Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/structure/test/Test_Transcript.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:e0f8dcca02ed |
|---|---|
| 1 import unittest | |
| 2 from SMART.Java.Python.structure.Interval import Interval | |
| 3 from SMART.Java.Python.structure.Transcript import Transcript | |
| 4 | |
| 5 class Test_Transcript(unittest.TestCase): | |
| 6 | |
| 7 def test_getSize(self): | |
| 8 transcript1 = Transcript() | |
| 9 transcript1.setDirection("+") | |
| 10 transcript1.setStart(2000) | |
| 11 transcript1.setEnd(3000) | |
| 12 transcript1.setChromosome("arm_X") | |
| 13 | |
| 14 self.assertEqual(transcript1.getSize(), 1001) | |
| 15 | |
| 16 transcript2 = Transcript() | |
| 17 transcript2.copy(transcript1) | |
| 18 self.assertEqual(transcript1.getSize(), 1001) | |
| 19 | |
| 20 transcript3 = Transcript() | |
| 21 transcript3.setDirection("+") | |
| 22 transcript3.setChromosome("arm_X") | |
| 23 | |
| 24 exon1 = Interval() | |
| 25 exon1.setDirection("+") | |
| 26 exon1.setChromosome("arm_X") | |
| 27 exon1.setStart(100) | |
| 28 exon1.setEnd(200) | |
| 29 transcript3.addExon(exon1) | |
| 30 | |
| 31 exon2 = Interval() | |
| 32 exon2.setDirection("+") | |
| 33 exon2.setChromosome("arm_X") | |
| 34 exon2.setStart(300) | |
| 35 exon2.setEnd(400) | |
| 36 transcript3.addExon(exon2) | |
| 37 | |
| 38 self.assertEqual(transcript3.getSize(), 203) | |
| 39 | |
| 40 | |
| 41 def test_overlapWithExons(self): | |
| 42 exon1_1 = Interval() | |
| 43 exon1_1.setChromosome("chr1") | |
| 44 exon1_1.setStart(100) | |
| 45 exon1_1.setEnd(200) | |
| 46 exon1_1.setDirection("+") | |
| 47 | |
| 48 exon1_2 = Interval() | |
| 49 exon1_2.setChromosome("chr1") | |
| 50 exon1_2.setStart(500) | |
| 51 exon1_2.setEnd(600) | |
| 52 exon1_2.setDirection("+") | |
| 53 | |
| 54 transcript1 = Transcript() | |
| 55 transcript1.setChromosome("chr1") | |
| 56 transcript1.setStart(100) | |
| 57 transcript1.setEnd(600) | |
| 58 transcript1.setDirection("+") | |
| 59 transcript1.addExon(exon1_1) | |
| 60 transcript1.addExon(exon1_2) | |
| 61 | |
| 62 exon2_1 = Interval() | |
| 63 exon2_1.copy(exon1_1) | |
| 64 | |
| 65 transcript2 = Transcript() | |
| 66 transcript2.setChromosome("chr1") | |
| 67 transcript2.setStart(100) | |
| 68 transcript2.setEnd(200) | |
| 69 transcript2.setDirection("+") | |
| 70 transcript2.addExon(exon2_1) | |
| 71 | |
| 72 self.assertTrue(transcript1.overlapWithExon(transcript2)) | |
| 73 | |
| 74 transcript2.reverse() | |
| 75 try: | |
| 76 self.assertFalse(transcript1.overlapWithExon(transcript2)) | |
| 77 except Exception: | |
| 78 pass | |
| 79 | |
| 80 transcript2.reverse() | |
| 81 transcript2.setChromosome("chr2") | |
| 82 self.assertFalse(transcript1.overlapWithExon(transcript2)) | |
| 83 | |
| 84 exon3_1 = Interval() | |
| 85 exon3_1.copy(exon1_1) | |
| 86 exon3_1.setEnd(400) | |
| 87 exon3_1.setStart(300) | |
| 88 | |
| 89 transcript3 = Transcript() | |
| 90 transcript3.setChromosome("chr1") | |
| 91 transcript3.setStart(300) | |
| 92 transcript3.setEnd(400) | |
| 93 transcript3.setDirection("+") | |
| 94 transcript3.addExon(exon3_1) | |
| 95 self.assertFalse(transcript1.overlapWithExon(transcript3)) | |
| 96 | |
| 97 | |
| 98 def test_merge(self): | |
| 99 exon1_1 = Interval() | |
| 100 exon1_1.setChromosome("chr1") | |
| 101 exon1_1.setStart(100) | |
| 102 exon1_1.setEnd(200) | |
| 103 exon1_1.setDirection("+") | |
| 104 | |
| 105 exon1_2 = Interval() | |
| 106 exon1_2.setChromosome("chr1") | |
| 107 exon1_2.setStart(500) | |
| 108 exon1_2.setEnd(600) | |
| 109 exon1_2.setDirection("+") | |
| 110 | |
| 111 transcript1 = Transcript() | |
| 112 transcript1.setChromosome("chr1") | |
| 113 transcript1.setEnd(600) | |
| 114 transcript1.setStart(100) | |
| 115 transcript1.setDirection("+") | |
| 116 transcript1.addExon(exon1_1) | |
| 117 transcript1.addExon(exon1_2) | |
| 118 | |
| 119 exon2_1 = Interval() | |
| 120 exon2_1.copy(exon1_1) | |
| 121 | |
| 122 transcript2 = Transcript() | |
| 123 transcript2.setChromosome("chr1") | |
| 124 transcript2.setEnd(200) | |
| 125 transcript2.setStart(100) | |
| 126 transcript2.setDirection("+") | |
| 127 transcript2.addExon(exon2_1) | |
| 128 | |
| 129 transcript1.merge(transcript2) | |
| 130 transcript1.sortExonsIncreasing() | |
| 131 exons = transcript1.getExons() | |
| 132 self.assertEqual(len(exons), 2) | |
| 133 exon1, exon2 = exons | |
| 134 self.assertEqual(exon1.getStart(), 100) | |
| 135 self.assertEqual(exon1.getEnd(), 200) | |
| 136 self.assertEqual(exon2.getStart(), 500) | |
| 137 self.assertEqual(exon2.getEnd(), 600) | |
| 138 | |
| 139 transcript2.setChromosome("chr2") | |
| 140 try: | |
| 141 transcript1.merge(transcript2) | |
| 142 self.fail() | |
| 143 except Exception: | |
| 144 pass | |
| 145 | |
| 146 exon3_1 = Interval() | |
| 147 exon3_1.copy(exon1_1) | |
| 148 exon3_1.setEnd(650) | |
| 149 exon3_1.setStart(550) | |
| 150 | |
| 151 transcript3 = Transcript() | |
| 152 transcript3.setChromosome("chr1") | |
| 153 transcript3.setEnd(650) | |
| 154 transcript3.setStart(550) | |
| 155 transcript3.setDirection("+") | |
| 156 transcript3.addExon(exon3_1) | |
| 157 | |
| 158 transcript1.merge(transcript3) | |
| 159 self.assertEqual(transcript1.getStart(), 100) | |
| 160 self.assertEqual(transcript1.getEnd(), 650) | |
| 161 exons = transcript1.getExons() | |
| 162 self.assertEqual(len(exons), 2) | |
| 163 exon1, exon2 = exons | |
| 164 self.assertEqual(exon1.getStart(), 100) | |
| 165 self.assertEqual(exon1.getEnd(), 200) | |
| 166 self.assertEqual(exon2.getStart(), 500) | |
| 167 self.assertEqual(exon2.getEnd(), 650) | |
| 168 | |
| 169 exon4_1 = Interval() | |
| 170 exon4_1.copy(exon1_1) | |
| 171 exon4_1.setEnd(400) | |
| 172 exon4_1.setStart(300) | |
| 173 | |
| 174 transcript4 = Transcript() | |
| 175 transcript4.setChromosome("chr1") | |
| 176 transcript4.setStart(300) | |
| 177 transcript4.setEnd(400) | |
| 178 transcript4.setDirection("+") | |
| 179 transcript4.addExon(exon4_1) | |
| 180 | |
| 181 transcript1.merge(transcript4) | |
| 182 self.assertEqual(transcript1.getStart(), 100) | |
| 183 self.assertEqual(transcript1.getEnd(), 650) | |
| 184 transcript1.sortExonsIncreasing() | |
| 185 exons = transcript1.getExons() | |
| 186 self.assertEqual(len(exons), 3) | |
| 187 exon1, exon2, exon3 = exons | |
| 188 self.assertEqual(exon1.getStart(), 100) | |
| 189 self.assertEqual(exon1.getEnd(), 200) | |
| 190 self.assertEqual(exon2.getStart(), 300) | |
| 191 self.assertEqual(exon2.getEnd(), 400) | |
| 192 self.assertEqual(exon3.getStart(), 500) | |
| 193 self.assertEqual(exon3.getEnd(), 650) | |
| 194 | |
| 195 | |
| 196 def test_extendStart(self): | |
| 197 transcript1 = Transcript() | |
| 198 transcript1.setStart(2000) | |
| 199 transcript1.setEnd(3000) | |
| 200 transcript1.setDirection("+") | |
| 201 transcript1.setChromosome("arm_X") | |
| 202 | |
| 203 transcript2 = Transcript() | |
| 204 transcript2.copy(transcript1) | |
| 205 transcript2.setDirection("-") | |
| 206 | |
| 207 transcript1.extendStart(1000) | |
| 208 transcript2.extendStart(1000) | |
| 209 | |
| 210 | |
| 211 self.assertEqual(transcript1.getDirection(), 1) | |
| 212 self.assertEqual(transcript1.getStart(), 1000) | |
| 213 self.assertEqual(transcript1.getEnd(), 3000) | |
| 214 self.assertEqual(transcript1.getChromosome(), "arm_X") | |
| 215 | |
| 216 self.assertEqual(transcript2.getDirection(), -1) | |
| 217 self.assertEqual(transcript2.getStart(), 2000) | |
| 218 self.assertEqual(transcript2.getEnd(), 4000) | |
| 219 self.assertEqual(transcript2.getChromosome(), "arm_X") | |
| 220 | |
| 221 | |
| 222 def test_restrictStart(self): | |
| 223 exon1_1 = Interval() | |
| 224 exon1_1.setChromosome("chr1") | |
| 225 exon1_1.setStart(100) | |
| 226 exon1_1.setEnd(200) | |
| 227 exon1_1.setDirection("+") | |
| 228 | |
| 229 exon1_2 = Interval() | |
| 230 exon1_2.setChromosome("chr1") | |
| 231 exon1_2.setStart(300) | |
| 232 exon1_2.setEnd(500) | |
| 233 exon1_2.setDirection("+") | |
| 234 | |
| 235 transcript1 = Transcript() | |
| 236 transcript1.setChromosome("chr1") | |
| 237 transcript1.setStart(100) | |
| 238 transcript1.setEnd(500) | |
| 239 transcript1.setDirection("+") | |
| 240 transcript1.addExon(exon1_1) | |
| 241 transcript1.addExon(exon1_2) | |
| 242 | |
| 243 transcript1.restrictStart(301) | |
| 244 exons = transcript1.getExons() | |
| 245 self.assertEqual(len(exons), 2) | |
| 246 exon1, exon2 = exons | |
| 247 self.assertEqual(exon1.getStart(), 100) | |
| 248 self.assertEqual(exon1.getEnd(), 200) | |
| 249 self.assertEqual(exon2.getStart(), 300) | |
| 250 self.assertEqual(exon2.getEnd(), 400) | |
| 251 | |
| 252 | |
| 253 def test__include(self): | |
| 254 iTranscript1 = Transcript() | |
| 255 iTranscript1.setName("transcript1") | |
| 256 iTranscript1.setChromosome("chr1") | |
| 257 iTranscript1.setStart(100) | |
| 258 iTranscript1.setEnd(200) | |
| 259 iTranscript1.setDirection("+") | |
| 260 | |
| 261 iTranscript2 = Transcript() | |
| 262 iTranscript2.copy(iTranscript1) | |
| 263 iTranscript2.setName("transcript2") | |
| 264 self.assertTrue(iTranscript1.include(iTranscript2)) | |
| 265 self.assertTrue(iTranscript2.include(iTranscript1)) | |
| 266 | |
| 267 iTranscript2.setChromosome("chr2") | |
| 268 self.assertFalse(iTranscript1.include(iTranscript2)) | |
| 269 self.assertFalse(iTranscript2.include(iTranscript1)) | |
| 270 | |
| 271 iTranscript2.setChromosome("chr1") | |
| 272 exon = Interval() | |
| 273 exon.setChromosome("chr1") | |
| 274 exon.setDirection("+") | |
| 275 exon.setStart(300) | |
| 276 exon.setEnd(400) | |
| 277 iTranscript1.addExon(exon) | |
| 278 self.assertTrue(iTranscript1.include(iTranscript2)) | |
| 279 self.assertFalse(iTranscript2.include(iTranscript1)) | |
| 280 | |
| 281 exon = Interval() | |
| 282 exon.setChromosome("chr1") | |
| 283 exon.setDirection("+") | |
| 284 exon.setStart(500) | |
| 285 exon.setEnd(600) | |
| 286 iTranscript2.addExon(exon) | |
| 287 self.assertFalse(iTranscript1.include(iTranscript2)) | |
| 288 self.assertFalse(iTranscript2.include(iTranscript1)) | |
| 289 | |
| 290 | |
| 291 def test__getDifference(self): | |
| 292 iTranscript1 = Transcript() | |
| 293 iTranscript1.setName("transcript1") | |
| 294 iTranscript1.setChromosome("chr1") | |
| 295 iTranscript1.setStart(100) | |
| 296 iTranscript1.setEnd(400) | |
| 297 iTranscript1.setDirection("+") | |
| 298 | |
| 299 iTranscript2 = Transcript() | |
| 300 iTranscript2.setName("transcript1") | |
| 301 iTranscript2.setChromosome("chr1") | |
| 302 iTranscript2.setStart(200) | |
| 303 iTranscript2.setEnd(400) | |
| 304 iTranscript2.setDirection("+") | |
| 305 | |
| 306 newTranscript = iTranscript1.getDifference(iTranscript2) | |
| 307 self.assertTrue(newTranscript.getStart(), 100) | |
| 308 self.assertTrue(newTranscript.getEnd(), 199) | |
| 309 exons = newTranscript.getExons() | |
| 310 self.assertTrue(len(exons), 1) | |
| 311 exon1 = exons[0] | |
| 312 self.assertTrue(exon1.getStart(), 100) | |
| 313 self.assertTrue(exon1.getEnd(), 199) | |
| 314 | |
| 315 iTranscript2 = Transcript() | |
| 316 iTranscript2.setName("transcript1") | |
| 317 iTranscript2.setChromosome("chr1") | |
| 318 iTranscript2.setStart(100) | |
| 319 iTranscript2.setEnd(200) | |
| 320 iTranscript2.setDirection("+") | |
| 321 | |
| 322 newTranscript = iTranscript1.getDifference(iTranscript2) | |
| 323 self.assertTrue(newTranscript.getStart(), 201) | |
| 324 self.assertTrue(newTranscript.getEnd(), 400) | |
| 325 exons = newTranscript.getExons() | |
| 326 self.assertTrue(len(exons), 1) | |
| 327 exon1 = exons[0] | |
| 328 self.assertTrue(exon1.getStart(), 201) | |
| 329 self.assertTrue(exon1.getEnd(), 400) | |
| 330 | |
| 331 iTranscript2 = Transcript() | |
| 332 iTranscript2.setName("transcript1") | |
| 333 iTranscript2.setChromosome("chr1") | |
| 334 iTranscript2.setStart(200) | |
| 335 iTranscript2.setEnd(300) | |
| 336 iTranscript2.setDirection("+") | |
| 337 | |
| 338 newTranscript = iTranscript1.getDifference(iTranscript2) | |
| 339 self.assertTrue(newTranscript.getStart(), 100) | |
| 340 self.assertTrue(newTranscript.getEnd(), 400) | |
| 341 exons = newTranscript.getExons() | |
| 342 self.assertTrue(len(exons), 2) | |
| 343 exon1, exon2 = exons | |
| 344 self.assertTrue(exon1.getStart(), 100) | |
| 345 self.assertTrue(exon1.getEnd(), 199) | |
| 346 self.assertTrue(exon2.getStart(), 301) | |
| 347 self.assertTrue(exon2.getEnd(), 400) | |
| 348 | |
| 349 | |
| 350 if __name__ == '__main__': | |
| 351 unittest.main() |