1 package jalview.ext.ensembl;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertFalse;
5 import static org.testng.AssertJUnit.assertTrue;
7 import jalview.datamodel.SequenceDummy;
8 import jalview.datamodel.SequenceFeature;
9 import jalview.datamodel.SequenceI;
10 import jalview.io.gff.SequenceOntologyFactory;
11 import jalview.io.gff.SequenceOntologyLite;
12 import jalview.util.MapList;
14 import java.util.List;
16 import org.testng.annotations.AfterClass;
17 import org.testng.annotations.BeforeClass;
18 import org.testng.annotations.Test;
20 public class EnsemblGenomeTest
22 @BeforeClass(alwaysRun = true)
25 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
28 @AfterClass(alwaysRun = true)
29 public void tearDown()
31 SequenceOntologyFactory.setInstance(null);
35 * Test that the genomic sequence part of genomic sequence is correctly
36 * identified by 'transcript' features (or subtypes) with the correct gene ID
38 @Test(groups = "Functional")
39 public void testGetGenomicRangesFromFeatures()
41 EnsemblGenome testee = new EnsemblGenome();
42 SequenceI genomic = new SequenceDummy("chr7");
43 genomic.setStart(10000);
44 genomic.setEnd(50000);
45 String transcriptId = "ABC123";
47 // transcript at (start+10000) length 501
48 SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
50 sf.setValue("ID", "transcript:" + transcriptId);
52 genomic.addSequenceFeature(sf);
54 // transcript (sub-type) at (start + 10500) length 101
55 sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
56 sf.setValue("ID", "transcript:" + transcriptId);
58 genomic.addSequenceFeature(sf);
60 // Ensembl treats NMD_transcript_variant as if transcript
61 // although strictly it is a sequence_variant in SO
62 sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
64 sf.setValue("ID", "transcript:" + transcriptId);
66 genomic.addSequenceFeature(sf);
68 // transcript with a different ID doesn't count
69 sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
70 sf.setValue("ID", "transcript:anotherOne");
71 genomic.addSequenceFeature(sf);
73 // parent of transcript feature doesn't count
74 sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
76 genomic.addSequenceFeature(sf);
78 MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
80 List<int[]> fromRanges = ranges.getFromRanges();
81 assertEquals(3, fromRanges.size());
82 // from ranges should be sorted by start order
83 assertEquals(10500, fromRanges.get(0)[0]);
84 assertEquals(10600, fromRanges.get(0)[1]);
85 assertEquals(11000, fromRanges.get(1)[0]);
86 assertEquals(12000, fromRanges.get(1)[1]);
87 assertEquals(20000, fromRanges.get(2)[0]);
88 assertEquals(20500, fromRanges.get(2)[1]);
89 // to range should start from given start numbering
90 List<int[]> toRanges = ranges.getToRanges();
91 assertEquals(1, toRanges.size());
92 assertEquals(23, toRanges.get(0)[0]);
93 assertEquals(1625, toRanges.get(0)[1]);
97 * Test the method that retains features except for 'transcript' (or
98 * sub-type), or those with parent other than the given id
100 @Test(groups = "Functional")
101 public void testRetainFeature()
103 String accId = "ABC123";
104 EnsemblGenome testee = new EnsemblGenome();
106 SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
108 assertFalse(testee.retainFeature(sf, accId));
110 sf.setType("mature_transcript");
111 assertFalse(testee.retainFeature(sf, accId));
113 sf.setType("NMD_transcript_variant");
114 assertFalse(testee.retainFeature(sf, accId));
116 // other feature with no parent is kept
117 sf.setType("anything");
118 assertTrue(testee.retainFeature(sf, accId));
120 // other feature with correct parent is kept
121 sf.setValue("Parent", "transcript:" + accId);
122 assertTrue(testee.retainFeature(sf, accId));
124 // other feature with wrong parent is not kept
125 sf.setValue("Parent", "transcript:XYZ");
126 assertFalse(testee.retainFeature(sf, accId));
130 * Test the method that picks out 'transcript' (or subtype) features with the
133 @Test(groups = "Functional")
134 public void testIdentifiesSequence()
136 String accId = "ABC123";
137 EnsemblGenome testee = new EnsemblGenome();
139 // transcript with no ID not valid
140 SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
142 assertFalse(testee.identifiesSequence(sf, accId));
144 // transcript with wrong ID not valid
145 sf.setValue("ID", "transcript");
146 assertFalse(testee.identifiesSequence(sf, accId));
148 // transcript with right ID is valid
149 sf.setValue("ID", "transcript:" + accId);
150 assertTrue(testee.identifiesSequence(sf, accId));
152 // transcript sub-type with right ID is valid
154 assertTrue(testee.identifiesSequence(sf, accId));
156 // Ensembl treats NMD_transcript_variant as if a transcript
157 sf.setType("NMD_transcript_variant");
158 assertTrue(testee.identifiesSequence(sf, accId));
162 assertFalse(testee.identifiesSequence(sf, accId));
166 assertFalse(testee.identifiesSequence(sf, accId));