Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/test/Test_GffParser.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 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