Mercurial > repos > chrisb > gap_all_glycan_tools

comparison extract_display_features/rings_fingerprinter/test_fingerprinter.py @ 0:89592faa2875 draft

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author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
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-1:000000000000 0:89592faa2875
1 __license__ = "MIT"
2
3 import unittest
4 import post_fingerprinter as fp
5
6
7 class SimpleUnitTest(unittest.TestCase):
8 def setUp(self):
9 import os
10
11 self.kcinput = {"rings": """ENTRY G00015 Glycan
12 NODE 8
13 1 Asn 20 0
14 2 GlcNAc 12 0
15 3 GlcNAc 3 0
16 4 Man -5 0
17 5 Man -12 5
18 6 Man -12 -5
19 7 GlcNAc -20 5
20 8 GlcNAc -20 -5
21 EDGE 7
22 1 2:b1 1
23 2 3:b1 2:4
24 3 4:b1 3:4
25 4 5:a1 4:6
26 5 6:a1 4:3
27 6 7:b1 5:2
28 7 8:b1 6:2
29 ///
30 ENTRY G00016 Glycan
31 NODE 9
32 1 Asn 20 3
33 2 GlcNAc 12 3
34 3 LFuc 4 8
35 4 GlcNAc 3 -2
36 5 Man -5 -2
37 6 Man -12 3
38 7 Man -12 -7
39 8 GlcNAc -20 3
40 9 GlcNAc -20 -7
41 EDGE 8
42 1 2:b1 1
43 2 3:a1 2:6
44 3 4:b1 2:4
45 4 5:b1 4:4
46 5 6:a1 5:6
47 6 7:a1 5:3
48 7 8:b1 6:2
49 8 9:b1 7:2
50 ///
51 ENTRY G00017 Glycan
52 NODE 11
53 1 Asn 24 3
54 2 GlcNAc 14 3
55 3 LFuc 7 8
56 4 GlcNAc 6 -2
57 5 Man -2 -2
58 6 Man -8 3
59 7 Man -8 -7
60 8 GlcNAc -16 3
61 9 GlcNAc -16 -7
62 10 Gal -24 3
63 11 Gal -24 -7
64 EDGE 10
65 1 2:b1 1
66 2 3:a1 2:6
67 3 4:b1 2:4
68 4 5:b1 4:4
69 5 6:a1 5:6
70 6 7:a1 5:3
71 7 8:b1 6:2
72 8 9:b1 7:2
73 9 10:b1 8:4
74 10 11:b1 9:4
75 ///
76 ENTRY G00018 Glycan
77 NODE 13
78 1 Asn 28 3
79 2 GlcNAc 18 3
80 3 LFuc 10 8
81 4 GlcNAc 9 -2
82 5 Man 1 -2
83 6 Man -5 4
84 7 Man -5 -8
85 8 GlcNAc -13 4
86 9 GlcNAc -13 -8
87 10 Gal -21 4
88 11 Gal -21 -8
89 12 Neu5Ac -29 4
90 13 Neu5Ac -29 -8
91 EDGE 12
92 1 2:b1 1
93 2 3:a1 2:6
94 3 4:b1 2:4
95 4 5:b1 4:4
96 5 6:a1 5:6
97 6 7:a1 5:3
98 7 8:b1 6:2
99 8 9:b1 7:2
100 9 10:b1 8:4
101 10 11:b1 9:4
102 11 12:a2 10:6
103 12 13:a2 11:6
104 ///
105 ENTRY G00019 Glycan
106 NODE 9
107 1 Asn 20 0
108 2 GlcNAc 12 0
109 3 GlcNAc 3 0
110 4 Man -5 0
111 5 Man -12 5
112 6 Man -12 -5
113 7 GlcNAc -15 0
114 8 GlcNAc -20 5
115 9 GlcNAc -20 -5
116 EDGE 8
117 1 2:b1 1
118 2 3:b1 2:4
119 3 4:b1 3:4
120 4 5:a1 4:6
121 5 6:a1 4:3
122 6 7:b1 4:4
123 7 8:b1 5:2
124 8 9:b1 6:2
125 ///
126 ENTRY G00020 Glycan
127 NODE 9
128 1 Asn 20 3
129 2 GlcNAc 11 3
130 3 GlcNAc 2 3
131 4 Man -6 3
132 5 Man -13 9
133 6 Man -13 -3
134 7 GlcNAc -21 9
135 8 GlcNAc -21 2
136 9 GlcNAc -21 -8
137 EDGE 8
138 1 2:b1 1
139 2 3:b1 2:4
140 3 4:b1 3:4
141 4 5:a1 4:6
142 5 6:a1 4:3
143 6 7:b1 5:2
144 7 8:b1 6:4
145 8 9:b1 6:2
146 ///
147 """
148 }
149 self.similaritymatrix = {
150 "rings": """G00015\t 1.000000\t 0.777778\t 0.460526\t 0.304348\t 0.564516\t 0.636364\t \nG00016\t 0.777778\t 1.000000\t 0.592105\t 0.391304\t 0.486111\t 0.538462\t \nG00017\t 0.460526\t 0.592105\t 1.000000\t 0.660870\t 0.339806\t 0.378947\t \nG00018\t 0.304348\t 0.391304\t 0.660870\t 1.000000\t 0.255319\t 0.268657\t \nG00019\t 0.564516\t 0.486111\t 0.339806\t 0.255319\t 1.000000\t 0.444444\t \nG00020\t 0.636364\t 0.538462\t 0.378947\t 0.268657\t 0.444444\t 1.000000\t """
151 }
152 os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http:
153 pass
154
155 def tearDown(self):
156 pass
157
158 def test_kcf_input(self):
159 import StringIO
160
161 kchandle = StringIO.StringIO(''.join(self.kcinput["rings"]))
162 h = fp.post_rings_fingerprinter(kchandle)
163 # print h
164 d = fp.extract_dendro_from_fingerprinter_output(h)
165 # print d
166 self.assertIn(self.similaritymatrix["rings"], h)
167 self.assertIn("|||G00015_G00016|_|G00019_G00020||_|G00017_G00018||", h)
168 self.assertIn("|||G00015_G00016|_|G00019_G00020||_|G00017_G00018||", d)
169
170 def test_empty_stream(self):
171 with self.assertRaises(IOError):
172 fp.post_rings_fingerprinter(None)
173 with self.assertRaises(IOError):
174 fp.post_rings_fingerprinter([])
175 with self.assertRaises(IOError):
176 fp.post_rings_fingerprinter("")
177 with self.assertRaises(IOError):
178 fp.extract_dendro_from_fingerprinter_output(None)
179 with self.assertRaises(IOError):
180 fp.extract_dendro_from_fingerprinter_output([])
181 with self.assertRaises(IOError):
182 fp.extract_dendro_from_fingerprinter_output("")
183
184
185 def run_tests():
186 unittest.main()
187
188
189 if __name__ == '__main__':
190 run_tests()