Mercurial > repos > yufei-luo > s_mart

comparison commons/core/writer/test/Test_Gff3Writer.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 from commons.core.writer.Gff3Writer import Gff3Writer
2 from SMART.Java.Python.structure.Transcript import Transcript
3 from SMART.Java.Python.structure.Interval import Interval
4 import unittest
5 import os
6 from SMART.Java.Python.misc import Utils
7
8 class Test_Gff3Writer(unittest.TestCase):
9
10 def test_writer(self):
11 obsFileName = "testGffWriter1.gff3"
12 writer = Gff3Writer(obsFileName)
13
14 transcript = Transcript()
15 transcript.setName("test1.1")
16 transcript.setChromosome("arm_X")
17 transcript.setStart(1000)
18 transcript.setEnd(4000)
19 transcript.setDirection("+")
20 transcript.setTagValue("ID", "test1.1-1")
21 transcript.setTagValue("occurrence", 1)
22 transcript.setTagValue("nbOccurrences", 2)
23
24 exon1 = Interval()
25 exon1.setChromosome("arm_X")
26 exon1.setStart(1000)
27 exon1.setEnd(2000)
28 exon1.setDirection("+")
29
30 exon2 = Interval()
31 exon2.setChromosome("arm_X")
32 exon2.setStart(3000)
33 exon2.setEnd(4000)
34 exon2.setDirection("+")
35
36 transcript.addExon(exon1)
37 transcript.addExon(exon2)
38
39 writer.addTranscript(transcript)
40 writer.write()
41 writer.close()
42
43 expFileName = "expFile.gff3"
44 f = open(expFileName, "w")
45 f.write("arm_X\tS-MART\ttranscript\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n")
46 f.write("arm_X\tS-MART\texon\t1000\t2000\t.\t+\t.\tID=test1.1-1-exon1;Name=test1.1-exon1;Parent=test1.1-1\n")
47 f.write("arm_X\tS-MART\texon\t3000\t4000\t.\t+\t.\tID=test1.1-1-exon2;Name=test1.1-exon2;Parent=test1.1-1\n")
48 f.close()
49
50 self.assertTrue(Utils.diff(expFileName, obsFileName))
51
52 os.remove(expFileName)
53 os.remove(obsFileName)
54
55 def test_writerAltNames(self):
56 obsFileName = "testGffWriter1.gff3"
57 writer = Gff3Writer(obsFileName,title="ALTSOURCE", feature="Match", featurePart="Match-Part")
58
59 transcript = Transcript()
60 transcript.setName("test1.1")
61 transcript.setChromosome("arm_X")
62 transcript.setStart(1000)
63 transcript.setEnd(4000)
64 transcript.setDirection("+")
65 transcript.setTagValue("ID", "test1.1-1")
66 transcript.setTagValue("occurrence", 1)
67 transcript.setTagValue("nbOccurrences", 2)
68
69 exon1 = Interval()
70 exon1.setChromosome("arm_X")
71 exon1.setStart(1000)
72 exon1.setEnd(2000)
73 exon1.setDirection("+")
74
75 exon2 = Interval()
76 exon2.setChromosome("arm_X")
77 exon2.setStart(3000)
78 exon2.setEnd(4000)
79 exon2.setDirection("+")
80
81 transcript.addExon(exon1)
82 transcript.addExon(exon2)
83
84 writer.addTranscript(transcript)
85 writer.write()
86 writer.close()
87
88 expFileName = "expFile.gff3"
89 f = open(expFileName, "w")
90 f.write("arm_X\tALTSOURCE\tMatch\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n")
91 f.write("arm_X\tALTSOURCE\tMatch-Part\t1000\t2000\t.\t+\t.\tID=test1.1-1-Match-Part1;Name=test1.1-Match-Part1;Parent=test1.1-1\n")
92 f.write("arm_X\tALTSOURCE\tMatch-Part\t3000\t4000\t.\t+\t.\tID=test1.1-1-Match-Part2;Name=test1.1-Match-Part2;Parent=test1.1-1\n")
93 f.close()
94
95 self.assertTrue(Utils.diff(expFileName, obsFileName))
96
97 os.remove(expFileName)
98 os.remove(obsFileName)
99
100 if __name__ == '__main__':
101 unittest.main()