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