Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/test/Test_GffParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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1 import unittest | |
2 from commons.core.parsing.GffParser import GffParser | |
3 | |
4 | |
5 class Test_GffParser(unittest.TestCase): | |
6 | |
7 | |
8 def test_Parser(self): | |
9 parser = GffParser("data/testGffParser1.gff3") | |
10 | |
11 self.assertEqual(parser.getNbTranscripts(), 3) | |
12 | |
13 cpt = 0 | |
14 for transcript in parser.getIterator(): | |
15 cpt += 1 | |
16 if cpt == 1: | |
17 self.assertEqual(transcript.getChromosome(), "arm_X") | |
18 self.assertEqual(transcript.getName(), "test1") | |
19 self.assertEqual(transcript.getStart(), 1000) | |
20 self.assertEqual(transcript.getEnd(), 2000) | |
21 self.assertEqual(transcript.getDirection(), 1) | |
22 self.assertEqual(transcript.getNbExons(), 1) | |
23 self.assertEqual(transcript.getTagValue("field"), "value1") | |
24 exons = transcript.getExons() | |
25 self.assertEqual(exons[0].getChromosome(), "arm_X") | |
26 self.assertEqual(exons[0].getStart(), 1000) | |
27 self.assertEqual(exons[0].getEnd(), 2000) | |
28 self.assertEqual(exons[0].getDirection(), 1) | |
29 self.assertEqual(transcript.getSize(), 1001) | |
30 elif cpt == 2: | |
31 self.assertEqual(transcript.getChromosome(), "arm_X") | |
32 self.assertEqual(transcript.getName(), "test2") | |
33 self.assertEqual(transcript.getStart(), 10000) | |
34 self.assertEqual(transcript.getEnd(), 20000) | |
35 self.assertEqual(transcript.getDirection(), -1) | |
36 self.assertEqual(transcript.getNbExons(), 2) | |
37 self.assertEqual(transcript.getTagValue("field"), "value2") | |
38 exons = transcript.getExons() | |
39 self.assertEqual(exons[0].getChromosome(), "arm_X") | |
40 self.assertEqual(exons[0].getStart(), 10000) | |
41 self.assertEqual(exons[0].getEnd(), 10100) | |
42 self.assertEqual(exons[0].getDirection(), -1) | |
43 self.assertEqual(transcript.getSize(), 9602) | |
44 if cpt == 3: | |
45 self.assertEqual(transcript.getChromosome(), "arm_X") | |
46 self.assertEqual(transcript.getName(), "test1.1") | |
47 self.assertEqual(transcript.getStart(), 1000) | |
48 self.assertEqual(transcript.getEnd(), 2000) | |
49 self.assertEqual(transcript.getDirection(), 1) | |
50 self.assertEqual(transcript.getNbExons(), 1) | |
51 self.assertEqual(transcript.getTagValue("ID"), "test1.1-1") | |
52 exons = transcript.getExons() | |
53 self.assertEqual(exons[0].getChromosome(), "arm_X") | |
54 self.assertEqual(exons[0].getStart(), 1000) | |
55 self.assertEqual(exons[0].getEnd(), 2000) | |
56 self.assertEqual(exons[0].getDirection(), 1) | |
57 self.assertEqual(transcript.getSize(), 1001) | |
58 | |
59 | |
60 if __name__ == '__main__': | |
61 unittest.main() | |
62 |