Mercurial > repos > yufei-luo > s_mart

comparison commons/core/coord/test/Test_Path.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 # 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 )