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.assertTrue;
27 import jalview.datamodel.SequenceDummy;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceI;
30 import jalview.io.gff.SequenceOntologyFactory;
31 import jalview.io.gff.SequenceOntologyLite;
32 import jalview.util.MapList;
34 import java.util.List;
36 import org.testng.Assert;
37 import org.testng.annotations.AfterClass;
38 import org.testng.annotations.BeforeClass;
39 import org.testng.annotations.Test;
41 public class EnsemblCdsTest
43 @BeforeClass(alwaysRun = true)
46 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
49 @AfterClass(alwaysRun = true)
50 public void tearDown()
52 SequenceOntologyFactory.setInstance(null);
56 * Test that the cdna part of genomic sequence is correctly identified by
57 * 'CDS' features (or subtypes) with the desired transcript as parent
59 @Test(groups = "Functional")
60 public void testGetGenomicRangesFromFeatures()
62 EnsemblCds testee = new EnsemblCds();
63 SequenceI genomic = new SequenceDummy("chr7");
64 genomic.setStart(10000);
65 genomic.setEnd(50000);
66 String transcriptId = "ABC123";
68 // CDS at (start+10000) length 501
69 SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
71 sf.setValue("Parent", "transcript:" + transcriptId);
73 genomic.addSequenceFeature(sf);
75 // CDS (sub-type) at (start + 10500) length 101
76 sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
77 sf.setValue("Parent", "transcript:" + transcriptId);
79 genomic.addSequenceFeature(sf);
81 // CDS belonging to a different transcript doesn't count
82 sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
83 sf.setValue("Parent", "transcript:anotherOne");
84 genomic.addSequenceFeature(sf);
86 // exon feature doesn't count
87 sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
88 genomic.addSequenceFeature(sf);
90 // mRNA_region feature doesn't count (parent of CDS)
91 sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
92 genomic.addSequenceFeature(sf);
94 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
96 List<int[]> fromRanges = ranges.getFromRanges();
97 assertEquals(2, fromRanges.size());
98 // from ranges should be sorted by start order
99 assertEquals(10500, fromRanges.get(0)[0]);
100 assertEquals(10600, fromRanges.get(0)[1]);
101 assertEquals(20000, fromRanges.get(1)[0]);
102 assertEquals(20500, fromRanges.get(1)[1]);
103 // to range should start from given start numbering
104 List<int[]> toRanges = ranges.getToRanges();
105 assertEquals(1, toRanges.size());
106 assertEquals(23, toRanges.get(0)[0]);
107 assertEquals(624, toRanges.get(0)[1]);
111 * Test the method that retains features except for 'CDS' (or subtypes), or
112 * features with parent other than the given id
114 @Test(groups = "Functional")
115 public void testRetainFeature()
117 String accId = "ABC123";
118 EnsemblCds testee = new EnsemblCds();
120 SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
122 assertFalse(testee.retainFeature(sf, accId));
124 sf.setType("CDS_predicted");
125 assertFalse(testee.retainFeature(sf, accId));
127 // other feature with no parent is retained
128 sf.setType("sequence_variant");
129 assertTrue(testee.retainFeature(sf, accId));
131 // other feature with desired parent is retained
132 sf.setValue("Parent", "transcript:" + accId);
133 assertTrue(testee.retainFeature(sf, accId));
135 // feature with wrong parent is not retained
136 sf.setValue("Parent", "transcript:XYZ");
137 assertFalse(testee.retainFeature(sf, accId));
141 * Test the method that picks out 'CDS' (or subtype) features with the
142 * accession id as parent
144 @Test(groups = "Functional")
145 public void testIdentifiesSequence()
147 String accId = "ABC123";
148 EnsemblCds testee = new EnsemblCds();
150 // cds with no parent not valid
151 SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
152 assertFalse(testee.identifiesSequence(sf, accId));
154 // cds with wrong parent not valid
155 sf.setValue("Parent", "transcript:XYZ");
156 assertFalse(testee.identifiesSequence(sf, accId));
158 // cds with right parent is valid
159 sf.setValue("Parent", "transcript:" + accId);
160 assertTrue(testee.identifiesSequence(sf, accId));
162 // cds sub-type with right parent is valid
163 sf.setType("CDS_predicted");
164 assertTrue(testee.identifiesSequence(sf, accId));
166 // transcript not valid:
167 sf.setType("transcript");
168 assertFalse(testee.identifiesSequence(sf, accId));
172 assertFalse(testee.identifiesSequence(sf, accId));
175 @Test(groups = "Functional")
176 public void testIsValidReference() throws Exception
178 EnsemblSequenceFetcher esq = new EnsemblCds();
179 Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
180 Assert.assertTrue(esq.isValidReference("ENST00000288602"));
181 Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
182 Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
183 Assert.assertFalse(esq.isValidReference("ENST0000288602"));
184 // non-human species have a 3 character identifier included:
185 Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));