Mercurial > repos > chrisb > gap_all_glycan_tools
comparison get_data/kegg_glycan/test_findKEGG.py @ 1:0a5e0df17054 draft default tip
Uploaded
author | chrisb |
---|---|
date | Fri, 06 May 2016 08:05:48 -0400 |
parents | 89592faa2875 |
children |
comparison
equal
deleted
inserted
replaced
0:89592faa2875 | 1:0a5e0df17054 |
---|---|
39 | 39 |
40 with self.assertRaises(urllib2.HTTPError): | 40 with self.assertRaises(urllib2.HTTPError): |
41 m = fk.find_entries_in_KEGG("john", "glucose") | 41 m = fk.find_entries_in_KEGG("john", "glucose") |
42 | 42 |
43 def test_unfindable_entry(self): | 43 def test_unfindable_entry(self): |
44 """should return None""" | 44 """should return an empty string""" |
45 m = fk.find_entries_in_KEGG("glycan", "sally") | 45 m = fk.find_entries_in_KEGG("glycan", "sally") |
46 self.assertIsNone(m) | 46 emptystring="" |
47 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") | |
47 | 48 |
48 def test_find_example(self): | 49 def test_find_example(self): |
49 m = fk.find_entries_in_KEGG("glycan", "glucose") | 50 m = fk.find_entries_in_KEGG("glycan", "glucose") |
50 self.assertIsNotNone(m) | 51 self.assertIsNotNone(m) |
51 self.assertIn("GDP-glucose", m) | 52 self.assertIn("GDP-glucose", m) |
52 | 53 |
53 def test_query_has_newlines(self): | 54 def test_query_has_newlines(self): |
54 """ | 55 """ |
55 should be fine and return entries | 56 Assume a new line query is an AND query. |
57 """ | |
58 m = fk.find_entries_in_KEGG("glycan", "glucose\nUDP") | |
59 self.assertIsNotNone(m) | |
60 print m | |
61 self.assertIn("UDP-D-glucose", m) | |
62 | |
63 def test_query_has_newlines_and_a_space(self): | |
64 """ | |
65 glucose\\n UDP. OR's should pass | |
56 """ | 66 """ |
57 m = fk.find_entries_in_KEGG("glycan", "glucose\n UDP") | 67 m = fk.find_entries_in_KEGG("glycan", "glucose\n UDP") |
58 self.assertIsNotNone(m) | 68 self.assertIsNotNone(m) |
59 self.assertIn("UDP-D-glucose", m) | 69 self.assertIn("UDP-D-glucose", m) |
60 | 70 |
71 def test_gene_specific_or(self): | |
72 """ | |
73 test "shiga toxin" returns. | |
74 /find/genes/"shiga toxin" for keywords "shiga toxin" | |
75 """ | |
76 m = fk.find_entries_in_KEGG("genes","shiga toxin") | |
77 self.assertIsNotNone(m) | |
78 #. not matching to all entries - that is silly, the db get updated! | |
79 self.assertIn("shiga", m) | |
80 self.assertIn("toxin", m) | |
81 self.assertNotIn("stm:STM0284",m) # should not be found in the OR query | |
82 | |
83 def test_gene_specific_and(self): | |
84 """ | |
85 test "shiga+toxin" returns. it should | |
86 /find/genes/shiga+toxin for keywords "shiga" and "toxin" | |
87 """ | |
88 m = fk.find_entries_in_KEGG("genes","shiga+toxin") | |
89 self.assertIsNotNone(m) | |
90 #. not matching to all entries - that is silly, the db get updated! | |
91 self.assertIn("shiga", m) | |
92 self.assertIn("toxin", m) | |
93 self.assertIn("stm:STM0284",m) # should be found in the AND query | |
94 | |
95 def test_enzyme_specific_1(self): | |
96 """ | |
97 test 2.4.99.1 returns | |
98 """ | |
99 m = fk.find_entries_in_KEGG("enzyme","2.4.99.1") | |
100 self.assertIsNotNone(m) | |
101 #. not matching to all entries - that is silly, the db get updated! | |
102 self.assertIn("2.4.99.1", m) | |
103 | |
104 def test_enzyme_specific_2(self): | |
105 """ | |
106 test 2.4.99.6 returns | |
107 """ | |
108 m = fk.find_entries_in_KEGG("enzyme","2.4.99.6") | |
109 self.assertIsNotNone(m) | |
110 #. not matching to all entries - that is silly, the db get updated! | |
111 self.assertIn("2.4.99.6", m) | |
112 | |
113 def test_enzyme_specific_3(self): | |
114 """ | |
115 test ec: 2.4.99.6 with space (tests stripping space functionality) | |
116 """ | |
117 m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.6") | |
118 self.assertIsNotNone(m) | |
119 #. not matching to all entries - that is silly, the db get updated! | |
120 self.assertIn("2.4.99.6", m) | |
121 | |
122 def test_enzyme_specific_4(self): | |
123 """ | |
124 test ec: 2.4.99. , should return 2.4.99.* | |
125 """ | |
126 m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.") | |
127 self.assertIsNotNone(m) | |
128 #. not matching to all entries - that is silly, the db get updated! | |
129 self.assertIn("2.4.99.1", m) | |
130 self.assertIn("2.4.99.6", m) | |
131 self.assertIn("2.4.99.11", m) | |
132 | |
133 def test_enzyme_specific_5(self): | |
134 """ | |
135 test ec: 2.4.99.1+2.4.99.6 . AND function, so returns nothing here. Do not expect an enzyme to be doubly classified. | |
136 """ | |
137 m = fk.find_entries_in_KEGG("enzyme","2.4.99.1+2.4.99.6") | |
138 self.assertIsNotNone(m) | |
139 emptystring="" | |
140 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") | |
141 | |
142 def test_enzyme_specific_6(self): | |
143 """ | |
144 test ec: 2.4.99.1 2.4.99.6 . OR function, should return something but does not (KEGG FAILURE?). | |
145 note that trying this without "" will return the AND function result which is incorrect. | |
146 """ | |
147 m = fk.find_entries_in_KEGG("enzyme","2.4.99.1 2.4.99.6") | |
148 self.assertIsNotNone(m) | |
149 #self.assertIn("2.4.99.1", m) | |
150 emptystring="" | |
151 print m | |
152 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") | |
153 | |
154 | |
155 def test_enzyme_specific_7(self): | |
156 """ | |
157 test deoxy+1.1.1. . AND function, that should return something | |
158 """ | |
159 m = fk.find_entries_in_KEGG("enzyme","deoxy+1.1.1") | |
160 self.assertIsNotNone(m) | |
161 print m | |
162 self.assertIn("deoxy", m) | |
163 self.assertIn("1.1.1", m) | |
164 | |
165 def test_enzyme_specific_8(self): | |
166 """ | |
167 test deoxy 1.1.1. . OR function. should return deoxy or 1.1.1. but does not (KEGG FAILURE?). i | |
168 note that trying this without "" will return the AND function result which is incorrect. | |
169 """ | |
170 m = fk.find_entries_in_KEGG("enzyme","deoxy 1.1.1") | |
171 self.assertIsNotNone(m) | |
172 emptystring="" | |
173 print m | |
174 self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") | |
175 |