qry1", "1", "100", "sbj1", "1", "100", "0.0", "135", "95.7" ) )
398 obs = self._align.areQrySbjOnOppositeStrands()
399 self.assertFalse( obs )
400 self._align.setFromTuple( ( "qry1", "600", "301", "sbj1", "1", "300", "0.0", "135", "95.7" ) )
401 obs = self._align.areQrySbjOnOppositeStrands()
402 self.assertTrue( obs )
403
404 def test_reverse(self):
405 line = "chr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2"
406 expLine = "chr1\t10\t1\tTE2\t17\t11\t1e-20\t30\t90.200000"
407
408 obsAlignInstance = Align()
409 obsAlignInstance.setFromString(line)
410 obsAlignInstance.reverse()
411 obsLine = obsAlignInstance.toString()
412
413 self.assertEquals(expLine, obsLine)
414
415 def test_getMapsOfQueryAndSubject(self):
416 self._align.setFromTuple( ( "qry1", "1", "100", "sbj1", "1", "100", "0.0", "135", "95.7" ) )
417
418 expMapQuery = Map()
419 expMapQuery.setFromTuple( ( "repet", "qry1", "1", "100" ) )
420 expMapSubject = Map()
421 expMapSubject.setFromTuple( ( "repet", "sbj1", "1", "100" ) )
422
423 obsMapQuery, obsMapSubject = self._align.getMapsOfQueryAndSubject()
424
425 self.assertEqual( expMapQuery, obsMapQuery )
426 self.assertEqual( expMapSubject, obsMapSubject )
427
428 def test_getBin_bin_level_9(self):
429 tuple = ("chr1","190000000","390000000","TE2","11","17","1e-20","30","90.2")
430 self._align.setFromTuple(tuple)
431 expRes = 100000000.0
432 obsRes = self._align.getBin()
433 self.assertEquals(expRes, obsRes)
434
435 def test_getBin_bin_level_8(self):
436 tuple = ("chr1","19000000","39000000","TE2","11","17","1e-20","30","90.2")
437 self._align.setFromTuple(tuple)
438 expRes = 100000000.0
439 obsRes = self._align.getBin()
440 self.assertEquals(expRes, obsRes)
441
442 def test_getBin_bin_level_7(self):
443 tuple = ("chr1","1900000","3900000","TE2","11","17","1e-20","30","90.2")
444 self._align.setFromTuple(tuple)
445 expRes = 10000000.0
446 obsRes = self._align.getBin()
447 self.assertEquals(expRes, obsRes)
448
449 def test_getBin_bin_level_6(self):
450 tuple = ("chr1","190000","390000","TE2","11","17","1e-20","30","90.2")
451 self._align.setFromTuple(tuple)
452 obsRes = self._align.getBin()
453 expRes = 1000000.0
454 self.assertEquals(expRes, obsRes)
455
456 def test_getBin_bin_level_5(self):
457 tuple = ("chr1","19000","39000","TE2","11","17","1e-20","30","90.2")
458 self._align.setFromTuple(tuple)
459 obsRes = self._align.getBin()
460 expRes = 100000.0
461 self.assertEquals(expRes, obsRes)
462
463 def test_getBin_bin_level_4(self):
464 tuple = ("chr1","1900","3900","TE2","11","17","1e-20","30","90.2")
465 self._align.setFromTuple(tuple)
466 obsRes = self._align.getBin()
467 expRes = 10000.0
468 self.assertEquals(expRes, obsRes)
469
470 def test_getBin_bin_level_3(self):
471 tuple = ("chr1","190","390","TE2","11","17","1e-20","30","90.2")
472 self._align.setFromTuple(tuple)
473 obsRes = self._align.getBin()
474 expRes = 1000.0
475 self.assertEquals(expRes, obsRes)
476
477 def test_getBin_bin_level_2(self):
478 tuple = ("chr1","19","39","TE2","11","17","1e-20","30","90.2")
479 self._align.setFromTuple(tuple)
480 obsRes = self._align.getBin()
481 expRes = 1000.0
482 self.assertEquals(expRes, obsRes)
483
484 def test_getBin_bin_level_1(self):
485 tuple = ("chr1","1","3","TE2","11","17","1e-20","30","90.2")
486 self._align.setFromTuple(tuple)
487 obsRes = self._align.getBin()
488 expRes = 1000.0
489 self.assertEquals(expRes, obsRes)
490
491
492 def test_switchQuerySubject_directS( self ):
493 tuple = ("chr1","1","3","TE2","11","17","1e-20","30","90.2")
494 self._align.setFromTuple( tuple )
495 exp = Align( Range("TE2","11","17"), Range("chr1","1","3"), "1e-20", "30", "90.2" )
496 self._align.switchQuerySubject()
497 self.assertEquals( exp, self._align )
498
499
500 def test_switchQuerySubject_reverseS( self ):
501 tuple = ("chr1","1","3","TE2","17","11","1e-20","30","90.2")
502 self._align.setFromTuple( tuple )
503 exp = Align( Range("TE2","11","17"), Range("chr1","3","1"), "1e-20", "30", "90.2" )
504 self._align.switchQuerySubject()
505 self.assertEquals( exp, self._align )
506
507
508 def test_toStringAsGff( self ):
509 self._align.setFromString( "chr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t85.2\n" )
510 exp = "chr1\tREPET\tmatch\t1\t10\t1e-20\t+\t.\tID=23;Target=TE3 11 17"
511 obs = self._align.toStringAsGff( ID="23" )
512 self.assertEqual( obs, exp )
513
514
515 test_suite = unittest.TestSuite()
516 test_suite.addTest( unittest.makeSuite( Test_Align ) )
517 if __name__ == "__main__":
518 unittest.TextTestRunner(verbosity=2).run( test_suite )