Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/test/Test_CoordsParser.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 769e306b7933 |
children |
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30:5677346472b5 | 31:0ab839023fe4 |
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1 import unittest | |
2 from commons.core.parsing.CoordsParser import CoordsParser | |
3 from SMART.Java.Python.mappingToCoordinates import MappingToCoordinates | |
4 | |
5 | |
6 class Test_CoordsParser(unittest.TestCase): | |
7 | |
8 | |
9 def test_Parser(self): | |
10 parser = CoordsParser("data/testCoordsParser.coords") | |
11 | |
12 cpt = 0 | |
13 for mapping in parser.getIterator(): | |
14 transcript = mapping.getTranscript() | |
15 cpt += 1 | |
16 if cpt == 1: | |
17 self.assertEqual(transcript.getChromosome(), "scaffold_1") | |
18 self.assertEqual(transcript.getName(), "gi|240254421:1-30427671") | |
19 self.assertEqual(transcript.getStart(), 1) | |
20 self.assertEqual(transcript.getEnd(), 6251) | |
21 self.assertEqual(transcript.getDirection(), -1) | |
22 self.assertEqual(transcript.getNbExons(), 1) | |
23 self.assertEqual(transcript.getTagValue("identity"), 89.030000000000001) | |
24 exons = transcript.getExons() | |
25 self.assertEqual(exons[0].getChromosome(), "scaffold_1") | |
26 self.assertEqual(exons[0].getStart(), 1) | |
27 self.assertEqual(exons[0].getEnd(), 6251) | |
28 self.assertEqual(exons[0].getDirection(), -1) | |
29 self.assertEqual(transcript.getSize(), 6251) | |
30 elif cpt == 2: | |
31 self.assertEqual(transcript.getChromosome(), "scaffold_1") | |
32 self.assertEqual(transcript.getName(), "gi|240254421:1-30427671") | |
33 self.assertEqual(transcript.getStart(), 9127) | |
34 self.assertEqual(transcript.getEnd(), 11947) | |
35 self.assertEqual(transcript.getDirection(), -1) | |
36 self.assertEqual(transcript.getNbExons(), 1) | |
37 self.assertEqual(transcript.getTagValue("identity"), 90.450000000000003) | |
38 exons = transcript.getExons() | |
39 self.assertEqual(exons[0].getChromosome(), "scaffold_1") | |
40 self.assertEqual(exons[0].getStart(), 9127) | |
41 self.assertEqual(exons[0].getEnd(), 11947) | |
42 self.assertEqual(exons[0].getDirection(), -1) | |
43 self.assertEqual(transcript.getSize(), 2821) | |
44 if cpt == 3: | |
45 self.assertEqual(transcript.getChromosome(), "scaffold_1") | |
46 self.assertEqual(transcript.getName(), "gi|240254421:1-30427671") | |
47 self.assertEqual(transcript.getStart(), 12201) | |
48 self.assertEqual(transcript.getEnd(), 12953) | |
49 self.assertEqual(transcript.getDirection(), -1) | |
50 self.assertEqual(transcript.getNbExons(), 1) | |
51 exons = transcript.getExons() | |
52 self.assertEqual(exons[0].getChromosome(), "scaffold_1") | |
53 self.assertEqual(exons[0].getStart(), 12201) | |
54 self.assertEqual(exons[0].getEnd(), 12953) | |
55 self.assertEqual(exons[0].getDirection(), -1) | |
56 self.assertEqual(transcript.getSize(), 753) | |
57 | |
58 def test_Parser_showcoord(self): | |
59 parser = CoordsParser("data/testCoordsParser_showcoord.coords") | |
60 expTranscriptCount = 1 | |
61 obsTranscriptCount = 0 | |
62 | |
63 for mapping in parser.getIterator(): | |
64 transcript = mapping.getTranscript() | |
65 obsTranscriptCount += 1 | |
66 self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001") | |
67 self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003") | |
68 self.assertEqual(transcript.getStart(), 296) | |
69 self.assertEqual(transcript.getEnd(), 2292) | |
70 self.assertEqual(transcript.getDirection(), 1) | |
71 self.assertEqual(transcript.getTagValue("identity"), 98.30) | |
72 self.assertEqual(transcript.getTagValue("target_pident"), 98.30) | |
73 self.assertEqual(transcript.getTagValue("target_pcover"), 3.32) | |
74 self.assertEqual(transcript.getTagValue("target_length"), 60273) | |
75 self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 1 2001") | |
76 self.assertEqual(transcript.getSize(), 1997) | |
77 | |
78 self.assertEquals(expTranscriptCount, obsTranscriptCount) | |
79 | |
80 def test_Parser_showcoord_promer(self): | |
81 parser = CoordsParser("data/testCoordsParser_showcoord_promer.coords") | |
82 expTranscriptCount = 1 | |
83 obsTranscriptCount = 0 | |
84 | |
85 for mapping in parser.getIterator(): | |
86 transcript = mapping.getTranscript() | |
87 obsTranscriptCount += 1 | |
88 self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001") | |
89 self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003") | |
90 self.assertEqual(transcript.getStart(), 291) | |
91 self.assertEqual(transcript.getEnd(), 1229) | |
92 self.assertEqual(transcript.getDirection(), -1) | |
93 self.assertEqual(transcript.getTagValue("identity"), 94.25) | |
94 self.assertEqual(transcript.getTagValue("target_pident"), 94.25) | |
95 self.assertEqual(transcript.getTagValue("target_pcover"), 1.56) | |
96 self.assertEqual(transcript.getTagValue("target_length"), 60273) | |
97 self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 939 1") | |
98 self.assertEqual(transcript.getSize(), 939) | |
99 | |
100 self.assertEquals(expTranscriptCount, obsTranscriptCount) | |
101 | |
102 | |
103 if __name__ == '__main__': | |
104 unittest.main() | |
105 |