--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNull;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Console;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.util.MapList;
+
+public class GenBankFileTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Console.initLogger();
+ }
+
+ /**
+ * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+ * one of them reverse strand
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse() throws MalformedURLException, IOException
+ {
+ File dataFile = new File("test/jalview/io/J03321.gb");
+ FileParse fp = new FileParse(dataFile.getAbsolutePath(),
+ DataSourceType.FILE);
+ EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
+ List<SequenceI> seqs = parser.getSeqs();
+
+ assertEquals(seqs.size(), 1);
+ SequenceI seq = seqs.get(0);
+ assertEquals(seq.getName(), "GenBankTest|J03321");
+ assertEquals(seq.getLength(), 7502);
+ assertEquals(seq.getDescription(),
+ "Chlamydia trachomatis plasmid pCHL1, complete sequence");
+
+ /*
+ * should be 9 CDS features (one is a 'join' of two exons)
+ */
+ Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
+ assertEquals(featureTypes.size(), 1);
+ assertTrue(featureTypes.contains("CDS"));
+
+ /*
+ * inspect some features (sorted just for convenience of test assertions)
+ */
+ List<SequenceFeature> features = seq.getFeatures()
+ .getAllFeatures("CDS");
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 9);
+
+ SequenceFeature sf = features.get(0);
+ assertEquals(sf.getBegin(), 1);
+ assertEquals(sf.getEnd(), 437);
+ assertEquals(sf.getDescription(),
+ "Exon 2 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ // this is the second exon of circular CDS!
+ assertEquals(sf.getValue("exon number"), 2);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+ assertEquals(sf.getValue("transl_table"), "11");
+
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 488);
+ assertEquals(sf.getEnd(), 1480);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91568.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "complement(488..1480)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), -1); // reverse strand!
+ assertEquals(sf.getValue("note"), "pGP8-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ sf = features.get(7);
+ assertEquals(sf.getBegin(), 6045);
+ assertEquals(sf.getEnd(), 6788);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91574.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "6045..6788");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * CDS at 7022-7502 is the first exon of the circular CDS
+ */
+ sf = features.get(8);
+ assertEquals(sf.getBegin(), 7022);
+ assertEquals(sf.getEnd(), 7502);
+ assertEquals(sf.getDescription(),
+ "Exon 1 for protein EMBLCDS:AAA91567.1");
+ assertEquals(sf.getFeatureGroup(), "GenBankTest");
+ assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
+ assertEquals(sf.getPhase(), "0");
+ assertEquals(sf.getStrand(), 1);
+ assertEquals(sf.getValue("note"), "pGP7-D");
+ assertEquals(sf.getValue("exon number"), 1);
+ assertEquals(sf.getValue("product"), "hypothetical protein");
+
+ /*
+ * GenBank doesn't declare accession or CDS xrefs;
+ * dbrefs are added by Jalview for
+ * xref to self : 1
+ * protein products: 8
+ */
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
+
+ assertEquals(dbrefs.size(), 9);
+ // xref to 'self':
+ DBRefEntry selfRef = new DBRefEntry("GENBANKTEST", "1", "J03321");
+ int[] range = new int[] { 1, seq.getLength() };
+ selfRef.setMap(new Mapping(null, range, range, 1, 1));
+ assertTrue(dbrefs.contains(selfRef));
+
+ /*
+ * dna should have dbref to itself, and to EMBLCDSPROTEIN
+ * for each /protein_id (synthesized as no UNIPROT xref)
+ */
+ // TODO check if we should synthesize EMBLCDSPROTEIN dbrefs
+ DBRefEntry dbref = dbrefs.get(0);
+ assertEquals(dbref.getSource(), "GENBANKTEST");
+ assertEquals(dbref.getAccessionId(), "J03321");
+ Mapping mapping = dbref.getMap();
+ assertNull(mapping.getTo());
+ MapList map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 7502);
+ assertEquals(map.getFromRatio(), 1);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for first CDS
+ dbref = dbrefs.get(1);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91567.1");
+ mapping = dbref.getMap();
+ SequenceI mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91567.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ String seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 305);
+ assertTrue(seqString.startsWith("MGSMAF"));
+ assertTrue(seqString.endsWith("QTPTIL"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 1);
+ assertEquals(map.getFromHighest(), 7502);
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 305);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+
+ // dbref to inferred EMBLCDSPROTEIN for last CDS
+ dbref = dbrefs.get(8);
+ assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
+ assertEquals(dbref.getAccessionId(), "AAA91574.1");
+ mapping = dbref.getMap();
+ mapTo = mapping.getTo();
+ assertEquals(mapTo.getName(), "AAA91574.1");
+ // the /product qualifier transfers to protein product description
+ assertEquals(mapTo.getDescription(), "hypothetical protein");
+ seqString = mapTo.getSequenceAsString();
+ assertEquals(seqString.length(), 247);
+ assertTrue(seqString.startsWith("MNKLK"));
+ assertTrue(seqString.endsWith("FKQKS"));
+ map = mapping.getMap();
+ assertEquals(map.getFromLowest(), 6045);
+ assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788
+ assertEquals(map.getToLowest(), 1);
+ assertEquals(map.getToHighest(), 247);
+ assertEquals(map.getFromRatio(), 3);
+ assertEquals(map.getToRatio(), 1);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff