Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_CombineTags.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 import unittest
2 import os
3 from optparse import OptionParser
4 from SMART.Java.Python.structure.Transcript import Transcript
5 from commons.core.parsing.ParserChooser import ParserChooser
6 from commons.core.parsing.GffParser import GffParser
7 from commons.core.writer.Gff3Writer import Gff3Writer
8 from SMART.Java.Python.CombineTags import CombineTags
9
10 class Test_F_CombineTags(unittest.TestCase):
11
12 def setUp(self):
13 self._inputFileName = "inputFileTest.gff3"
14 self._outputFileName = "outputFileTest.gff3"
15 self._tag1 = "tag1"
16 self._tag2 = "tag2"
17 self._outputTag = "outputTag"
18
19 def tearDown(self):
20 os.remove(self._inputFileName)
21 os.remove(self._outputFileName)
22
23 def test_plus(self):
24 transcript = self._createDummyTranscript()
25 transcript.setTagValue(self._tag1, 1)
26 transcript.setTagValue(self._tag2, 2)
27 self._writeTranscript(transcript)
28 combiner = CombineTags(0)
29 combiner.setInputFile(self._inputFileName, "gff3")
30 combiner.setOutputFile(self._outputFileName)
31 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
32 combiner.setOperation("plus")
33 combiner.run()
34 self._testOutputTag(3)
35
36 def test_minus(self):
37 transcript = self._createDummyTranscript()
38 transcript.setTagValue(self._tag1, 2)
39 transcript.setTagValue(self._tag2, 1)
40 self._writeTranscript(transcript)
41 combiner = CombineTags(0)
42 combiner.setInputFile(self._inputFileName, "gff3")
43 combiner.setOutputFile(self._outputFileName)
44 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
45 combiner.setOperation("minus")
46 combiner.run()
47 self._testOutputTag(1)
48
49 def test_times(self):
50 transcript = self._createDummyTranscript()
51 transcript.setTagValue(self._tag1, 6)
52 transcript.setTagValue(self._tag2, 3)
53 self._writeTranscript(transcript)
54 combiner = CombineTags(0)
55 combiner.setInputFile(self._inputFileName, "gff3")
56 combiner.setOutputFile(self._outputFileName)
57 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
58 combiner.setOperation("times")
59 combiner.run()
60 self._testOutputTag(18)
61
62 def test_div(self):
63 transcript = self._createDummyTranscript()
64 transcript.setTagValue(self._tag1, 6)
65 transcript.setTagValue(self._tag2, 3)
66 self._writeTranscript(transcript)
67 combiner = CombineTags(0)
68 combiner.setInputFile(self._inputFileName, "gff3")
69 combiner.setOutputFile(self._outputFileName)
70 combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
71 combiner.setOperation("div")
72 combiner.run()
73 self._testOutputTag(2)
74
75 def test_default(self):
76 transcript = self._createDummyTranscript()
77 transcript.setTagValue(self._tag1, 1)
78 self._writeTranscript(transcript)
79 combiner = CombineTags(0)
80 combiner.setInputFile(self._inputFileName, "gff3")
81 combiner.setOutputFile(self._outputFileName)
82 combiner.setTags(self._tag1, self._tag2, self._outputTag, 0)
83 combiner.setOperation("plus")
84 combiner.run()
85 self._testOutputTag(0)
86
87 def _createDummyTranscript(self):
88 transcript = Transcript()
89 transcript.setChromosome("chr1")
90 transcript.setName("test1")
91 transcript.setEnd(200)
92 transcript.setStart(100)
93 transcript.setDirection("+")
94 return transcript
95
96 def _testOutputTag(self, value):
97 parser = GffParser(self._outputFileName, 0)
98 for transcript in parser.getIterator():
99 self.assertEquals(float(transcript.getTagValue(self._outputTag)), value)
100 parser.close()
101
102 def _writeTranscript(self, transcript):
103 f = open(self._inputFileName, "w")
104 f.write(transcript.printGff3("test"))
105 f.close()
106
107
108 if __name__ == "__main__":
109 unittest.main()