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comparison smart_toolShed/commons/core/coord/test/Test_PathUtils.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 from commons.core.coord.PathUtils import PathUtils
36 from commons.core.coord.Path import Path
37 from commons.core.coord.Set import Set
38 from commons.core.utils.FileUtils import FileUtils
39 from commons.core.coord.Range import Range
40 from commons.core.coord.Align import Align
41
42
43 class Test_PathUtils ( unittest.TestCase ):
44
45 def test_getSetListFromQueries( self ):
46 set1 = Set(1,"TE2","chr1",1,10)
47 set2 = Set(1,"TE2","chr1",10,1)
48 set3 = Set(1,"TE3","chr4",12,22)
49
50 expList = [set1, set2, set3]
51
52 tuple1 = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2")
53 tuple2 = ("1","chr1","10","1","TE2","11","17","1e-20","30","90.2")
54 tuple3 = ("1","chr4","12","22","TE3","11","17","1e-20","30","90.2")
55
56 pathList = self._makePathListFromTupleList( [ tuple1, tuple2, tuple3 ] )
57
58 obsList = PathUtils.getSetListFromQueries( pathList )
59
60 self.assertEquals( expList, obsList )
61
62
63 def test_getSetListFromQueries_on_empty_list( self ):
64 expList = []
65 obsList = PathUtils.getSetListFromQueries( [] )
66
67 self.assertEquals( expList, obsList )
68
69
70 def test_getSetListFromQueries_on_list_size1( self ):
71 set1 = Set(1,"TE2","chr1",1,10)
72
73 expList = [set1]
74
75 tuple1 = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2")
76 path1 = Path()
77 path1.setFromTuple(tuple1)
78
79 pathList = [path1]
80 obsList = PathUtils.getSetListFromQueries( pathList )
81
82 self.assertEquals( expList, obsList )
83
84
85 def test_getRangeListFromSubjects_initiallyOrdered_directStrand( self ):
86 tuple1 = ("1","chr1","1","10","TE2","1","10","1e-20","30","90.2")
87 tuple2 = ("1","chr1","21","30","TE2","11","20","1e-20","30","90.2")
88 tuple3 = ("1","chr1","41","50","TE2","21","30","1e-20","30","90.2")
89 lPaths = self._makePathListFromTupleList( [ tuple1, tuple2, tuple3 ] )
90
91 iSet1 = Range( "TE2", 1, 10 )
92 iSet2 = Range( "TE2", 11, 20 )
93 iSet3 = Range( "TE2", 21, 30 )
94 lExp = [ iSet1, iSet2, iSet3 ]
95
96 lObs = PathUtils.getRangeListFromSubjects( lPaths )
97
98 self.assertEquals( lExp, lObs )
99
100
101 def test_getRangeListFromSubjects_initiallyUnordered_directStrand( self ):
102 tuple1 = ("1","chr1","1","10","TE2","1","10","1e-20","30","90.2")
103 tuple2 = ("1","chr1","41","50","TE2","21","30","1e-20","30","90.2")
104 tuple3 = ("1","chr1","21","30","TE2","11","20","1e-20","30","90.2")
105 lPaths = self._makePathListFromTupleList( [ tuple1, tuple2, tuple3 ] )
106
107 iSet1 = Range( "TE2", 1, 10 )
108 iSet2 = Range( "TE2", 11, 20 )
109 iSet3 = Range( "TE2", 21, 30 )
110 lExp = [ iSet1, iSet2, iSet3 ]
111
112 lObs = PathUtils.getRangeListFromSubjects( lPaths )
113
114 self.assertEquals( lExp, lObs )
115
116
117 def test_getRangeListFromSubjects_initiallyUnordered_reverseStrand( self ):
118 tuple1 = ("1","chr1","1","10","TE2","10","1","1e-20","30","90.2")
119 tuple2 = ("1","chr1","41","50","TE2","30","21","1e-20","30","90.2")
120 tuple3 = ("1","chr1","21","30","TE2","20","11","1e-20","30","90.2")
121 lPaths = self._makePathListFromTupleList( [ tuple1, tuple2, tuple3 ] )
122
123 iSet3 = Range( "TE2", 30, 21 )
124 iSet2 = Range( "TE2", 20, 11 )
125 iSet1 = Range( "TE2", 10, 1 )
126 lExp = [ iSet1, iSet2, iSet3 ]
127
128 lObs = PathUtils.getRangeListFromSubjects( lPaths )
129
130 self.assertEquals( lExp, lObs )
131
132
133 def test_getQueryMinMaxFromPathList( self ):
134 tuple1 = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2")
135 tuple2 = ("1","chr1","10","1","TE2","11","17","1e-20","30","90.2")
136 tuple3 = ("1","chr4","12","22","TE3","11","17","1e-20","30","90.2")
137
138 pathList = self._makePathListFromTupleList([tuple1, tuple2, tuple3])
139
140 obsTuple = PathUtils.getQueryMinMaxFromPathList( pathList )
141 expTuple = (1,22)
142
143 self.assertEquals(expTuple, obsTuple)
144
145 def test_getQueryMinMaxFromPathList_on_empty_list( self ):
146 obsTuple = PathUtils.getQueryMinMaxFromPathList( [] )
147 expTuple = (-1,-1)
148 self.assertEquals( expTuple, obsTuple )
149
150 def test_getQueryMinMaxFromPathList_on_list_size1( self ):
151 tuple1 = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2")
152 path1 = Path()
153 path1.setFromTuple(tuple1)
154
155 pathList = [path1]
156 obsTuple = PathUtils.getQueryMinMaxFromPathList( pathList )
157
158 expTuple = (1,10)
159
160 self.assertEquals(expTuple, obsTuple)
161
162 def test_getSubjectMinMaxFromPathList( self ):
163 tuple1 = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2")
164 tuple2 = ("1","chr1","10","1","TE2","17","11","1e-20","30","90.2")
165 tuple3 = ("1","chr4","12","22","TE3","22","34","1e-20","30","90.2")
166
167 pathList = self._makePathListFromTupleList([tuple1, tuple2, tuple3])
168 obsTuple = PathUtils.getSubjectMinMaxFromPathList(pathList)
169
170 expTuple = (11,34)
171
172 self.assertEquals(expTuple, obsTuple)
173
174 def test_getSubjectMinMaxFromPathList_on_empty_list( self ):
175 obsTuple = PathUtils.getSubjectMinMaxFromPathList([])
176 expTuple = (-1,-1)
177 self.assertEquals(expTuple, obsTuple)
178
179 def test_getSubjectMinMaxFromPathList_on_list_size1( self ):
180 tuple1 = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2")
181 path1 = Path()
182 path1.setFromTuple(tuple1)
183
184 pathList = [path1]
185 obsTuple = PathUtils.getSubjectMinMaxFromPathList(pathList)
186
187 expTuple = (11,17)
188
189 self.assertEquals(expTuple, obsTuple)
190
191 def test_areQueriesOverlappingBetweenPathLists_list2_empty( self ):
192 tuple1 = ("1","chr1","100","110","TE2","15","10","1e-20","30","90.2")
193 tuple2 = ("1","chr1","200","220","TE2","15","10","1e-20","30","90.2")
194 tuple3 = ("1","chr1","300","330","TE2","15","10","1e-20","30","90.2")
195 pathList1 = self._makePathListFromTupleList([tuple1, tuple2, tuple3])
196
197 pathList2 = []
198
199 expRes = False
200 obsRes = PathUtils.areQueriesOverlappingBetweenPathLists( pathList1, pathList2 )
201
202 self.assertEquals( expRes, obsRes )
203
204 def test_areQueriesOverlappingBetweenPathLists_list2_size1( self ):
205 tuple1 = ("1","chr1","9","11","TE2","150","200","1e-20","30","90.2")
206 tuple2 = ("1","chr1","20","22","TE2","150","200","1e-20","30","90.2")
207 tuple3 = ("1","chr1","30","33","TE2","150","200","1e-20","30","90.2")
208 pathList1 = self._makePathListFromTupleList( [ tuple1, tuple2, tuple3 ] )
209
210 tuple11 = ("1","chr1","8","11","TE2","150","200","1e-20","30","90.2")
211 pathList2 = self._makePathListFromTupleList( [ tuple11 ] )
212
213 expRes = True
214 obsRes = PathUtils.areQueriesOverlappingBetweenPathLists( pathList1, pathList2 )
215
216 self.assertEquals( expRes, obsRes )
217
218 def test_areQueriesOverlappingBetweenPathLists_list1_greater_list2( self ):
219 tuple1 = ("1","chr1","100","110","TE2","15","10","1e-20","30","90.2")
220 tuple2 = ("1","chr1","200","220","TE2","15","10","1e-20","30","90.2")
221 tuple3 = ("1","chr1","300","330","TE2","15","10","1e-20","30","90.2")
222 pathList1 = self._makePathListFromTupleList( [ tuple1, tuple2, tuple3 ] )
223
224 tuple11 = ("1","chr1","10","11","TE2","150","200","1e-20","30","90.2")
225 tuple22 = ("1","chr1","20","22","TE2","150","200","1e-20","30","90.2")
226 tuple33 = ("1","chr1","30","33","TE2","150","200","1e-20","30","90.2")
227 pathList2 = self._makePathListFromTupleList( [ tuple11, tuple22, tuple33 ] )
228
229 expRes = False
230 obsRes = PathUtils.areQueriesOverlappingBetweenPathLists( pathList1, pathList2 )
231
232 self.assertEquals( expRes, obsRes )
233
234 def test_areQueriesOverlappingBetweenPathLists_unordered_first_item_of_list1_greater_second_item_smaller( self ):
235 tuple1 = ("1","chr1","400","440","TE2","15","10","1e-20","30","90.2")
236 tuple2 = ("1","chr1","1","11","TE2","15","10","1e-20","30","90.2")
237 pathList1 = self._makePathListFromTupleList( [ tuple1, tuple2 ] )
238
239 tuple11 = ("1","chr1","15","17","TE2","150","200","1e-20","30","90.2")
240 tuple22 = ("1","chr1","20","22","TE2","150","200","1e-20","30","90.2")
241 tuple33 = ("1","chr1","30","33","TE2","150","200","1e-20","30","90.2")
242 pathList2 = self._makePathListFromTupleList( [ tuple11, tuple22, tuple33 ] )
243
244 expRes = False
245 obsRes = PathUtils.areQueriesOverlappingBetweenPathLists( pathList1, pathList2 )
246
247 self.assertEquals( expRes, obsRes )
248
249 def test_areQueriesOverlappingBetweenPathLists_unorderd_second_item_of_list1_overlap_first_item( self ):
250 tuple1 = ("1","chr1","400","440","TE2","15","10","1e-20","30","90.2")
251 tuple2 = ("1","chr1","1","18","TE2","15","10","1e-20","30","90.2")
252 pathList1 = self._makePathListFromTupleList( [ tuple1, tuple2 ] )
253
254 tuple11 = ("1","chr1","15","17","TE2","150","200","1e-20","30","90.2")
255 tuple22 = ("1","chr1","20","22","TE2","150","200","1e-20","30","90.2")
256 tuple33 = ("1","chr1","30","33","TE2","150","200","1e-20","30","90.2")
257 pathList2 = self._makePathListFromTupleList( [ tuple11, tuple22, tuple33 ] )
258
259 expRes = True
260 obsRes = PathUtils.areQueriesOverlappingBetweenPathLists( pathList1, pathList2 )
261
262 self.assertEquals( expRes, obsRes )
263
264 def test_areQueriesOverlappingBetweenPathLists_last_item_list1_overlap_last_item_list2( self ):
265 tuple1 = ("1","chr1","400","440","TE2","15","10","1e-20","30","90.2")
266 tuple2 = ("1","chr1","320","340","TE2","15","10","1e-20","30","90.2")
267 pathList1 = self._makePathListFromTupleList( [ tuple1, tuple2 ] )
268
269 tuple11 = ("1","chr1","100","110","TE2","150","200","1e-20","30","90.2")
270 tuple22 = ("1","chr1","200","220","TE2","150","200","1e-20","30","90.2")
271 tuple33 = ("1","chr1","300","330","TE2","150","200","1e-20","30","90.2")
272 pathList2 = self._makePathListFromTupleList( [ tuple11, tuple22, tuple33 ] )
273
274 expRes = True
275 obsRes = PathUtils.areQueriesOverlappingBetweenPathLists( pathList1, pathList2 )
276
277 self.assertEquals( expRes, obsRes )
278
279 def test_writeListInFile( self ):
280 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
281 line2 = ("1\tchr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
282 line3 = ("1\tchr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
283
284 expFileName = "expFileName.path"
285 expFileHandle = open ( expFileName, 'w' )
286 expFileHandle.write(line1)
287 expFileHandle.write(line2)
288 expFileHandle.write(line3)
289 expFileHandle.close()
290
291 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
292 line2 = ("1\tchr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
293 line3 = ("1\tchr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
294
295 obsFileName = "obsFileName.path"
296 obsPathList = self._makePathListFromStringList( [ line1, line2, line3 ] )
297
298 PathUtils.writeListInFile( obsPathList, obsFileName )
299
300 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
301
302 os.remove( obsFileName )
303 os.remove( expFileName )
304
305 def test_writeListInFile_in_append_mode( self ):
306 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
307 line2 = ("1\tchr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
308 line3 = ("1\tchr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
309 line4 = ("1\tchr1\t400\t410\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
310 line5 = ("1\tchr1\t500\t520\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
311 line6 = ("1\tchr1\t600\t630\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
312
313 expFileName = "expFileName.path"
314 expFileHandle = open ( expFileName, 'w' )
315 expFileHandle.write(line1)
316 expFileHandle.write(line2)
317 expFileHandle.write(line3)
318 expFileHandle.write(line4)
319 expFileHandle.write(line5)
320 expFileHandle.write(line6)
321 expFileHandle.close()
322
323 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
324 line2 = ("1\tchr1\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
325 line3 = ("1\tchr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.200000\n")
326 line4 = ("1\tchr1\t400\t410\tTE2\t150\t200\t1e-20\t30\t90.2\n")
327 line5 = ("1\tchr1\t500\t520\tTE2\t150\t200\t1e-20\t30\t90.2\n")
328 line6 = ("1\tchr1\t600\t630\tTE2\t150\t200\t1e-20\t30\t90.2\n")
329
330 obsFileName = "obsFileName.path"
331 obsFileHandle = open( obsFileName, 'w' )
332 obsFileHandle.write(line1)
333 obsFileHandle.write(line2)
334 obsFileHandle.write(line3)
335 obsFileHandle.close()
336
337 obsPathList = self._makePathListFromStringList( [ line4, line5, line6 ] )
338
339 PathUtils.writeListInFile( obsPathList, obsFileName, "a" )
340
341 self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
342
343 os.remove(obsFileName)
344 os.remove(expFileName)
345
346 def test_getPathListWithoutDuplicates_empty_list( self ):
347 pathList = []
348 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
349
350 expPathList = []
351
352 self.assertEquals( expPathList, obsPathList )
353
354 def test_getPathListWithoutDuplicates_list_size1( self ):
355 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
356 pathList = self._makePathListFromStringList([line1])
357
358 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
359
360 expPathList = pathList
361
362 self.assertEquals( expPathList, obsPathList )
363
364 def test_getPathListWithoutDuplicates_list_with_only_doublons( self ):
365 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
366 line2 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
367 line3 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
368 line4 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
369 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4 ] )
370
371 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
372
373 expPathList = self._makePathListFromStringList( [ line1 ] )
374
375 self.assertEquals( expPathList, obsPathList )
376
377 def test_getPathListWithoutDuplicates_list_with_doublons_at_start_and_at_end( self ):
378 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
379 line2 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
380 line3 = ("1\tchr1\t300\t310\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
381 line4 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
382 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4 ] )
383
384 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
385
386 expPathList = self._makePathListFromStringList( [ line1, line2, line3 ] )
387 expPathList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( expPathList )
388
389 self.assertEquals( expPathList, obsPathList )
390
391 def test_getPathListWithoutDuplicates_list_with_contiguus_doublons( self ):
392 line1 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
393 line2 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
394 line3 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
395 line4 = ("1\tchr1\t300\t310\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
396 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4 ] )
397
398 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
399
400 expPathList = self._makePathListFromStringList( [ line1, line2, line4 ] )
401 expPathList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( expPathList )
402
403 self.assertEquals( expPathList, obsPathList )
404
405 def test_getPathListWithoutDuplicates_list_with_one_doublon( self ):
406 line1 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
407 line2 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
408 line3 = ("1\tchr1\t210\t250\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
409 line4 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
410 line5 = ("1\tchr1\t300\t310\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
411 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4, line5 ] )
412
413 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
414
415 expPathList = self._makePathListFromStringList( [ line1, line2, line3, line5 ] )
416 expPathList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( expPathList )
417
418 self.assertEquals( expPathList, obsPathList )
419
420 def test_getPathListWithoutDuplicates_list_with_two_doublons( self ):
421 line1 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
422 line2 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
423 line3 = ("1\tchr1\t210\t250\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
424 line4 = ("1\tchr1\t230\t250\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
425 line5 = ("1\tchr1\t210\t250\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
426 line6 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
427 line7 = ("1\tchr1\t300\t310\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
428 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4, line5, line6, line7 ] )
429
430 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
431
432 expPathList = self._makePathListFromStringList( [ line1, line2, line3, line4, line7 ] )
433 expPathList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( expPathList )
434
435 self.assertEquals( expPathList, obsPathList )
436
437 def test_getPathListWithoutDuplicates_list_with_two_doublons_useOnlyCoord_is_False_different_id( self ):
438 line1 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
439 line2 = ("2\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
440 line3 = ("3\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
441 line4 = ("4\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
442 line5 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
443 line6 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
444 line7 = ("5\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
445 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4, line5, line6, line7 ] )
446
447 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList )
448
449 expPathList = self._makePathListFromStringList( [ line1, line2, line3, line4, line7 ] )
450 expPathList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( expPathList )
451
452 self.assertEquals( expPathList, obsPathList )
453
454 def test_getPathListWithoutDuplicates_list_with_two_doublons_useOnlyCoord_is_True_different_id( self ):
455 line1 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
456 line2 = ("2\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
457 line3 = ("3\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
458 line4 = ("4\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
459 line5 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
460 line6 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
461 line7 = ("5\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
462 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4, line5, line6, line7 ] )
463
464 obsPathList = PathUtils.getPathListWithoutDuplicates( pathList, True )
465
466 expPathList = self._makePathListFromStringList( [ line1 ] )
467 expPathList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( expPathList )
468
469 self.assertEquals( expPathList, obsPathList )
470
471 def test_path_getDictOfListsWithIdAsKey_empty_list( self ):
472 pathList = []
473
474 obsDict = PathUtils.getDictOfListsWithIdAsKey( pathList )
475 expDict = {}
476
477 self.assertEquals( expDict, obsDict )
478
479 def test_path_getDictOfListsWithIdAsKey_list_size1( self ):
480 line1 = ( "1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
481 pathList = self._makePathListFromStringList( [ line1 ] )
482
483 obsDict = PathUtils.getDictOfListsWithIdAsKey( pathList )
484
485 expPathInstance = Path()
486 expPathInstance.setFromString( line1 )
487 expDict = { 1: [ expPathInstance ] }
488
489 self.assertEquals( expDict, obsDict )
490
491 def test_getDictOfListsWithIdAsKey_ids_only_once( self ):
492 line1 = ( "1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
493 line2 = ( "2\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
494 line3 = ( "3\tchr1\t210\t250\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
495
496 pathList = self._makePathListFromStringList( [ line1, line2, line3 ] )
497
498 obsDict = PathUtils.getDictOfListsWithIdAsKey( pathList )
499
500 expPathInstance1 = Path()
501 expPathInstance1.setFromString( line1 )
502
503 expPathInstance2 = Path()
504 expPathInstance2.setFromString( line2 )
505
506 expPathInstance3 = Path()
507 expPathInstance3.setFromString( line3 )
508
509 expDict = { 1: [ expPathInstance1 ], 2: [ expPathInstance2 ], 3: [ expPathInstance3 ] }
510
511 self.assertEquals( expDict, obsDict )
512
513 def test_getDictOfListsWithIdAsKey_ids_more_than_only_once( self ):
514 line1 = ( "1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
515 line2 = ( "2\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
516 line3 = ( "3\tchr1\t210\t250\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
517
518 line4 = ( "1\tchr1\t100\t120\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
519 line5 = ( "2\tchr1\t200\t220\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
520 line6 = ( "3\tchr1\t210\t260\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
521
522 line7 = ( "1\tchr1\t110\t120\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
523 line8 = ( "2\tchr1\t210\t220\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
524 line9 = ( "3\tchr1\t220\t260\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
525
526 pathList = self._makePathListFromStringList( [ line1, line2, line3, line4, line5, line6, line7, line8, line9 ] )
527
528 obsDict = PathUtils.getDictOfListsWithIdAsKey( pathList )
529
530 expPathInstance1 = Path()
531 expPathInstance1.setFromString( line1 )
532
533 expPathInstance2 = Path()
534 expPathInstance2.setFromString( line2 )
535
536 expPathInstance3 = Path()
537 expPathInstance3.setFromString( line3 )
538
539 expPathInstance4 = Path()
540 expPathInstance4.setFromString( line4 )
541
542 expPathInstance5 = Path()
543 expPathInstance5.setFromString( line5 )
544
545 expPathInstance6 = Path()
546 expPathInstance6.setFromString( line6 )
547
548 expPathInstance7 = Path()
549 expPathInstance7.setFromString( line7 )
550
551 expPathInstance8 = Path()
552 expPathInstance8.setFromString( line8 )
553
554 expPathInstance9 = Path()
555 expPathInstance9.setFromString( line9 )
556
557 expDict = { 1: [ expPathInstance1, expPathInstance4, expPathInstance7 ], 2 :[ expPathInstance2, expPathInstance5, expPathInstance8 ], 3: [ expPathInstance3, expPathInstance6, expPathInstance9 ] }
558
559 self.assertEquals( expDict, obsDict )
560
561 def test_getPathListUnjoinedBasedOnQuery_listToKeep_empty_listToUnjoin_empty( self ):
562 pathListToKeep = []
563 pathListToUnjoin = []
564
565 expList = []
566
567 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
568
569 self.assertEquals( expList, obsList )
570
571 def test_getPathListUnjoinedBasedOnQuery_listToKeep_empty_listToUnjoin_size1( self ):
572 pathListToKeep = []
573
574 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
575 pathListToUnjoin = self._makePathListFromStringList( [ line1 ] )
576
577 expList = [ pathListToUnjoin ]
578
579 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
580
581 self.assertEquals( expList, obsList )
582
583 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_empty( self ):
584 lineKeep1 = ("1\tchr1\t1\t11\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
585 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
586
587 pathListToUnjoin = []
588
589 expList = []
590
591 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
592
593 self.assertEquals( expList, obsList )
594
595 def test_getPathListUnjoinedBasedOnQuery_listToKeep_empty( self ):
596 pathListToKeep = []
597
598 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
599 line2 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
600 line3 = ("1\tchr1\t250\t280\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
601 pathListToUnjoin = self._makePathListFromStringList( [ line1, line2, line3 ] )
602
603 expList = [ pathListToUnjoin ]
604
605 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
606
607 self.assertEquals( expList, obsList )
608
609 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_size1( self ):
610 lineKeep1 = ("1\tchr1\t1\t11\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
611 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
612
613 lineUnjoin1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
614 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1 ] )
615
616 expList = [ pathListToUnjoin ]
617
618 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
619
620 self.assertEquals( expList, obsList )
621
622 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_size2_noSplit_minKeep( self ):
623 lineKeep1 = ("1\tchr1\t1\t10\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
624 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
625
626 lineUnjoin1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
627 lineUnjoin2 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
628 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2 ] )
629
630 expList = [ pathListToUnjoin ]
631
632 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
633
634 self.assertEquals( expList, obsList )
635
636 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_size3_noSplit_minKeep( self ):
637 lineKeep1 = ("1\tchr1\t1\t10\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
638 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
639
640 lineUnjoin1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
641 lineUnjoin2 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
642 lineUnjoin3 = ("1\tchr1\t250\t280\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
643 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2, lineUnjoin3 ] )
644
645 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
646
647 expList = [ pathListToUnjoin ]
648
649 self.assertEquals( expList, obsList )
650
651 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_size2_noSplit_minUnjoin( self ):
652 lineKeep1 = ("1\tchr1\t101\t150\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
653 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
654
655 lineUnjoin1 = ("1\tchr1\t1\t10\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
656 lineUnjoin2 = ("1\tchr1\t21\t40\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
657 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2 ] )
658
659 expList = [ pathListToUnjoin ]
660
661 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
662
663 self.assertEquals( expList, obsList )
664
665 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size3_listToUnjoin_size2_oneSplit_minKeep( self ):
666 lineKeep1 = ("1\tchr1\t1\t10\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
667 lineKeep2 = ("1\tchr1\t21\t30\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
668 lineKeep3 = ("1\tchr1\t61\t70\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
669 pathListToKeep = self._makePathListFromStringList( [ lineKeep1, lineKeep2, lineKeep3 ] )
670
671 lineUnjoin1 = ("1\tchr1\t41\t50\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
672 lineUnjoin2 = ("1\tchr1\t81\t90\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
673 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2 ] )
674
675 expList = []
676 expList.append( self._makePathListFromStringList( [ lineUnjoin1 ] ) )
677 expList.append( self._makePathListFromStringList( [ lineUnjoin2 ] ) )
678
679 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
680
681 self.assertEquals( expList, obsList )
682
683 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size3_listToUnjoin_size3_twoSplits_minUnjoin( self ):
684 lineKeep1 = ("1\tchr1\t21\t30\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
685 lineKeep2 = ("1\tchr1\t41\t50\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
686 lineKeep3 = ("1\tchr1\t81\t90\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
687 pathListToKeep = self._makePathListFromStringList( [ lineKeep1, lineKeep2, lineKeep3 ] )
688
689 lineUnjoin1 = ("1\tchr1\t1\t10\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
690 lineUnjoin2 = ("1\tchr1\t61\t70\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
691 lineUnjoin3 = ("1\tchr1\t101\t110\tTE2\t150\t90\t0.000000\t30\t90.200000\n")
692 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2, lineUnjoin3 ] )
693
694 expList = []
695 expList.append( self._makePathListFromStringList( [ lineUnjoin1 ] ) )
696 expList.append( self._makePathListFromStringList( [ lineUnjoin2 ] ) )
697 expList.append( self._makePathListFromStringList( [ lineUnjoin3 ] ) )
698
699 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
700
701 self.assertEquals( expList, obsList )
702
703 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_size2_split( self ):
704 lineKeep1 = ("1\tchr1\t51\t80\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
705 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
706
707 lineUnjoin1 = ("1\tchr1\t21\t40\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
708 lineUnjoin2 = ("1\tchr1\t101\t150\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
709 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2 ] )
710
711 expList = []
712 expList.append( self._makePathListFromStringList( [ lineUnjoin1 ] ) )
713 expList.append( self._makePathListFromStringList( [ lineUnjoin2 ] ) )
714
715 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
716
717 self.assertEquals( expList, obsList )
718
719 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size2_listToUnjoin_size2_split( self ):
720 lineKeep1 = ("1\tchr1\t1\t15\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
721 lineKeep2 = ("1\tchr1\t81\t130\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
722 pathListToKeep = self._makePathListFromStringList( [ lineKeep1, lineKeep2 ] )
723
724 lineUnjoin1 = ("1\tchr1\t21\t40\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
725 lineUnjoin2 = ("1\tchr1\t201\t250\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
726 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2 ] )
727
728 expList = []
729 expList.append( self._makePathListFromStringList( [ lineUnjoin1 ] ) )
730 expList.append( self._makePathListFromStringList( [ lineUnjoin2 ] ) )
731
732 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
733
734 self.assertEquals( expList, obsList )
735
736 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_ordered_OneSplit( self ):
737 lineKeep1 = ("1\tchr1\t120\t180\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
738 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
739
740 lineUnjoin1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
741 lineUnjoin2 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
742 lineUnjoin3 = ("1\tchr1\t250\t280\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
743 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2, lineUnjoin3 ] )
744
745 expList = []
746 expList.append( self._makePathListFromStringList( [ lineUnjoin1 ] ) )
747 expList.append( self._makePathListFromStringList( [ lineUnjoin2, lineUnjoin3 ] ) )
748
749 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
750
751 self.assertEquals( expList, obsList )
752
753 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size1_listToUnjoin_unordered_OneSplit( self ):
754 lineKeep1 = ("1\tchr1\t120\t180\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
755 pathListToKeep = self._makePathListFromStringList( [ lineKeep1 ] )
756
757 lineUnjoin1 = ("1\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
758 lineUnjoin2 = ("1\tchr1\t250\t280\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
759 lineUnjoin3 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
760 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2, lineUnjoin3 ] )
761
762 expList = []
763 expList.append( self._makePathListFromStringList( [ lineUnjoin3 ] ) )
764 expList.append( self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2 ] ) )
765
766 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
767
768 self.assertEquals( expList, obsList )
769
770 def test_getPathListUnjoinedBasedOnQuery_listToKeep_size2_listToUnjoin_size4_twoSplits( self ):
771 lineKeep1 = ("1\tchr1\t21\t30\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
772 lineKeep2 = ("1\tchr1\t81\t90\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
773 pathListToKeep = self._makePathListFromStringList( [ lineKeep1, lineKeep2 ] )
774
775 lineUnjoin1 = ("1\tchr1\t1\t10\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
776 lineUnjoin2 = ("1\tchr1\t41\t50\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
777 lineUnjoin3 = ("1\tchr1\t61\t70\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
778 lineUnjoin4 = ("1\tchr1\t101\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
779 pathListToUnjoin = self._makePathListFromStringList( [ lineUnjoin1, lineUnjoin2, lineUnjoin3, lineUnjoin4 ] )
780
781 expList = []
782 expList.append( self._makePathListFromStringList( [ lineUnjoin1 ] ) )
783 expList.append( self._makePathListFromStringList( [ lineUnjoin2, lineUnjoin3 ] ) )
784 expList.append( self._makePathListFromStringList( [ lineUnjoin4 ] ) )
785
786 obsList = PathUtils.getPathListUnjoinedBasedOnQuery( pathListToKeep, pathListToUnjoin )
787
788 self.assertEquals( expList, obsList )
789
790 def test_changeIdInList_empty_list ( self ):
791 pathList = []
792
793 PathUtils.changeIdInList(pathList,1)
794
795 obsList = pathList
796 expList = []
797
798 self.assertEquals(expList, obsList)
799
800 def test_changeIdInList_list_size1 ( self ):
801 line1 = ("1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
802 line2 = ("2\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n")
803
804 pathList = self._makePathListFromStringList([line1])
805 PathUtils.changeIdInList(pathList,2)
806
807 expPathList = pathList
808
809 obsPathList = self._makePathListFromStringList([line2])
810
811 self.assertEquals(expPathList, obsPathList)
812
813 def test_changeIdInList( self ):
814 line1 = ( "1\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
815 line2 = ( "2\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
816 line3 = ( "3\tchr1\t300\t310\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
817
818 pathList = self._makePathListFromStringList( [ line1, line2, line3 ] )
819 PathUtils.changeIdInList( pathList, 2 )
820 obsPathList = pathList
821
822 line11 = ( "2\tchr1\t100\t110\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
823 line22 = ( "2\tchr1\t200\t210\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
824 line33 = ( "2\tchr1\t300\t310\tTE2\t150\t200\t0.000000\t30\t90.200000\n" )
825
826 expPathList = self._makePathListFromStringList( [ line11, line22, line33 ] )
827
828 self.assertEquals( expPathList, obsPathList )
829
830
831 def test_getIdentityFromPathList( self ):
832 p1 = Path()
833 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
834 p2 = Path()
835 p2.setFromTuple( ( "2", "qry1", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
836 lPaths = [ p1, p2 ]
837 exp = ( 90.0 * ( 100-1+1) + 91.2 * (350-121+1) ) / ( (100-1+1) + (350-121+1) ) # 90.836363636363643
838 obs = PathUtils.getIdentityFromPathList( lPaths )
839 self.assertEqual( exp, obs )
840
841
842 def test_getIdentityFromPathList_withOverlap( self ):
843 p1 = Path()
844 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
845 p2 = Path()
846 p2.setFromTuple( ( "2", "qry1", "21", "80", "sbj1", "21", "80", "0.0", "176", "91.2" ) )
847 p3 = Path()
848 p3.setFromTuple( ( "2", "qry1", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
849 lPaths = [ p1, p2, p3 ]
850 exp = ( 91.2 * ( 100-1+1) + 91.2 * (350-121+1) ) / ( (100-1+1) + (350-121+1) )
851 obs = PathUtils.getIdentityFromPathList( lPaths )
852 self.assertEqual( exp, obs )
853
854
855 def test_getIdentityFromPathList_diffQueries( self ):
856 p1 = Path()
857 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
858 p2 = Path()
859 p2.setFromTuple( ( "2", "qry2", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
860 lPaths = [ p1, p2 ]
861 try:
862 obs = PathUtils.getIdentityFromPathList( lPaths )
863 except:
864 pass
865
866
867 def test_getIdentityFromPathList_diffSubjects_check( self ):
868 p1 = Path()
869 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
870 p2 = Path()
871 p2.setFromTuple( ( "1", "qry1", "121", "350", "sbj2", "101", "200", "0.0", "176", "91.2" ) )
872 lPaths = [ p1, p2 ]
873 try:
874 obs = PathUtils.getIdentityFromPathList( lPaths, True )
875 except:
876 pass
877
878
879 def test_getIdentityFromPathList_diffSubjects_noCheck( self ):
880 p1 = Path()
881 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
882 p2 = Path()
883 p2.setFromTuple( ( "1", "qry1", "121", "350", "sbj2", "101", "200", "0.0", "176", "91.2" ) )
884 lPaths = [ p1, p2 ]
885 exp = ( 90.0 * ( 100-1+1) + 91.2 * (350-121+1) ) / ( (100-1+1) + (350-121+1) ) # 90.836363636363643
886 obs = PathUtils.getIdentityFromPathList( lPaths, False )
887 self.assertEqual( exp, obs )
888
889
890 def test_getPathListSortedByIncreasingMinQueryThenMaxQuery_alreadyOrdered_diffIdentifier( self ):
891 p1 = Path()
892 p1.setFromTuple( ( "1", "qry1", "1", "10", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
893 p2 = Path()
894 p2.setFromTuple( ( "2", "qry1", "21", "30", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
895 lPaths = [ p1, p2 ]
896
897 expList = [ p1, p2 ]
898
899 obsList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths )
900
901 self.assertEqual( expList, obsList )
902
903 def test_getPathListSortedByIncreasingMinQueryThenMaxQuery_unordered_diffIdentifier( self ):
904 p1 = Path()
905 p1.setFromTuple( ( "2", "qry1", "21", "30", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
906 p2 = Path()
907 p2.setFromTuple( ( "1", "qry1", "1", "10", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
908 lPaths = [ p1, p2 ]
909
910 expList = [ p2, p1 ]
911
912 obsList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths )
913
914 self.assertEqual( expList, obsList )
915
916 def test_getPathListSortedByIncreasingMinQueryThenMaxQuery_unordered_sameIdentifier( self ):
917 p1 = Path()
918 p1.setFromTuple( ( "1", "qry1", "21", "30", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
919 p2 = Path()
920 p2.setFromTuple( ( "1", "qry1", "1", "10", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
921 lPaths = [ p1, p2 ]
922
923 expList = [ p2, p1 ]
924
925 obsList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths )
926
927 self.assertEqual( expList, obsList )
928
929 def test_getPathListSortedByIncreasingMinQueryThenMaxQuery_unordered_overlapping( self ):
930 p1 = Path()
931 p1.setFromTuple( ( "1", "qry1", "6", "15", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
932 p2 = Path()
933 p2.setFromTuple( ( "2", "qry1", "1", "10", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
934 lPaths = [ p1, p2 ]
935
936 expList = [ p2, p1 ]
937
938 obsList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths )
939
940 self.assertEqual( expList, obsList )
941
942 def test_getPathListSortedByIncreasingMinQueryThenMaxQuery_unordered_sameMin_threeSets( self ):
943 p1 = Path()
944 p1.setFromTuple( ( "1", "qry1", "1", "15", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
945 p2 = Path()
946 p2.setFromTuple( ( "2", "qry1", "1", "10", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
947 p3 = Path()
948 p3.setFromTuple( ( "2", "qry1", "1", "12", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
949 lPaths = [ p1, p2, p3 ]
950
951 expList = [ p2, p3, p1 ]
952
953 obsList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths )
954
955 self.assertEqual( expList, obsList )
956
957 def test_getPathListSortedByIncreasingMinQueryThenMaxQuery_unordered_included( self ):
958 p1 = Path()
959 p1.setFromTuple( ( "1", "qry1", "2", "4", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
960 p2 = Path()
961 p2.setFromTuple( ( "2", "qry1", "1", "5", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
962 lPaths = [ p1, p2 ]
963
964 expList = [ p2, p1 ]
965
966 obsList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQuery( lPaths )
967
968 self.assertEqual( expList, obsList )
969
970 def test_getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier_sameCoord_diffId( self ):
971 p1 = Path()
972 p1.setFromTuple( ( "1", "qry1", "1", "5", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
973 p2 = Path()
974 p2.setFromTuple( ( "2", "qry1", "1", "5", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
975 lPaths = [ p2, p1 ]
976
977 expList = [ p1, p2 ]
978
979 obsList = PathUtils.getPathListSortedByIncreasingMinQueryThenMaxQueryThenIdentifier( lPaths )
980
981 self.assertEqual( expList, obsList )
982
983 def test_getListOfDistinctIdentifiers( self ):
984 p1 = Path()
985 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
986 p2 = Path()
987 p2.setFromTuple( ( "2", "qry1", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
988 p3 = Path()
989 p3.setFromTuple( ( "2", "qry1", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
990 lPaths = [ p1, p2, p3 ]
991 lExp = [ 1, 2 ]
992 lObs = PathUtils.getListOfDistinctIdentifiers( lPaths )
993 lExp.sort()
994 lObs.sort()
995 self.assertEqual( lObs, lExp )
996
997 def test_getListOfDistinctQueryNames( self ):
998 p1 = Path()
999 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
1000 p2 = Path()
1001 p2.setFromTuple( ( "2", "qry2", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
1002 p3 = Path()
1003 p3.setFromTuple( ( "2", "qry2", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
1004 lPaths = [ p1, p2, p3 ]
1005 lExp = [ "qry1", "qry2" ]
1006 lObs = PathUtils.getListOfDistinctQueryNames( lPaths )
1007 lExp.sort()
1008 lObs.sort()
1009 self.assertEqual( lObs, lExp )
1010
1011 def test_getListOfDistinctSubjectNames( self ):
1012 p1 = Path()
1013 p1.setFromTuple( ( "1", "qry1", "1", "100", "sbj1", "1", "100", "0.0", "239", "90.0" ) )
1014 p2 = Path()
1015 p2.setFromTuple( ( "2", "qry2", "121", "350", "sbj1", "101", "200", "0.0", "176", "91.2" ) )
1016 p3 = Path()
1017 p3.setFromTuple( ( "2", "qry2", "121", "350", "sbj2", "101", "200", "0.0", "176", "91.2" ) )
1018 lPaths = [ p1, p2, p3 ]
1019 lExp = [ "sbj1", "sbj2" ]
1020 lObs = PathUtils.getListOfDistinctSubjectNames( lPaths )
1021 lExp.sort()
1022 lObs.sort()
1023 self.assertEqual( lObs, lExp )
1024
1025 def test_getListOfJoinCoordinatesOnQuery_returnCoord( self ):
1026 p1a = Path()
1027 p1a.setFromTuple( ( "1", "qry1", "1", "500", "sbj1", "1", "500", "0.0", "532", "95.0" ) )
1028 p1b = Path()
1029 p1b.setFromTuple( ( "1", "qry1", "701", "900", "sbj1", "501", "700", "0.0", "232", "95.3" ) )
1030 lExp = [ [ 501, 700 ] ]
1031 lPaths = [ p1a, p1b ]
1032 lObs = PathUtils.getListOfJoinCoordinatesOnQuery( lPaths )
1033 lExp.sort()
1034 lObs.sort()
1035 self.assertEqual( lObs, lExp )
1036
1037 def test_getListOfJoinCoordinatesOnQuery_overlap( self ):
1038 p1a = Path()
1039 p1a.setFromTuple( ( "1", "qry1", "1", "500", "sbj1", "1", "500", "0.0", "532", "95.0" ) )
1040 p1b = Path()
1041 p1b.setFromTuple( ( "1", "qry1", "491", "900", "sbj1", "501", "770", "0.0", "232", "95.3" ) )
1042 lExp = []
1043 lPaths = [ p1a, p1b ]
1044 minLength = 100
1045 lObs = PathUtils.getListOfJoinCoordinatesOnQuery( lPaths, minLength )
1046 lExp.sort()
1047 lObs.sort()
1048 self.assertEqual( lObs, lExp )
1049
1050 def test_getListOfJoinCoordinates_tooShort( self ):
1051 p1a = Path()
1052 p1a.setFromTuple( ( "1", "qry1", "1", "500", "sbj1", "1", "500", "0.0", "532", "95.0" ) )
1053 p1b = Path()
1054 p1b.setFromTuple( ( "1", "qry1", "551", "900", "sbj1", "501", "750", "0.0", "232", "95.3" ) )
1055 lExp = []
1056 lPaths = [ p1a, p1b ]
1057 minLength = 100
1058 lObs = PathUtils.getListOfJoinCoordinatesOnQuery( lPaths, minLength )
1059 lExp.sort()
1060 lObs.sort()
1061 self.assertEqual( lObs, lExp )
1062
1063 def test_getLengthOnQueryFromPathList( self ):
1064 p1 = Path()
1065 p1.setFromTuple( ( "1", "qry1", "1", "70", "sbj1", "1", "70", "0.0", "132", "95.0" ) )
1066 p2 = Path()
1067 p2.setFromTuple( ( "2", "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1068 lPaths = [ p1, p2 ]
1069 exp = 90
1070 obs = PathUtils.getLengthOnQueryFromPathList( lPaths )
1071 self.assertEqual( obs, exp )
1072
1073 def test_convertPathFileIntoAlignFile( self ):
1074 pathFile = "dummyPathFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1075 pathFileHandler = open( pathFile, "w" )
1076 pathFileHandler.write( "3\tchr2\t250\t151\tseq5\t1\t100\t1e-31\t147\t98.3\n" )
1077 pathFileHandler.close()
1078
1079 expFile = "dummyExpFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1080 expFileHandler = open( expFile, "w" )
1081 expFileHandler.write( "chr2\t151\t250\tseq5\t100\t1\t1e-31\t147\t98.300000\n" )
1082 expFileHandler.close()
1083
1084 obsFile = "dummyObsFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1085
1086 PathUtils.convertPathFileIntoAlignFile( pathFile, obsFile )
1087
1088 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1089
1090 for f in [ pathFile, expFile, obsFile ]:
1091 if os.path.exists( f ):
1092 os.remove ( f )
1093
1094 def test_convertPathFileIntoMapFileWithQueryCoordsOnly( self ):
1095 pathFile = "dummyPathFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1096 pathFileHandler = open( pathFile, "w" )
1097 pathFileHandler.write( "3\tchr2\t250\t151\tseq5\t1\t100\t1e-31\t147\t98.3\n" )
1098 pathFileHandler.write( "4\tchr2\t191\t230\tseq8\t237\t387\t1e-11\t187\t95.3\n" )
1099 pathFileHandler.write( "3\tchr2\t500\t301\tseq5\t101\t300\t1e-81\t247\t96.2\n" )
1100 pathFileHandler.close()
1101
1102 expFile = "dummyExpFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1103 expFileHandler = open( expFile, "w" )
1104 expFileHandler.write( "seq5\tchr2\t250\t151\n" )
1105 expFileHandler.write( "seq8\tchr2\t191\t230\n" )
1106 expFileHandler.write( "seq5\tchr2\t500\t301\n" )
1107 expFileHandler.close()
1108
1109 obsFile = "dummyObsFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1110
1111 PathUtils.convertPathFileIntoMapFileWithQueryCoordsOnly( pathFile, obsFile )
1112
1113 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1114
1115 for f in [ pathFile, expFile, obsFile ]:
1116 if os.path.exists( f ):
1117 os.remove( f )
1118
1119
1120 def test_mergeMatchesOnQueries( self ):
1121 pathFile = "dummyPathFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1122 pathFileHandler = open( pathFile, "w" )
1123 pathFileHandler.write( "3\tchr2\t250\t151\tseq5\t1\t100\t1e-31\t147\t98.3\n" )
1124 pathFileHandler.write( "4\tchr2\t230\t191\tseq8\t237\t387\t1e-11\t187\t95.3\n" )
1125 pathFileHandler.write( "3\tchr2\t500\t301\tseq5\t101\t300\t1e-81\t247\t96.2\n" )
1126 pathFileHandler.close()
1127
1128 expFile = "dummyExpFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1129 expFileHandler = open( expFile, "w" )
1130 expFileHandler.write( "0\tchr2\t151\t250\tseq5\t0\t0\t0.0\t0\t0\n" )
1131 expFileHandler.write( "0\tchr2\t301\t500\tseq5\t0\t0\t0.0\t0\t0\n" )
1132 expFileHandler.close()
1133
1134 obsFile = "dummyObsFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1135
1136 PathUtils.mergeMatchesOnQueries( pathFile, obsFile )
1137
1138 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1139
1140 for f in [ pathFile, expFile, obsFile ]:
1141 if os.path.exists( f ):
1142 os.remove( f )
1143
1144
1145 def test_filterPathListOnChainLength( self ):
1146 p1a = Path()
1147 p1a.setFromTuple( ( "1", "qry1", "1", "12", "sbj1", "1", "12", "0.0", "132", "95.0" ) )
1148 p1b = Path()
1149 p1b.setFromTuple( ( "1", "qry1", "15", "30", "sbj1", "13", "28", "0.0", "132", "95.0" ) )
1150 p2 = Path()
1151 p2.setFromTuple( ( "2", "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1152 p3 = Path()
1153 p3.setFromTuple( ( "3", "qry2", "1", "12", "sbj3", "15", "1", "0.0", "132", "95.0" ) )
1154 lPaths = [ p1a, p1b, p2, p3 ]
1155 lExp = [ p1a, p1b, p2 ]
1156 lObs = PathUtils.filterPathListOnChainLength( lPaths, 20 )
1157 self.assertEqual( lExp, lObs )
1158
1159 def test_getPathListFromFile(self):
1160 file = "dummyFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1161 fileHandler = open( file, "w" )
1162 fileHandler.write( "1\tchr2\t151\t250\tseq5\t0\t0\t0.0\t0\t0\n" )
1163 fileHandler.write( "2\tchr2\t301\t500\tseq5\t0\t0\t0.0\t0\t0\n" )
1164 fileHandler.close()
1165 p1 = Path()
1166 p1.setFromTuple( ( "1", "chr2", "151", "250", "seq5", "0", "0", "0.0", "0", "0" ) )
1167 p2 = Path()
1168 p2.setFromTuple( ( "2", "chr2", "301", "500", "seq5", "0", "0", "0.0", "0", "0" ) )
1169 expLPath = [ p1, p2 ]
1170 obsLPath = PathUtils.getPathListFromFile(file)
1171 expLPathSorted = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength(expLPath)
1172 obsLPathSorted = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength(obsLPath)
1173 os.remove(file)
1174 self.assertEqual( expLPathSorted, obsLPathSorted )
1175
1176 def test_getPathListFromFile_empty_file(self):
1177 file = "dummyFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1178 fileHandler = open( file, "w" )
1179 fileHandler.close()
1180 expLPath = []
1181 obsLPath = PathUtils.getPathListFromFile(file)
1182 expLPathSorted = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength(expLPath)
1183 obsLPathSorted = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength(obsLPath)
1184 os.remove(file)
1185 self.assertEqual( expLPathSorted, obsLPathSorted )
1186
1187 def test_convertPathFileIntoAlignFileViaPathrange_sortedInput( self ):
1188 p1a = Path()
1189 p1a.setFromTuple( ( "1", "qry1", "1", "12", "sbj1", "1", "12", "0.0", "132", "95.0" ) )
1190 p1b = Path()
1191 p1b.setFromTuple( ( "1", "qry1", "16", "30", "sbj1", "13", "28", "1e-270", "150", "97.0" ) )
1192 p2 = Path()
1193 p2.setFromTuple( ( "2", "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1194 inFile = "dummyInFile"
1195 inF = open( inFile, "w" )
1196 for iPath in [ p1a, p1b, p2 ]:
1197 iPath.write( inF )
1198 inF.close()
1199
1200 expFile = "dummyExpFile"
1201 expF = open( expFile, "w" )
1202 a1 = Align()
1203 a1.setFromTuple( ( "qry1", "1", "30", "sbj1", "1", "28", "0.0", "282", str((95*12+97*15)/float(12+15)) ) )
1204 a2 = Align()
1205 a2.setFromTuple( ( "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1206 for iAlign in [ a1, a2 ]:
1207 iAlign.write( expF )
1208 expF.close()
1209
1210 obsFile = "dummyObsFile"
1211
1212 PathUtils.convertPathFileIntoAlignFileViaPathrange( inFile, obsFile, 0 )
1213
1214 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1215
1216 for f in [ inFile, expFile, obsFile ]:
1217 os.remove( f )
1218
1219
1220 def test_convertPathFileIntoAlignFileViaPathrange_unsortedInput( self ):
1221 p1a = Path()
1222 p1a.setFromTuple( ( "1", "qry1", "1", "12", "sbj1", "1", "12", "0.0", "132", "95.0" ) )
1223 p1b = Path()
1224 p1b.setFromTuple( ( "1", "qry1", "16", "30", "sbj1", "13", "28", "0.0", "150", "97.0" ) )
1225 p2 = Path()
1226 p2.setFromTuple( ( "2", "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1227 inFile = "dummyInFile"
1228 inF = open( inFile, "w" )
1229 for iPath in [ p1b, p2, p1a ]:
1230 iPath.write( inF )
1231 inF.close()
1232
1233 expFile = "dummyExpFile"
1234 expF = open( expFile, "w" )
1235 a1 = Align()
1236 a1.setFromTuple( ( "qry1", "1", "30", "sbj1", "1", "28", "0.0", "282", str((95*12+97*15)/float(12+15)) ) )
1237 a2 = Align()
1238 a2.setFromTuple( ( "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1239 for iAlign in [ a1, a2 ]:
1240 iAlign.write( expF )
1241 expF.close()
1242
1243 obsFile = "dummyObsFile"
1244
1245 PathUtils.convertPathFileIntoAlignFileViaPathrange( inFile, obsFile, 0 )
1246
1247 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1248
1249 for f in [ inFile, expFile, obsFile ]:
1250 os.remove( f )
1251
1252
1253 def test_convertPathFileIntoAlignFileViaPathrange_sortedInput_subjectReverseStrand( self ):
1254 p1a = Path()
1255 p1a.setFromTuple( ( "1", "qry1", "1", "12", "sbj1", "12", "1", "0.0", "132", "95.0" ) )
1256 p1b = Path()
1257 p1b.setFromTuple( ( "1", "qry1", "16", "30", "sbj1", "28", "13", "0.0", "150", "97.0" ) )
1258 p2 = Path()
1259 p2.setFromTuple( ( "2", "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1260 inFile = "dummyInFile"
1261 inF = open( inFile, "w" )
1262 for iPath in [ p1a, p1b, p2 ]:
1263 iPath.write( inF )
1264 inF.close()
1265
1266 expFile = "dummyExpFile"
1267 expF = open( expFile, "w" )
1268 a1 = Align()
1269 a1.setFromTuple( ( "qry1", "1", "30", "sbj1", "28", "1", "0.0", "282", str((95*12+97*15)/float(12+15)) ) )
1270 a2 = Align()
1271 a2.setFromTuple( ( "qry1", "51", "90", "sbj2", "40", "1", "0.0", "132", "95.0" ) )
1272 for iAlign in [ a1, a2 ]:
1273 iAlign.write( expF )
1274 expF.close()
1275
1276 obsFile = "dummyObsFile"
1277
1278 PathUtils.convertPathFileIntoAlignFileViaPathrange( inFile, obsFile, 0 )
1279
1280 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1281
1282 for f in [ inFile, expFile, obsFile ]:
1283 os.remove( f )
1284
1285
1286 def test_splitPathListByQueryName_empty_list( self ):
1287 lPath = []
1288
1289 obsLPath = PathUtils.splitPathListByQueryName( lPath )
1290
1291 expLPath = []
1292
1293 self.assertEquals( expLPath, obsLPath )
1294
1295
1296 def test_splitPathListByQueryName( self ):
1297 iPath1 = Path()
1298 iPath1.setFromString("1\tchr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1299 iPath2 = Path()
1300 iPath2.setFromString("2\tchr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1301 iPath3 = Path()
1302 iPath3.setFromString("3\tchr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1303 lPath = [ iPath1, iPath2, iPath3 ]
1304
1305 obsLPath = PathUtils.splitPathListByQueryName( lPath )
1306
1307 expLPath = [ [ iPath1, iPath3 ],
1308 [ iPath2 ] ]
1309
1310 self.assertEquals( expLPath, obsLPath )
1311
1312
1313 def test_splitPathListByQueryName_last_align_alone( self ):
1314 iPath1 = Path()
1315 iPath1.setFromString("1\tchr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1316 iPath2 = Path()
1317 iPath2.setFromString("2\tchr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1318 iPath3 = Path()
1319 iPath3.setFromString("3\tchr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1320 iPath4 = Path()
1321 iPath4.setFromString("4\tchr3\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1322 iPath5 = Path()
1323 iPath5.setFromString("5\tchr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1324 iPath6 = Path()
1325 iPath6.setFromString("6\tchr1\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1326 iPath7 = Path()
1327 iPath7.setFromString("7\tchr1\t100\t110\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1328 iPath8 = Path()
1329 iPath8.setFromString("8\tchr2\t200\t220\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1330 iPath9 = Path()
1331 iPath9.setFromString("9\tchr4\t300\t330\tTE2\t150\t200\t1e-20\t30\t90.2\n")
1332 lPath = [ iPath1, iPath2, iPath3, iPath4, iPath5, iPath6, iPath7, iPath8, iPath9 ]
1333
1334 obsLPath = PathUtils.splitPathListByQueryName( lPath )
1335
1336 expLPath = [ [ iPath1, iPath3, iPath6, iPath7 ],
1337 [ iPath2, iPath5, iPath8 ],
1338 [ iPath4 ],
1339 [ iPath9 ] ]
1340
1341 self.assertEquals( expLPath, obsLPath )
1342
1343
1344 def test_getPathListSortedByIncreasingQueryMinThenInvQueryLength_alreadyOrdered_diffIdentifier( self ):
1345 iPath1 = Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 )
1346 iPath2 = Path( 2, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 )
1347 lPaths = [ iPath1, iPath2 ]
1348
1349 lExp = [ Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 ),
1350 Path( 2, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 ) ]
1351
1352 lObs = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
1353
1354 self.assertEquals( lExp, lObs )
1355
1356
1357 def test_getPathListSortedByIncreasingQueryMinThenInvQueryLength_unordered_diffIdentifier( self ):
1358 iPath1 = Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 )
1359 iPath2 = Path( 2, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 )
1360 lPaths = [ iPath2, iPath1 ]
1361
1362 lExp = [ Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 ),
1363 Path( 2, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 ) ]
1364
1365 lObs = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
1366
1367 self.assertEquals( lExp, lObs )
1368
1369
1370 def test_getPathListSortedByIncreasingQueryMinThenInvQueryLength_unordered_sameIdentifier( self ):
1371 iPath1a = Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 )
1372 iPath1b = Path( 1, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 )
1373 lPaths = [ iPath1b, iPath1a ]
1374
1375 lExp = [ Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 ),
1376 Path( 1, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 ) ]
1377
1378 lObs = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
1379
1380 self.assertEquals( lExp, lObs )
1381
1382
1383 def test_getPathListSortedByIncreasingQueryMinThenInvQueryLength_unordered_overlapping( self ):
1384 iPath1 = Path( 1, Range("qry1",1,6), Range("sbj1",1,6), 0.0, 10, 98.7 )
1385 iPath2 = Path( 2, Range("qry1",5,10), Range("sbj1",5,10), 0.0, 10, 98.7 )
1386 lPaths = [ iPath2, iPath1 ]
1387
1388 lExp = [ Path( 1, Range("qry1",1,6), Range("sbj1",1,6), 0.0, 10, 98.7 ),
1389 Path( 2, Range("qry1",5,10), Range("sbj1",5,10), 0.0, 10, 98.7 ) ]
1390
1391 lObs = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
1392
1393 self.assertEquals( lExp, lObs )
1394
1395
1396 def test_getPathListSortedByIncreasingQueryMinThenInvQueryLength_threePaths_2sameMin( self ):
1397 iPath1 = Path( 1, Range("qry1",1,6), Range("sbj1",1,6), 0.0, 10, 98.7 )
1398 iPath2 = Path( 2, Range("qry1",5,12), Range("sbj1",5,12), 0.0, 10, 98.7 )
1399 iPath3 = Path( 3, Range("qry1",5,10), Range("sbj1",5,10), 0.0, 10, 98.7 )
1400 lPaths = [ iPath3, iPath2, iPath1 ]
1401
1402 lExp = [ Path( 1, Range("qry1",1,6), Range("sbj1",1,6), 0.0, 10, 98.7 ),
1403 Path( 2, Range("qry1",5,12), Range("sbj1",5,12), 0.0, 10, 98.7 ),
1404 Path( 3, Range("qry1",5,10), Range("sbj1",5,10), 0.0, 10, 98.7 ) ]
1405
1406 lObs = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
1407
1408 self.assertEquals( lExp, lObs )
1409
1410
1411 def test_getPathListSortedByIncreasingQueryMinThenInvQueryLength_unordered_included( self ):
1412 iPath1 = Path( 1, Range("qry1",1,6), Range("sbj1",1,6), 0.0, 10, 98.7 )
1413 iPath2 = Path( 2, Range("qry1",2,5), Range("sbj1",2,5), 0.0, 10, 98.7 )
1414 lPaths = [ iPath2, iPath1 ]
1415
1416 lExp = [ Path( 1, Range("qry1",1,6), Range("sbj1",1,6), 0.0, 10, 98.7 ),
1417 Path( 2, Range("qry1",2,5), Range("sbj1",2,5), 0.0, 10, 98.7 ) ]
1418
1419 lObs = PathUtils.getPathListSortedByIncreasingQueryMinThenInvQueryLength( lPaths )
1420
1421 self.assertEquals( lExp, lObs )
1422
1423
1424 def test_mergePathsInList_emptyList( self ):
1425 lPaths = []
1426 lExp = []
1427 lObs = PathUtils.mergePathsInList( lPaths )
1428 self.assertEquals( lExp, lObs )
1429
1430
1431 def test_mergePathsInList_onePath( self ):
1432 iPath1 = Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 )
1433 lPaths = [ iPath1 ]
1434 lExp = [ Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 ) ]
1435 lObs = PathUtils.mergePathsInList( lPaths )
1436 self.assertEquals( lExp, lObs )
1437
1438
1439 def test_mergePathsInList_noOverlap( self ):
1440 iPath1 = Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 )
1441 iPath2 = Path( 1, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 )
1442 lPaths = [ iPath1, iPath2 ]
1443
1444 lExp = [ Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 ),
1445 Path( 1, Range("qry1",21,30), Range("sbj1",11,20), 0.0, 10, 98.7 ) ]
1446
1447 lObs = PathUtils.mergePathsInList( lPaths )
1448
1449 self.assertEquals( lExp, lObs )
1450
1451
1452 def test_mergePathsInList_withOverlap( self ):
1453 iPath1 = Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 )
1454 iPath2 = Path( 1, Range("qry1",6,15), Range("sbj1",6,15), 0.0, 10, 98.7 )
1455 lPaths = [ iPath2, iPath1 ]
1456
1457 lExp = [ Path( 1, Range("qry1",1,15), Range("sbj1",1,15), 0.0, 10, 98.7 ) ]
1458
1459 lObs = PathUtils.mergePathsInList( lPaths )
1460
1461 self.assertEquals( lExp, lObs )
1462
1463
1464 def test_mergePathsInList_withOverlap_reverseOnly( self ):
1465 iPath1 = Path( 1, Range("qry1",10,1), Range("sbj1",10,1), 0.0, 10, 98.7 )
1466 iPath2 = Path( 1, Range("qry1",15,6), Range("sbj1",15,6), 0.0, 10, 98.7 )
1467 lPaths = [ iPath2, iPath1 ]
1468
1469 lExp = [ Path( 1, Range("qry1",15,1), Range("sbj1",15,1), 0.0, 10, 98.7 ) ]
1470
1471 lObs = PathUtils.mergePathsInList( lPaths )
1472
1473 self.assertEquals( lExp, lObs )
1474
1475
1476 def test_mergePathsInList_withOverlap_directAndReverse( self ):
1477 iPath1 = Path( 1, Range("qry1",10,1), Range("sbj1",10,1), 0.0, 10, 98.7 )
1478 iPath2 = Path( 1, Range("qry1",15,6), Range("sbj1",15,6), 0.0, 10, 98.7 )
1479 iPath3 = Path( 1, Range("qry1",2,5), Range("sbj1",2,5), 0.0, 10, 98.7 )
1480 lPaths = [ iPath3, iPath2, iPath1 ]
1481
1482 lExp = [ Path( 1, Range("qry1",15,1), Range("sbj1",15,1), 0.0, 10, 98.7 ) ]
1483
1484 lObs = PathUtils.mergePathsInList( lPaths )
1485
1486 self.assertEquals( lExp, lObs )
1487
1488
1489 def test_mergePathsInList_diffQueries_withOverlap( self ):
1490 iPath1 = Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 )
1491 iPath2 = Path( 2, Range("qry2",6,15), Range("sbj1",6,15), 0.0, 10, 98.7 )
1492 lPaths = [ iPath2, iPath1 ]
1493
1494 lExp = [ Path( 1, Range("qry1",1,10), Range("sbj1",1,10), 0.0, 10, 98.7 ),
1495 Path( 2, Range("qry2",6,15), Range("sbj1",6,15), 0.0, 10, 98.7 ) ]
1496
1497 lObs = PathUtils.mergePathsInList( lPaths )
1498
1499 self.assertEquals( lExp, lObs )
1500
1501
1502 def test_mergePathsInList_nonOverlappingSubjects( self ):
1503 iPath1 = Path( 1, Range("qry1",398,491), Range("sbj1",10,112), 0.0, 10, 98.7 )
1504 iPath2 = Path( 1, Range("qry1",451,492), Range("sbj1",124,169), 0.0, 10, 98.7 )
1505 iPath3 = Path( 1, Range("qry1",493,531), Range("sbj1",249,294), 0.0, 10, 98.7 )
1506 lPaths = [ iPath3, iPath2, iPath1 ]
1507
1508 lExp = [ Path( 1, Range("qry1",398,491), Range("sbj1",10,112), 0.0, 10, 98.7 ),
1509 Path( 1, Range("qry1",451,492), Range("sbj1",124,169), 0.0, 10, 98.7 ),
1510 Path( 1, Range("qry1",493,531), Range("sbj1",249,294), 0.0, 10, 98.7 ) ]
1511
1512 lObs = PathUtils.mergePathsInList( lPaths )
1513
1514 self.assertEquals( lExp, lObs )
1515
1516
1517 def test_mergePathsInListUsingQueryCoordsOnly( self ):
1518 iPath1 = Path( 1, Range("qry1",398,491), Range("sbj1",10,112), 0.0, 10, 98.7 )
1519 iPath2 = Path( 1, Range("qry1",451,492), Range("sbj1",124,169), 0.0, 10, 98.7 )
1520 iPath3 = Path( 1, Range("qry1",493,531), Range("sbj1",249,294), 0.0, 10, 98.7 )
1521 lPaths = [ iPath3, iPath2, iPath1 ]
1522
1523 lExp = [ Path( 1, Range("qry1",398,492), Range("sbj1",10,169), 0.0, 10, 98.7 ),
1524 Path( 1, Range("qry1",493,531), Range("sbj1",249,294), 0.0, 10, 98.7 ) ]
1525
1526 lObs = PathUtils.mergePathsInListUsingQueryCoordsOnly( lPaths )
1527
1528 self.assertEquals( lExp, lObs )
1529
1530
1531 def test_convertPathFileIntoGffFile( self ):
1532 p1 = Path()
1533 p1.setFromTuple( ( "1", "qry1", "12", "1", "sbj1", "1", "12", "0.0", "132", "95.0" ) )
1534 p2a = Path()
1535 p2a.setFromTuple( ( "2", "qry1", "16", "30", "sbj2", "1", "15", "1e-270", "150", "97.0" ) )
1536 p2b = Path()
1537 p2b.setFromTuple( ( "2", "qry1", "51", "90", "sbj2", "21", "60", "0.0", "132", "95.9" ) )
1538 inFile = "dummyInFile"
1539 PathUtils.writeListInFile( [ p1, p2a, p2b ], inFile, "w" )
1540
1541 expFile = "dummyExpFile"
1542 expF = open( expFile, "w" )
1543 expF.write( "qry1\tREPET\tmatch\t1\t12\t0\t-\t.\tID=1;Target=sbj1 1 12\n" )
1544 expF.write( "qry1\tREPET\tmatch\t16\t90\t0\t+\t.\tID=ms2;Target=sbj2 1 60\n" )
1545 expF.write( "qry1\tREPET\tmatch_part\t16\t30\t1e-270\t+\t.\tID=mp2-1;Parent=ms2;Target=sbj2 1 15\n" )
1546 expF.write( "qry1\tREPET\tmatch_part\t51\t90\t0\t+\t.\tID=mp2-2;Parent=ms2;Target=sbj2 21 60\n" )
1547 expF.close()
1548
1549 obsFile = "dummyObsFile"
1550
1551 PathUtils.convertPathFileIntoGffFile( inFile, obsFile )
1552
1553 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1554
1555 for f in [ inFile, expFile, obsFile ]:
1556 os.remove( f )
1557
1558
1559 def test_convertPathFileIntoSetFile( self ):
1560 pathFile = "dummyPathFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1561 pathFileHandler = open( pathFile, "w" )
1562 pathFileHandler.write( "3\tchr2\t250\t151\tseq5\t1\t100\t1e-31\t147\t98.3\n" )
1563 pathFileHandler.close()
1564
1565 expFile = "dummyExpFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1566 expFileHandler = open( expFile, "w" )
1567 expFileHandler.write( "3\tseq5\tchr2\t250\t151\n" )
1568 expFileHandler.close()
1569
1570 obsFile = "dummyObsFile_%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
1571
1572 PathUtils.convertPathFileIntoSetFile( pathFile, obsFile )
1573
1574 self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
1575
1576 for f in [ pathFile, expFile, obsFile ]:
1577 if os.path.exists( f ):
1578 os.remove ( f )
1579
1580
1581 def test_removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName(self):
1582 pathFile = "dummyPathFile"
1583 f = open(pathFile, "w")
1584 f.write("1\tG4\t1\t3856\tAtha5Chr4_Pals_Piler_3590_69_MAP_3\t1\t3856\t0\t7642\t99.9741\n")
1585 f.write("1\tG4\t1\t3856\tAtha5Chr4_Pals_Piler_3590_69_MAP_3\t100\t3956\t0\t7642\t99.9741\n")
1586 f.write("2\trooA\t1\t386\tAtha5Chr4_Pals_Piler_3589_69_MAP_3\t1\t386\t6.3e-220\t758\t99.4819\n")
1587 f.write("3\trooA\t7236\t7621\tAtha5Chr4_Pals_Piler_3536_69_MAP_3\t1\t386\t6.3e-220\t758\t99.4819\n")
1588 f.write("4\trooA\t387\t7235\tAtha5Chr4_Pals_Piler_3596_69_MAP_3\t1\t6849\t0\t13580\t99.9854\n")
1589 f.write("5\taurora-element\t4046\t4257\tAtha5Chr4_Pals_Piler_3540_69_MAP_3\t1\t204\t6.1e-80\t300\t96.5686\n")
1590 f.write("6\taurora-element\t274\t381\tAtha5Chr4_Pals_Piler_3595_23_MAP_3\t177\t284\t0\t191\t97.2222\n")
1591 f.write("6\taurora-element\t116\t287\tAtha5Chr4_Pals_Piler_3595_30_MAP_3\t3\t170\t0\t290\t98.8095\n")
1592 f.write("7\taurora-element\t393\t902\tAtha5Chr4_Pals_Piler_3595_31_MAP_3\t1467\t1945\t0\t873\t97.2441\n")
1593 f.write("7\taurora-element\t393\t902\tAtha5Chr4_Pals_Piler_3595_31_MAP_3\t276\t100784\t0\t869\t98.1211\n")
1594 f.write("7\taurora-element\t1387\t2271\tAtha5Chr4_Pals_Piler_3595_31_MAP_3\t276\t10780\t0\t1576\t97.6244\n")
1595 f.write("8\taurora-element\t2486\t2828\tAtha5Chr4_Pals_Piler_3595_50_MAP_3\t4301\t4641\t0\t585\t97.3607\n")
1596 f.write("9\taurora-element\t2265\t2483\tAtha5Chr4_Pals_Piler_3595_62_MAP_3\t3999\t4218\t0\t361\t96.347\n")
1597 f.write("10\taurora-element\t2834\t4045\tAtha5Chr4_Pals_Piler_3595_69_MAP_3\t4800\t6011\t0\t2074\t97.0248\n")
1598 f.write("11\taurora-element\t2\t113\tAtha5Chr4_Pals_Piler_3598_69_MAP_3\t205\t317\t8.5e-37\t157\t93.75\n")
1599 f.write("11\taurora-element\t2\t113\tAtha5Chr4_Pals_Piler_3598_69_MAP_3\t305\t417\t8.5e-37\t157\t93.75\n")
1600 f.write("11\taurora-element\t2\t113\tAtha5Chr4_Pals_Piler_3598_69_MAP_3\t305\t417\t8.5e-37\t157\t93.75\n")
1601 f.close()
1602
1603 obsPathFile = "obsDummyPathFile"
1604 PathUtils.removeInPathFileDuplicatedPathOnQueryNameQueryCoordAndSubjectName(pathFile, obsPathFile)
1605
1606 expPathFile = "expDummyPathFile"
1607 f = open(expPathFile, "w")
1608 f.write("1\tG4\t1\t3856\tAtha5Chr4_Pals_Piler_3590_69_MAP_3\t1\t3856\t0\t7642\t99.974100\n")
1609 f.write("2\trooA\t1\t386\tAtha5Chr4_Pals_Piler_3589_69_MAP_3\t1\t386\t6.3e-220\t758\t99.481900\n")
1610 f.write("3\trooA\t7236\t7621\tAtha5Chr4_Pals_Piler_3536_69_MAP_3\t1\t386\t6.3e-220\t758\t99.481900\n")
1611 f.write("4\trooA\t387\t7235\tAtha5Chr4_Pals_Piler_3596_69_MAP_3\t1\t6849\t0\t13580\t99.985400\n")
1612 f.write("5\taurora-element\t4046\t4257\tAtha5Chr4_Pals_Piler_3540_69_MAP_3\t1\t204\t6.1e-80\t300\t96.568600\n")
1613 f.write("6\taurora-element\t274\t381\tAtha5Chr4_Pals_Piler_3595_23_MAP_3\t177\t284\t0\t191\t97.222200\n")
1614 f.write("6\taurora-element\t116\t287\tAtha5Chr4_Pals_Piler_3595_30_MAP_3\t3\t170\t0\t290\t98.809500\n")
1615 f.write("7\taurora-element\t393\t902\tAtha5Chr4_Pals_Piler_3595_31_MAP_3\t1467\t1945\t0\t873\t97.244100\n")
1616 f.write("7\taurora-element\t1387\t2271\tAtha5Chr4_Pals_Piler_3595_31_MAP_3\t276\t10780\t0\t1576\t97.624400\n")
1617 f.write("8\taurora-element\t2486\t2828\tAtha5Chr4_Pals_Piler_3595_50_MAP_3\t4301\t4641\t0\t585\t97.360700\n")
1618 f.write("9\taurora-element\t2265\t2483\tAtha5Chr4_Pals_Piler_3595_62_MAP_3\t3999\t4218\t0\t361\t96.347000\n")
1619 f.write("10\taurora-element\t2834\t4045\tAtha5Chr4_Pals_Piler_3595_69_MAP_3\t4800\t6011\t0\t2074\t97.024800\n")
1620 f.write("11\taurora-element\t2\t113\tAtha5Chr4_Pals_Piler_3598_69_MAP_3\t205\t317\t8.5e-37\t157\t93.750000\n")
1621 f.close()
1622
1623 self.assertTrue(FileUtils.are2FilesIdentical(expPathFile, obsPathFile))
1624
1625 os.remove(pathFile)
1626 os.remove(expPathFile)
1627 os.remove(obsPathFile)
1628
1629
1630 def test_getPathListWithoutDuplicatesOnQueryCoord(self):
1631 iPath1 = Path(1, Range("qry1",398,491), Range("sbj1",10,112), 0.0, 10, 98.7)
1632 iPath2 = Path(1, Range("qry1",451,492), Range("sbj1",124,169), 0.0, 10, 98.7)
1633 iPath3 = Path(1, Range("qry1",451,492), Range("sbj1",249,294), 0.0, 10, 98.7)
1634 lPaths = [iPath3, iPath2, iPath1]
1635
1636 obslPaths = PathUtils.getPathListWithoutDuplicatesOnQueryCoord(lPaths)
1637
1638 explPaths = [iPath1, iPath3]
1639
1640 self.assertEquals(explPaths, obslPaths)
1641
1642
1643 def _makePathListFromTupleList ( self, tupleList ):
1644 pathList = []
1645 for tuple in tupleList:
1646 path = Path()
1647 path.setFromTuple(tuple)
1648 pathList.append(path)
1649 return pathList
1650
1651 def _makePathListFromStringList (self, stringList):
1652 pathList = []
1653 for string in stringList:
1654 path = Path()
1655 path.setFromString(string)
1656 pathList.append(path)
1657 return pathList
1658
1659 def _show (self, list):
1660 for item in list:
1661 print item.toString()
1662
1663
1664 test_suite = unittest.TestSuite()
1665 test_suite.addTest( unittest.makeSuite( Test_PathUtils ) )
1666 if __name__ == "__main__":
1667 unittest.TextTestRunner(verbosity=2).run( test_suite )