Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/align/tests/Test_AlignListUtils.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 os
2 import unittest
3 from commons.pyRepetUnit.align.AlignList import AlignList
4 from commons.pyRepetUnit.align.AlignListUtils import AlignListUtils
5 from commons.core.utils.FileUtils import FileUtils
6 from commons.core.coord.Range import Range
7 from commons.core.coord.Align import Align
8
9 class Test_AlignListUtils (unittest.TestCase):
10
11 def setUp(self):
12 self.inputFileName = "dummyAlignFile.align"
13 self.outputFileName = "dummyAlignFile.out"
14
15 def testRead(self):
16 f = open(self.inputFileName, "w")
17 f.write("blumeria_Grouper_590_20:NoCat_1\t91\t108\tDUF234\t5\t22\t2.6e-60\t0\t3.2\n")
18 f.write("blumeria_Grouper_590_20:NoCat_1\t111\t119\tDUF1414\t1\t9\t6.3\t0\t2.9\n")
19 f.close()
20 alignRead = AlignListUtils()
21 tableauAlignInstance = alignRead.read(self.inputFileName)
22 self.assertEquals(tableauAlignInstance.get(0).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1")
23 self.assertEquals(tableauAlignInstance.get(0).range_query.start, 91)
24 self.assertEquals(tableauAlignInstance.get(0).range_query.end, 108)
25 self.assertEquals(tableauAlignInstance.get(0).range_subject.seqname, "DUF234")
26 self.assertEquals(tableauAlignInstance.get(0).range_subject.start, 5)
27 self.assertEquals(tableauAlignInstance.get(0).range_subject.end, 22)
28 self.assertEquals(tableauAlignInstance.get(0).e_value, 2.6e-60)
29 self.assertEquals(tableauAlignInstance.get(0).score, 0)
30 self.assertEquals(tableauAlignInstance.get(0).identity, 3.2)
31 self.assertEquals(tableauAlignInstance.get(1).range_query.seqname, "blumeria_Grouper_590_20:NoCat_1")
32 self.assertEquals(tableauAlignInstance.get(1).range_query.start, 111)
33 self.assertEquals(tableauAlignInstance.get(1).range_query.end, 119)
34 self.assertEquals(tableauAlignInstance.get(1).range_subject.seqname, "DUF1414")
35 self.assertEquals(tableauAlignInstance.get(1).range_subject.start, 1)
36 self.assertEquals(tableauAlignInstance.get(1).range_subject.end, 9)
37 self.assertEquals(tableauAlignInstance.get(1).e_value, 6.3)
38 self.assertEquals(tableauAlignInstance.get(1).score, 0)
39 self.assertEquals(tableauAlignInstance.get(1).identity, 2.9)
40 os.system("rm " + self.inputFileName)
41
42 def testWrite(self):
43 f = open("expectedAlignFile.align", "w")
44 f.write("biduleChouetteQuery\t20\t55\tbiduleChouetteSubject\t2\t15\t0.005\t20\t0.000000\n")
45 f.write("trucBiduleQuery\t110\t155\ttrucBiduleSubject\t1\t35\t2\t1\t0.000000\n")
46 f.write("dummyQuery\t1\t65\tdummySubject\t1\t25\t2.6e-60\t50\t0.000000\n")
47 f.close()
48 listAlignInstance = AlignList()
49 align1 = Align()
50 align1.range_query = Range("biduleChouetteQuery", 20, 55)
51 align1.range_subject = Range("biduleChouetteSubject", 2, 15)
52 align1.e_value = 0.005
53 align1.score = 20
54 listAlignInstance.append(align1)
55 align2 = Align()
56 align2.range_query = Range("trucBiduleQuery", 110, 155)
57 align2.range_subject = Range("trucBiduleSubject", 1, 35)
58 align2.e_value = 2
59 align2.score = 1.5
60 listAlignInstance.append(align2)
61 align3 = Align()
62 align3.range_query = Range("dummyQuery", 1, 65)
63 align3.range_subject = Range("dummySubject", 1, 25)
64 align3.e_value = 2.6e-60
65 align3.score = 50
66 listAlignInstance.append(align3)
67 f = open(self.outputFileName, "w")
68 alignUtils = AlignListUtils()
69 alignUtils.write(listAlignInstance, self.outputFileName)
70 self.assertTrue(FileUtils.are2FilesIdentical(self.outputFileName, "expectedAlignFile.align"))
71 os.system("rm " + self.outputFileName)
72 os.system("rm expectedAlignFile.align")
73
74 def testFilterOnAMinimalScore(self):
75 listAlignInstance = AlignList()
76 align1 = Align()
77 align1.range_query = Range("biduleChouetteQuery", 20, 55)
78 align1.range_subject = Range("biduleChouetteSubject", 2, 15)
79 align1.e_value = 5
80 align1.score = -0.5
81 listAlignInstance.append(align1)
82 align2 = Align()
83 align2.range_query = Range("trucBiduleQuery", 110, 155)
84 align2.range_subject = Range("trucBiduleSubject", 1, 35)
85 align2.e_value = 2
86 align2.score = -2.0
87 listAlignInstance.append(align2)
88 align3 = Align()
89 align3.range_query = Range("dummyQuery", 1, 65)
90 align3.range_subject = Range("dummySubject", 1, 25)
91 align3.e_value = 2.6e-60
92 align3.score = 50
93 listAlignInstance.append(align3)
94 expectedAlignInstance = align3
95 alignUtils = AlignListUtils()
96 alignUtils.filterOnAMinimalScore(listAlignInstance, 0)
97 self.assertEquals(listAlignInstance.get(0), expectedAlignInstance)
98
99 if __name__ == "__main__" :
100 unittest.main()