X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;fp=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;h=35b378b4668bdcd1f39f7fcb1d4f4f645311d9fa;hb=b055047e4c383cd11d8d86c5e75dc4f0e425d6ef;hp=0000000000000000000000000000000000000000;hpb=60418a01c0fd5c38fba873b3a275e503ed3e29e6;p=jalview.git diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java new file mode 100644 index 0000000..35b378b --- /dev/null +++ b/test/jalview/io/EmblFlatFileTest.java @@ -0,0 +1,326 @@ +package jalview.io; + +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertSame; +import static org.testng.AssertJUnit.fail; +import static org.testng.AssertJUnit.assertNull; + +import java.io.File; +import java.io.IOException; +import java.net.MalformedURLException; +import java.util.Arrays; +import java.util.List; +import java.util.Set; + +import org.testng.annotations.Test; + +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 EmblFlatFileTest +{ + /** + * 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.embl.txt"); + FileParse fp = new FileParse(dataFile.getAbsolutePath(), DataSourceType.FILE); + EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest"); + parser.parse(); + List seqs = parser.getSeqs(); + + assertEquals(seqs.size(), 1); + SequenceI seq = seqs.get(0); + assertEquals(seq.getName(), "EmblTest|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 featureTypes = seq.getFeatures().getFeatureTypes(); + assertEquals(featureTypes.size(), 1); + assertTrue(featureTypes.contains("CDS")); + + /* + * inspect some features (sorted just for convenience of test assertions) + */ + List 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(), "EmblTest"); + 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(), "EmblTest"); + 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(), "EmblTest"); + 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(), "EmblTest"); + 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"); + + /* + * Verify DBRefs, whether declared in the file or added by Jalview. + * There are 4 'direct' (DR) dbrefs, and numerous CDS /db_xref entries + * (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'. + * Sample a few here. Note DBRefEntry constructor capitalises source. + */ + List dbrefs = Arrays.asList(seq.getDBRefs()); + + assertEquals(dbrefs.size(), 32); + // xref to 'self': + DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321"); + int[] range = new int[] { 1, seq.getLength() }; + selfRef.setMap(new Mapping(null, range, range, 1, 1)); + assertTrue(dbrefs.contains(selfRef)); + + // 1st DR line; note trailing period is removed + assertTrue(dbrefs.contains(new DBRefEntry("MD5", "0", + "d4c4942a634e3df4995fd5ac75c26a61"))); + // the 4th DR line: + assertTrue( + dbrefs.contains(new DBRefEntry("EUROPEPMC", "0", "PMC87941"))); + // from the first CDS feature + assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19"))); + // from the last CDS feature + assertTrue( + dbrefs.contains(new DBRefEntry("INTERPRO", "0", "IPR005350"))); + + /* + * verify mappings to, and sequences for, UNIPROT proteins + */ + int uniprotCount = 0; + List ranges; + for (DBRefEntry dbref : dbrefs) + { + if ("UNIPROT".equals(dbref.getSource())) + { + uniprotCount++; + Mapping mapping = dbref.getMap(); + assertNotNull(mapping); + MapList map = mapping.getMap(); + String mappedToName = mapping.getTo().getName(); + if ("UNIPROT|P0CE16".equals(mappedToName)) + { + assertEquals((ranges = map.getFromRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 1579); + assertEquals(ranges.get(0)[1], 2934); + assertEquals((ranges = map.getToRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 1); + assertEquals(ranges.get(0)[1], 451); + // CDS /product carries over as protein product description + assertEquals(mapping.getTo().getDescription(), + "hypothetical protein"); + } + else if ("UNIPROT|P0CE17".equals(mappedToName)) + { + assertEquals((ranges = map.getFromRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 2928); + assertEquals(ranges.get(0)[1], 3992); + assertEquals((ranges = map.getToRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 1); + assertEquals(ranges.get(0)[1], 354); + } + else if ("UNIPROT|P0CE18".equals(mappedToName)) + { + assertEquals((ranges = map.getFromRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 4054); + assertEquals(ranges.get(0)[1], 4848); + assertEquals((ranges = map.getToRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 1); + assertEquals(ranges.get(0)[1], 264); + } + else if ("UNIPROT|P0CE19".equals(mappedToName)) + { + // join(7022..7502,1..437) + assertEquals((ranges = map.getFromRanges()).size(), 2); + assertEquals(ranges.get(0)[0], 7022); + assertEquals(ranges.get(0)[1], 7502); + assertEquals(ranges.get(1)[0], 1); + assertEquals(ranges.get(1)[1], 437); + assertEquals((ranges = map.getToRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 1); + assertEquals(ranges.get(0)[1], 305); + } + else if ("UNIPROT|P0CE20".equals(mappedToName)) + { + // complement(488..1480) + assertEquals((ranges = map.getFromRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 1480); + assertEquals(ranges.get(0)[1], 488); + assertEquals((ranges = map.getToRanges()).size(), 1); + assertEquals(ranges.get(0)[0], 1); + assertEquals(ranges.get(0)[1], 330); + } + else if (!"UNIPROT|P0CE23".equals(mappedToName) + && !"UNIPROT|P10559".equals(mappedToName) + && !"UNIPROT|P10560".equals(mappedToName)) + { + fail("Unexpected UNIPROT dbref to " + mappedToName); + } + } + } + assertEquals(uniprotCount, 8); + } + + @Test(groups = "Functional") + public void testParse_codonStartNot1() + { + // TODO verify CDS-to-protein mapping for CDS with /codon_start=2 + // example: https://www.ebi.ac.uk/ena/browser/api/embl/EU498516 + } + + /** + * Test for the case that the EMBL CDS has no UNIPROT xref. In this case + * Jalview should synthesize an xref to EMBLCDSPROTEIN in the hope this will + * allow Get Cross-References. + * + * @throws IOException + */ + @Test(groups = "Functional") + public void testParse_noUniprotXref() throws IOException + { + // MN908947 cut down to 40BP, one CDS, length 5 peptide for test purposes + String data = "ID MN908947; SV 3; linear; genomic RNA; STD; VRL; 20 BP.\n" + + "DE Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,\n" + + "FT CDS 3..17\n" + + "FT /protein_id=\"QHD43415.1\"\n" + + "FT /product=\"orf1ab polyprotein\"\n" + + "FT /translation=\"MRKLD\n" + + "SQ Sequence 7496 BP; 2450 A; 1290 C; 1434 G; 2322 T; 0 other;\n" + + " ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga 40\n"; + FileParse fp = new FileParse(data, DataSourceType.PASTE); + EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest"); + parser.parse(); + List seqs = parser.getSeqs(); + assertEquals(seqs.size(), 1); + SequenceI seq = seqs.get(0); + List dbrefs = Arrays.asList(seq.getDBRefs()); + + /* + * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1 + */ + assertEquals(dbrefs.size(), 2); + + // dbref to self + DBRefEntry dbref = dbrefs.get(0); + assertEquals(dbref.getSource(), "EMBLTEST"); + assertEquals(dbref.getAccessionId(), "MN908947"); + Mapping mapping = dbref.getMap(); + assertNull(mapping.getTo()); + MapList map = mapping.getMap(); + assertEquals(map.getFromLowest(), 1); + assertEquals(map.getFromHighest(), 40); + assertEquals(map.getToLowest(), 1); + assertEquals(map.getToHighest(), 40); + assertEquals(map.getFromRatio(), 1); + assertEquals(map.getToRatio(), 1); + + // dbref to inferred EMBLCDSPROTEIN: + dbref = dbrefs.get(1); + assertEquals(dbref.getSource(), "EMBLCDSPROTEIN"); + assertEquals(dbref.getAccessionId(), "QHD43415.1"); + mapping = dbref.getMap(); + SequenceI mapTo = mapping.getTo(); + assertEquals(mapTo.getName(), "QHD43415.1"); + assertEquals(mapTo.getDescription(), "orf1ab polyprotein"); + assertEquals(mapTo.getSequenceAsString(), "MRKLD"); + map = mapping.getMap(); + assertEquals(map.getFromLowest(), 3); + assertEquals(map.getFromHighest(), 17); + assertEquals(map.getToLowest(), 1); + assertEquals(map.getToHighest(), 5); + assertEquals(map.getFromRatio(), 3); + assertEquals(map.getToRatio(), 1); + } + + @Test(groups = "Functional") + public void testAdjustForProteinLength() + { + int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp + + // exact length match: + assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons)); + + // match if we assume exons include stop codon not in protein: + assertSame(exons, EmblFlatFile.adjustForProteinLength(5, exons)); + + // truncate last exon by 6bp + int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons); + assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated)); + + // remove last exon and truncate preceding by 1bp (so 3bp in total) + truncated = EmblFlatFile.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 = EmblFlatFile.adjustForProteinLength(4, exons); + assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated)); + + // what if exons are too short for protein? + truncated = EmblFlatFile.adjustForProteinLength(7, exons); + assertSame(exons, truncated); + } +}