6
|
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
|