Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/seq/test/Test_AlignedBioseqDB.py @ 0:e0f8dcca02ed
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 |
| parents | |
| children |
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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 sys | |
| 34 import os | |
| 35 import time | |
| 36 from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB | |
| 37 from commons.core.seq.Bioseq import Bioseq | |
| 38 from commons.core.utils.FileUtils import FileUtils | |
| 39 from commons.core.coord.Align import Align | |
| 40 from commons.core.coord.Range import Range | |
| 41 from commons.core.stat.Stat import Stat | |
| 42 | |
| 43 | |
| 44 class Test_AlignedBioseqDB( unittest.TestCase ): | |
| 45 | |
| 46 def setUp( self ): | |
| 47 self._i = AlignedBioseqDB() | |
| 48 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) | |
| 49 | |
| 50 | |
| 51 def tearDown( self ): | |
| 52 self._i = None | |
| 53 self._uniqId = "" | |
| 54 | |
| 55 | |
| 56 def test_getLength(self): | |
| 57 iAlignedBioseqDB = AlignedBioseqDB() | |
| 58 | |
| 59 iBioseq1 = Bioseq( "seq1", "AGCGGACGATGCAGCATGCGAATGACGAT" ) | |
| 60 iAlignedBioseqDB.setData([iBioseq1]) | |
| 61 | |
| 62 expLenght = 29 | |
| 63 obsLength = iAlignedBioseqDB.getLength() | |
| 64 | |
| 65 self.assertEquals(expLenght, obsLength) | |
| 66 | |
| 67 | |
| 68 def test_getSeqLengthWithoutGaps( self ): | |
| 69 iAlignedBioseqDB = AlignedBioseqDB() | |
| 70 iAlignedBioseqDB.add( Bioseq( "seq3", | |
| 71 "AGCG-GACGATGCAGCAT--GCGAATGA--CGAT" ) ) | |
| 72 expLenght = 29 | |
| 73 obsLength = iAlignedBioseqDB.getSeqLengthWithoutGaps( "seq3" ) | |
| 74 | |
| 75 self.assertEquals(expLenght, obsLength) | |
| 76 | |
| 77 | |
| 78 def test_getListOccPerSite(self): | |
| 79 iBioseq1 = Bioseq( "seq1", "AGAAA") | |
| 80 iBioseq2 = Bioseq( "seq2", "TCAAG") | |
| 81 iBioseq3 = Bioseq( "seq3", "GGTAC") | |
| 82 iBioseq4 = Bioseq( "seq4", "CCTTA") | |
| 83 | |
| 84 iAlignedBioseqDB = AlignedBioseqDB() | |
| 85 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 86 | |
| 87 expList = [ | |
| 88 | |
| 89 {"A":1, "T":1, "G":1, "C":1}, | |
| 90 | |
| 91 {"G":2, "C":2}, | |
| 92 | |
| 93 {"A":2, "T":2 }, | |
| 94 | |
| 95 {"A":3, "T":1 }, | |
| 96 | |
| 97 {"A":2, "G":1, "C":1} | |
| 98 ] | |
| 99 | |
| 100 obsList = iAlignedBioseqDB.getListOccPerSite() | |
| 101 | |
| 102 self.assertEquals(expList, obsList) | |
| 103 | |
| 104 | |
| 105 def test_getListOccPerSite_with_none_sequence(self): | |
| 106 iBioseq1 = Bioseq( "seq1", "AGAAA") | |
| 107 iBioseq2 = Bioseq( "seq2", "TCAAG") | |
| 108 iBioseq3 = Bioseq( "seq3", "GGTAC") | |
| 109 iBioseq4 = Bioseq( "seq4", None) | |
| 110 iBioseq5 = Bioseq( "seq5", "CCTTA") | |
| 111 | |
| 112 iAlignedBioseqDB = AlignedBioseqDB() | |
| 113 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4, iBioseq5]) | |
| 114 | |
| 115 expList = [ | |
| 116 {"A":1, "T":1, "G":1}, | |
| 117 {"G":2, "C":1}, | |
| 118 {"A":2, "T":1 }, | |
| 119 {"A":3}, | |
| 120 {"A":1, "G":1, "C":1}, | |
| 121 ] | |
| 122 | |
| 123 obsList = iAlignedBioseqDB.getListOccPerSite() | |
| 124 | |
| 125 self.assertEquals(expList, obsList) | |
| 126 | |
| 127 | |
| 128 def test_getListOccPerSite_on_three_sequence(self): | |
| 129 iBioseq1 = Bioseq( "seq1", "AGAAA") | |
| 130 iBioseq2 = Bioseq( "seq2", "TCAAG") | |
| 131 iBioseq3 = Bioseq( "seq3", "GGTAC") | |
| 132 | |
| 133 iAlignedBioseqDB = AlignedBioseqDB() | |
| 134 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) | |
| 135 | |
| 136 expList = [ | |
| 137 {"A":1, "T":1, "G":1}, | |
| 138 {"G":2, "C":1}, | |
| 139 {"A":2, "T":1 }, | |
| 140 {"A":3}, | |
| 141 {"A":1, "G":1, "C":1}, | |
| 142 ] | |
| 143 | |
| 144 obsList = iAlignedBioseqDB.getListOccPerSite() | |
| 145 | |
| 146 self.assertEquals(expList, obsList) | |
| 147 | |
| 148 | |
| 149 def test_getConsensus_with_minNbNt_greater_than_nbInSeq(self): | |
| 150 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 151 iBioseq2 = Bioseq("seq2", "TGCA") | |
| 152 iBioseq3 = Bioseq("seq3", "TACT") | |
| 153 | |
| 154 iAlignedBioseqDB = AlignedBioseqDB() | |
| 155 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) | |
| 156 | |
| 157 expConsensus = Bioseq("consensus= length=4 nbAlign=3","TGCT") | |
| 158 obsConsensus = iAlignedBioseqDB.getConsensus(5) | |
| 159 | |
| 160 self.assertEquals(expConsensus, obsConsensus) | |
| 161 | |
| 162 | |
| 163 def test_getConsensus_with_minPropNt_greater_than_1(self): | |
| 164 isSysExitRaised = False | |
| 165 | |
| 166 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 167 iBioseq2 = Bioseq("seq2", "TGCA") | |
| 168 iBioseq3 = Bioseq("seq3", "TACT") | |
| 169 | |
| 170 iAlignedBioseqDB = AlignedBioseqDB() | |
| 171 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) | |
| 172 | |
| 173 expFileName = "expFileName" | |
| 174 expFileHandler = open(expFileName,"w") | |
| 175 expMessage = "ERROR: minPropNt=2.00 should be a proportion (below 1.0)\n" | |
| 176 expFileHandler.write(expMessage) | |
| 177 expFileHandler.close() | |
| 178 | |
| 179 obsFileName = "obsFileName" | |
| 180 obsFileHandler = open(obsFileName,"w") | |
| 181 | |
| 182 stdoutRef = sys.stdout | |
| 183 sys.stdout = obsFileHandler | |
| 184 | |
| 185 try: | |
| 186 iAlignedBioseqDB.getConsensus(2,2) | |
| 187 except SystemExit: | |
| 188 isSysExitRaised = True | |
| 189 | |
| 190 obsFileHandler.close() | |
| 191 expFileHandler.close() | |
| 192 | |
| 193 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
| 194 self.assertTrue( isSysExitRaised ) | |
| 195 | |
| 196 sys.stdout = stdoutRef | |
| 197 os.remove ( obsFileName ) | |
| 198 os.remove ( expFileName ) | |
| 199 stdoutRef = sys.stdout | |
| 200 | |
| 201 | |
| 202 def test_getConsensus_with_AlignBioseqInstance_size_1(self): | |
| 203 isSysExitRaised = False | |
| 204 | |
| 205 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 206 | |
| 207 iAlignedBioseqDB = AlignedBioseqDB() | |
| 208 iAlignedBioseqDB.setData([iBioseq1]) | |
| 209 | |
| 210 expFileName = "expFileName" | |
| 211 expFileHandler = open(expFileName,"w") | |
| 212 expMessage = "ERROR: can't make a consensus with less than 2 sequences\n" | |
| 213 expFileHandler.write(expMessage) | |
| 214 expFileHandler.close() | |
| 215 | |
| 216 obsFileName = "obsFileName" | |
| 217 obsFileHandler = open(obsFileName,"w") | |
| 218 | |
| 219 stdoutRef = sys.stdout | |
| 220 sys.stdout = obsFileHandler | |
| 221 | |
| 222 try: | |
| 223 iAlignedBioseqDB.getConsensus(4) | |
| 224 except SystemExit: | |
| 225 isSysExitRaised = True | |
| 226 | |
| 227 obsFileHandler.close() | |
| 228 expFileHandler.close() | |
| 229 | |
| 230 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
| 231 self.assertTrue( isSysExitRaised ) | |
| 232 | |
| 233 sys.stdout = stdoutRef | |
| 234 os.remove ( obsFileName ) | |
| 235 os.remove ( expFileName ) | |
| 236 stdoutRef = sys.stdout | |
| 237 | |
| 238 | |
| 239 def test_getConsensus_with_gap_assertion_on_warning_msg(self): | |
| 240 iBioseq1 = Bioseq("seq1", "A-GA-T") | |
| 241 iBioseq2 = Bioseq("seq2", "T-GC-A") | |
| 242 iBioseq3 = Bioseq("seq3", "T-AC-T") | |
| 243 | |
| 244 iAlignedBioseqDB = AlignedBioseqDB() | |
| 245 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) | |
| 246 | |
| 247 expFileName = "expFileName" | |
| 248 expFileHandler = open(expFileName,"w") | |
| 249 expMessage = "WARNING: 2 sites were removed (33.33%)\n" | |
| 250 expFileHandler.write(expMessage) | |
| 251 expFileHandler.close() | |
| 252 | |
| 253 obsFileName = "obsFileName" | |
| 254 obsFileHandler = open(obsFileName,"w") | |
| 255 | |
| 256 stdoutRef = sys.stdout | |
| 257 sys.stdout = obsFileHandler | |
| 258 | |
| 259 iAlignedBioseqDB.getConsensus(2) | |
| 260 | |
| 261 obsFileHandler.close() | |
| 262 expFileHandler.close() | |
| 263 | |
| 264 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
| 265 | |
| 266 sys.stdout = stdoutRef | |
| 267 os.remove ( obsFileName ) | |
| 268 os.remove ( expFileName ) | |
| 269 stdoutRef = sys.stdout | |
| 270 | |
| 271 | |
| 272 def test_getConsensus_with_gap_assertion_on_result(self): | |
| 273 iBioseq1 = Bioseq("seq1", "A-GA-T") | |
| 274 iBioseq2 = Bioseq("seq2", "T-GC-A") | |
| 275 iBioseq3 = Bioseq("seq3", "T-AC-T") | |
| 276 | |
| 277 iAlignedBioseqDB = AlignedBioseqDB() | |
| 278 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) | |
| 279 | |
| 280 expConsensus = Bioseq("consensus= length=4 nbAlign=3","TGCT") | |
| 281 obsConsensus = iAlignedBioseqDB.getConsensus(2) | |
| 282 | |
| 283 self.assertEquals(expConsensus, obsConsensus) | |
| 284 | |
| 285 | |
| 286 def test_getConsensus_with_gaps_and_no_consensus_built_assertion_on_result(self): | |
| 287 iBioseq1 = Bioseq("seq1", "A--A-T") | |
| 288 iBioseq2 = Bioseq("seq2", "----A-") | |
| 289 iBioseq3 = Bioseq("seq3", "--A---") | |
| 290 | |
| 291 iAlignedBioseqDB = AlignedBioseqDB() | |
| 292 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) | |
| 293 | |
| 294 expConsensus = None | |
| 295 obsConsensus = iAlignedBioseqDB.getConsensus(2) | |
| 296 self.assertEquals(expConsensus, obsConsensus) | |
| 297 | |
| 298 | |
| 299 def test_getConsensus_with_gaps_and_no_consensus_built_assertion_on_warning_messages(self): | |
| 300 iBioseq1 = Bioseq("seq1", "A--A-T") | |
| 301 iBioseq2 = Bioseq("seq2", "----A-") | |
| 302 iBioseq3 = Bioseq("seq3", "--A---") | |
| 303 | |
| 304 iAlignedBioseqDB = AlignedBioseqDB() | |
| 305 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3]) | |
| 306 | |
| 307 expFileName = "expFileName" | |
| 308 expFileHandler = open(expFileName,"w") | |
| 309 expMessage1 = "WARNING: 1 site was removed (16.67%)\n" | |
| 310 expMessage2 = "WARNING: no consensus can be built (no sequence left)\n" | |
| 311 expFileHandler.write(expMessage1) | |
| 312 expFileHandler.write(expMessage2) | |
| 313 expFileHandler.close() | |
| 314 | |
| 315 obsFileName = "obsFileName" | |
| 316 obsFileHandler = open(obsFileName,"w") | |
| 317 | |
| 318 stdoutRef = sys.stdout | |
| 319 sys.stdout = obsFileHandler | |
| 320 | |
| 321 iAlignedBioseqDB.getConsensus(2) | |
| 322 | |
| 323 obsFileHandler.close() | |
| 324 expFileHandler.close() | |
| 325 | |
| 326 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
| 327 | |
| 328 sys.stdout = stdoutRef | |
| 329 os.remove ( obsFileName ) | |
| 330 os.remove ( expFileName ) | |
| 331 stdoutRef = sys.stdout | |
| 332 | |
| 333 | |
| 334 def test_getConsensus_with_unacceptable_N_proportion_assertion_on_result(self): | |
| 335 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 336 iBioseq2 = Bioseq("seq2", "CCCA") | |
| 337 iBioseq3 = Bioseq("seq3", "TTCT") | |
| 338 iBioseq4 = Bioseq("seq4", "TTAT") | |
| 339 | |
| 340 iAlignedBioseqDB = AlignedBioseqDB() | |
| 341 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 342 | |
| 343 expConsensus = None | |
| 344 obsConsensus = iAlignedBioseqDB.getConsensus(2,0.75) | |
| 345 | |
| 346 self.assertEquals(expConsensus, obsConsensus) | |
| 347 | |
| 348 | |
| 349 def test_getConsensus_with_unacceptable_N_proportion_assertion_on_warning_msg(self): | |
| 350 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 351 iBioseq2 = Bioseq("seq2", "CCCA") | |
| 352 iBioseq3 = Bioseq("seq3", "TTCT") | |
| 353 iBioseq4 = Bioseq("seq4", "TTAT") | |
| 354 | |
| 355 iAlignedBioseqDB = AlignedBioseqDB() | |
| 356 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 357 | |
| 358 expFileName = "expFileName" | |
| 359 expFileHandler = open(expFileName,"w") | |
| 360 expMessage = "WARNING: no consensus can be built (75% of N's >= 40%)\n" | |
| 361 expFileHandler.write(expMessage) | |
| 362 expFileHandler.close() | |
| 363 | |
| 364 obsFileName = "obsFileName" | |
| 365 obsFileHandler = open(obsFileName,"w") | |
| 366 | |
| 367 stdoutRef = sys.stdout | |
| 368 sys.stdout = obsFileHandler | |
| 369 | |
| 370 iAlignedBioseqDB.getConsensus(2,0.75) | |
| 371 | |
| 372 obsFileHandler.close() | |
| 373 expFileHandler.close() | |
| 374 | |
| 375 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
| 376 | |
| 377 sys.stdout = stdoutRef | |
| 378 os.remove ( obsFileName ) | |
| 379 os.remove ( expFileName ) | |
| 380 stdoutRef = sys.stdout | |
| 381 | |
| 382 | |
| 383 def test_getConsensus_with_acceptable_N_proportion_assertion_on_warning_msg(self): | |
| 384 iBioseq1 = Bioseq("seq1", "AGATAA") | |
| 385 iBioseq2 = Bioseq("seq2", "CTCAAA") | |
| 386 iBioseq3 = Bioseq("seq3", "TTCTAA") | |
| 387 iBioseq4 = Bioseq("seq4", "GTATCC") | |
| 388 | |
| 389 iAlignedBioseqDB = AlignedBioseqDB() | |
| 390 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 391 | |
| 392 expFileName = "expFileName" | |
| 393 expFileHandler = open(expFileName,"w") | |
| 394 expMessage = "WARNING: 33% of N's\n" | |
| 395 expFileHandler.write(expMessage) | |
| 396 expFileHandler.close() | |
| 397 | |
| 398 obsFileName = "obsFileName" | |
| 399 obsFileHandler = open(obsFileName,"w") | |
| 400 | |
| 401 stdoutRef = sys.stdout | |
| 402 sys.stdout = obsFileHandler | |
| 403 | |
| 404 iAlignedBioseqDB.getConsensus(2,0.6) | |
| 405 | |
| 406 obsFileHandler.close() | |
| 407 expFileHandler.close() | |
| 408 | |
| 409 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) ) | |
| 410 | |
| 411 sys.stdout = stdoutRef | |
| 412 os.remove ( obsFileName ) | |
| 413 os.remove ( expFileName ) | |
| 414 stdoutRef = sys.stdout | |
| 415 | |
| 416 | |
| 417 def test_getConsensus_with_acceptable_N_proportion_assertion_on_result(self): | |
| 418 iBioseq1 = Bioseq("seq1", "AGATAA") | |
| 419 iBioseq2 = Bioseq("seq2", "CTCAAA") | |
| 420 iBioseq3 = Bioseq("seq3", "TTCTAA") | |
| 421 iBioseq4 = Bioseq("seq4", "GTATCC") | |
| 422 | |
| 423 iAlignedBioseqDB = AlignedBioseqDB() | |
| 424 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 425 | |
| 426 expConsensus = Bioseq("consensus= length=6 nbAlign=4","NTNTAA") | |
| 427 obsConsensus = iAlignedBioseqDB.getConsensus(2,0.6) | |
| 428 | |
| 429 self.assertEquals(expConsensus, obsConsensus) | |
| 430 | |
| 431 | |
| 432 def test_getConsensus_with_chimeric_seq_in_alignment(self): | |
| 433 iBioseq1 = Bioseq("seq1", "AGAGTTGTAA") | |
| 434 iBioseq2 = Bioseq("seq2", "ATC----AAA") | |
| 435 iBioseq3 = Bioseq("seq3", "ATC----TAA") | |
| 436 iBioseq4 = Bioseq("seq4", "GTC----TAA") | |
| 437 | |
| 438 iAlignedBioseqDB = AlignedBioseqDB() | |
| 439 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 440 | |
| 441 expConsensus = Bioseq("consensus= length=6 nbAlign=4","ATCTAA") | |
| 442 obsConsensus = iAlignedBioseqDB.getConsensus(2) | |
| 443 | |
| 444 self.assertEquals(expConsensus, obsConsensus) | |
| 445 | |
| 446 | |
| 447 def test_getConsensus_with_SATannot_data(self): | |
| 448 iBioseq1 = Bioseq("MbS69Gr8Cl511 chunk21 {Fragment} 165740..165916", "--TTTAGCCGAAGTCCATATGAGTCTTTGTGTTTGTATCTTCTAACAAGGAAACACTACTTAGGCTTTTAGGATAAGATTGCGGTTTAAGTTCTTATACTCAATCATACACATGACATCAAGTCATATTCGAATCCAAAACTCTAAGCAAGCTTCTTCTTGCTTCTCAAA-GCTTTGATG") | |
| 449 iBioseq2 = Bioseq("MbS68Gr8Cl511 chunk21 {Fragment} 165916..166092", "GGTCTAGCCGAAGTCCATATGAGTCTTTGTCTTTGTATCTTCTAACAAGAAAACACTACTTAGGCTTTTAGGATAAGGTTGCAGTTTAAGTTTTTATACTAAATCATACACATCACATCAAGTCATATTCGACTCCCAAACACTAACCAAGCTTCTT--TGCTTCTCAAC-GCTTTGATG") | |
| 450 iBioseq3 = Bioseq("MbS67Gr8Cl511 chunk21 {Fragment} 166093..166269", "-GTTTAGCCGAAGTCCATATGAGTCGTTGTGTTTGTATCTTCTAACAAGGAAACACTACTTACGCTTTTAGGATAAGATTGTTGTTTAAGTTCTTATACTTAATCATACACATGACATAAAGTCATATTCGACTCCAAAACACTAATCAAGCTTCTTCTTGCTTCTCAAA-GCTTTGTT-") | |
| 451 iBioseq4 = Bioseq("MbS66Gr8Cl511 chunk21 {Fragment} 173353..173529", "--TTTAGCAAAATTCTATATGAGTCTTTATCTTTGTATCTTCTAACAAGGAAACACTACTTAGGCTTTTAGGATAAGGTTGCGGGTTAAGTTCTTATACTCAATCATACACATGATATCAAGTCATATTCGACTCCAAAACACTAACCAAGCTTCTTCTTGCTTCTTAAAAGCTTTGAA-") | |
| 452 | |
| 453 iAlignedBioseqDB = AlignedBioseqDB() | |
| 454 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 455 | |
| 456 expConsensus = Bioseq("consensus= length=178 nbAlign=4 pile=511 pyramid=8", "GTTTAGCCGAAGTCCATATGAGTCTTTGTNTTTGTATCTTCTAACAAGGAAACACTACTTAGGCTTTTAGGATAAGNTTGCNGTTTAAGTTCTTATACTNAATCATACACATGACATCAAGTCATATTCGACTCCAAAACACTAANCAAGCTTCTTCTTGCTTCTCAAAGCTTTGATG") | |
| 457 obsConsensus = iAlignedBioseqDB.getConsensus(2, 0.6, isHeaderSAtannot=True) | |
| 458 | |
| 459 self.assertEquals(expConsensus, obsConsensus) | |
| 460 | |
| 461 | |
| 462 def test_getEntropy_equal_zero(self): | |
| 463 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 464 iBioseq2 = Bioseq("seq2", "AGAT") | |
| 465 iBioseq3 = Bioseq("seq3", "AGAT") | |
| 466 iBioseq4 = Bioseq("seq4", "AGAT") | |
| 467 | |
| 468 iAlignedBioseqDB = AlignedBioseqDB() | |
| 469 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 470 | |
| 471 expStats = Stat() | |
| 472 expStats._min = 0 | |
| 473 expStats._max = 0 | |
| 474 expStats._sum = 0 | |
| 475 expStats._sumOfSquares = 0 | |
| 476 expStats._n = 4 | |
| 477 expStats._lValues = [0, 0, 0, 0] | |
| 478 | |
| 479 obsStats = iAlignedBioseqDB.getEntropy() | |
| 480 | |
| 481 self.assertEquals(expStats, obsStats) | |
| 482 | |
| 483 | |
| 484 def test_getEntropy_different_nucl(self): | |
| 485 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 486 iBioseq2 = Bioseq("seq2", "CTCA") | |
| 487 iBioseq3 = Bioseq("seq3", "TTCT") | |
| 488 iBioseq4 = Bioseq("seq4", "GTAT") | |
| 489 | |
| 490 iAlignedBioseqDB = AlignedBioseqDB() | |
| 491 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 492 | |
| 493 expStats = Stat() | |
| 494 expStats._min = 0.81127812445913283 | |
| 495 expStats._max = 2.0 | |
| 496 expStats._sum = 4.62255624892 | |
| 497 expStats._sumOfSquares = 6.31634439045 | |
| 498 expStats._n = 4 | |
| 499 expStats._lValues = [2.0, 0.81127812445913283, 1.0, 0.81127812445913283] | |
| 500 | |
| 501 obsStats = iAlignedBioseqDB.getEntropy() | |
| 502 | |
| 503 self.assertEquals(expStats, obsStats) | |
| 504 | |
| 505 | |
| 506 def test_getEntropy_different_nucl_with_N(self): | |
| 507 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 508 iBioseq2 = Bioseq("seq2", "CNCA") | |
| 509 iBioseq3 = Bioseq("seq3", "TTNT") | |
| 510 iBioseq4 = Bioseq("seq4", "GTNT") | |
| 511 | |
| 512 iAlignedBioseqDB = AlignedBioseqDB() | |
| 513 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 514 | |
| 515 expStats = Stat() | |
| 516 expStats._min = 0.811278124459 | |
| 517 expStats._max = 2 | |
| 518 expStats._sum = 6.11387090595 | |
| 519 expStats._sumOfSquares = 10.1629200457 | |
| 520 expStats._n = 4 | |
| 521 expStats._lValues = [2, 1.4913146570363986, 1.8112781244591329, 0.81127812445913283] | |
| 522 | |
| 523 obsStats = iAlignedBioseqDB.getEntropy() | |
| 524 | |
| 525 self.assertEquals(expStats, obsStats) | |
| 526 | |
| 527 | |
| 528 def test_getEntropy_different_nucl_with_gap(self): | |
| 529 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 530 iBioseq2 = Bioseq("seq2", "C-CA") | |
| 531 iBioseq3 = Bioseq("seq3", "T--T") | |
| 532 iBioseq4 = Bioseq("seq4", "-TNT") | |
| 533 | |
| 534 iAlignedBioseqDB = AlignedBioseqDB() | |
| 535 iAlignedBioseqDB.setData([iBioseq1, iBioseq2, iBioseq3, iBioseq4]) | |
| 536 | |
| 537 expStats = Stat() | |
| 538 expStats._min = 0.811278124459 | |
| 539 expStats._max = 1.65002242165 | |
| 540 expStats._sum = 5.04626304683 | |
| 541 expStats._sumOfSquares = 6.89285231586 | |
| 542 expStats._n = 4 | |
| 543 expStats._lValues = [1.5849625007211561, 1.0, 1.6500224216483541, 0.81127812445913283] | |
| 544 | |
| 545 obsStats = iAlignedBioseqDB.getEntropy() | |
| 546 | |
| 547 self.assertEquals(expStats, obsStats) | |
| 548 | |
| 549 | |
| 550 def test_saveAsBinaryMatrix( self ): | |
| 551 iBioseq1 = Bioseq("seq1", "AGAT") | |
| 552 iBioseq2 = Bioseq("seq2", "C-CA") | |
| 553 iBioseq3 = Bioseq("seq3", "T--T") | |
| 554 iBioseq4 = Bioseq("seq4", "-TNT") | |
| 555 | |
| 556 self._i.setData( [ iBioseq1, iBioseq2, iBioseq3, iBioseq4 ] ) | |
| 557 | |
| 558 expFile = "dummyExpFile_%s" % ( self._uniqId ) | |
| 559 expFileHandler = open( expFile, "w" ) | |
| 560 expFileHandler.write( "seq1\t1\t1\t1\t1\n" ) | |
| 561 expFileHandler.write( "seq2\t1\t0\t1\t1\n" ) | |
| 562 expFileHandler.write( "seq3\t1\t0\t0\t1\n" ) | |
| 563 expFileHandler.write( "seq4\t0\t1\t1\t1\n" ) | |
| 564 expFileHandler.close() | |
| 565 | |
| 566 obsFile = "dummyObsFile_%s" % ( self._uniqId ) | |
| 567 self._i.saveAsBinaryMatrix( obsFile ) | |
| 568 | |
| 569 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) ) | |
| 570 for f in [ expFile, obsFile ]: | |
| 571 os.remove( f ) | |
| 572 | |
| 573 | |
| 574 def test_getAlignList( self ): | |
| 575 iBioseq1 = Bioseq( "seq1", "AGAAT" ) | |
| 576 iBioseq2 = Bioseq( "seq2", "-G-AC" ) | |
| 577 self._i.setData( [ iBioseq1, iBioseq2 ] ) | |
| 578 | |
| 579 iAlign1 = Align( Range( "seq1", 2, 2 ), | |
| 580 Range( "seq2", 1, 1 ), | |
| 581 0, 1, 100 ) | |
| 582 iAlign2 = Align( Range( "seq1", 4, 5 ), | |
| 583 Range( "seq2", 2, 3 ), | |
| 584 0, 1, 50 ) | |
| 585 lExp = [ iAlign1, iAlign2 ] | |
| 586 | |
| 587 lObs = self._i.getAlignList( "seq1", "seq2" ) | |
| 588 self.assertEquals( lExp, lObs ) | |
| 589 | |
| 590 | |
| 591 def test_removeGaps(self): | |
| 592 iBioseq1 = Bioseq( "seq1", "AGAAT-" ) | |
| 593 iBioseq2 = Bioseq( "seq2", "AG-ACG" ) | |
| 594 self._i.setData( [ iBioseq1, iBioseq2 ] ) | |
| 595 | |
| 596 exp = AlignedBioseqDB() | |
| 597 exp.setData( [ Bioseq( "seq1", "AGAAT" ), | |
| 598 Bioseq( "seq2", "AGACG" ) ] ) | |
| 599 | |
| 600 self._i.removeGaps() | |
| 601 | |
| 602 self.assertEquals(exp, self._i) | |
| 603 | |
| 604 def test_computeMeanPcentIdentity_between_two_sequences_50pcent(self): | |
| 605 iBioseq1 = Bioseq( "seq1", "AGAAT-" ) | |
| 606 iBioseq2 = Bioseq( "seq2", "AG-ACG" ) | |
| 607 self._i.setData( [ iBioseq1, iBioseq2 ] ) | |
| 608 expIdentity = 50.0 | |
| 609 obsIdentity = self._i.computeMeanPcentIdentity() | |
| 610 self.assertEquals(expIdentity, obsIdentity) | |
| 611 | |
| 612 def test_computeMeanPcentIdentity_between_two_sequences_57pcent(self): | |
| 613 iBioseq1 = Bioseq( "seq1", "AGAAT-T" ) | |
| 614 iBioseq2 = Bioseq( "seq2", "AG-ACGT" ) | |
| 615 self._i.setData( [ iBioseq1, iBioseq2 ] ) | |
| 616 expIdentity = 57.0 | |
| 617 obsIdentity = self._i.computeMeanPcentIdentity() | |
| 618 self.assertEquals(expIdentity, obsIdentity) | |
| 619 | |
| 620 def test_compueNeamPcentIdentity_between_two_sequences_gaps_on_same_position(self): | |
| 621 iBioseq1 = Bioseq( "seq1", "AGAAT-T" ) | |
| 622 iBioseq2 = Bioseq( "seq2", "AG-AC-T" ) | |
| 623 self._i.setData( [ iBioseq1, iBioseq2 ] ) | |
| 624 expIdentity = 57.0 | |
| 625 obsIdentity = self._i.computeMeanPcentIdentity() | |
| 626 self.assertEquals(expIdentity, obsIdentity) | |
| 627 | |
| 628 def test_computeMeanPcentIdentity_between_three_sequences_50_pcent(self): | |
| 629 iBioseqRef = Bioseq( "seqRef", "AGAAT-" ) | |
| 630 iBioseq1 = Bioseq( "seq1", "AG-ACG" ) | |
| 631 iBioseq2 = Bioseq( "seq2", "AG-ACG" ) | |
| 632 | |
| 633 self._i.setData( [ iBioseqRef, iBioseq1, iBioseq2 ] ) | |
| 634 | |
| 635 expIdentity = 50.0 | |
| 636 obsIdentity = self._i.computeMeanPcentIdentity() | |
| 637 self.assertEquals(expIdentity, obsIdentity) | |
| 638 | |
| 639 def test_computeMeanPcentIdentity_between_three_sequences_42_pcent(self): | |
| 640 iBioseqRef = Bioseq( "seqRef", "AGAAT-" ) | |
| 641 iBioseq1 = Bioseq( "seq1", "AG-ACG" ) | |
| 642 iBioseq2 = Bioseq( "seq2", "AG-CC-" ) | |
| 643 | |
| 644 self._i.setData( [ iBioseqRef, iBioseq1, iBioseq2 ] ) | |
| 645 | |
| 646 expIdentity = 42.0 | |
| 647 obsIdentity = self._i.computeMeanPcentIdentity() | |
| 648 self.assertEquals(expIdentity, obsIdentity) | |
| 649 | |
| 650 #TODO: test with tthis data: | |
| 651 #>BlastclustCluster2Mb1_chunk7 (dbseq-nr 1) [101523,104351] | |
| 652 #------------------------------------------------------------ | |
| 653 #------------------------------------------------------------ | |
| 654 #------------------------------------------------------------ | |
| 655 #------------------------------------------------------------ | |
| 656 #------------------------------------------------------------ | |
| 657 #------------------------------------------------------------ | |
| 658 #-------------------------------TAAATCCAACACTGAGAAGAATTATTTAA | |
| 659 #AGAAGGTTTTTATTTAACTTCTTTATTCGGATATCAGTTTAAGACTAAAA-TTCA-AATG | |
| 660 #TAAATTGGATTGAGGAGAAGCCTCAGTATTTTAACAATATTTGTATTTCGGGAGGGCCTC | |
| 661 #GCTTTTGGATTCTTAAGATTAGGAAAAGATTCAAAGAGAGCAGTCAAATCTGCTTATGTC | |
| 662 #AGGCTTTAGGATTTTTACAAGAACGGCTAAGTGCCGCTGCCAAAGAATTCTTTATTAGAA | |
| 663 #ACGGACGCTGCGCAGCTGGGATACATTATGGAAATAACTTAAGTGCATTACTGTTTTCTT | |
| 664 #TGAAATAATTGAAGTGGCCGATTTGGACCACCCAAATACGTACCTCCCCTTCCCTTAAAG | |
| 665 #TGAAACCTATACTTGGGCTGGGATTGATAGATATTGTATGGAAAATGGAGTTTGTTCTAT | |
| 666 #TTCTATTTGTTGTGGTATGTTTTGATTTTTTCTTATTTTAAGTTTTGCATACAGCAACAT | |
| 667 #AA--ATGGCATAA--ATTATACATA-TCTTAAATATAAGTACAATAAAATTAGTCA--AT | |
| 668 #TATTACAATGGTCATTAGTATG-TAAAGTGTAAT-ATTGTTCTC-TGA-AATCATCTTAA | |
| 669 #CATTGGCGTTGTGTTTTACAATTTTTATTTTTGTTATATTAAGTGGTGTGTCAAGTGGTG | |
| 670 #TCAAATCTATTTCTGGTTTTAACATATTTTCACTTAAAATTATACTATTGATTTCTATTT | |
| 671 #TGCATTGCATTACTCCTTTCATTTTGTTTTCTTCTATTTTTATATTATTAATTGAATTTG | |
| 672 #GGTAATTTTGGTTATGAATGGTTTGGGTTAAGTTCCAGTAATTTGTAATAATTTAAGTTT | |
| 673 #AGTAATTTTGGGTTAAACAAGTCAAGTCTGGAAAGCTGGCATAGCCATTCTAAATCTTCT | |
| 674 #ACGTATTCCGTAAACTGCATTAGCTAGAACAAAAGTGGTTATTTTCATAGTTCTGTTTTT | |
| 675 #TTGGTTTCTTAAGTAAT--TAAT--TTGTATGTTTGATCAAAAAGGGTAACTATTATTTT | |
| 676 #TGTAAT--TAATAACTGATTGGACATTTTTCAACAATTTTCTGTCAATTAGCAT----AT | |
| 677 #CGTAATTATTAGAA-AATACTATT--TCTGGGTAA-CATAATCAAGTCGTTCAAGGTAAT | |
| 678 #AGGGCCATT-TAATGTTAA-AACTTCACTTCTACTATTTTGTATGGGAAGA--CAAAATA | |
| 679 #TATTTTCAT--TGATCATATTAATTGTGGAAGCCATTTGTATGTGTACCCTTTGTATACT | |
| 680 #ATTTTTAAGCATTCGTGTTGTCCGGGGCTGTTGACCGAAAATTTTCGTTTAGTTCAGAAT | |
| 681 #TATTTTGATTTTGTTCATTATTAATGTGTACGGGTTGGACCTGTTGTTGCCCTTCATTAA | |
| 682 #TGAACCCATGATTTTGATATGGATTGTATTGATTTTGGTCATAATACTGTTGTTCGTAGG | |
| 683 #TTGGGTCTGAAATAATTAGGTACGTGCCACATTGGTGGGTTGTAAGTCGTCTGCTCTGAT | |
| 684 #AGCTAGGTCTAAATGGTTGAATGTATTGATTAAAATTAGGCTGGAAGGGTTGGGAATATT | |
| 685 #GTGGGTAACTTGGGCGAGTTTGAACGTTTGTATTGAATTTATGTGCTTTCGAATTCTGAT | |
| 686 #TAAAATTTGAATTTTTATTACGGTATTCTGGGTTTATAAAATTCAAAATTAATGAGTTTT | |
| 687 #TCATAAATTCCCTCATTTTGTGCAATGGTTATTAAGGATCTTAAGTCTGTAATA-TCGTG | |
| 688 #ATGAG-ATAA-AATAGTAAATATAGTAG-AGTCTTTA--ATAGCCTGAATAAAAATAAGA | |
| 689 #AAATCCGATTGGTTACCTTCCAGGTGTAGTTTCGAAATTAATAATTGACGTCGTCTTTCC | |
| 690 #CCTTCTTCGGAGAATGTTTTTAGGTTTCCTCTGTATGGTGTCTCCCTGAAGCTCTCCAGA | |
| 691 #AGTTTGTAGTTTGGTGTTTGAGTTTTAAATTCCGCGATGAGTCTTGCTTTGAGGGTAGGC | |
| 692 #CAATGCTCGGAAGTCCCAAAGATCGTATTATCCGTCCAAGTTACTTTTGATGGCTCCCAG | |
| 693 #TAGAATCCTCTGTTTACGAAAATTACGTAAATCCACTCTGCTGACGACGGTGTGAAGTGT | |
| 694 #TTCTGGATCACCCTTAAATGTCATAATGTCTTTAAGCTGCCGACGGGCTTCGGCAAGGTT | |
| 695 #GTTGTCTCTTAGCGCAACGATTTAAGGTGCGGCAATAATTATAATAATTGGTTGAGACAT | |
| 696 #TTTTATTGTAAAATTTTAAATTTTGTGTTTTATTGTTTTATTGTTTCGAATTCAATGCTA | |
| 697 #TTATTTATTTTTTTTTTTGTTTTCTAGTTTCACTTTTTTTTTTATTGTATTGCTTTATTG | |
| 698 #TTCTTATTTTATTTTTATATGTTGGTTTTAAAACTTAGTTGCCTTTGGACTTAATGTTTT | |
| 699 #TGTTTCGTATTTCACTTCCACTTTAAATTGGATAACAGAATTGGAATTAAAATCCAAGTT | |
| 700 #GAAGAGTTTCCACGAATTTATTTGGGAAATGTTTCGAGCACTGGAATCCAGTGACTGGAT | |
| 701 #TATAAAATTTAACTTATTTCC-ACTCGAAGGTTCTTTTTT--CGG--------ATACTTT | |
| 702 #TTGTATCAGT--TGACTAAGAGCAACACTGAGAAGAATTATTTAAAGAAGGTTTTTATTT | |
| 703 #AACTTCTTTATTCGGATATCAGTTTAAGACTAAAA-TTCA-AATGTAAATTGGATTGAGG | |
| 704 #AGAAGCCTCAGTATT--TCAACAATATTTGTATT--TCGGGAGGGCCTCGCTCTTGGAT- | |
| 705 #-TCTTAAGATTAGGAAAAAATTCA-AAGAGAGCAGTCA-AATC-TGCTTATGTCAGGCTT | |
| 706 #TAGGATTTTTACAAGAAGGGC-TAAGTGCCGCTGAAACGGATGC---------------- | |
| 707 #------------------------------------------------------------ | |
| 708 #------------------------------------------------------------ | |
| 709 #------------ | |
| 710 #>BlastclustCluster2Mb2_chunk7 (dbseq-nr 1) [99136,100579] | |
| 711 #GTAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATA | |
| 712 #ATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATA | |
| 713 #ATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATC | |
| 714 #ATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATA | |
| 715 #ATCATAATAATCATAATAATCATAATAATCATAATAATAATAATAATCATAATCATAATC | |
| 716 #ATAATAAGCGATAAAAAAATTAAAAAATAAAAATTAAAACCCACTGCAATCACGTTGGAC | |
| 717 #GGCGAGTCACAGACGTCAGAATAGTGGTGCGTAAATCCAACGCCGAGAAGAATTACTTCA | |
| 718 #AGAAGGTTTTTATTGAACTTCTTTATTCGGATATCAGTTTAAGACTAAAAATTAATAATC | |
| 719 #ATAAT---AATCATAATAATCATAATAATCATAATAATCATAATAAT------------- | |
| 720 #------------------------------------------------------------ | |
| 721 #------------------------------------------------------------ | |
| 722 #------------------------------------------------------------ | |
| 723 #------------------------------------------------------------ | |
| 724 #------------------------------------------------------------ | |
| 725 #-----------------------------------------------CATA-ATAATCAT | |
| 726 #AATAAT--CATAATAATCATA-ATAATCATAATAATCATAATAATCATAATAATCATAAT | |
| 727 #AATCATAATAATCATAATAATCATAA----TAATCATAATAATCATAATAATCATAATAA | |
| 728 #------------------------------------------------------------ | |
| 729 #------------------------------------------------------------ | |
| 730 #------------------------------------------------------------ | |
| 731 #------------------------------------------------------------ | |
| 732 #------------------------------------------------------------ | |
| 733 #------------------------------------------------------------ | |
| 734 #------TCATAA-TAATCATAATAATCGTAA---TAATCATAA----TAATCATAATAAT | |
| 735 #CATAATAATCATAA-TAAT----CAT-----AATAATCAT-----AATAATCATAATAAT | |
| 736 #CATAATAATCATAATAATCATAATAATCATAATAATCATAAT-AA-TCAT--AA--TAAT | |
| 737 #-----CATAATAATCATAATAA--TCA----TAATAATC---AT---AATAATCATAATA | |
| 738 #-AT---CATAATAATCATAATAATC----------------------------------- | |
| 739 #------------------------------------------------------------ | |
| 740 #------------------------------------------------------------ | |
| 741 #------------------------------------------------------------ | |
| 742 #------------------------------------------------------------ | |
| 743 #------------------------------------------------------------ | |
| 744 #------------------------------------------------------------ | |
| 745 #-----------------------------------ATAATAATCATAAT-AATCA----- | |
| 746 #TAATAA------TCATAAT----AATCATAAT-AATCATAATAA-TCA-TAATAATCATA | |
| 747 #ATAATCATAATAATCATAATAATAATAATAATCATAATCATAATCATAATAAGCATAAAA | |
| 748 #AAAT-------------------------------------------------------- | |
| 749 #------------------------------------------------------------ | |
| 750 #------------------------------------------------------------ | |
| 751 #------------------------------------------------------------ | |
| 752 #------------------------------------------------------------ | |
| 753 #------------------------------------------------------------ | |
| 754 #------------------------------------------------------------ | |
| 755 #------------------------------------------------------------ | |
| 756 #------------------------------------------------------------ | |
| 757 #------------------------------------------------------------ | |
| 758 #------------------------------------------------------------ | |
| 759 #------------------------------------------------------------ | |
| 760 #TAAAAAATAAAAATTAAAACCCACTGCAA---TCACGTTGGACGGCGAGTCACAGACGTC | |
| 761 #A-GAAT-AGTGGTGCGTAAATCCAACGCCGAGAAGAATTACTTCAAGAAGGTTTTTATTG | |
| 762 #AACTTCTTTATTCGGATATCAGTTTAAGACTAAAAATTAATAATCATAAT---AATCATA | |
| 763 #ATAA---TCA-TAATAATCAT-AATAATCATAATAATCATAA-----TAA-TCATA-ATA | |
| 764 #ATCATAATAATCATAATAA--TCATAATA-ATCA-TAATAATCATAATAATCATAATCAT | |
| 765 #CATAATAATCATAATAAT--CATAA-T-------AATC--ATAATAATCATAATAATCAT | |
| 766 #AATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAAT | |
| 767 #CATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAATAATCATAAT | |
| 768 #AATCATAATAAT | |
| 769 | |
| 770 test_suite = unittest.TestSuite() | |
| 771 test_suite.addTest( unittest.makeSuite( Test_AlignedBioseqDB ) ) | |
| 772 if __name__ == "__main__": | |
| 773 unittest.TextTestRunner(verbosity=2).run( test_suite ) |