2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.ensembl;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNull;
26 import static org.testng.AssertJUnit.assertTrue;
28 import jalview.datamodel.Sequence;
29 import jalview.datamodel.SequenceDummy;
30 import jalview.datamodel.SequenceFeature;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.JvOptionPane;
33 import jalview.io.gff.SequenceOntologyFactory;
34 import jalview.io.gff.SequenceOntologyLite;
35 import jalview.util.MapList;
37 import java.util.List;
39 import org.testng.Assert;
40 import org.testng.annotations.AfterClass;
41 import org.testng.annotations.BeforeClass;
42 import org.testng.annotations.Test;
44 public class EnsemblCdnaTest
47 @BeforeClass(alwaysRun = true)
48 public void setUpJvOptionPane()
50 JvOptionPane.setInteractiveMode(false);
51 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54 @BeforeClass(alwaysRun = true)
57 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
60 @AfterClass(alwaysRun = true)
61 public void tearDown()
63 SequenceOntologyFactory.setInstance(null);
67 * Test that the cdna part of genomic sequence is correctly identified by
68 * 'exon' features (or subtypes) - reverse strand case.
70 @Test(groups = "Functional")
71 public void testGetGenomicRangesFromFeatures_reverseStrand()
73 EnsemblCdna testee = new EnsemblCdna();
74 SequenceI genomic = new SequenceDummy("chr7");
75 genomic.setStart(10000);
76 genomic.setEnd(50000);
77 String transcriptId = "ABC123";
79 // exon at (start+10000) length 501
80 SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
82 sf.setValue("Parent", transcriptId);
84 genomic.addSequenceFeature(sf);
86 // exon (sub-type) at (start + exon_variant) length 101
87 sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
88 sf.setValue("Parent", transcriptId);
90 genomic.addSequenceFeature(sf);
92 // exon belonging to a different transcript doesn't count
93 sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
94 sf.setValue("Parent", "anotherOne");
95 genomic.addSequenceFeature(sf);
97 // transcript feature doesn't count
98 sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
99 genomic.addSequenceFeature(sf);
101 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
103 List<int[]> fromRanges = ranges.getFromRanges();
104 assertEquals(2, fromRanges.size());
107 * from ranges should be sorted by start order descending
108 * and hold mappings from reverse strand sense
110 assertEquals(20500, fromRanges.get(0)[0]);
111 assertEquals(20000, fromRanges.get(0)[1]);
112 assertEquals(10600, fromRanges.get(1)[0]);
113 assertEquals(10500, fromRanges.get(1)[1]);
114 // to range should start from given start numbering
115 List<int[]> toRanges = ranges.getToRanges();
116 assertEquals(1, toRanges.size());
117 assertEquals(23, toRanges.get(0)[0]);
118 assertEquals(624, toRanges.get(0)[1]);
122 * Test that the cdna part of genomic sequence is correctly identified by
123 * 'exon' features (or subtypes) with the desired transcript as parent
125 @Test(groups = "Functional")
126 public void testGetGenomicRangesFromFeatures()
128 EnsemblCdna testee = new EnsemblCdna();
129 SequenceI genomic = new SequenceDummy("chr7");
130 genomic.setStart(10000);
131 genomic.setEnd(50000);
132 String transcriptId = "ABC123";
134 // exon at (start+10000) length 501
135 SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
137 sf.setValue("Parent", transcriptId);
139 genomic.addSequenceFeature(sf);
141 // exon (sub-type) at (start + exon_variant) length 101
142 sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
143 sf.setValue("Parent", transcriptId);
145 genomic.addSequenceFeature(sf);
147 // exon belonging to a different transcript doesn't count
148 sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
149 sf.setValue("Parent", "anotherOne");
150 genomic.addSequenceFeature(sf);
152 // transcript feature doesn't count
153 sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
154 sf.setStrand("-"); // weird but ignored
155 genomic.addSequenceFeature(sf);
157 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
159 List<int[]> fromRanges = ranges.getFromRanges();
160 assertEquals(2, fromRanges.size());
161 // from ranges should be sorted by start order
162 assertEquals(10500, fromRanges.get(0)[0]);
163 assertEquals(10600, fromRanges.get(0)[1]);
164 assertEquals(20000, fromRanges.get(1)[0]);
165 assertEquals(20500, fromRanges.get(1)[1]);
166 // to range should start from given start numbering
167 List<int[]> toRanges = ranges.getToRanges();
168 assertEquals(1, toRanges.size());
169 assertEquals(23, toRanges.get(0)[0]);
170 assertEquals(624, toRanges.get(0)[1]);
174 * The method under test should give up and return null if both forward and
175 * reverse strands are present in the features of interest
177 @Test(groups = "Functional")
178 public void testGetGenomicRangesFromFeatures_mixedStrand()
180 EnsemblCdna testee = new EnsemblCdna();
181 SequenceI genomic = new SequenceDummy("chr7");
182 genomic.setStart(10000);
183 genomic.setEnd(50000);
184 String transcriptId = "ABC123";
186 SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
188 sf.setValue("Parent", "transcript:" + transcriptId);
190 genomic.addSequenceFeature(sf);
192 sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
193 sf.setValue("Parent", "transcript:" + transcriptId);
195 genomic.addSequenceFeature(sf);
197 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
203 * Test the method that retains features except for 'transcript' (or
204 * subtypes), or features with parent other than the given id
206 @Test(groups = "Functional")
207 public void testRetainFeature()
209 String accId = "ABC123";
210 EnsemblCdna testee = new EnsemblCdna();
212 SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
214 assertFalse(testee.retainFeature(sf, accId));
216 sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
218 assertFalse(testee.retainFeature(sf, accId));
220 sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
222 assertFalse(testee.retainFeature(sf, accId));
224 // other feature with no parent is retained
225 sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
226 assertTrue(testee.retainFeature(sf, accId));
228 // other feature with desired parent is retained
229 sf.setValue("Parent", accId);
230 assertTrue(testee.retainFeature(sf, accId));
232 // test is not case-sensitive
233 assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
235 // feature with wrong parent is not retained
236 sf.setValue("Parent", "XYZ");
237 assertFalse(testee.retainFeature(sf, accId));
241 * Test the method that picks out 'exon' (or subtype) features with the
242 * accession id as parent
244 @Test(groups = "Functional")
245 public void testGetIdentifyingFeatures()
247 String accId = "ABC123";
248 SequenceI seq = new Sequence(accId, "MKLNFRQIE");
250 // exon with no parent: not valid
251 SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null);
252 seq.addSequenceFeature(sf1);
254 // exon with wrong parent: not valid
255 SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
256 sf2.setValue("Parent", "XYZ");
257 seq.addSequenceFeature(sf2);
259 // exon with right parent is valid
260 SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
261 sf3.setValue("Parent", accId);
262 seq.addSequenceFeature(sf3);
264 // exon sub-type with right parent is valid
265 SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
267 sf4.setValue("Parent", accId);
268 seq.addSequenceFeature(sf4);
270 // transcript not valid:
271 SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
273 sf5.setValue("Parent", accId);
274 seq.addSequenceFeature(sf5);
277 SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
279 sf6.setValue("Parent", accId);
280 seq.addSequenceFeature(sf6);
282 List<SequenceFeature> sfs = new EnsemblCdna()
283 .getIdentifyingFeatures(seq, accId);
284 assertFalse(sfs.contains(sf1));
285 assertFalse(sfs.contains(sf2));
286 assertTrue(sfs.contains(sf3));
287 assertTrue(sfs.contains(sf4));
288 assertFalse(sfs.contains(sf5));
289 assertFalse(sfs.contains(sf6));
292 @Test(groups = "Functional")
293 public void testIsValidReference() throws Exception
295 EnsemblSequenceFetcher esq = new EnsemblCdna();
296 Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
297 Assert.assertTrue(esq.isValidReference("ENST00000288602"));
298 Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
299 Assert.assertFalse(esq.isValidReference("ENSP00000288602"));
300 Assert.assertFalse(esq.isValidReference("ENST0000288602"));
301 // non-human species having a 3 character identifier included:
302 Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));