Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/structure/test/Test_Transcript.py @ 6:769e306b7933

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
parents
children
comparison
equal deleted inserted replaced
5:ea3082881bf8 6:769e306b7933
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()