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 |
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date | Wed, 23 Mar 2016 14:35:56 -0400 |
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-1:000000000000 | 0:89592faa2875 |
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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() |