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comparison commons/core/checker/test/Test_CheckerUtils.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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30:5677346472b5 31:0ab839023fe4
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 ConfigParser
35 from commons.core.checker.CheckerUtils import CheckerUtils
36 from commons.core.checker.CheckerException import CheckerException
37 from ConfigParser import NoOptionError
38 from ConfigParser import NoSectionError
39
40 class Test_CheckerUtils( unittest.TestCase ):
41
42 def setUp(self):
43 self.queueFileName = "queueName.txt"
44 self.configFileName = "dummyConfig.cfg"
45
46 def tearDown(self):
47 if os.path.exists(self.queueFileName):
48 os.remove(self.queueFileName)
49 if os.path.exists(self.configFileName):
50 os.remove(self.configFileName)
51
52 def test_isBlastNameInBlastValues( self ):
53 correctValueList = [ "blastn", "blastp", "blastx", "tblastn", "tblastx" ]
54 for value in correctValueList:
55 self.assertFalse( CheckerUtils.isBlastNameNotInBlastValues( value ) )
56
57 incorrectValueList = [ "badbalst", "wublast" ]
58 for value in incorrectValueList:
59 self.assertTrue( CheckerUtils.isBlastNameNotInBlastValues( value ) )
60
61 def test_isNotTRUEisNotFALSE( self ):
62 correctValueList = [ "TRUE", "FALSE" ]
63 for value in correctValueList:
64 self.assertFalse( CheckerUtils.isNotTRUEisNotFALSE( value ) )
65
66 incorrectValueList = [ "True", "False" ]
67 for value in incorrectValueList:
68 self.assertTrue( CheckerUtils.isNotTRUEisNotFALSE( value ) )
69
70 def test_isRessourceNotExists( self ):
71 fileName = "dummyFile.txt"
72 self.assertTrue( CheckerUtils.isRessourceNotExits( fileName ) )
73 os.system( "touch %s" % ( fileName ) )
74 self.assertFalse( CheckerUtils.isRessourceNotExits( fileName ) )
75 os.remove( fileName )
76
77 def test_isNotAeValueWithOneDigit2DecimalsAtLeast( self ):
78 correctEValueList = [ "5e-32", "7e-45", "1e-2122", "9e-32" ]
79 for value in correctEValueList:
80 self.assertFalse( CheckerUtils.isNotAeValueWithOneDigit2DecimalsAtLeast( value ) )
81
82 incorrecEValueStr = [ "10e-32", "2e-3", "2e-2", "1", "cxhhe" ]
83 for value in incorrecEValueStr:
84 self.assertTrue( CheckerUtils.isNotAeValueWithOneDigit2DecimalsAtLeast( value ) )
85
86 def test_isNotADigit( self ):
87 correctDigitList = [ "1", "21", "345" ]
88 for value in correctDigitList:
89 self.assertFalse( CheckerUtils.isNotANumber( value ) )
90
91 incorrectDigitList = [ "A", "dfdf", "((((" ]
92 for value in incorrectDigitList:
93 self.assertTrue( CheckerUtils.isNotANumber( value ) )
94
95 def test_isExecutableInUserPath( self ):
96 exeName = "ls"
97 self.assertTrue( CheckerUtils.isExecutableInUserPath( exeName ) )
98
99 exeName = "hsvegdtefaobfbcheta"
100 self.assertFalse( CheckerUtils.isExecutableInUserPath( exeName ) )
101
102 def test_isExecutableInUserPath_case_endsWith( self ):
103 exeName = "s"
104 self.assertFalse( CheckerUtils.isExecutableInUserPath( exeName ) )
105
106 def test_isQueueNameValid_valid(self):
107 cmd = "qconf -sql > " + self.queueFileName
108 os.system(cmd)
109 f = open(self.queueFileName, "r")
110 lQueueNames = f.readlines()
111 f.close()
112 if lQueueNames == []:
113 print "Warning you need SGE installed\n"
114 else:
115 self.assertTrue(CheckerUtils.isQueueNameValid(lQueueNames[0].strip()))
116
117 def test_isQueueNameValid_not_valid(self):
118 cmd = "qconf -sql > " + self.queueFileName
119 os.system(cmd)
120 f = open(self.queueFileName, "r")
121 lQueueNames = f.readlines()
122 f.close()
123 if lQueueNames == []:
124 print "Warning you need SGE installed\n"
125 else:
126 self.assertFalse(CheckerUtils.isQueueNameValid("dummyQueueName"))
127
128 def test_isQueueNameValid_valid_with_parameter(self):
129 cmd = "qconf -sql > " + self.queueFileName
130 os.system(cmd)
131 f = open(self.queueFileName, "r")
132 lQueueNames = f.readlines()
133 f.close()
134 if lQueueNames == []:
135 print "Warning you need SGE installed\n"
136 else:
137 queueNameWithParameter = lQueueNames[0].strip() + " test=TRUE"
138 self.assertTrue(CheckerUtils.isQueueNameValid(queueNameWithParameter))
139
140 def test_isCharAlphanumOrUnderscore_valid(self):
141 project_name = "Project_Name"
142 self.assertTrue(CheckerUtils.isCharAlphanumOrUnderscore(project_name))
143
144 def test_isCharAlphanumOrUnderscore_not_valid(self):
145 project_name = "Project_Name,"
146 self.assertFalse(CheckerUtils.isCharAlphanumOrUnderscore(project_name))
147
148 def test_isMax15Char_valid(self):
149 project_name = "Project_Name"
150 self.assertTrue(CheckerUtils.isMax15Char(project_name))
151
152 def test_isMax15Char_not_valid(self):
153 project_name = "Project_Name_tooLong"
154 self.assertFalse(CheckerUtils.isMax15Char(project_name))
155
156 def test_checkSectionInConfigFile_empty_section(self):
157 sectionName = "sectionName"
158 line = "[" + sectionName + "]"
159 configFile = open(self.configFileName, "w")
160 configFile.write(line)
161 configFile.close()
162 configFile = open(self.configFileName, "r")
163
164 config = ConfigParser.ConfigParser()
165 config.readfp(configFile)
166
167 isSectionExceptionRaised = False
168 try:
169 CheckerUtils.checkSectionInConfigFile(config, sectionName)
170 except NoSectionError:
171 isSectionExceptionRaised = True
172 configFile.close()
173 self.assertFalse(isSectionExceptionRaised)
174
175 def test_checkSectionInConfigFile(self):
176 sectionName = "sectionName"
177 lines = "[" + sectionName + "]\ndummyOption : dummyOption\n"
178 configFile = open(self.configFileName, "w")
179 configFile.write(lines)
180 configFile.close()
181 configFile = open(self.configFileName, "r")
182
183 config = ConfigParser.ConfigParser()
184 config.readfp(configFile)
185
186 isSectionExceptionRaised = False
187 try:
188 CheckerUtils.checkSectionInConfigFile(config, sectionName)
189 except NoSectionError:
190 isSectionExceptionRaised = True
191 configFile.close()
192 self.assertFalse(isSectionExceptionRaised)
193
194 def test_checkSectionInConfigFile_not_valid(self):
195 sectionName = "sectionName"
196 line = " "
197 configFile = open(self.configFileName, "w")
198 configFile.write(line)
199 configFile.close()
200 configFile = open(self.configFileName, "r")
201
202 config = ConfigParser.ConfigParser()
203 config.readfp(configFile)
204
205 isSectionExceptionRaised = False
206 try:
207 CheckerUtils.checkSectionInConfigFile(config, sectionName)
208 except NoSectionError:
209 isSectionExceptionRaised = True
210 configFile.close()
211 self.assertTrue(isSectionExceptionRaised)
212
213 def test_checkOptionInSectionInConfigFile(self):
214 optionName = "optionName"
215 sectionName = "sectionName"
216 configFile = open(self.configFileName, "w")
217 configFile.write("[" + sectionName + "]\n")
218 configFile.write(optionName + ": ")
219 configFile.close()
220 configFile = open(self.configFileName, "r")
221
222 config = ConfigParser.ConfigParser()
223 config.readfp(configFile)
224
225 isSectionExceptionRaised = False
226 try:
227 CheckerUtils.checkOptionInSectionInConfigFile(config, sectionName, optionName)
228 except NoOptionError:
229 isSectionExceptionRaised = True
230 configFile.close()
231 self.assertFalse(isSectionExceptionRaised)
232
233 def test_checkOptionInSectionInConfigFile_not_present(self):
234 optionName = " "
235 sectionName = "sectionName"
236 configFile = open(self.configFileName, "w")
237 configFile.write("[" + sectionName + "]\n")
238 configFile.write(optionName)
239 configFile.close()
240 configFile = open(self.configFileName, "r")
241
242 config = ConfigParser.ConfigParser()
243 config.readfp(configFile)
244
245 isSectionExceptionRaised = False
246 try:
247 CheckerUtils.checkOptionInSectionInConfigFile(config, sectionName, optionName)
248 except NoOptionError:
249 isSectionExceptionRaised = True
250 configFile.close()
251 self.assertTrue(isSectionExceptionRaised)
252
253 def test_checkOptionInSectionInConfigFile_not_in_the_right_section(self):
254 optionName = "optionName"
255 rightSection = "dummySection2"
256 configFile = open(self.configFileName, "w")
257 configFile.write("[dummySection1]\n")
258 configFile.write(optionName + ": \n")
259 configFile.write("[" + rightSection + "]")
260 configFile.close()
261 configFile = open(self.configFileName, "r")
262
263 config = ConfigParser.ConfigParser()
264 config.readfp(configFile)
265
266 isSectionExceptionRaised = False
267 try:
268 CheckerUtils.checkOptionInSectionInConfigFile(config, rightSection, optionName)
269 except NoOptionError:
270 isSectionExceptionRaised = True
271 configFile.close()
272 self.assertTrue(isSectionExceptionRaised)
273
274 def test_checkConfigVersion_different_version_between_changeLog_and_configFile(self):
275 changeLogFileName = "dummyCHANGELOG"
276
277 self._writeChangeLogFile(changeLogFileName)
278 self._writeConfigFile("repet_version: 1.3.5\n")
279
280 changeLogFileHandler = open(changeLogFileName, "r")
281 configFileHandler = open(self.configFileName, "r")
282 config = ConfigParser.ConfigParser()
283 config.readfp(configFileHandler)
284
285 self.assertRaises(CheckerException, CheckerUtils.checkConfigVersion, changeLogFileHandler, config)
286
287 changeLogFileHandler.close()
288 configFileHandler.close()
289 os.remove(changeLogFileName)
290
291 def test_checkConfigVersion_same_version_between_changeLog_and_configFile(self):
292 changeLogFileName = "dummyCHANGELOG"
293 self._writeChangeLogFile(changeLogFileName)
294 self._writeConfigFile("repet_version: 1.3.6\n")
295
296 changeLogFileHandler = open(changeLogFileName, "r")
297 configFileHandler = open(self.configFileName, "r")
298 config = ConfigParser.ConfigParser()
299 config.readfp(configFileHandler)
300
301 isCheckerExceptionRaised = False
302 try:
303 CheckerUtils.checkConfigVersion(changeLogFileHandler, config)
304 except CheckerException:
305 isCheckerExceptionRaised = True
306 self.assertFalse(isCheckerExceptionRaised)
307
308 changeLogFileHandler.close()
309 configFileHandler.close()
310 os.remove(changeLogFileName)
311
312 def test_getVersionFromChangelogFile(self):
313 changeLogFileName = "dummyCHANGELOG"
314 self._writeChangeLogFile(changeLogFileName)
315 obsVer = CheckerUtils.getVersionFromChangelogFile(changeLogFileName)
316 expVer = "1.3.6"
317
318 self.assertEquals(obsVer, expVer)
319
320 os.remove(changeLogFileName)
321
322 def test_checkConfigVersion_check_exception_message(self):
323 changeLogFileName = "dummyCHANGELOG"
324 self._writeChangeLogFile(changeLogFileName)
325 self._writeConfigFile("repet_version: 1.3.5\n")
326
327 changeLogFileHandler = open(changeLogFileName, "r")
328 configFileHandler = open(self.configFileName, "r")
329 config = ConfigParser.ConfigParser()
330 config.readfp(configFileHandler)
331
332 checkerExceptionInstance = None
333 try:
334 CheckerUtils.checkConfigVersion(changeLogFileHandler, config)
335 except CheckerException, e:
336 checkerExceptionInstance = e
337
338 expMessage = "*** Error: wrong config file version. Expected version num is 1.3.6 but actual in config file is 1.3.5"
339 obsMessage = checkerExceptionInstance.msg
340
341 self.assertEquals(expMessage, obsMessage)
342
343 def test_checkHeaders_first_header_with_question_mark(self):
344 fastaFileName = "dummyFasta.fa"
345 self._writeFastaFile_first_header_with_question_mark(fastaFileName)
346 fastaFileHandler = open(fastaFileName,"r")
347 isExceptionRaised = False
348 try:
349 CheckerUtils.checkHeaders(fastaFileHandler)
350 except CheckerException, e:
351 isExceptionRaised = True
352
353 fastaFileHandler.close()
354 os.remove(fastaFileName)
355
356 self.assertTrue(isExceptionRaised)
357
358 expMessages = ["DmelChr4_Bla?ster_Piler_0.0_Map_3"]
359 obsMessages = e.getMessages()
360
361 self.assertEquals(expMessages, obsMessages)
362
363 def test_checkHeaders_with_2_wrong_headers(self):
364 fastaFileName = "dummyFasta.fa"
365 self._writeFastaFile_with_2_wrong_headers(fastaFileName)
366 fastaFileHandler = open(fastaFileName,"r")
367 isExceptionRaised = False
368 try:
369 CheckerUtils.checkHeaders(fastaFileHandler)
370 except CheckerException, e:
371 isExceptionRaised = True
372
373 fastaFileHandler.close()
374 os.remove(fastaFileName)
375
376 self.assertTrue(isExceptionRaised)
377
378 expMessages = ["DmelChr4_Bla?ster_Piler_0.0_Map_3","DmelChr4_Bla!ster_Piler_1.0_Map_9"]
379 obsMessages = e.getMessages()
380
381 self.assertEquals(expMessages, obsMessages)
382
383 def test_checkHeaders_with_pipe(self):
384 fastaFileName = "dummyFasta.fa"
385 self._writeFastaFile_with_pipe(fastaFileName)
386 fastaFileHandler = open(fastaFileName,"r")
387 isExceptionRaised = False
388 try:
389 CheckerUtils.checkHeaders(fastaFileHandler)
390 except CheckerException, e:
391 isExceptionRaised = True
392
393 fastaFileHandler.close()
394 os.remove(fastaFileName)
395
396 self.assertTrue(isExceptionRaised)
397
398 expMessages = ["DmelC|hr4_Blas-ter_Piler_1.0_Map_9"]
399 obsMessages = e.getMessages()
400
401 self.assertEquals(expMessages, obsMessages)
402
403 def test_checkHeaders_with_equal(self):
404 fastaFileName = "dummyFasta.fa"
405 self._writeFastaFile_with_equal(fastaFileName)
406 fastaFileHandler = open(fastaFileName,"r")
407 isExceptionRaised = False
408 try:
409 CheckerUtils.checkHeaders(fastaFileHandler)
410 except CheckerException, e:
411 isExceptionRaised = True
412
413 fastaFileHandler.close()
414 os.remove(fastaFileName)
415
416 self.assertTrue(isExceptionRaised)
417
418 expMessages = ["DmelC:hr4_Blas=ter_Piler_1.0_Map_9"]
419 obsMessages = e.getMessages()
420
421 self.assertEquals(expMessages, obsMessages)
422
423 def test_checkHeaders_all_headers_ok(self):
424 fastaFileName = "dummyFasta.fa"
425 self._writeFastaFile_all_headers_ok(fastaFileName)
426 fastaFileHandler = open(fastaFileName,"r")
427 isExceptionRaised = False
428 try:
429 CheckerUtils.checkHeaders(fastaFileHandler)
430 except CheckerException:
431 isExceptionRaised = True
432
433 fastaFileHandler.close()
434 os.remove(fastaFileName)
435
436 self.assertFalse(isExceptionRaised)
437
438 def _writeFastaFile_first_header_with_question_mark(self, fastaFileName):
439 fastaFileHandler = open(fastaFileName, "w")
440 fastaFileHandler.write(">DmelChr4_Bla?ster_Piler_0.0_Map_3\n")
441 fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
442 fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
443 fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
444 fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
445 fastaFileHandler.write(">DmelChr4_Blaster_Piler_1.0_Map_9\n")
446 fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
447 fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
448 fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
449 fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
450 fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
451 fastaFileHandler.close()
452
453 def _writeFastaFile_with_2_wrong_headers(self, fastaFileName):
454 fastaFileHandler = open(fastaFileName, "w")
455 fastaFileHandler.write(">DmelChr4_Bla?ster_Piler_0.0_Map_3\n")
456 fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
457 fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
458 fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
459 fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
460 fastaFileHandler.write(">DmelChr4_Bla!ster_Piler_1.0_Map_9\n")
461 fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
462 fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
463 fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
464 fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
465 fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
466 fastaFileHandler.close()
467
468 def _writeFastaFile_all_headers_ok(self, fastaFileName):
469 fastaFileHandler = open(fastaFileName, "w")
470 fastaFileHandler.write(">DmelChr4_Blaster_Piler_0.0_Map_3\n")
471 fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
472 fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
473 fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
474 fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
475 fastaFileHandler.write(">DmelC:hr4_Blas-ter_Piler_1.0_Map_9\n")
476 fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
477 fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
478 fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
479 fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
480 fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
481 fastaFileHandler.close()
482
483 def _writeFastaFile_with_pipe(self, fastaFileName):
484 fastaFileHandler = open(fastaFileName, "w")
485 fastaFileHandler.write(">DmelChr4_Blaster_Piler_0.0_Map_3\n")
486 fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
487 fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
488 fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
489 fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
490 fastaFileHandler.write(">DmelC|hr4_Blas-ter_Piler_1.0_Map_9\n")
491 fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
492 fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
493 fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
494 fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
495 fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
496 fastaFileHandler.close()
497
498 def _writeFastaFile_with_equal(self, fastaFileName):
499 fastaFileHandler = open(fastaFileName, "w")
500 fastaFileHandler.write(">DmelChr4_Blaster_Piler_0.0_Map_3\n")
501 fastaFileHandler.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
502 fastaFileHandler.write("TTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGA\n")
503 fastaFileHandler.write("GCTGAGAGCGCTACAGCGAACAGCTCTTTTCTACACATAAAGTGATAGCAGACAACTGTA\n")
504 fastaFileHandler.write("TGTGTGCACACGTGTGCTCATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTCAAA\n")
505 fastaFileHandler.write(">DmelC:hr4_Blas=ter_Piler_1.0_Map_9\n")
506 fastaFileHandler.write("AGTTTAAAAACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGC\n")
507 fastaFileHandler.write("ACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTACTCTCTTTCCGCTCACTCCCGCTG\n")
508 fastaFileHandler.write("AGAGCGTAAGAAATCTAAAAATATAATTTGCTTGCTTGTGTGAGTAAAAACAAGAGACGA\n")
509 fastaFileHandler.write("GAACGCGTATAAGTGTGCGTGTTGTGCTAGAAGACGATTTTCGGGACCGAAATCAATTCT\n")
510 fastaFileHandler.write("GATCGAAGAAACGAATTTACATGGTACATATTAGGGTAGTTTTTGCCAATTTCCTAGCAA\n")
511 fastaFileHandler.close()
512
513 def _writeChangeLogFile(self, changeLogFileName ):
514 changeLogFileHandler = open(changeLogFileName, "w")
515 changeLogFileHandler.write("ChangeLog of REPET\n")
516 changeLogFileHandler.write("\n")
517 changeLogFileHandler.write("\n")
518 changeLogFileHandler.write("\n")
519 changeLogFileHandler.write("REPET release 1.3.6\n")
520 changeLogFileHandler.write("(release date XX/XX/2010)\n")
521 changeLogFileHandler.write("\n")
522 changeLogFileHandler.close()
523
524 def _writeConfigFile(self, lineVersion):
525 configFileHandler = open(self.configFileName, "w")
526 configFileHandler.write("[repet_env]\n")
527 configFileHandler.write(lineVersion)
528 configFileHandler.write("repet_host: <your_MySQL_host>\n")
529 configFileHandler.close()
530
531
532 test_suite = unittest.TestSuite()
533 test_suite.addTest( unittest.makeSuite( Test_CheckerUtils ) )
534 if __name__ == "__main__":
535 unittest.TextTestRunner(verbosity=2).run( test_suite )