Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/coord/test/Test_Path.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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1 # Copyright INRA (Institut National de la Recherche Agronomique) | |
2 # http://www.inra.fr | |
3 # http://urgi.versailles.inra.fr | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 | |
31 | |
32 import unittest | |
33 from commons.core.coord.Path import Path | |
34 from commons.core.coord.Align import Align | |
35 from commons.core.coord.Set import Set | |
36 | |
37 | |
38 class Test_Path( unittest.TestCase ): | |
39 | |
40 def setUp( self ): | |
41 self._path = Path() | |
42 | |
43 def test_setFromTuple( self ): | |
44 line = "1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2" | |
45 self._path.setFromTuple( line.split("\t") ) | |
46 self.assertEqual( self._path.id, 1 ) | |
47 self.assertEqual( self._path.range_query.seqname, "chr1" ) | |
48 self.assertEqual( self._path.range_query.start, 1 ) | |
49 self.assertEqual( self._path.range_query.end, 10 ) | |
50 self.assertEqual( self._path.range_subject.seqname, "TE2" ) | |
51 self.assertEqual( self._path.range_subject.start, 11 ) | |
52 self.assertEqual( self._path.range_subject.end, 17 ) | |
53 self.assertEqual( self._path.e_value, float("1e-20") ) | |
54 self.assertEqual( self._path.score, float("30") ) | |
55 self.assertEqual( self._path.identity, float("90.2") ) | |
56 | |
57 def test___eq__( self ): | |
58 self._path.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) | |
59 o = Path() | |
60 o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) | |
61 self.assertEqual( self._path, o ) | |
62 o.setFromString( "2\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) | |
63 self.assertNotEqual( self._path, o ) | |
64 o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t3000000\t90.2\n" ) | |
65 self.assertNotEqual( self._path, o ) | |
66 | |
67 def test_canMerge( self ): | |
68 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") | |
69 self._path.setFromTuple(tuple) | |
70 tuple = ("2", "chr1","2", "9","TE2","10","13","1e-20","30","90.2") | |
71 o = Path() | |
72 o.setFromTuple(tuple) | |
73 self.assertTrue(self._path.canMerge(o)) | |
74 | |
75 def test_canMerge_on_same_id ( self ): | |
76 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") | |
77 self._path.setFromTuple(tuple) | |
78 tuple = ("1", "chr1","2", "9","TE2","10","13","1e-20","30","90.2") | |
79 o = Path() | |
80 o.setFromTuple(tuple) | |
81 self.assertFalse(self._path.canMerge(o)) | |
82 | |
83 def test_canMerge_on_same_chr( self ): | |
84 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") | |
85 self._path.setFromTuple(tuple) | |
86 tuple = ("2", "chr2","2", "9","TE2","10","13","1e-20","30","90.2") | |
87 o = Path() | |
88 o.setFromTuple(tuple) | |
89 self.assertFalse(self._path.canMerge(o)) | |
90 | |
91 def test_canMerge_on_diff_subj( self ): | |
92 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") | |
93 self._path.setFromTuple(tuple) | |
94 tuple = ("2", "chr1","2", "9","TE3","10","13","1e-20","30","90.2") | |
95 o = Path() | |
96 o.setFromTuple(tuple) | |
97 self.assertFalse(self._path.canMerge(o)) | |
98 | |
99 def test_canMerge_on_queries_that_do_not_overlap( self ): | |
100 tuple = ("1", "chr1","5", "11","TE2","11","17","1e-20","30","90.2") | |
101 self._path.setFromTuple(tuple) | |
102 tuple = ("2", "chr1","1", "4","TE2","10","13","1e-20","30","90.2") | |
103 o = Path() | |
104 o.setFromTuple(tuple) | |
105 self.assertFalse(self._path.canMerge(o)) | |
106 | |
107 def test_canMerge_on_subjects_that_do_not_overlap( self ): | |
108 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") | |
109 self._path.setFromTuple(tuple) | |
110 tuple = ("2", "chr1","2", "9","TE2","1","10","1e-20","30","90.2") | |
111 o = Path() | |
112 o.setFromTuple(tuple) | |
113 self.assertFalse(self._path.canMerge(o)) | |
114 | |
115 def test_getSubjectAsSetOfQuery( self ): | |
116 tuple = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2") | |
117 self._path.setFromTuple(tuple) | |
118 exp = Set(1,"TE2","chr1",1,10) | |
119 obs = self._path.getSubjectAsSetOfQuery() | |
120 self.assertEqual( exp, obs ) | |
121 | |
122 def test_getSubjectAsSetOfQuery_on_neg_strand( self ): | |
123 tuple = ("1","chr1","10","1","TE2","11","17","1e-20","30","90.2") | |
124 self._path.setFromTuple(tuple) | |
125 exp = Set(1,"TE2","chr1",10,1) | |
126 obs = self._path.getSubjectAsSetOfQuery() | |
127 self.assertEqual( exp, obs ) | |
128 | |
129 def test_toString( self ): | |
130 self._path.setFromString( "1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t85.2\n" ) | |
131 exp = "1\tchr1\t1\t10\tTE3\t11\t17\t%g\t30\t%f" % ( 1e-20, 85.2 ) | |
132 obs = self._path.toString() | |
133 self.assertEqual( obs, exp ) | |
134 | |
135 def test_getAlignInstance( self ): | |
136 self._path.setFromTuple( ( "2", "chr3", "250", "151", "seq5", "1", "100", "1e-32", "147", "87.9" ) ) | |
137 expAlign = Align() | |
138 expAlign.setFromTuple( ( "chr3", "151", "250", "seq5", "100", "1", "1e-32", "147", "87.9" ) ) | |
139 obsAlign = self._path.getAlignInstance() | |
140 self.assertEqual( expAlign, obsAlign ) | |
141 | |
142 | |
143 test_suite = unittest.TestSuite() | |
144 test_suite.addTest( unittest.makeSuite( Test_Path ) ) | |
145 if __name__ == "__main__": | |
146 unittest.TextTestRunner(verbosity=2).run( test_suite ) |