Source code

001/**
002 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
003 *
004 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
006 * Veterinary Studies, University of Edinburgh.
007 *
008 * Project hosted at: http://jensembl.sourceforge.net
009 *
010 * This is free software: you can redistribute it and/or modify
011 * it under the terms of the GNU General Public License (version 3) as published by
012 * the Free Software Foundation.
013 *
014 * This software is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
021 */
022package uk.ac.roslin.ensembl.demo;
023
024import java.util.Collection;
025import java.util.List;
026import uk.ac.roslin.ensembl.config.DBConnection.DataSource;
027import uk.ac.roslin.ensembl.dao.database.DBRegistry;
028import uk.ac.roslin.ensembl.dao.database.DBSpecies;
029import uk.ac.roslin.ensembl.datasourceaware.DAXRef;
030import uk.ac.roslin.ensembl.datasourceaware.core.DAGene;
031import uk.ac.roslin.ensembl.datasourceaware.core.DATranscript;
032import uk.ac.roslin.ensembl.datasourceaware.core.DATranslation;
033import uk.ac.roslin.ensembl.model.core.Species;
034
035public class Synonyms {
036
037    public static void main(String[] args) throws Exception {
038
039        
040        DBRegistry reg2 = DBRegistry.createRegistryForDataSourceCurrentRelease(DataSource.ENSEMBLBACTERIA);
041        
042        Collection<? extends Species> setOfEverySpeciesByAlias = reg2.getSetOfEverySpeciesByAlias("k-12");
043        
044        System.out.println("there are "+setOfEverySpeciesByAlias.size()+" species with name 'k-12'.");
045        
046        Collection<? extends Species> setOfSpeciesByAlias = reg2.getSetOfSpeciesByAlias("k-12");       
047        
048        System.out.println("there are "+setOfSpeciesByAlias.size()+" CURRENT species with name 'k-12'.");
049        
050        DBSpecies ek = reg2.getSpeciesByAlias("escherichia_coli_str_k_12_substr_mg1655");
051        
052        System.out.println("ek.getGenesForExactName(\"thrL\")");
053        
054        List<DAGene> genesForExactName = ek.getGenesForExactName("thrL");
055
056        System.out.println("count is: "+genesForExactName.size());
057        
058        for (DAGene g : genesForExactName) {
059
060            System.out.println("GENE: " + g.getStableID());
061
062            System.out.println("DisplayXref displayID: " + g.getDisplayXRef().getDisplayID());
063            System.out.println("DisplayXref primary accession: " + g.getDisplayXRef().getPrimaryAccession());
064            System.out.println("DisplayXref version: " + g.getDisplayXRef().getVersion());
065            System.out.println("DisplayXref database: " + g.getDisplayXRef().getDBDisplayName());
066            System.out.println("DisplayXref db version: " + g.getDisplayXRef().getDBVersion());
067            System.out.println("DisplayXref description: " + g.getDisplayXRef().getDescription());
068            System.out.print("DisplayXref synonyms (method1): ");
069            for (String s : g.getDisplayXRef().getSynonyms()) {
070                System.out.print(s + " | ");
071            }
072            System.out.println("");
073            System.out.print("DisplayXref synonyms (method2): ");
074            for (String s : g.getSynonyms(g.getDisplayXRef())) {
075                System.out.print(s + " | ");
076            }
077            System.out.println("");
078            System.out.println("VEGA XREFS");
079
080            for (DAXRef x : g.getVegaXRefs()) {
081                System.out.println(" displayID: " + x.getDisplayID());
082                System.out.println(" primary accession: " + x.getPrimaryAccession());
083                System.out.println(" version: " + x.getVersion());
084                System.out.println(" database: " + x.getDBDisplayName());
085                System.out.println(" db version: " + x.getDBVersion());
086                System.out.println(" description: " + x.getDescription());
087                System.out.print("Synonyms: ");
088                for (String s : x.getSynonyms()) {
089                    System.out.print(s + " | ");
090                }
091                System.out.println("");
092            }
093
094            System.out.print("ALL SYNONYMS: ");
095
096            for (String s : g.getAllSynonyms()) {
097                System.out.print(s + " | ");
098            }
099            System.out.println("");
100
101        }
102
103        System.out.println("");
104        System.out.println("----------------------------------");
105        System.out.println("");        
106        
107        
108        DBRegistry reg = DBRegistry.createRegistryForDataSource(DataSource.ENSEMBLDB);
109        DBSpecies hs = reg.getSpeciesByAlias("human");
110        
111        System.out.println("hs.getGenesForExactName(\"MAPK13\")");
112        
113        genesForExactName = hs.getGenesForExactName("MAPK13");
114
115        System.out.println("count is: "+genesForExactName.size());
116        
117        for (DAGene g : genesForExactName) {
118
119            System.out.println("GENE: " + g.getStableID());
120
121            System.out.println("DisplayXref displayID: " + g.getDisplayXRef().getDisplayID());
122            System.out.println("DisplayXref primary accession: " + g.getDisplayXRef().getPrimaryAccession());
123            System.out.println("DisplayXref version: " + g.getDisplayXRef().getVersion());
124            System.out.println("DisplayXref database: " + g.getDisplayXRef().getDBDisplayName());
125            System.out.println("DisplayXref db version: " + g.getDisplayXRef().getDBVersion());
126            System.out.println("DisplayXref description: " + g.getDisplayXRef().getDescription());
127            System.out.print("DisplayXref synonyms (method1): ");
128            for (String s : g.getDisplayXRef().getSynonyms()) {
129                System.out.print(s + " | ");
130            }
131            System.out.println("");
132            System.out.print("DisplayXref synonyms (method2): ");
133            for (String s : g.getSynonyms(g.getDisplayXRef())) {
134                System.out.print(s + " | ");
135            }
136            System.out.println("");
137            System.out.println("VEGA XREFS");
138
139            for (DAXRef x : g.getVegaXRefs()) {
140                System.out.println(" displayID: " + x.getDisplayID());
141                System.out.println(" primary accession: " + x.getPrimaryAccession());
142                System.out.println(" version: " + x.getVersion());
143                System.out.println(" database: " + x.getDBDisplayName());
144                System.out.println(" db version: " + x.getDBVersion());
145                System.out.println(" description: " + x.getDescription());
146                System.out.print("Synonyms: ");
147                for (String s : x.getSynonyms()) {
148                    System.out.print(s + " | ");
149                }
150                System.out.println("");
151            }
152
153            System.out.print("ALL SYNONYMS: ");
154
155            for (String s : g.getAllSynonyms()) {
156                System.out.print(s + " | ");
157            }
158            System.out.println("");
159
160        }
161        System.out.println("");
162        System.out.println("----------------------------------");
163        System.out.println("");
164        
165        
166        System.out.println("hs.getGenesForExactName(\"SAPK4\");");
167        //SAPK4 is infact an a synonym
168        genesForExactName = hs.getGenesForExactName("SAPK4");
169        System.out.println("count is: "+genesForExactName.size());
170        for (DAGene g : genesForExactName) {
171
172            System.out.println("GENE: " + g.getStableID());
173
174            System.out.println("DisplayXref displayID: " + g.getDisplayXRef().getDisplayID());
175            System.out.println("DisplayXref primary accession: " + g.getDisplayXRef().getPrimaryAccession());
176            System.out.println("DisplayXref version: " + g.getDisplayXRef().getVersion());
177            System.out.println("DisplayXref database: " + g.getDisplayXRef().getDBDisplayName());
178            System.out.println("DisplayXref db version: " + g.getDisplayXRef().getDBVersion());
179            System.out.println("DisplayXref description: " + g.getDisplayXRef().getDescription());
180            System.out.print("DisplayXref synonyms (method1): ");
181            for (String s : g.getDisplayXRef().getSynonyms()) {
182                System.out.print(s + " | ");
183            }
184            System.out.println("");
185            System.out.print("DisplayXref synonyms (method2): ");
186            for (String s : g.getSynonyms(g.getDisplayXRef())) {
187                System.out.print(s + " | ");
188            }
189            System.out.println("");
190            System.out.println("VEGA XREFS");
191
192            for (DAXRef x : g.getVegaXRefs()) {
193                System.out.println(" displayID: " + x.getDisplayID());
194                System.out.println(" primary accession: " + x.getPrimaryAccession());
195                System.out.println(" version: " + x.getVersion());
196                System.out.println(" database: " + x.getDBDisplayName());
197                System.out.println(" db version: " + x.getDBVersion());
198                System.out.println(" description: " + x.getDescription());
199                System.out.print("Synonyms: ");
200                for (String s : x.getSynonyms()) {
201                    System.out.print(s + " | ");
202                }
203                System.out.println("");
204            }
205
206            System.out.print("ALL SYNONYMS: ");
207
208            for (String s : g.getAllSynonyms()) {
209                System.out.print(s + " | ");
210            }
211            System.out.println("");
212        }
213        
214        System.out.println("");
215        System.out.println("----------------------------------");
216        System.out.println("");
217        
218        System.out.println("hs.getGenesForNameBeginning(\"MAPK13\");");
219        //SAPK4 is infact an a synonym
220        genesForExactName = hs.getGenesForNameBeginning("MAPK13");
221        System.out.println("count is: "+genesForExactName.size());
222        for (DAGene g : genesForExactName) {
223
224            System.out.println("GENE: " + g.getStableID());
225
226            System.out.println("DisplayXref displayID: " + g.getDisplayXRef().getDisplayID());
227            System.out.println("DisplayXref primary accession: " + g.getDisplayXRef().getPrimaryAccession());
228            System.out.println("DisplayXref version: " + g.getDisplayXRef().getVersion());
229            System.out.println("DisplayXref database: " + g.getDisplayXRef().getDBDisplayName());
230            System.out.println("DisplayXref db version: " + g.getDisplayXRef().getDBVersion());
231            System.out.println("DisplayXref description: " + g.getDisplayXRef().getDescription());
232            System.out.print("DisplayXref synonyms (method1): ");
233            for (String s : g.getDisplayXRef().getSynonyms()) {
234                System.out.print(s + " | ");
235            }
236            System.out.println("");
237            System.out.print("DisplayXref synonyms (method2): ");
238            for (String s : g.getSynonyms(g.getDisplayXRef())) {
239                System.out.print(s + " | ");
240            }
241            System.out.println("");
242            System.out.println("VEGA XREFS");
243
244            for (DAXRef x : g.getVegaXRefs()) {
245                System.out.println(" displayID: " + x.getDisplayID());
246                System.out.println(" primary accession: " + x.getPrimaryAccession());
247                System.out.println(" version: " + x.getVersion());
248                System.out.println(" database: " + x.getDBDisplayName());
249                System.out.println(" db version: " + x.getDBVersion());
250                System.out.println(" description: " + x.getDescription());
251                System.out.print("Synonyms: ");
252                for (String s : x.getSynonyms()) {
253                    System.out.print(s + " | ");
254                }
255                System.out.println("");
256            }
257
258            System.out.print("ALL SYNONYMS: ");
259
260            for (String s : g.getAllSynonyms()) {
261                System.out.print(s + " | ");
262            }
263            System.out.println("");
264
265        }
266        
267        System.out.println("");
268        System.out.println("----------------------------------");
269        System.out.println("");
270        
271        System.out.println("hs.getGenesForNameBeginning(\"MAPK1\");");
272        //SAPK4 is infact an a synonym
273        genesForExactName = hs.getGenesForNameBeginning("MAPK1");
274        System.out.println("count is: "+genesForExactName.size());
275        for (DAGene g : genesForExactName) {
276
277            System.out.println("GENE: " + g.getStableID());
278
279            System.out.println("DisplayXref displayID: " + g.getDisplayXRef().getDisplayID());
280            System.out.println("DisplayXref primary accession: " + g.getDisplayXRef().getPrimaryAccession());
281            System.out.println("DisplayXref version: " + g.getDisplayXRef().getVersion());
282            System.out.println("DisplayXref database: " + g.getDisplayXRef().getDBDisplayName());
283            System.out.println("DisplayXref db version: " + g.getDisplayXRef().getDBVersion());
284            System.out.println("DisplayXref description: " + g.getDisplayXRef().getDescription());
285            System.out.print("DisplayXref synonyms (method1): ");
286            for (String s : g.getDisplayXRef().getSynonyms()) {
287                System.out.print(s + " | ");
288            }
289            System.out.println("");
290            System.out.print("DisplayXref synonyms (method2): ");
291            for (String s : g.getSynonyms(g.getDisplayXRef())) {
292                System.out.print(s + " | ");
293            }
294            System.out.println("");
295            System.out.println("VEGA XREFS");
296
297            for (DAXRef x : g.getVegaXRefs()) {
298                System.out.println(" displayID: " + x.getDisplayID());
299                System.out.println(" primary accession: " + x.getPrimaryAccession());
300                System.out.println(" version: " + x.getVersion());
301                System.out.println(" database: " + x.getDBDisplayName());
302                System.out.println(" db version: " + x.getDBVersion());
303                System.out.println(" description: " + x.getDescription());
304                System.out.print("Synonyms: ");
305                for (String s : x.getSynonyms()) {
306                    System.out.print(s + " | ");
307                }
308                System.out.println("");
309            }
310
311            System.out.print("ALL SYNONYMS: ");
312
313            for (String s : g.getAllSynonyms()) {
314                System.out.print(s + " | ");
315            }
316            System.out.println("");
317
318        }
319        
320        System.out.println("");
321        System.out.println("----------------------------------");
322        System.out.println("");
323        
324        
325        System.out.println("hs.getGenesForNameBeginning(\"SAPK\", \"57\");");
326        //SAPK4 is infact an a synonym
327         genesForExactName = hs.getGenesForNameBeginning("SAPK", "57");
328        System.out.println("count is: "+genesForExactName.size());
329        
330        int count  = 1;
331        for (DAGene g : genesForExactName) {
332
333            System.out.println("GENE: " + count++ +"  -  "+ g.getStableID());
334
335            System.out.println("DisplayXref displayID: " + g.getDisplayXRef().getDisplayID());
336            System.out.println("DisplayXref primary accession: " + g.getDisplayXRef().getPrimaryAccession());
337            System.out.println("DisplayXref version: " + g.getDisplayXRef().getVersion());
338            System.out.println("DisplayXref database: " + g.getDisplayXRef().getDBDisplayName());
339            System.out.println("DisplayXref db version: " + g.getDisplayXRef().getDBVersion());
340            System.out.println("DisplayXref description: " + g.getDisplayXRef().getDescription());
341            System.out.print("DisplayXref synonyms (method1): ");
342            for (String s : g.getDisplayXRef().getSynonyms()) {
343                System.out.print(s + " | ");
344            }
345            System.out.println("");
346            System.out.print("DisplayXref synonyms (method2): ");
347            for (String s : g.getSynonyms(g.getDisplayXRef())) {
348                System.out.print(s + " | ");
349            }
350            System.out.println("");
351            System.out.println("VEGA XREFS");
352
353            for (DAXRef x : g.getVegaXRefs()) {
354                System.out.println(" displayID: " + x.getDisplayID());
355                System.out.println(" primary accession: " + x.getPrimaryAccession());
356                System.out.println(" version: " + x.getVersion());
357                System.out.println(" database: " + x.getDBDisplayName());
358                System.out.println(" db version: " + x.getDBVersion());
359                System.out.println(" description: " + x.getDescription());
360                System.out.print("Synonyms: ");
361                for (String s : x.getSynonyms()) {
362                    System.out.print(s + " | ");
363                }
364                System.out.println("");
365            }
366
367            System.out.print("ALL SYNONYMS: ");
368
369            for (String s : g.getAllSynonyms()) {
370                System.out.print(s + " | ");
371            }
372            System.out.println("");
373        }
374        
375        System.out.println("");
376        System.out.println("----------------------------------");
377        System.out.println("");
378        
379        
380            DAGene gene = hs.getGeneByStableID("ENSG00000156711");
381
382            System.out.println("GENE: " + gene.getStableID());
383
384            System.out.println("DisplayXref displayID: " + gene.getDisplayXRef().getDisplayID());
385            System.out.println("DisplayXref primary accession: " + gene.getDisplayXRef().getPrimaryAccession());
386            System.out.println("DisplayXref version: " + gene.getDisplayXRef().getVersion());
387            System.out.println("DisplayXref database: " + gene.getDisplayXRef().getDBDisplayName());
388            System.out.println("DisplayXref db version: " + gene.getDisplayXRef().getDBVersion());
389            System.out.println("DisplayXref description: " + gene.getDisplayXRef().getDescription());
390            System.out.print("DisplayXref synonyms (method1): ");
391            for (String s : gene.getDisplayXRef().getSynonyms()) {
392                System.out.print(s + " | ");
393            }
394            System.out.println("");
395            System.out.print("DisplayXref synonyms (method2): ");
396            for (String s : gene.getSynonyms(gene.getDisplayXRef())) {
397                System.out.print(s + " | ");
398            }
399            System.out.println("");
400            System.out.println("VEGA XREFS");
401
402            for (DAXRef x : gene.getVegaXRefs()) {
403                System.out.println(" displayID: " + x.getDisplayID());
404                System.out.println(" primary accession: " + x.getPrimaryAccession());
405                System.out.println(" version: " + x.getVersion());
406                System.out.println(" database: " + x.getDBDisplayName());
407                System.out.println(" db version: " + x.getDBVersion());
408                System.out.println(" description: " + x.getDescription());
409                System.out.print("Synonyms: ");
410                for (String s : x.getSynonyms()) {
411                    System.out.print(s + " | ");
412                }
413                System.out.println("");
414            }
415
416            System.out.print("ALL SYNONYMS: ");
417
418            for (String s : gene.getAllSynonyms()) {
419                System.out.print(s + " | ");
420            }
421            System.out.println("");
422            System.out.println("");
423            System.out.println("");
424
425            DATranscript transcript = hs.getTranscriptByStableID("ENST00000368759");
426            System.out.println("TRANSCRIPT: " + transcript.getStableID());
427
428            System.out.println("DisplayXref displayID: " + transcript.getDisplayXRef().getDisplayID());
429            System.out.println("DisplayXref primary accession: " + transcript.getDisplayXRef().getPrimaryAccession());
430            System.out.println("DisplayXref version: " + transcript.getDisplayXRef().getVersion());
431            System.out.println("DisplayXref database: " + transcript.getDisplayXRef().getDBDisplayName());
432            System.out.println("DisplayXref db version: " + transcript.getDisplayXRef().getDBVersion());
433            System.out.println("DisplayXref description: " + transcript.getDisplayXRef().getDescription());
434            System.out.print("DisplayXref synonyms (method1): ");
435            for (String s : transcript.getDisplayXRef().getSynonyms()) {
436                System.out.print(s + " | ");
437            }
438            System.out.println("");
439            System.out.print("DisplayXref synonyms (method2): ");
440            for (String s : transcript.getSynonyms(transcript.getDisplayXRef())) {
441                System.out.print(s + " | ");
442            }
443            System.out.println("");
444            System.out.println("VEGA XREFS");
445
446            for (DAXRef x : transcript.getVegaXRefs()) {
447                System.out.println(" displayID: " + x.getDisplayID());
448                System.out.println(" primary accession: " + x.getPrimaryAccession());
449                System.out.println(" version: " + x.getVersion());
450                System.out.println(" database: " + x.getDBDisplayName());
451                System.out.println(" db version: " + x.getDBVersion());
452                System.out.println(" description: " + x.getDescription());
453                System.out.print("Synonyms: ");
454                for (String s : x.getSynonyms()) {
455                    System.out.print(s + " | ");
456                }
457                System.out.println("");
458            }
459
460            System.out.print("ALL SYNONYMS: ");
461
462            for (String s : transcript.getAllSynonyms()) {
463                System.out.print(s + " | ");
464            }
465            System.out.println("");
466            System.out.println("");
467            System.out.println("");
468
469            DATranslation translation = hs.getTranslationByStableID("ENSP00000261584");
470            System.out.println("TRANSLATION: " + translation.getStableID());
471
472
473            System.out.println("");
474            System.out.println("VEGA XREFS");
475
476            for (DAXRef x : translation.getVegaXRefs()) {
477                System.out.println(" displayID: " + x.getDisplayID());
478                System.out.println(" primary accession: " + x.getPrimaryAccession());
479                System.out.println(" version: " + x.getVersion());
480                System.out.println(" database: " + x.getDBDisplayName());
481                System.out.println(" db version: " + x.getDBVersion());
482                System.out.println(" description: " + x.getDescription());
483                System.out.print("Synonyms: ");
484                for (String s : x.getSynonyms()) {
485                    System.out.print(s + " | ");
486                }
487                System.out.println("");
488            }
489
490            System.out.print("ALL SYNONYMS: ");
491
492            for (String s : translation.getAllSynonyms()) {
493                System.out.print(s + " | ");
494            }
495            System.out.println("");
496
497        }
498    }