1 package jalview.ws.phyre2;
3 import jalview.datamodel.Sequence;
4 import jalview.datamodel.SequenceI;
5 import jalview.ext.jmol.JmolParser;
6 import jalview.io.DataSourceType;
7 import jalview.io.StructureFile;
9 import java.io.IOException;
10 import java.util.Arrays;
11 import java.util.HashMap;
13 import org.testng.Assert;
14 import org.testng.annotations.Test;
16 public class Phyre2ClientTest
18 private Phyre2Client phyre2Client = null;
23 @Test(groups = { "Functional" })
24 public void getPhyre2FastaMappingTest()
26 String phyre2ModelFile = "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb";
27 String fastaMappingFile = "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta";
29 SequenceI testSeq = new Sequence(
31 "MASVSATMISTSFMPRKPAVTSLKPIPNVGEALFGLKSANGGKVTCMASYKVKLITPDGPIEF"
32 + "DCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQL"
33 + "EEGWVLTCVAYPQSDVTIETHKEAELVG", 1, 144);
35 HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();
36 // PDB sequence starts with residue 48
37 expectedMapping.put(48, new int[] { 48, 1 });
38 expectedMapping.put(49, new int[] { 49, 6 });
39 expectedMapping.put(50, new int[] { 50, 12 });
40 expectedMapping.put(51, new int[] { 51, 24 });
41 expectedMapping.put(52, new int[] { 52, 33 });
42 expectedMapping.put(53, new int[] { 53, 40 });
43 expectedMapping.put(54, new int[] { 54, 49 });
44 expectedMapping.put(55, new int[] { 55, 57 });
45 expectedMapping.put(56, new int[] { 56, 65 });
46 expectedMapping.put(57, new int[] { 57, 72 });
47 expectedMapping.put(58, new int[] { 58, 79 });
48 expectedMapping.put(59, new int[] { 59, 87 });
49 // residues 60, 61 absent in PDB file
50 // residues 62, 63 also skipped in map (is this right?)
51 expectedMapping.put(64, new int[] { 62, 91 });
52 expectedMapping.put(65, new int[] { 63, 100 });
53 expectedMapping.put(66, new int[] { 64, 111 });
54 expectedMapping.put(67, new int[] { 65, 119 });
55 expectedMapping.put(68, new int[] { 66, 125 });
56 expectedMapping.put(69, new int[] { 67, 132 });
57 expectedMapping.put(70, new int[] { 68, 140 });
58 expectedMapping.put(71, new int[] { 69, 148 });
59 expectedMapping.put(72, new int[] { 70, 155 });
60 expectedMapping.put(73, new int[] { 71, 167 });
61 expectedMapping.put(74, new int[] { 72, 175 });
62 expectedMapping.put(75, new int[] { 73, 183 });
63 expectedMapping.put(76, new int[] { 74, 191 });
64 expectedMapping.put(77, new int[] { 75, 200 });
65 expectedMapping.put(78, new int[] { 76, 205 });
66 expectedMapping.put(79, new int[] { 77, 214 });
67 expectedMapping.put(80, new int[] { 78, 223 });
68 expectedMapping.put(81, new int[] { 79, 228 });
69 expectedMapping.put(82, new int[] { 80, 232 });
70 expectedMapping.put(83, new int[] { 81, 242 });
71 expectedMapping.put(84, new int[] { 82, 250 });
72 expectedMapping.put(85, new int[] { 83, 258 });
73 expectedMapping.put(86, new int[] { 84, 265 });
74 expectedMapping.put(87, new int[] { 85, 277 });
75 expectedMapping.put(88, new int[] { 86, 283 });
76 expectedMapping.put(89, new int[] { 87, 289 });
77 expectedMapping.put(90, new int[] { 88, 300 });
78 expectedMapping.put(91, new int[] { 89, 305 });
79 expectedMapping.put(92, new int[] { 90, 309 });
80 expectedMapping.put(93, new int[] { 91, 315 });
81 expectedMapping.put(94, new int[] { 92, 321 });
82 expectedMapping.put(95, new int[] { 93, 327 });
83 expectedMapping.put(96, new int[] { 94, 333 });
84 expectedMapping.put(97, new int[] { 95, 339 });
85 expectedMapping.put(98, new int[] { 96, 344 });
86 expectedMapping.put(99, new int[] { 97, 348 });
87 expectedMapping.put(100, new int[] { 98, 357 });
88 expectedMapping.put(101, new int[] { 99, 365 });
89 expectedMapping.put(102, new int[] { 100, 370 });
90 expectedMapping.put(103, new int[] { 101, 374 });
91 expectedMapping.put(104, new int[] { 102, 378 });
92 expectedMapping.put(105, new int[] { 103, 383 });
93 expectedMapping.put(106, new int[] { 104, 390 });
94 expectedMapping.put(107, new int[] { 105, 398 });
95 expectedMapping.put(108, new int[] { 106, 407 });
96 expectedMapping.put(109, new int[] { 107, 414 });
97 expectedMapping.put(110, new int[] { 108, 422 });
98 expectedMapping.put(111, new int[] { 109, 426 });
99 expectedMapping.put(112, new int[] { 110, 434 });
100 expectedMapping.put(113, new int[] { 111, 445 });
101 expectedMapping.put(114, new int[] { 112, 453 });
102 expectedMapping.put(115, new int[] { 113, 461 });
103 // residue 116 absent in PDB file
104 expectedMapping.put(117, new int[] { 114, 469 });
105 expectedMapping.put(118, new int[] { 115, 477 });
106 // residue 119 gets removed as mapped to 116 - is this right?
107 expectedMapping.put(120, new int[] { 117, 486 });
108 expectedMapping.put(121, new int[] { 118, 495 });
109 expectedMapping.put(122, new int[] { 119, 504 });
110 expectedMapping.put(123, new int[] { 120, 508 });
111 expectedMapping.put(124, new int[] { 121, 522 });
112 expectedMapping.put(125, new int[] { 122, 529 });
113 expectedMapping.put(126, new int[] { 123, 537 });
114 expectedMapping.put(127, new int[] { 124, 544 });
115 expectedMapping.put(128, new int[] { 125, 550 });
116 expectedMapping.put(129, new int[] { 126, 557 });
117 expectedMapping.put(130, new int[] { 127, 562 });
118 expectedMapping.put(131, new int[] { 128, 574 });
119 expectedMapping.put(132, new int[] { 129, 581 });
120 expectedMapping.put(133, new int[] { 130, 590 });
121 expectedMapping.put(134, new int[] { 131, 596 });
122 expectedMapping.put(135, new int[] { 132, 604 });
123 expectedMapping.put(136, new int[] { 133, 611 });
124 expectedMapping.put(137, new int[] { 134, 618 });
125 expectedMapping.put(138, new int[] { 135, 626 });
126 expectedMapping.put(139, new int[] { 136, 635 });
127 expectedMapping.put(140, new int[] { 137, 642 });
128 expectedMapping.put(141, new int[] { 138, 652 });
129 expectedMapping.put(142, new int[] { 139, 661 });
130 expectedMapping.put(143, new int[] { 140, 670 });
131 // residue 144 absent in PDB file
133 StructureFile structureFile;
136 structureFile = new JmolParser(phyre2ModelFile, DataSourceType.FILE);
137 phyre2Client = new Phyre2Client(structureFile);
138 phyre2Client.setFastaMappingFile(fastaMappingFile);
139 } catch (IOException e1)
141 e1.printStackTrace();
143 Assert.assertNotNull(phyre2Client);
144 Assert.assertNotNull(testSeq);
145 Assert.assertNotNull(expectedMapping);
148 HashMap<Integer, int[]> actualMapping = phyre2Client
149 .getPhyre2FastaMapping(testSeq, null);
151 Assert.assertEquals(testSeq.getStart(), 1);
152 Assert.assertEquals(testSeq.getEnd(), 144);
153 testMappings(actualMapping, expectedMapping);
154 } catch (Exception e)
157 Assert.fail("Exception thrown while performing Phyre2 model mapping...");
161 @Test(groups = { "Functional" })
162 public void getPhyre2FastaMappingTest2()
164 String phyre2ModelFile = "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.pdb";
165 String fastaMappingFile = "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.fasta";
167 SequenceI testSeq = new Sequence(
169 "APPPCFSSPLRLRVAVAKPLAAPMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDL",
172 HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();
173 // PDB sequence starts with residue 33
174 expectedMapping.put(45, new int[] { 33, 1 });
175 expectedMapping.put(46, new int[] { 34, 6 });
176 expectedMapping.put(47, new int[] { 35, 13 });
177 expectedMapping.put(48, new int[] { 36, 25 });
178 expectedMapping.put(49, new int[] { 37, 33 });
179 expectedMapping.put(50, new int[] { 38, 40 });
180 expectedMapping.put(51, new int[] { 39, 49 });
181 expectedMapping.put(52, new int[] { 40, 57 });
182 expectedMapping.put(53, new int[] { 41, 65 });
183 expectedMapping.put(54, new int[] { 42, 72 });
184 expectedMapping.put(55, new int[] { 43, 79 });
185 expectedMapping.put(56, new int[] { 44, 88 });
186 expectedMapping.put(57, new int[] { 45, 92 });
187 expectedMapping.put(58, new int[] { 46, 101 });
188 expectedMapping.put(59, new int[] { 47, 108 });
189 expectedMapping.put(60, new int[] { 48, 117 });
190 expectedMapping.put(61, new int[] { 49, 125 });
191 expectedMapping.put(62, new int[] { 50, 134 });
192 expectedMapping.put(63, new int[] { 51, 141 });
193 expectedMapping.put(64, new int[] { 52, 148 });
194 expectedMapping.put(65, new int[] { 53, 156 });
195 expectedMapping.put(66, new int[] { 54, 164 });
196 expectedMapping.put(67, new int[] { 55, 171 });
197 expectedMapping.put(68, new int[] { 56, 183 });
198 expectedMapping.put(69, new int[] { 57, 191 });
199 expectedMapping.put(70, new int[] { 58, 199 });
200 expectedMapping.put(71, new int[] { 59, 207 });
201 expectedMapping.put(72, new int[] { 60, 218 });
202 expectedMapping.put(73, new int[] { 61, 223 });
203 expectedMapping.put(74, new int[] { 62, 232 });
204 expectedMapping.put(75, new int[] { 63, 241 });
205 expectedMapping.put(76, new int[] { 64, 250 });
206 expectedMapping.put(77, new int[] { 65, 254 });
207 expectedMapping.put(78, new int[] { 66, 262 });
208 expectedMapping.put(79, new int[] { 67, 270 });
209 expectedMapping.put(80, new int[] { 68, 278 });
210 expectedMapping.put(81, new int[] { 69, 285 });
211 expectedMapping.put(82, new int[] { 70, 296 });
212 expectedMapping.put(83, new int[] { 71, 302 });
213 expectedMapping.put(84, new int[] { 72, 308 });
214 expectedMapping.put(85, new int[] { 73, 319 });
215 expectedMapping.put(86, new int[] { 74, 324 });
216 expectedMapping.put(87, new int[] { 75, 328 });
217 expectedMapping.put(88, new int[] { 76, 334 });
218 expectedMapping.put(89, new int[] { 77, 340 });
219 expectedMapping.put(90, new int[] { 78, 346 });
220 expectedMapping.put(91, new int[] { 79, 352 });
221 expectedMapping.put(92, new int[] { 80, 358 });
222 expectedMapping.put(93, new int[] { 81, 363 });
223 expectedMapping.put(94, new int[] { 82, 367 });
224 expectedMapping.put(95, new int[] { 83, 376 });
225 expectedMapping.put(96, new int[] { 84, 383 });
226 expectedMapping.put(97, new int[] { 85, 390 });
227 expectedMapping.put(98, new int[] { 86, 396 });
228 expectedMapping.put(99, new int[] { 87, 400 });
229 expectedMapping.put(100, new int[] { 88, 406 });
230 expectedMapping.put(101, new int[] { 89, 413 });
231 expectedMapping.put(102, new int[] { 90, 421 });
232 expectedMapping.put(103, new int[] { 91, 430 });
233 expectedMapping.put(104, new int[] { 92, 436 });
234 expectedMapping.put(105, new int[] { 93, 444 });
235 expectedMapping.put(106, new int[] { 94, 453 });
236 expectedMapping.put(107, new int[] { 95, 459 });
237 expectedMapping.put(108, new int[] { 96, 470 });
238 expectedMapping.put(109, new int[] { 97, 478 });
239 expectedMapping.put(110, new int[] { 98, 486 });
240 expectedMapping.put(111, new int[] { 99, 494 });
241 expectedMapping.put(112, new int[] { 100, 502 });
242 expectedMapping.put(113, new int[] { 101, 511 });
243 expectedMapping.put(114, new int[] { 102, 518 });
244 expectedMapping.put(115, new int[] { 103, 523 });
245 expectedMapping.put(116, new int[] { 104, 531 });
246 expectedMapping.put(117, new int[] { 105, 535 });
247 expectedMapping.put(118, new int[] { 106, 549 });
248 expectedMapping.put(119, new int[] { 107, 556 });
249 expectedMapping.put(120, new int[] { 108, 564 });
250 expectedMapping.put(121, new int[] { 109, 571 });
251 expectedMapping.put(122, new int[] { 110, 577 });
252 expectedMapping.put(123, new int[] { 111, 582 });
253 expectedMapping.put(124, new int[] { 112, 587 });
254 expectedMapping.put(125, new int[] { 113, 599 });
255 expectedMapping.put(126, new int[] { 114, 606 });
256 expectedMapping.put(127, new int[] { 115, 613 });
257 expectedMapping.put(128, new int[] { 116, 619 });
258 expectedMapping.put(129, new int[] { 117, 627 });
259 expectedMapping.put(130, new int[] { 118, 634 });
260 expectedMapping.put(131, new int[] { 119, 641 });
261 expectedMapping.put(132, new int[] { 120, 649 });
262 expectedMapping.put(133, new int[] { 121, 658 });
263 expectedMapping.put(134, new int[] { 122, 665 });
264 expectedMapping.put(135, new int[] { 123, 675 });
265 expectedMapping.put(136, new int[] { 124, 684 });
266 expectedMapping.put(137, new int[] { 125, 693 });
267 expectedMapping.put(138, new int[] { 126, 701 });
268 expectedMapping.put(139, new int[] { 127, 709 });
270 StructureFile structureFile;
273 structureFile = new JmolParser(phyre2ModelFile, DataSourceType.FILE);
274 phyre2Client = new Phyre2Client(structureFile);
275 phyre2Client.setFastaMappingFile(fastaMappingFile);
276 } catch (IOException e1)
278 e1.printStackTrace();
280 Assert.assertNotNull(phyre2Client);
281 Assert.assertNotNull(testSeq);
282 Assert.assertNotNull(expectedMapping);
285 HashMap<Integer, int[]> actualMapping = phyre2Client
286 .getPhyre2FastaMapping(testSeq, null);
288 Assert.assertEquals(testSeq.getStart(), 13);
289 Assert.assertEquals(testSeq.getEnd(), 139);
290 Assert.assertEquals(actualMapping, expectedMapping);
291 testMappings(actualMapping, expectedMapping);
292 } catch (Exception e)
295 Assert.fail("Exception thrown while performing Phyre2 model mapping...");
299 public void testMappings(HashMap<Integer, int[]> actualMapping,
300 HashMap<Integer, int[]> expectedMapping)
302 System.out.println("Expected Mapping size: " + expectedMapping.size());
303 System.out.println("Actual Mapping size: " + actualMapping.size());
305 Assert.assertEquals(actualMapping.size(), expectedMapping.size());
307 Assert.assertEquals(actualMapping.keySet(), expectedMapping.keySet());
309 for (int key : expectedMapping.keySet())
311 System.out.println(key + " ---> [" + expectedMapping.get(key)[0]
312 + ", " + expectedMapping.get(key)[1] + "] = ["
313 + actualMapping.get(key)[0] + ", "
314 + actualMapping.get(key)[1] + "]");
315 Assert.assertTrue(Arrays.equals(expectedMapping.get(key),
316 actualMapping.get(key)));