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package jalview.io.vcf; |
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import static org.testng.Assert.assertEquals; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.Mapping; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.features.SequenceFeatures; |
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import jalview.gui.AlignFrame; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import jalview.io.gff.Gff3Helper; |
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import jalview.io.gff.SequenceOntologyI; |
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import jalview.util.MapList; |
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import java.io.File; |
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import java.io.IOException; |
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import java.io.PrintWriter; |
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import java.util.List; |
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import java.util.Map; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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| 98.6% |
Uncovered Elements: 5 (368) |
Complexity: 10 |
Complexity Density: 0.03 |
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public class VCFLoaderTest |
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{ |
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private static final float DELTA = 0.00001f; |
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private static final String FASTA = "" |
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+ |
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">gene1/1-25 chromosome:GRCh38:17:45051610:45051634:1\n" |
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+ "CAAGCTGGCGGACGAGAGTGTGACA\n" |
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+ ">transcript1/1-18\n--AGCTGGCG----AGAGTGTGAC-\n" |
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+ ">gene2/1-25 chromosome:GRCh38:17:45051610:45051634:-1\n" |
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+ "TGTCACACTCTCGTCCGCCAGCTTG\n" |
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+ ">transcript2/1-18\n" + "-GTCACACTCT----CGCCAGCT--\n" |
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+ ">gene3/1-25 chromosome:GRCh38:5:45051610:45051634:1\n" |
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+ "CAAGCTGGCGGACGAGAGTGTGACA\n" |
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+ ">transcript3/1-18\n--AGCTGGCG----AGAGTGTGAC-\n" |
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+ ">transcript4/1-18\n-----TGG-GGACGAGAGTGTGA-A\n"; |
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private static final String[] VCF = { "##fileformat=VCFv4.2", |
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"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">", |
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"##reference=Homo_sapiens/GRCh38", |
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"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO", |
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"17\t45051611\t.\tA\tT,C\t1666.64\tRF\tAC=15;AF=5.0e-03,4.0e-03", |
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"17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" }; |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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@BeforeClass... |
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public void setUp() |
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{ |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
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Cache.setProperty("VCF_FIELDS", ".*"); |
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Cache.setProperty("VEP_FIELDS", ".*"); |
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Cache.initLogger(); |
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} |
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| 100% |
Uncovered Elements: 0 (66) |
Complexity: 2 |
Complexity Density: 0.03 |
1PASS
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@Test(groups = "Functional")... |
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public void testDoLoad() throws IOException |
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{ |
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AlignmentI al = buildAlignment(); |
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File f = makeVcf(); |
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VCFLoader loader = new VCFLoader(f.getPath()); |
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loader.doLoad(al.getSequencesArray(), null); |
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List<SequenceFeature> geneFeatures = al.getSequenceAt(0) |
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.getSequenceFeatures(); |
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SequenceFeatures.sortFeatures(geneFeatures, true); |
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assertEquals(geneFeatures.size(), 4); |
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SequenceFeature sf = geneFeatures.get(0); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 2); |
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assertEquals(sf.getEnd(), 2); |
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assertEquals(sf.getScore(), 4.0e-03, DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C"); |
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assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
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sf = geneFeatures.get(1); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 2); |
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assertEquals(sf.getEnd(), 2); |
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assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 5.0e-03, DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T"); |
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sf = geneFeatures.get(2); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 4); |
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assertEquals(sf.getEnd(), 4); |
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assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 2.0e-03, DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C"); |
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sf = geneFeatures.get(3); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 4); |
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assertEquals(sf.getEnd(), 4); |
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assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 3.0e-03, DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA"); |
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List<SequenceFeature> transcriptFeatures = al.getSequenceAt(1) |
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.getSequenceFeatures(); |
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assertEquals(transcriptFeatures.size(), 2); |
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sf = transcriptFeatures.get(0); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 2); |
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assertEquals(sf.getEnd(), 2); |
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assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 2.0e-03, DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C"); |
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sf = transcriptFeatures.get(1); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 2); |
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assertEquals(sf.getEnd(), 2); |
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assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 3.0e-03, DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA"); |
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DBRefEntry[] dbRefs = al.getSequenceAt(1).getDBRefs(); |
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SequenceI peptide = null; |
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for (DBRefEntry dbref : dbRefs) |
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{ |
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if (dbref.getMap().getMap().getFromRatio() == 3) |
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{ |
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peptide = dbref.getMap().getTo(); |
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} |
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} |
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List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures(); |
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assertEquals(proteinFeatures.size(), 1); |
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sf = proteinFeatures.get(0); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 1); |
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assertEquals(sf.getEnd(), 1); |
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assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); |
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assertEquals(sf.getDescription(), "p.Ser1Thr"); |
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} |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
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private File makeVcf() throws IOException... |
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{ |
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File f = File.createTempFile("Test", ".vcf"); |
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f.deleteOnExit(); |
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PrintWriter pw = new PrintWriter(f); |
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for (String vcfLine : VCF) |
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{ |
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pw.println(vcfLine); |
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} |
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pw.close(); |
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return f; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (46) |
Complexity: 1 |
Complexity Density: 0.02 |
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private AlignmentI buildAlignment()... |
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{ |
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AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA, |
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DataSourceType.PASTE); |
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AlignmentI alignment = af.getViewport().getAlignment(); |
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SequenceI gene1 = alignment.findName("gene1"); |
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int[] to = new int[] { 45051610, 45051634 }; |
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int[] from = new int[] { gene1.getStart(), gene1.getEnd() }; |
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gene1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to, |
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1, 1)); |
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to = new int[] { 45051612, 45051619, 45051624, 45051633 }; |
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SequenceI transcript1 = alignment.findName("transcript1"); |
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from = new int[] { transcript1.getStart(), transcript1.getEnd() }; |
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transcript1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList( |
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from, to, |
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1, 1)); |
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SequenceI gene2 = alignment.findName("gene2"); |
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to = new int[] { 45051634, 45051610 }; |
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from = new int[] { gene2.getStart(), gene2.getEnd() }; |
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gene2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to, |
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1, 1)); |
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to = new int[] { 45051633, 45051624, 45051619, 45051612 }; |
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SequenceI transcript2 = alignment.findName("transcript2"); |
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from = new int[] { transcript2.getStart(), transcript2.getEnd() }; |
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transcript2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList( |
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from, to, |
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1, 1)); |
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SequenceI peptide1 = new Sequence("ENSP001", "SWRECD"); |
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MapList mapList = new MapList(new int[] { 1, 18 }, new int[] { 1, 6 }, |
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3, 1); |
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Mapping map = new Mapping(peptide1, mapList); |
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DBRefEntry product = new DBRefEntry("", "", "ENSP001", map); |
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transcript1.addDBRef(product); |
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SequenceI peptide2 = new Sequence("ENSP002", "VTLSPA"); |
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mapList = new MapList(new int[] { 1, 18 }, new int[] { 1, 6 }, 3, 1); |
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map = new Mapping(peptide2, mapList); |
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product = new DBRefEntry("", "", "ENSP002", map); |
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transcript2.addDBRef(product); |
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SequenceI gene3 = alignment.findName("gene3"); |
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to = new int[] { 45051610, 45051634 }; |
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from = new int[] { gene3.getStart(), gene3.getEnd() }; |
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gene3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(from, to, |
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1, 1)); |
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SequenceI transcript3 = alignment.findName("transcript3"); |
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to = new int[] { 45051612, 45051619, 45051624, 45051633 }; |
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from = new int[] { transcript3.getStart(), transcript3.getEnd() }; |
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transcript3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList( |
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from, to, |
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1, 1)); |
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SequenceI transcript4 = alignment.findName("transcript4"); |
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to = new int[] { 45051615, 45051617, 45051619, 45051632, 45051634, |
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45051634 }; |
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from = new int[] { transcript4.getStart(), transcript4.getEnd() }; |
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transcript4.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList( |
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from, to, |
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1, 1)); |
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SequenceI peptide3 = new Sequence("ENSP003", "SWRECD"); |
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mapList = new MapList(new int[] { 1, 18 }, new int[] { 1, 6 }, 3, 1); |
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map = new Mapping(peptide3, mapList); |
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product = new DBRefEntry("", "", "ENSP003", map); |
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transcript3.addDBRef(product); |
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return alignment; |
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} |
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@throws |
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| 100% |
Uncovered Elements: 0 (66) |
Complexity: 2 |
Complexity Density: 0.03 |
1PASS
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1 |
@Test(groups = "Functional")... |
313 |
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public void testDoLoad_reverseStrand() throws IOException |
314 |
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{ |
315 |
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AlignmentI al = buildAlignment(); |
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File f = makeVcf(); |
318 |
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VCFLoader loader = new VCFLoader(f.getPath()); |
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loader.doLoad(al.getSequencesArray(), null); |
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List<SequenceFeature> geneFeatures = al.getSequenceAt(2) |
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.getSequenceFeatures(); |
329 |
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SequenceFeatures.sortFeatures(geneFeatures, true); |
330 |
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assertEquals(geneFeatures.size(), 4); |
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335 |
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SequenceFeature sf = geneFeatures.get(3); |
336 |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
337 |
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assertEquals(sf.getBegin(), 24); |
338 |
1 |
assertEquals(sf.getEnd(), 24); |
339 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
340 |
1 |
assertEquals(sf.getScore(), 5.0e-03, DELTA); |
341 |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A"); |
342 |
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346 |
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sf = geneFeatures.get(2); |
347 |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
348 |
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assertEquals(sf.getBegin(), 24); |
349 |
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assertEquals(sf.getEnd(), 24); |
350 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
351 |
1 |
assertEquals(sf.getScore(), 4.0e-03, DELTA); |
352 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,G"); |
353 |
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354 |
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355 |
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356 |
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357 |
1 |
sf = geneFeatures.get(1); |
358 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
359 |
1 |
assertEquals(sf.getBegin(), 22); |
360 |
1 |
assertEquals(sf.getEnd(), 22); |
361 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
362 |
1 |
assertEquals(sf.getScore(), 2.0e-03, DELTA); |
363 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G"); |
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366 |
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369 |
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370 |
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371 |
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372 |
1 |
sf = geneFeatures.get(0); |
373 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
374 |
1 |
assertEquals(sf.getBegin(), 21); |
375 |
1 |
assertEquals(sf.getEnd(), 21); |
376 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
377 |
1 |
assertEquals(sf.getScore(), 3.0e-03, DELTA); |
378 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT"); |
379 |
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380 |
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381 |
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382 |
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383 |
1 |
List<SequenceFeature> transcriptFeatures = al.getSequenceAt(3) |
384 |
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.getSequenceFeatures(); |
385 |
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assertEquals(transcriptFeatures.size(), 2); |
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1 |
sf = transcriptFeatures.get(0); |
391 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
392 |
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assertEquals(sf.getBegin(), 16); |
393 |
1 |
assertEquals(sf.getEnd(), 16); |
394 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
395 |
1 |
assertEquals(sf.getScore(), 3.0e-03, DELTA); |
396 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT"); |
397 |
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398 |
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399 |
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400 |
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401 |
1 |
sf = transcriptFeatures.get(1); |
402 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
403 |
1 |
assertEquals(sf.getBegin(), 17); |
404 |
1 |
assertEquals(sf.getEnd(), 17); |
405 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT); |
406 |
1 |
assertEquals(sf.getScore(), 2.0e-03, DELTA); |
407 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G"); |
408 |
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409 |
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410 |
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411 |
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412 |
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413 |
1 |
DBRefEntry[] dbRefs = al.getSequenceAt(3).getDBRefs(); |
414 |
1 |
SequenceI peptide = null; |
415 |
1 |
for (DBRefEntry dbref : dbRefs) |
416 |
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{ |
417 |
2 |
if (dbref.getMap().getMap().getFromRatio() == 3) |
418 |
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{ |
419 |
1 |
peptide = dbref.getMap().getTo(); |
420 |
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} |
421 |
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} |
422 |
1 |
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures(); |
423 |
1 |
assertEquals(proteinFeatures.size(), 1); |
424 |
1 |
sf = proteinFeatures.get(0); |
425 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
426 |
1 |
assertEquals(sf.getBegin(), 6); |
427 |
1 |
assertEquals(sf.getEnd(), 6); |
428 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); |
429 |
1 |
assertEquals(sf.getDescription(), "p.Ala6Gly"); |
430 |
|
} |
431 |
|
|
432 |
|
|
433 |
|
|
434 |
|
|
435 |
|
|
436 |
|
|
437 |
|
@throws |
438 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (133) |
Complexity: 2 |
Complexity Density: 0.02 |
1PASS
|
|
439 |
1 |
@Test(groups = "Functional")... |
440 |
|
public void testDoLoad_vepCsq() throws IOException |
441 |
|
{ |
442 |
1 |
AlignmentI al = buildAlignment(); |
443 |
|
|
444 |
1 |
VCFLoader loader = new VCFLoader("test/jalview/io/vcf/testVcf.vcf"); |
445 |
|
|
446 |
|
|
447 |
|
|
448 |
|
|
449 |
|
|
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
1 |
loader.doLoad(al.getSequencesArray(), null); |
455 |
|
|
456 |
|
|
457 |
|
|
458 |
|
|
459 |
1 |
List<SequenceFeature> geneFeatures = al.findName("gene3") |
460 |
|
.getSequenceFeatures(); |
461 |
1 |
SequenceFeatures.sortFeatures(geneFeatures, true); |
462 |
1 |
assertEquals(geneFeatures.size(), 7); |
463 |
1 |
SequenceFeature sf = geneFeatures.get(0); |
464 |
1 |
assertEquals(sf.getBegin(), 1); |
465 |
1 |
assertEquals(sf.getEnd(), 1); |
466 |
1 |
assertEquals(sf.getScore(), 0.1f, DELTA); |
467 |
1 |
assertEquals(sf.getValue("alleles"), "C,A"); |
468 |
|
|
469 |
1 |
Map map = (Map) sf.getValue("CSQ"); |
470 |
1 |
assertEquals(map.size(), 9); |
471 |
|
|
472 |
1 |
sf = geneFeatures.get(1); |
473 |
1 |
assertEquals(sf.getBegin(), 5); |
474 |
1 |
assertEquals(sf.getEnd(), 5); |
475 |
1 |
assertEquals(sf.getScore(), 0.2f, DELTA); |
476 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
477 |
1 |
map = (Map) sf.getValue("CSQ"); |
478 |
1 |
assertEquals(map.size(), 9); |
479 |
|
|
480 |
1 |
sf = geneFeatures.get(2); |
481 |
1 |
assertEquals(sf.getBegin(), 9); |
482 |
1 |
assertEquals(sf.getEnd(), 11); |
483 |
1 |
assertEquals(sf.getScore(), 0.3f, DELTA); |
484 |
1 |
assertEquals(sf.getValue("alleles"), "CGG,C"); |
485 |
1 |
map = (Map) sf.getValue("CSQ"); |
486 |
1 |
assertEquals(map.size(), 9); |
487 |
|
|
488 |
1 |
sf = geneFeatures.get(3); |
489 |
1 |
assertEquals(sf.getBegin(), 13); |
490 |
1 |
assertEquals(sf.getEnd(), 13); |
491 |
1 |
assertEquals(sf.getScore(), 0.5f, DELTA); |
492 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
493 |
1 |
map = (Map) sf.getValue("CSQ"); |
494 |
1 |
assertEquals(map.size(), 9); |
495 |
|
|
496 |
1 |
sf = geneFeatures.get(4); |
497 |
1 |
assertEquals(sf.getBegin(), 13); |
498 |
1 |
assertEquals(sf.getEnd(), 13); |
499 |
1 |
assertEquals(sf.getScore(), 0.4f, DELTA); |
500 |
1 |
assertEquals(sf.getValue("alleles"), "C,G"); |
501 |
1 |
map = (Map) sf.getValue("CSQ"); |
502 |
1 |
assertEquals(map.size(), 9); |
503 |
|
|
504 |
1 |
sf = geneFeatures.get(5); |
505 |
1 |
assertEquals(sf.getBegin(), 17); |
506 |
1 |
assertEquals(sf.getEnd(), 17); |
507 |
1 |
assertEquals(sf.getScore(), 0.7f, DELTA); |
508 |
1 |
assertEquals(sf.getValue("alleles"), "A,G"); |
509 |
1 |
map = (Map) sf.getValue("CSQ"); |
510 |
1 |
assertEquals(map.size(), 9); |
511 |
|
|
512 |
1 |
sf = geneFeatures.get(6); |
513 |
1 |
assertEquals(sf.getBegin(), 17); |
514 |
1 |
assertEquals(sf.getEnd(), 17); |
515 |
1 |
assertEquals(sf.getScore(), 0.6f, DELTA); |
516 |
1 |
assertEquals(sf.getValue("alleles"), "A,AC"); |
517 |
1 |
map = (Map) sf.getValue("CSQ"); |
518 |
1 |
assertEquals(map.size(), 9); |
519 |
|
|
520 |
|
|
521 |
|
|
522 |
|
|
523 |
|
|
524 |
|
|
525 |
|
|
526 |
1 |
List<SequenceFeature> transcriptFeatures = al.findName("transcript3") |
527 |
|
.getSequenceFeatures(); |
528 |
1 |
SequenceFeatures.sortFeatures(transcriptFeatures, true); |
529 |
1 |
assertEquals(transcriptFeatures.size(), 3); |
530 |
1 |
sf = transcriptFeatures.get(0); |
531 |
1 |
assertEquals(sf.getBegin(), 3); |
532 |
1 |
assertEquals(sf.getEnd(), 3); |
533 |
1 |
assertEquals(sf.getScore(), 0.2f, DELTA); |
534 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
535 |
|
|
536 |
1 |
map = (Map) sf.getValue("CSQ"); |
537 |
1 |
assertEquals(map.size(), 9); |
538 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3"); |
539 |
|
|
540 |
1 |
sf = transcriptFeatures.get(1); |
541 |
1 |
assertEquals(sf.getBegin(), 11); |
542 |
1 |
assertEquals(sf.getEnd(), 11); |
543 |
1 |
assertEquals(sf.getScore(), 0.7f, DELTA); |
544 |
1 |
assertEquals(sf.getValue("alleles"), "A,G"); |
545 |
1 |
assertEquals(map.size(), 9); |
546 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3"); |
547 |
|
|
548 |
1 |
sf = transcriptFeatures.get(2); |
549 |
1 |
assertEquals(sf.getBegin(), 11); |
550 |
1 |
assertEquals(sf.getEnd(), 11); |
551 |
1 |
assertEquals(sf.getScore(), 0.6f, DELTA); |
552 |
1 |
assertEquals(sf.getValue("alleles"), "A,AC"); |
553 |
1 |
assertEquals(map.size(), 9); |
554 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3"); |
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
1 |
DBRefEntry[] dbRefs = al.findName("transcript3").getDBRefs(); |
564 |
1 |
SequenceI peptide = null; |
565 |
1 |
for (DBRefEntry dbref : dbRefs) |
566 |
|
{ |
567 |
2 |
if (dbref.getMap().getMap().getFromRatio() == 3) |
568 |
|
{ |
569 |
1 |
peptide = dbref.getMap().getTo(); |
570 |
|
} |
571 |
|
} |
572 |
1 |
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures(); |
573 |
1 |
SequenceFeatures.sortFeatures(proteinFeatures, true); |
574 |
1 |
assertEquals(proteinFeatures.size(), 2); |
575 |
1 |
sf = proteinFeatures.get(0); |
576 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
577 |
1 |
assertEquals(sf.getBegin(), 1); |
578 |
1 |
assertEquals(sf.getEnd(), 1); |
579 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT); |
580 |
1 |
assertEquals(sf.getDescription(), "agC/agT"); |
581 |
1 |
sf = proteinFeatures.get(1); |
582 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
583 |
1 |
assertEquals(sf.getBegin(), 4); |
584 |
1 |
assertEquals(sf.getEnd(), 4); |
585 |
1 |
assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT); |
586 |
1 |
assertEquals(sf.getDescription(), "p.Glu4Gly"); |
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
|
592 |
1 |
transcriptFeatures = al.findName("transcript4").getSequenceFeatures(); |
593 |
1 |
SequenceFeatures.sortFeatures(transcriptFeatures, true); |
594 |
1 |
assertEquals(transcriptFeatures.size(), 4); |
595 |
1 |
sf = transcriptFeatures.get(0); |
596 |
1 |
assertEquals(sf.getBegin(), 7); |
597 |
1 |
assertEquals(sf.getEnd(), 7); |
598 |
1 |
assertEquals(sf.getScore(), 0.5f, DELTA); |
599 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
600 |
1 |
assertEquals(map.size(), 9); |
601 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
602 |
|
|
603 |
1 |
sf = transcriptFeatures.get(1); |
604 |
1 |
assertEquals(sf.getBegin(), 7); |
605 |
1 |
assertEquals(sf.getEnd(), 7); |
606 |
1 |
assertEquals(sf.getScore(), 0.4f, DELTA); |
607 |
1 |
assertEquals(sf.getValue("alleles"), "C,G"); |
608 |
1 |
assertEquals(map.size(), 9); |
609 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
610 |
|
|
611 |
1 |
sf = transcriptFeatures.get(2); |
612 |
1 |
assertEquals(sf.getBegin(), 11); |
613 |
1 |
assertEquals(sf.getEnd(), 11); |
614 |
1 |
assertEquals(sf.getScore(), 0.7f, DELTA); |
615 |
1 |
assertEquals(sf.getValue("alleles"), "A,G"); |
616 |
1 |
assertEquals(map.size(), 9); |
617 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
618 |
|
|
619 |
1 |
sf = transcriptFeatures.get(3); |
620 |
1 |
assertEquals(sf.getBegin(), 11); |
621 |
1 |
assertEquals(sf.getEnd(), 11); |
622 |
1 |
assertEquals(sf.getScore(), 0.6f, DELTA); |
623 |
1 |
assertEquals(sf.getValue("alleles"), "A,AC"); |
624 |
1 |
assertEquals(map.size(), 9); |
625 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
626 |
|
} |
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
@throws |
633 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (39) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
634 |
1 |
@Test(groups = "Functional")... |
635 |
|
public void testLoadVCFContig() throws IOException |
636 |
|
{ |
637 |
1 |
VCFLoader loader = new VCFLoader( |
638 |
|
"test/jalview/io/vcf/testVcf2.vcf"); |
639 |
|
|
640 |
1 |
SequenceI seq = loader.loadVCFContig("contig123"); |
641 |
1 |
assertEquals(seq.getLength(), 15); |
642 |
1 |
assertEquals(seq.getSequenceAsString(), "AAAAACCCCCGGGGG"); |
643 |
1 |
List<SequenceFeature> features = seq.getSequenceFeatures(); |
644 |
1 |
SequenceFeatures.sortFeatures(features, true); |
645 |
1 |
assertEquals(features.size(), 2); |
646 |
1 |
SequenceFeature sf = features.get(0); |
647 |
1 |
assertEquals(sf.getBegin(), 8); |
648 |
1 |
assertEquals(sf.getEnd(), 8); |
649 |
1 |
assertEquals(sf.getDescription(), "C,A"); |
650 |
1 |
sf = features.get(1); |
651 |
1 |
assertEquals(sf.getBegin(), 12); |
652 |
1 |
assertEquals(sf.getEnd(), 12); |
653 |
1 |
assertEquals(sf.getDescription(), "G,T"); |
654 |
|
|
655 |
1 |
seq = loader.loadVCFContig("contig789"); |
656 |
1 |
assertEquals(seq.getLength(), 25); |
657 |
1 |
assertEquals(seq.getSequenceAsString(), "GGGGGTTTTTAAAAACCCCCGGGGG"); |
658 |
1 |
features = seq.getSequenceFeatures(); |
659 |
1 |
SequenceFeatures.sortFeatures(features, true); |
660 |
1 |
assertEquals(features.size(), 2); |
661 |
1 |
sf = features.get(0); |
662 |
1 |
assertEquals(sf.getBegin(), 2); |
663 |
1 |
assertEquals(sf.getEnd(), 2); |
664 |
1 |
assertEquals(sf.getDescription(), "G,T"); |
665 |
1 |
sf = features.get(1); |
666 |
1 |
assertEquals(sf.getBegin(), 21); |
667 |
1 |
assertEquals(sf.getEnd(), 21); |
668 |
1 |
assertEquals(sf.getDescription(), "G,A"); |
669 |
|
|
670 |
1 |
seq = loader.loadVCFContig("contig456"); |
671 |
1 |
assertEquals(seq.getLength(), 20); |
672 |
1 |
assertEquals(seq.getSequenceAsString(), "CCCCCGGGGGTTTTTAAAAA"); |
673 |
1 |
features = seq.getSequenceFeatures(); |
674 |
1 |
SequenceFeatures.sortFeatures(features, true); |
675 |
1 |
assertEquals(features.size(), 1); |
676 |
1 |
sf = features.get(0); |
677 |
1 |
assertEquals(sf.getBegin(), 15); |
678 |
1 |
assertEquals(sf.getEnd(), 15); |
679 |
1 |
assertEquals(sf.getDescription(), "T,C"); |
680 |
|
} |
681 |
|
} |