--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
+import jalview.xml.binding.embl.EntryType;
+import jalview.xml.binding.embl.EntryType.Feature;
+import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.embl.XrefType;
+
+import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class EmblSourceTest
+{
+
+ // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
+ // dna and translations truncated for convenience
+ static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
+ + "<ROOT>"
+ + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
+ + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
+ + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
+ + " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
+ + " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
+ + "<secondaryAccession>X07574</secondaryAccession>"
+ + "<description>C. trachomatis plasmid</description>"
+ + "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
+ + "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
+ + "<xref db=\"MD5\" id=\"ac73317\" />"
+ /*
+ * first CDS (range and translation changed to keep test data manageable)
+ */
+ + "<feature name=\"CDS\" location=\"complement(46..57)\">"
+ // test the case of >1 cross-ref to the same database (JAL-2029)
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
+ + "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value></qualifier>"
+ + "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MLCF</value></qualifier>"
+ + "</feature>"
+ /*
+ * second CDS (range and translation changed to keep test data manageable)
+ */
+ + "<feature name=\"CDS\" location=\"4..15\">"
+ + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
+ + "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
+ + "</feature>"
+ /*
+ * third CDS is made up - has no xref - code should synthesize
+ * one to an assumed EMBLCDSPROTEIN accession
+ */
+ + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
+ + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
+ + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
+ + "</feature>"
+ /*
+ * sequence (modified for test purposes)
+ * emulates EMBL XML 1.2 which splits sequence data every 60 characters
+ * see EmblSequence.setSequence
+ */
+ + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
+ + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
+ + "</sequence></entry></ROOT>";
+
+ @Test(groups = "Functional")
+ public void testGetCdsRanges()
+ {
+ EmblSource testee = new EmblSource();
+
+ /*
+ * Make a (CDS) Feature with 5 locations
+ */
+ Feature cds = new Feature();
+ cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
+
+ int[] exons = testee.getCdsRanges("EMBL", cds);
+ assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
+ Arrays.toString(exons));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSequence()
+ {
+ // not the whole sequence but enough for this test...
+ List<SequenceI> peptides = new ArrayList<>();
+ List<EntryType> entries = EmblSourceTest.getEmblEntries();
+ assertEquals(1, entries.size());
+ EntryType entry = entries.get(0);
+ EmblSource testee = new EmblSource();
+ String sourceDb = "EMBL";
+ SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
+
+ /*
+ * newline has been removed from sequence
+ */
+ String seq = dna.getSequenceAsString();
+ assertEquals(
+ "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
+ seq);
+
+ /*
+ * peptides should now have five entries:
+ * EMBL product and two Uniprot accessions for the first CDS / translation
+ * EMBL product and one Uniprot accession for the second CDS / "
+ * EMBL product only for the third
+ */
+ assertEquals(6, peptides.size());
+ assertEquals("CAA30420.1", peptides.get(0).getName());
+ assertEquals("MLCF", peptides.get(0).getSequenceAsString());
+ assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
+ assertEquals("MLCF", peptides.get(1).getSequenceAsString());
+ assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
+ assertEquals("MLCF", peptides.get(2).getSequenceAsString());
+ assertEquals("CAA30421.1", peptides.get(3).getName());
+ assertEquals("MSSS", peptides.get(3).getSequenceAsString());
+ assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
+ assertEquals("MSSS", peptides.get(4).getSequenceAsString());
+ assertEquals("CAA12345.6", peptides.get(5).getName());
+ assertEquals("MSS", peptides.get(5).getSequenceAsString());
+
+ /*
+ * verify dna sequence has dbrefs
+ * - to 'self' (synthesized dbref)
+ * - to EuropePMC
+ * - to MD5 (with null version as "0")
+ * - with CDS mappings to the peptide 'products'
+ */
+ MapList mapToSelf = new MapList(new int[] { 1, 57 },
+ new int[]
+ { 1, 57 }, 1, 1);
+ MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
+ 3, 1);
+ MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
+ 3, 1);
+ MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
+ 1, 3 }, 3, 1);
+
+ DBRefEntry[] dbrefs = dna.getDBRefs();
+ assertEquals(7, dbrefs.length);
+
+ DBRefEntry dbRefEntry = dbrefs[0];
+ assertEquals("EMBL", dbRefEntry.getSource());
+ assertEquals("X07547", dbRefEntry.getAccessionId());
+ assertEquals("1", dbRefEntry.getVersion());
+ assertNotNull(dbRefEntry.getMap());
+ assertNull(dbRefEntry.getMap().getTo());
+ assertEquals(mapToSelf, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[1];
+ // DBRefEntry constructor puts dbSource in upper case
+ assertEquals("EUROPEPMC", dbRefEntry.getSource());
+ assertEquals("PMC107176", dbRefEntry.getAccessionId());
+ assertEquals("9573186", dbRefEntry.getVersion());
+ assertNull(dbRefEntry.getMap());
+
+ dbRefEntry = dbrefs[2];
+ assertEquals("MD5", dbRefEntry.getSource());
+ assertEquals("ac73317", dbRefEntry.getAccessionId());
+ assertEquals("0", dbRefEntry.getVersion());
+ assertNull(dbRefEntry.getMap());
+
+ dbRefEntry = dbrefs[3];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("B0BCM4", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
+ assertEquals(cds1Map, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[4];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("P0CE20", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
+ assertEquals(cds1Map, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[5];
+ assertEquals("UNIPROT", dbRefEntry.getSource());
+ assertEquals("B0BCM3", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
+ assertEquals(cds2Map, dbRefEntry.getMap().getMap());
+
+ dbRefEntry = dbrefs[6];
+ assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
+ assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
+ assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
+ assertEquals(cds3Map, dbRefEntry.getMap().getMap());
+
+ /*
+ * verify peptides have dbrefs
+ * - to EMBL sequence (with inverse 1:3 cds mapping)
+ * - to EMBLCDS (with 1:3 mapping)
+ * - direct (no mapping) to other protein accessions
+ */
+ MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
+ 1, 12 }, 1, 3);
+ MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
+ 1, 9 }, 1, 3);
+
+ // dbrefs for first CDS EMBL product CAA30420.1
+ dbrefs = peptides.get(0).getDBRefs();
+ assertEquals(5, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
+ // TODO: verify getPrimaryDBRefs() for peptide products
+ assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+ dbrefs[3]);
+ assertNull(dbrefs[3].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+ dbrefs[4]);
+ assertNull(dbrefs[4].getMap());
+
+ // dbrefs for first CDS first Uniprot xref
+ dbrefs = peptides.get(1).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for first CDS second Uniprot xref
+ dbrefs = peptides.get(2).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for second CDS EMBL product CAA30421.1
+ dbrefs = peptides.get(3).getDBRefs();
+ assertEquals(4, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
+ assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+ dbrefs[3]);
+ assertNull(dbrefs[3].getMap());
+
+ // dbrefs for second CDS second Uniprot xref
+ dbrefs = peptides.get(4).getDBRefs();
+ assertEquals(2, dbrefs.length);
+ assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+ dbrefs[0]);
+ assertNull(dbrefs[0].getMap());
+ assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+ assertEquals("X07547", dbrefs[1].getAccessionId());
+ assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
+
+ // dbrefs for third CDS inferred EMBL product CAA12345.6
+ dbrefs = peptides.get(5).getDBRefs();
+ assertEquals(3, dbrefs.length);
+ assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+ assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
+ assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+ assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
+ assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
+ assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+ assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
+ assertNull(dbrefs[2].getMap());
+ }
+
+ @Test(groups = "Functional")
+ public void testAdjustForProteinLength()
+ {
+ int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
+
+ // exact length match:
+ assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
+
+ // match if we assume exons include stop codon not in protein:
+ assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
+
+ // truncate last exon by 6bp
+ int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
+ assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+
+ // remove last exon and truncate preceding by 1bp
+ truncated = EmblXmlSource.adjustForProteinLength(3, exons);
+ assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+
+ // exact removal of exon case:
+ exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
+ truncated = EmblXmlSource.adjustForProteinLength(4, exons);
+ assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+
+ // what if exons are too short for protein?
+ truncated = EmblXmlSource.adjustForProteinLength(7, exons);
+ assertSame(exons, truncated);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetEmblEntries()
+ {
+ List<EntryType> entries = EmblSourceTest.getEmblEntries();
+ assertEquals(1, entries.size());
+ EntryType entry = entries.get(0);
+
+ assertEquals("X07547", entry.getAccession());
+ assertEquals("C. trachomatis plasmid", entry.getDescription());
+ assertEquals("STD", entry.getDataClass());
+ assertEquals("PRO", entry.getTaxonomicDivision());
+ assertEquals("1999-02-10", entry.getLastUpdated().toString());
+ assertEquals(58, entry.getLastUpdatedRelease().intValue());
+ assertEquals("1988-11-10", entry.getFirstPublic().toString());
+ assertEquals(18, entry.getFirstPublicRelease().intValue());
+ assertEquals("genomic DNA", entry.getMoleculeType());
+ assertEquals(1, entry.getVersion().intValue());
+ assertEquals(8, entry.getEntryVersion().intValue());
+ assertEquals("linear", entry.getTopology());
+ assertEquals(7499, entry.getSequenceLength().intValue());
+ assertEquals(2, entry.getKeyword().size());
+ assertEquals("plasmid", entry.getKeyword().get(0));
+ assertEquals("unidentified reading frame", entry.getKeyword().get(1));
+
+ /*
+ * dbrefs
+ */
+ assertEquals(2, entry.getXref().size());
+ XrefType dbref = entry.getXref().get(0);
+ assertEquals("EuropePMC", dbref.getDb());
+ assertEquals("PMC107176", dbref.getId());
+ assertEquals("9573186", dbref.getSecondaryId());
+ dbref = entry.getXref().get(1);
+ assertEquals("MD5", dbref.getDb());
+ assertEquals("ac73317", dbref.getId());
+ assertNull(dbref.getSecondaryId());
+
+ /*
+ * three sequence features for CDS
+ */
+ assertEquals(3, entry.getFeature().size());
+ /*
+ * first CDS
+ */
+ Feature ef = entry.getFeature().get(0);
+ assertEquals("CDS", ef.getName());
+ assertEquals("complement(46..57)", ef.getLocation());
+ assertEquals(2, ef.getXref().size());
+ dbref = ef.getXref().get(0);
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
+ assertEquals("B0BCM4", dbref.getId());
+ assertEquals("2.1", dbref.getSecondaryId());
+ dbref = ef.getXref().get(1);
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
+ assertEquals("P0CE20", dbref.getId());
+ assertNull(dbref.getSecondaryId());
+ // CDS feature qualifiers
+ assertEquals(3, ef.getQualifier().size());
+ Qualifier q = ef.getQualifier().get(0);
+ assertEquals("note", q.getName());
+ assertEquals("ORF 8 (AA 1-330)", q.getValue());
+ q = ef.getQualifier().get(1);
+ assertEquals("protein_id", q.getName());
+ assertEquals("CAA30420.1", q.getValue());
+ q = ef.getQualifier().get(2);
+ assertEquals("translation", q.getName());
+ assertEquals("MLCF", q.getValue());
+
+ /*
+ * second CDS
+ */
+ ef = entry.getFeature().get(1);
+ assertEquals("CDS", ef.getName());
+ assertEquals("4..15", ef.getLocation());
+ assertEquals(1, ef.getXref().size());
+ dbref = ef.getXref().get(0);
+ assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
+ assertEquals("B0BCM3", dbref.getId());
+ assertNull(dbref.getSecondaryId());
+ assertEquals(2, ef.getQualifier().size());
+ q = ef.getQualifier().get(0);
+ assertEquals("protein_id", q.getName());
+ assertEquals("CAA30421.1", q.getValue());
+ q = ef.getQualifier().get(1);
+ assertEquals("translation", q.getName());
+ assertEquals("MSSS", q.getValue());
+
+ /*
+ * third CDS
+ */
+ ef = entry.getFeature().get(2);
+ assertEquals("CDS", ef.getName());
+ assertEquals("join(4..6,10..15)", ef.getLocation());
+ assertNotNull(ef.getXref());
+ assertTrue(ef.getXref().isEmpty());
+ assertEquals(2, ef.getQualifier().size());
+ q = ef.getQualifier().get(0);
+ assertEquals("protein_id", q.getName());
+ assertEquals("CAA12345.6", q.getValue());
+ q = ef.getQualifier().get(1);
+ assertEquals("translation", q.getName());
+ assertEquals("MSS", q.getValue());
+
+ /*
+ * Sequence - raw data before removal of newlines
+ */
+ String seq = entry.getSequence();
+ assertEquals(
+ "GGTATGTCCTCTAGTACAAAC\n"
+ + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
+ seq);
+
+ /*
+ * getSequence() converts empty DBRefEntry.version to "0"
+ */
+ assertNull(entry.getXref().get(1).getSecondaryId());
+ assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
+ }
+
+ static List<EntryType> getEmblEntries()
+ {
+ return new EmblSource()
+ .getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff