1 package jalview.datamodel.xdb.embl;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertNotNull;
5 import static org.testng.AssertJUnit.assertNull;
6 import static org.testng.AssertJUnit.assertSame;
8 import jalview.analysis.SequenceIdMatcher;
9 import jalview.datamodel.DBRefEntry;
10 import jalview.datamodel.DBRefSource;
11 import jalview.datamodel.SequenceI;
12 import jalview.util.MapList;
14 import java.util.ArrayList;
15 import java.util.Arrays;
16 import java.util.List;
18 import org.testng.annotations.Test;
20 public class EmblEntryTest
22 @Test(groups = "Functional")
23 public void testGetCdsRanges()
25 EmblEntry testee = new EmblEntry();
28 * Make a (CDS) Feature with 5 locations
30 EmblFeature cds = new EmblFeature();
31 cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
33 int[] exons = testee.getCdsRanges(cds);
34 assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
35 Arrays.toString(exons));
38 @Test(groups = "Functional")
39 public void testParseCodingFeature()
41 // not the whole sequence but enough for this test...
42 List<SequenceI> peptides = new ArrayList<SequenceI>();
43 SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
44 EmblEntry ef = EmblTestHelper.getEmblFile();
46 // assertEquals(1, ef.getEntries().size());
47 // EmblEntry testee = ef.getEntries().get(0);
48 String sourceDb = "EMBL";
49 SequenceI dna = ef.makeSequence(sourceDb);
52 * parse three CDS features, with two/one/no Uniprot cross-refs
54 for (EmblFeature feature : ef.getFeatures())
56 if ("CDS".equals(feature.getName()))
58 ef.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
63 * peptides should now have five entries:
64 * EMBL product and two Uniprot accessions for the first CDS / translation
65 * EMBL product and one Uniprot accession for the second CDS / "
66 * EMBL product only for the third
68 assertEquals(6, peptides.size());
69 assertEquals("CAA30420.1", peptides.get(0).getName());
70 assertEquals("MLCF", peptides.get(0).getSequenceAsString());
71 assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
72 assertEquals("MLCF", peptides.get(1).getSequenceAsString());
73 assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
74 assertEquals("MLCF", peptides.get(2).getSequenceAsString());
75 assertEquals("CAA30421.1", peptides.get(3).getName());
76 assertEquals("MSSS", peptides.get(3).getSequenceAsString());
77 assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
78 assertEquals("MSSS", peptides.get(4).getSequenceAsString());
79 assertEquals("CAA12345.6", peptides.get(5).getName());
80 assertEquals("MSS", peptides.get(5).getSequenceAsString());
83 * verify dna sequence has dbrefs with CDS mappings to the peptide 'products'
85 MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
87 MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
89 MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
91 DBRefEntry[] dbrefs = dna.getDBRefs();
92 assertEquals(4, dbrefs.length);
93 DBRefEntry dbRefEntry = dbrefs[0];
94 assertEquals("UNIPROT", dbRefEntry.getSource());
95 assertEquals("B0BCM4", dbRefEntry.getAccessionId());
96 assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
97 assertEquals(cds1Map, dbRefEntry.getMap().getMap());
99 dbRefEntry = dbrefs[1];
100 assertEquals("UNIPROT", dbRefEntry.getSource());
101 assertEquals("P0CE20", dbRefEntry.getAccessionId());
102 assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
103 assertEquals(cds1Map, dbRefEntry.getMap().getMap());
105 dbRefEntry = dbrefs[2];
106 assertEquals("UNIPROT", dbRefEntry.getSource());
107 assertEquals("B0BCM3", dbRefEntry.getAccessionId());
108 assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
109 assertEquals(cds2Map, dbRefEntry.getMap().getMap());
111 dbRefEntry = dbrefs[3];
112 assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
113 assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
114 assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
115 assertEquals(cds3Map, dbRefEntry.getMap().getMap());
118 * verify peptides have dbrefs
119 * - to EMBL sequence (with inverse 1:3 cds mapping)
120 * - to EMBLCDS (with 1:3 mapping)
121 * - direct (no mapping) to other protein accessions
123 MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
125 MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
128 // dbrefs for first CDS EMBL product CAA30420.1
129 dbrefs = peptides.get(0).getDBRefs();
130 assertEquals(5, dbrefs.length);
131 assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
132 assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
133 // TODO: verify getPrimaryDBRefs() for peptide products
134 assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
135 assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
136 assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
137 assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
138 assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
139 assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
140 assertNull(dbrefs[2].getMap());
141 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
143 assertNull(dbrefs[3].getMap());
144 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
146 assertNull(dbrefs[4].getMap());
148 // dbrefs for first CDS first Uniprot xref
149 dbrefs = peptides.get(1).getDBRefs();
150 assertEquals(2, dbrefs.length);
151 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
153 assertNull(dbrefs[0].getMap());
154 assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
155 assertEquals("X07547", dbrefs[1].getAccessionId());
156 assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
158 // dbrefs for first CDS second Uniprot xref
159 dbrefs = peptides.get(2).getDBRefs();
160 assertEquals(2, dbrefs.length);
161 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
163 assertNull(dbrefs[0].getMap());
164 assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
165 assertEquals("X07547", dbrefs[1].getAccessionId());
166 assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
168 // dbrefs for second CDS EMBL product CAA30421.1
169 dbrefs = peptides.get(3).getDBRefs();
170 assertEquals(4, dbrefs.length);
171 assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
172 assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
173 assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
174 assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
175 assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
176 assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
177 assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
178 assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
179 assertNull(dbrefs[2].getMap());
180 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
182 assertNull(dbrefs[3].getMap());
184 // dbrefs for second CDS second Uniprot xref
185 dbrefs = peptides.get(4).getDBRefs();
186 assertEquals(2, dbrefs.length);
187 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
189 assertNull(dbrefs[0].getMap());
190 assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
191 assertEquals("X07547", dbrefs[1].getAccessionId());
192 assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
194 // dbrefs for third CDS inferred EMBL product CAA12345.6
195 dbrefs = peptides.get(5).getDBRefs();
196 assertEquals(3, dbrefs.length);
197 assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
198 assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
199 assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
200 assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
201 assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
202 assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
203 assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
204 assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
205 assertNull(dbrefs[2].getMap());
208 @Test(groups = "Functional")
209 public void testAdjustForProteinLength()
211 int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
213 // exact length match:
214 assertSame(exons, EmblEntry.adjustForProteinLength(6, exons));
216 // match if we assume exons include stop codon not in protein:
217 assertSame(exons, EmblEntry.adjustForProteinLength(5, exons));
219 // truncate last exon by 6bp
220 int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
221 assertEquals("[11, 15, 21, 25, 31, 32]",
222 Arrays.toString(truncated));
224 // remove last exon and truncate preceding by 1bp
225 truncated = EmblEntry.adjustForProteinLength(3, exons);
226 assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
228 // exact removal of exon case:
229 exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
230 truncated = EmblEntry.adjustForProteinLength(4, exons);
231 assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
233 // what if exons are too short for protein?
234 truncated = EmblEntry.adjustForProteinLength(7, exons);
235 assertSame(exons, truncated);