Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/structure/test/Test_Interval.py @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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| 1 import unittest | |
| 2 from SMART.Java.Python.structure.Interval import Interval | |
| 3 | |
| 4 class Test_Interval(unittest.TestCase): | |
| 5 | |
| 6 def setUp(self): | |
| 7 self.iInterval = Interval() | |
| 8 self.iInterval1 = Interval() | |
| 9 self.iInterval2 = Interval() | |
| 10 | |
| 11 def test__init__(self): | |
| 12 self.iInterval.setChromosome("chromosome") | |
| 13 self.iInterval.setName("sequence") | |
| 14 self.iInterval.setStart(0) | |
| 15 self.iInterval.setEnd(123) | |
| 16 obsStart = self.iInterval.getStart() | |
| 17 obsEnd = self.iInterval.getEnd() | |
| 18 expStart = 0 | |
| 19 expEnd = 123 | |
| 20 | |
| 21 self.assertEqual(expStart, obsStart) | |
| 22 self.assertEqual(expEnd, obsEnd) | |
| 23 | |
| 24 def test_copy(self): | |
| 25 self.iInterval1.setName("interval1") | |
| 26 self.iInterval1.setChromosome("chr1") | |
| 27 self.iInterval1.setStart(100) | |
| 28 self.iInterval1.setEnd(300) | |
| 29 self.iInterval1.setDirection("+") | |
| 30 | |
| 31 self.iInterval2.copy(self.iInterval1) | |
| 32 self.assertEqual(self.iInterval2.getName(), "interval1") | |
| 33 self.assertEqual(self.iInterval2.getChromosome(), "chr1") | |
| 34 self.assertEqual(self.iInterval2.getStart(), 100) | |
| 35 self.assertEqual(self.iInterval2.getEnd(), 300) | |
| 36 self.assertEqual(self.iInterval2.getDirection(), 1) | |
| 37 | |
| 38 self.iInterval1.setStart(200) | |
| 39 self.assertEqual(self.iInterval2.getStart(), 100) | |
| 40 | |
| 41 def test_getDirection(self): | |
| 42 self.iInterval1.setName("interval1") | |
| 43 self.iInterval1.setChromosome("chr1") | |
| 44 self.iInterval1.setStart(100) | |
| 45 self.iInterval1.setEnd(300) | |
| 46 self.iInterval1.setDirection("+") | |
| 47 expDirect = 1 | |
| 48 self.assertEquals(expDirect,self.iInterval1.getDirection()) | |
| 49 | |
| 50 #!!!! Warning: two methods getStart() and getEnd() give the information maximum and minimum in interval.!!!!# | |
| 51 #In case strand = "+", start < end; strand = "-", start > end | |
| 52 def test_setStartEnd(self): | |
| 53 self.iInterval1 = Interval() | |
| 54 self.iInterval1.setName("interval1") | |
| 55 self.iInterval1.setChromosome("chr1") | |
| 56 self.iInterval1.setStart(100) | |
| 57 self.iInterval1.setEnd(300) | |
| 58 self.iInterval1.setDirection("+") | |
| 59 | |
| 60 self.assertEqual(self.iInterval1.getName(), "interval1") | |
| 61 self.assertEqual(self.iInterval1.getChromosome(), "chr1") | |
| 62 self.assertEqual(self.iInterval1.getStart(),100) | |
| 63 self.assertEqual(self.iInterval1.getEnd(), 300) | |
| 64 self.assertEqual(self.iInterval1.getDirection(), 1) | |
| 65 | |
| 66 self.iInterval1.setStart(200) | |
| 67 self.assertEqual(self.iInterval1.getStart(), 200) | |
| 68 self.assertEqual(self.iInterval1.getEnd(), 300) | |
| 69 | |
| 70 self.iInterval1.setEnd(300) | |
| 71 self.iInterval1.setStart(100) | |
| 72 self.assertEqual(self.iInterval1.getStart(), 100) | |
| 73 self.assertEqual(self.iInterval1.getEnd(), 300) | |
| 74 | |
| 75 self.iInterval1.setEnd(1200) | |
| 76 self.iInterval1.setStart(1000) | |
| 77 self.assertEqual(self.iInterval1.getStart(), 1000) | |
| 78 self.assertEqual(self.iInterval1.getEnd(), 1200) | |
| 79 | |
| 80 self.iInterval1.reverse() | |
| 81 self.assertEqual(self.iInterval1.getDirection(), -1) | |
| 82 self.assertEqual(self.iInterval1.getStart(), 1000) | |
| 83 self.assertEqual(self.iInterval1.getEnd(), 1200) | |
| 84 | |
| 85 self.iInterval1.setStart(1100) | |
| 86 self.assertEqual(self.iInterval1.getStart(), 1100) | |
| 87 self.assertEqual(self.iInterval1.getEnd(), 1200) | |
| 88 | |
| 89 self.iInterval1.setEnd(2200) | |
| 90 self.iInterval1.setStart(2000) | |
| 91 self.assertEqual(self.iInterval1.getStart(), 2000) | |
| 92 self.assertEqual(self.iInterval1.getEnd(), 2200) | |
| 93 | |
| 94 self.iInterval1.setStart(1000) | |
| 95 self.iInterval1.setEnd(1200) | |
| 96 self.assertEqual(self.iInterval1.getStart(), 1000) | |
| 97 self.assertEqual(self.iInterval1.getEnd(), 1200) | |
| 98 | |
| 99 def test_reverse(self): | |
| 100 self.iInterval1 = Interval() | |
| 101 self.iInterval1.setName("interval1") | |
| 102 self.iInterval1.setChromosome("chr1") | |
| 103 self.iInterval1.setStart(100) | |
| 104 self.iInterval1.setEnd(200) | |
| 105 self.iInterval1.setDirection("+") | |
| 106 self.iInterval1.reverse() | |
| 107 self.assertEqual(self.iInterval1.getStart(), 100) | |
| 108 self.assertEqual(self.iInterval1.getEnd(), 200) | |
| 109 self.assertEqual(self.iInterval1.getDirection(), -1) | |
| 110 | |
| 111 def test_overlapWith(self): | |
| 112 self.iInterval1 = Interval() | |
| 113 self.iInterval1.setName("interval1") | |
| 114 self.iInterval1.setChromosome("chr1") | |
| 115 self.iInterval1.setStart(100) | |
| 116 self.iInterval1.setEnd(200) | |
| 117 self.iInterval1.setDirection("+") | |
| 118 | |
| 119 self.iInterval2 = Interval() | |
| 120 self.iInterval2.copy(self.iInterval1) | |
| 121 self.iInterval2.setName("interval2") | |
| 122 | |
| 123 self.assertTrue(self.iInterval1.overlapWith(self.iInterval2)) | |
| 124 | |
| 125 self.iInterval2.setChromosome("chr2") | |
| 126 try: | |
| 127 self.iInterval1.overlapWith(self.iInterval2) | |
| 128 self.fail() | |
| 129 except Exception: | |
| 130 pass | |
| 131 | |
| 132 self.iInterval2.setChromosome("chr1") | |
| 133 self.iInterval2.setEnd(400) | |
| 134 self.iInterval2.setStart(300) | |
| 135 self.assertFalse(self.iInterval1.overlapWith(self.iInterval2)) | |
| 136 | |
| 137 self.iInterval2.setStart(200) | |
| 138 self.assertTrue(self.iInterval1.overlapWith(self.iInterval2)) | |
| 139 | |
| 140 def test_isIncludeIn(self): | |
| 141 self.iInterval1 = Interval() | |
| 142 self.iInterval1.setName("interval1") | |
| 143 self.iInterval1.setChromosome("chr1") | |
| 144 self.iInterval1.setStart(100) | |
| 145 self.iInterval1.setEnd(200) | |
| 146 self.iInterval1.setDirection("+") | |
| 147 | |
| 148 self.iInterval2 = Interval() | |
| 149 self.iInterval2.setName("interval2") | |
| 150 self.iInterval2.setChromosome("chr1") | |
| 151 self.iInterval2.setStart(80) | |
| 152 self.iInterval2.setEnd(280) | |
| 153 self.iInterval2.setDirection("+") | |
| 154 self.assertTrue(self.iInterval1.isIncludeIn(self.iInterval2)) | |
| 155 | |
| 156 def test_getDistance(self): | |
| 157 self.iInterval1 = Interval() | |
| 158 self.iInterval1.setName("interval1") | |
| 159 self.iInterval1.setChromosome("chr1") | |
| 160 self.iInterval1.setStart(100) | |
| 161 self.iInterval1.setEnd(200) | |
| 162 self.iInterval1.setDirection("+") | |
| 163 | |
| 164 self.iInterval2 = Interval() | |
| 165 self.iInterval2.copy(self.iInterval1) | |
| 166 self.iInterval2.setName("interval2") | |
| 167 | |
| 168 self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 0) | |
| 169 self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 0) | |
| 170 | |
| 171 self.iInterval2.setChromosome("chr2") | |
| 172 try: | |
| 173 self.iInterval1.getDistance(self.iInterval2) | |
| 174 self.fail() | |
| 175 except Exception: | |
| 176 pass | |
| 177 | |
| 178 self.iInterval2.setChromosome("chr1") | |
| 179 self.iInterval2.setEnd(400) | |
| 180 self.iInterval2.setStart(300) | |
| 181 self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 100) | |
| 182 self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 100) | |
| 183 | |
| 184 def test_getRelativeDistance(self): | |
| 185 self.iInterval1 = Interval() | |
| 186 self.iInterval1.setName("interval1") | |
| 187 self.iInterval1.setChromosome("chr1") | |
| 188 self.iInterval1.setStart(100) | |
| 189 self.iInterval1.setEnd(200) | |
| 190 self.iInterval1.setDirection("+") | |
| 191 | |
| 192 self.iInterval2 = Interval() | |
| 193 self.iInterval2.copy(self.iInterval1) | |
| 194 self.iInterval2.setName("interval2") | |
| 195 | |
| 196 self.assertEqual(self.iInterval1.getDistance(self.iInterval2), 0) | |
| 197 self.assertEqual(self.iInterval2.getDistance(self.iInterval1), 0) | |
| 198 | |
| 199 self.iInterval2.setChromosome("chr2") | |
| 200 try: | |
| 201 self.iInterval1.getDistance(self.iInterval2) | |
| 202 self.fail() | |
| 203 except Exception: | |
| 204 pass | |
| 205 | |
| 206 self.iInterval2.setChromosome("chr1") | |
| 207 self.iInterval2.setEnd(400) | |
| 208 self.iInterval2.setStart(300) | |
| 209 self.assertEqual(self.iInterval1.getRelativeDistance(self.iInterval2), 100) | |
| 210 self.assertEqual(self.iInterval2.getRelativeDistance(self.iInterval1), -100) | |
| 211 | |
| 212 def test_merge(self): | |
| 213 self.iInterval1 = Interval() | |
| 214 self.iInterval1.setName("interval1") | |
| 215 self.iInterval1.setChromosome("chr1") | |
| 216 self.iInterval1.setStart(100) | |
| 217 self.iInterval1.setEnd(200) | |
| 218 self.iInterval1.setDirection("+") | |
| 219 | |
| 220 self.iInterval2 = Interval() | |
| 221 self.iInterval2.copy(self.iInterval1) | |
| 222 self.iInterval2.setName("interval2") | |
| 223 self.iInterval2.merge(self.iInterval1) | |
| 224 | |
| 225 self.assertEqual(self.iInterval1, self.iInterval2) | |
| 226 | |
| 227 self.iInterval2.setChromosome("chr2") | |
| 228 expMessage = "Cannot merge '%s' and '%s' for they are on different chromosomes." % (str(self.iInterval2), str(self.iInterval1)) | |
| 229 isExceptionRaised = False | |
| 230 try: | |
| 231 self.iInterval2.merge(self.iInterval1) | |
| 232 except Exception, e: | |
| 233 isExceptionRaised = True | |
| 234 obsMessage = str(e) | |
| 235 | |
| 236 self.assertTrue(isExceptionRaised) | |
| 237 self.assertEquals(expMessage, obsMessage) | |
| 238 #Warning! Both two intervals should be on the same chromosome and direction. | |
| 239 self.iInterval2.setChromosome("chr1") | |
| 240 self.iInterval2.setStart(300) | |
| 241 self.iInterval2.setEnd(400) | |
| 242 self.iInterval2.merge(self.iInterval1) | |
| 243 self.assertEqual(self.iInterval2.getStart(), 100) | |
| 244 self.assertEqual(self.iInterval2.getEnd(), 400) | |
| 245 self.assertEqual(self.iInterval2.getChromosome(), "chr1") | |
| 246 | |
| 247 def test_include(self): | |
| 248 iInterval1 = Interval() | |
| 249 iInterval1.setName("interval1") | |
| 250 iInterval1.setChromosome("chr1") | |
| 251 iInterval1.setStart(100) | |
| 252 iInterval1.setEnd(200) | |
| 253 iInterval1.setDirection("+") | |
| 254 | |
| 255 iInterval2 = Interval() | |
| 256 iInterval2.copy(iInterval1) | |
| 257 iInterval2.setName("interval2") | |
| 258 self.assertTrue(iInterval1.include(iInterval2)) | |
| 259 self.assertTrue(iInterval2.include(iInterval1)) | |
| 260 | |
| 261 iInterval2.setChromosome("chr2") | |
| 262 self.assertFalse(iInterval1.include(iInterval2)) | |
| 263 self.assertFalse(iInterval2.include(iInterval1)) | |
| 264 | |
| 265 iInterval2.setChromosome("chr1") | |
| 266 iInterval1.setStart(1) | |
| 267 self.assertTrue(iInterval1.include(iInterval2)) | |
| 268 self.assertFalse(iInterval2.include(iInterval1)) | |
| 269 | |
| 270 iInterval1.setStart(100) | |
| 271 iInterval1.setEnd(300) | |
| 272 self.assertTrue(iInterval1.include(iInterval2)) | |
| 273 self.assertFalse(iInterval2.include(iInterval1)) | |
| 274 | |
| 275 | |
| 276 def test_getDifference(self): | |
| 277 iInterval1 = Interval() | |
| 278 iInterval1.setName("interval1") | |
| 279 iInterval1.setChromosome("chr1") | |
| 280 iInterval1.setStart(100) | |
| 281 iInterval1.setEnd(400) | |
| 282 iInterval1.setDirection("+") | |
| 283 | |
| 284 iInterval2 = Interval() | |
| 285 iInterval2.copy(iInterval1) | |
| 286 iInterval2.setName("interval2") | |
| 287 self.assertEqual(iInterval1.getDifference(iInterval2), []) | |
| 288 self.assertEqual(iInterval2.getDifference(iInterval1), []) | |
| 289 | |
| 290 iInterval2.setChromosome("chr2") | |
| 291 results = iInterval1.getDifference(iInterval2) | |
| 292 self.assertEqual(len(results), 1) | |
| 293 resultInterval = results[0] | |
| 294 self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) | |
| 295 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) | |
| 296 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) | |
| 297 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) | |
| 298 | |
| 299 iInterval2.setChromosome("chr1") | |
| 300 iInterval2.setEnd(300) | |
| 301 results = iInterval1.getDifference(iInterval2) | |
| 302 self.assertEqual(len(results), 1) | |
| 303 resultInterval = results[0] | |
| 304 self.assertEqual(resultInterval.getStart(), 301) | |
| 305 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) | |
| 306 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) | |
| 307 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) | |
| 308 | |
| 309 iInterval2.setDirection("-") | |
| 310 results = iInterval1.getDifference(iInterval2, True) | |
| 311 self.assertEqual(len(results), 1) | |
| 312 resultInterval = results[0] | |
| 313 self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) | |
| 314 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) | |
| 315 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) | |
| 316 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) | |
| 317 | |
| 318 iInterval2.setDirection("+") | |
| 319 iInterval2.setStart(200) | |
| 320 results = iInterval1.getDifference(iInterval2) | |
| 321 self.assertEqual(len(results), 2) | |
| 322 resultInterval1, resultInterval2 = results | |
| 323 self.assertEqual(resultInterval1.getStart(), iInterval1.getStart()) | |
| 324 self.assertEqual(resultInterval1.getEnd(), 199) | |
| 325 self.assertEqual(resultInterval1.getDirection(), iInterval1.getDirection()) | |
| 326 self.assertEqual(resultInterval1.getChromosome(), iInterval1.getChromosome()) | |
| 327 self.assertEqual(resultInterval2.getStart(), 301) | |
| 328 self.assertEqual(resultInterval2.getEnd(), iInterval1.getEnd()) | |
| 329 self.assertEqual(resultInterval2.getDirection(), iInterval1.getDirection()) | |
| 330 self.assertEqual(resultInterval2.getChromosome(), iInterval1.getChromosome()) | |
| 331 | |
| 332 iInterval2.setEnd(2000) | |
| 333 iInterval2.setStart(1000) | |
| 334 results = iInterval1.getDifference(iInterval2) | |
| 335 self.assertEqual(len(results), 1) | |
| 336 resultInterval = results[0] | |
| 337 self.assertEqual(resultInterval.getStart(), iInterval1.getStart()) | |
| 338 self.assertEqual(resultInterval.getEnd(), iInterval1.getEnd()) | |
| 339 self.assertEqual(resultInterval.getDirection(), iInterval1.getDirection()) | |
| 340 self.assertEqual(resultInterval.getChromosome(), iInterval1.getChromosome()) | |
| 341 | |
| 342 def test_mergeWithDifferentStrand(self): | |
| 343 self.iInterval1 = Interval() | |
| 344 self.iInterval1.setName("interval1") | |
| 345 self.iInterval1.setChromosome("chr1") | |
| 346 self.iInterval1.setStart(100) | |
| 347 self.iInterval1.setEnd(200) | |
| 348 self.iInterval1.setDirection("+") | |
| 349 | |
| 350 self.iInterval2 = Interval() | |
| 351 self.iInterval2.setName("interval2") | |
| 352 self.iInterval2.setChromosome("chr1") | |
| 353 self.iInterval2.setStart(300) | |
| 354 self.iInterval2.setEnd(400) | |
| 355 self.iInterval2.setDirection("-") | |
| 356 | |
| 357 expMessage = "Cannot merge '%s' and '%s' for they are on different strands." % (str(self.iInterval2), str(self.iInterval1)) | |
| 358 isExceptionRaised = False | |
| 359 try: | |
| 360 self.iInterval2.merge(self.iInterval1) | |
| 361 except Exception, e: | |
| 362 isExceptionRaised = True | |
| 363 obsMessage = str(e) | |
| 364 | |
| 365 self.assertTrue(isExceptionRaised) | |
| 366 self.assertEquals(expMessage, obsMessage) | |
| 367 | |
| 368 if __name__ == "__main__": | |
| 369 unittest.main() |