X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;h=2465f27559efee7e20a562a6f5377d08bc57fd55;hp=b1023d1079977a05e6fba99950570786df31d4a0;hb=4bc5011afd8738293cd11d7fe8f28baf894c9051;hpb=d4ed63b811b2b57149af11ba0ccbe11c6845acba diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java index b1023d1..2465f27 100644 --- a/test/jalview/io/EmblFlatFileTest.java +++ b/test/jalview/io/EmblFlatFileTest.java @@ -2,23 +2,37 @@ 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.assertNull; +import static org.testng.AssertJUnit.assertSame; +import static org.testng.AssertJUnit.fail; 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.BeforeClass; import org.testng.annotations.Test; +import jalview.bin.Cache; 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 { + @BeforeClass(alwaysRun = true) + public void setUp() + { + Cache.initLogger(); + } + /** * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features, * one of them reverse strand @@ -30,7 +44,7 @@ public class EmblFlatFileTest public void testParse() throws MalformedURLException, IOException { File dataFile = new File("test/jalview/io/J03321.embl.txt"); - FileParse fp = new FileParse(dataFile, DataSourceType.FILE); + FileParse fp = new FileParse(dataFile.getAbsolutePath(), DataSourceType.FILE); EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest"); parser.parse(); List seqs = parser.getSeqs(); @@ -39,7 +53,8 @@ public class EmblFlatFileTest SequenceI seq = seqs.get(0); assertEquals(seq.getName(), "EmblTest|J03321"); assertEquals(seq.getLength(), 7502); - assertEquals(seq.getDescription(), "Chlamydia trachomatis plasmid pCHL1, complete sequence"); + assertEquals(seq.getDescription(), + "Chlamydia trachomatis plasmid pCHL1, complete sequence"); /* * should be 9 CDS features (one is a 'join' of two exons) @@ -47,15 +62,15 @@ public class EmblFlatFileTest 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); + SequenceFeatures.sortFeatures(features, true); assertEquals(features.size(), 9); - + SequenceFeature sf = features.get(0); assertEquals(sf.getBegin(), 1); assertEquals(sf.getEnd(), 437); @@ -70,7 +85,7 @@ public class EmblFlatFileTest 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); @@ -83,7 +98,7 @@ public class EmblFlatFileTest 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); @@ -96,7 +111,7 @@ public class EmblFlatFileTest 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 */ @@ -114,31 +129,220 @@ public class EmblFlatFileTest assertEquals(sf.getValue("product"), "hypothetical protein"); /* - * Jalview adds a dbref to 'self', and there are 4 'direct' (DR) dbrefs, - * and numerous CDS /db_xref entries (some e.g. INTERPRO are duplicates) - * sample a few here - * Note DBRefEntry constructor capitalises source + * 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 = seq.getDBRefs(); + 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()}; + 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; note canonicalisation to "UNIPROT" + // from the first CDS feature assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19"))); - assertTrue(dbrefs.contains(new DBRefEntry("UNIPROT", "0", "P0CE19"))); // from the last CDS feature - assertTrue(dbrefs.contains(new DBRefEntry("INTERPRO", "0", "IPR005350"))); + 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], 2931); + 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], 3989); + 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], 4845); + 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], 434); + 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], 491); + 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); + } - // todo: mappings to, and sequences for, UNIPROT proteins + @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 + // plus an additional (invented) test case: + // - multi-line /product qualifier including escaped quotes + 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 \"\"foobar\"\" \"\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"); + // the /product qualifier transfers to protein product description + assertEquals(mapTo.getDescription(), "orf1ab polyprotein \"foobar\""); + 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 + + int[] exons_nostop = new int[] { 11, 15, 21, 25, 31, 35 }; // 15 bp + // exact length match: + assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons)); + + // trimmed if we assume exons include stop codon not in protein: + assertEquals(Arrays.toString(exons_nostop), Arrays.toString(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); + } + + @Test(groups = "Functional") + public void testRemoveQuotes() + { + assertNull(EmblFlatFile.removeQuotes(null)); + assertEquals(EmblFlatFile.removeQuotes("No quotes here"), "No quotes here"); + assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""), "Enclosing quotes"); + assertEquals(EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""), "Escaped \"quotes\" example"); } }