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package jalview.io.vcf; |
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import static jalview.io.gff.SequenceOntologyI.SEQUENCE_VARIANT; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.Assert.assertNull; |
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import static org.testng.Assert.assertTrue; |
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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.FeatureAttributes; |
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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.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.BeforeTest; |
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import org.testng.annotations.Test; |
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| 100% |
Uncovered Elements: 0 (393) |
Complexity: 11 |
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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"##INFO=<ID=AC_Female,Number=A,Type=Integer,Description=\"Allele count in Female genotypes\"", |
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"##INFO=<ID=AF_AFR,Number=A,Type=Float,Description=\"Allele Frequency among African/African American genotypes\"", |
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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\trs384765\tA\tT,C\t1666.64\tRF;XYZ\tAC=15;AF=5.0e-03,4.0e-03;AC_Female=12,3d;AF_AFR=low,2.3e-4", |
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"17\t45051613\t.\tG\tGA,C\t1666.65\t.\tAC=15;AF=3.0e-03,2.0e-03", |
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"17\t45051615\t.\tG\tC\t1666.66\tRF\tAC=16;AF=." }; |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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@BeforeClass(alwaysRun = true)... |
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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.setProperty("VCF_ASSEMBLY", "GRCh38=GRCh38"); |
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Cache.initLogger(); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@BeforeTest(alwaysRun = true)... |
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public void setUpBeforeTest() |
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{ |
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FeatureAttributes.getInstance().clear(); |
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} |
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| 100% |
Uncovered Elements: 0 (84) |
Complexity: 2 |
Complexity Density: 0.02 |
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 = makeVcfFile(); |
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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(), 5); |
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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(), 0f); |
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assertEquals(sf.getValue("AF"), "4.0e-03"); |
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assertEquals(sf.getValue("AF_AFR"), "2.3e-4"); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C"); |
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assertEquals(sf.getType(), SEQUENCE_VARIANT); |
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assertEquals(sf.getValue("POS"), "45051611"); |
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assertEquals(sf.getValue("ID"), "rs384765"); |
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assertEquals(sf.getValue("QUAL"), "1666.64"); |
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assertEquals(sf.getValue("FILTER"), "RF;XYZ"); |
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assertNull(sf.getValue("AC_Female")); |
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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(), SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 0f); |
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assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03, |
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DELTA); |
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assertEquals(sf.getValue("AC_Female"), "12"); |
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assertNull(sf.getValue("AC_AFR")); |
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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(), SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 0f); |
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assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03, |
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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(), SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 0f); |
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assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03, |
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DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA"); |
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assertNull(sf.getValue("ID")); |
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assertNull(sf.getValue("FILTER")); |
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sf = geneFeatures.get(4); |
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assertEquals(sf.getFeatureGroup(), "VCF"); |
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assertEquals(sf.getBegin(), 6); |
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assertEquals(sf.getEnd(), 6); |
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assertEquals(sf.getType(), SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 0f); |
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assertNull(sf.getValue("AF")); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C"); |
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List<SequenceFeature> transcriptFeatures = al.getSequenceAt(1) |
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.getSequenceFeatures(); |
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assertEquals(transcriptFeatures.size(), 3); |
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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(), SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 0f); |
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assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03, |
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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(), SEQUENCE_VARIANT); |
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assertEquals(sf.getScore(), 0f); |
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assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03, |
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DELTA); |
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assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA"); |
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List<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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assertTrue(proteinFeatures.isEmpty()); |
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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 makeVcfFile() 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); |
313 |
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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 }; |
320 |
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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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327 |
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SequenceI transcript3 = alignment.findName("transcript3"); |
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to = new int[] { 45051612, 45051619, 45051624, 45051633 }; |
329 |
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from = new int[] { transcript3.getStart(), transcript3.getEnd() }; |
330 |
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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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337 |
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SequenceI transcript4 = alignment.findName("transcript4"); |
338 |
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to = new int[] { 45051615, 45051617, 45051619, 45051632, 45051634, |
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45051634 }; |
340 |
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from = new int[] { transcript4.getStart(), transcript4.getEnd() }; |
341 |
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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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348 |
3 |
SequenceI peptide3 = new Sequence("ENSP003", "SWRECD"); |
349 |
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mapList = new MapList(new int[] { 1, 18 }, new int[] { 1, 6 }, 3, 1); |
350 |
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map = new Mapping(peptide3, mapList); |
351 |
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product = new DBRefEntry("", "", "ENSP003", map); |
352 |
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transcript3.addDBRef(product); |
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return alignment; |
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} |
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362 |
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@throws |
363 |
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| 100% |
Uncovered Elements: 0 (67) |
Complexity: 2 |
Complexity Density: 0.03 |
1PASS
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364 |
1 |
@Test(groups = "Functional")... |
365 |
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public void testDoLoad_reverseStrand() throws IOException |
366 |
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{ |
367 |
1 |
AlignmentI al = buildAlignment(); |
368 |
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369 |
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File f = makeVcfFile(); |
370 |
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371 |
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VCFLoader loader = new VCFLoader(f.getPath()); |
372 |
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loader.doLoad(al.getSequencesArray(), null); |
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List<SequenceFeature> geneFeatures = al.getSequenceAt(2) |
380 |
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.getSequenceFeatures(); |
381 |
1 |
SequenceFeatures.sortFeatures(geneFeatures, true); |
382 |
1 |
assertEquals(geneFeatures.size(), 5); |
383 |
1 |
SequenceFeature sf; |
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sf = geneFeatures.get(1); |
393 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
394 |
1 |
assertEquals(sf.getBegin(), 21); |
395 |
1 |
assertEquals(sf.getEnd(), 21); |
396 |
1 |
assertEquals(sf.getType(), SEQUENCE_VARIANT); |
397 |
1 |
assertEquals(sf.getScore(), 0f); |
398 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT"); |
399 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03, |
400 |
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DELTA); |
401 |
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402 |
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403 |
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404 |
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405 |
1 |
sf = geneFeatures.get(2); |
406 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
407 |
1 |
assertEquals(sf.getBegin(), 22); |
408 |
1 |
assertEquals(sf.getEnd(), 22); |
409 |
1 |
assertEquals(sf.getType(), SEQUENCE_VARIANT); |
410 |
1 |
assertEquals(sf.getScore(), 0f); |
411 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G"); |
412 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03, |
413 |
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DELTA); |
414 |
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415 |
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416 |
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417 |
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418 |
1 |
sf = geneFeatures.get(3); |
419 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
420 |
1 |
assertEquals(sf.getBegin(), 24); |
421 |
1 |
assertEquals(sf.getEnd(), 24); |
422 |
1 |
assertEquals(sf.getType(), SEQUENCE_VARIANT); |
423 |
1 |
assertEquals(sf.getScore(), 0f); |
424 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,G"); |
425 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03, |
426 |
|
DELTA); |
427 |
|
|
428 |
|
|
429 |
|
|
430 |
|
|
431 |
1 |
sf = geneFeatures.get(4); |
432 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
433 |
1 |
assertEquals(sf.getBegin(), 24); |
434 |
1 |
assertEquals(sf.getEnd(), 24); |
435 |
1 |
assertEquals(sf.getType(), SEQUENCE_VARIANT); |
436 |
1 |
assertEquals(sf.getScore(), 0f); |
437 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A"); |
438 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03, |
439 |
|
DELTA); |
440 |
|
|
441 |
|
|
442 |
|
|
443 |
|
|
444 |
1 |
List<SequenceFeature> transcriptFeatures = al.getSequenceAt(3) |
445 |
|
.getSequenceFeatures(); |
446 |
1 |
assertEquals(transcriptFeatures.size(), 3); |
447 |
|
|
448 |
|
|
449 |
|
|
450 |
|
|
451 |
1 |
sf = transcriptFeatures.get(1); |
452 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
453 |
1 |
assertEquals(sf.getBegin(), 16); |
454 |
1 |
assertEquals(sf.getEnd(), 16); |
455 |
1 |
assertEquals(sf.getType(), SEQUENCE_VARIANT); |
456 |
1 |
assertEquals(sf.getScore(), 0f); |
457 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT"); |
458 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03, |
459 |
|
DELTA); |
460 |
|
|
461 |
|
|
462 |
|
|
463 |
|
|
464 |
1 |
sf = transcriptFeatures.get(2); |
465 |
1 |
assertEquals(sf.getFeatureGroup(), "VCF"); |
466 |
1 |
assertEquals(sf.getBegin(), 17); |
467 |
1 |
assertEquals(sf.getEnd(), 17); |
468 |
1 |
assertEquals(sf.getType(), SEQUENCE_VARIANT); |
469 |
1 |
assertEquals(sf.getScore(), 0f); |
470 |
1 |
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G"); |
471 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03, |
472 |
|
DELTA); |
473 |
|
|
474 |
|
|
475 |
|
|
476 |
|
|
477 |
|
|
478 |
1 |
List<DBRefEntry> dbRefs = al.getSequenceAt(3).getDBRefs(); |
479 |
1 |
SequenceI peptide = null; |
480 |
1 |
for (DBRefEntry dbref : dbRefs) |
481 |
|
{ |
482 |
2 |
if (dbref.getMap().getMap().getFromRatio() == 3) |
483 |
|
{ |
484 |
1 |
peptide = dbref.getMap().getTo(); |
485 |
|
} |
486 |
|
} |
487 |
1 |
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures(); |
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
1 |
assertTrue(proteinFeatures.isEmpty()); |
493 |
|
} |
494 |
|
|
495 |
|
|
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
@throws |
501 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (136) |
Complexity: 2 |
Complexity Density: 0.01 |
1PASS
|
|
502 |
1 |
@Test(groups = "Functional")... |
503 |
|
public void testDoLoad_vepCsq() throws IOException |
504 |
|
{ |
505 |
1 |
AlignmentI al = buildAlignment(); |
506 |
|
|
507 |
1 |
VCFLoader loader = new VCFLoader("test/jalview/io/vcf/testVcf.vcf"); |
508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
|
|
515 |
|
|
516 |
|
|
517 |
1 |
loader.doLoad(al.getSequencesArray(), null); |
518 |
|
|
519 |
|
|
520 |
|
|
521 |
|
|
522 |
1 |
List<SequenceFeature> geneFeatures = al.findName("gene3") |
523 |
|
.getSequenceFeatures(); |
524 |
1 |
SequenceFeatures.sortFeatures(geneFeatures, true); |
525 |
1 |
assertEquals(geneFeatures.size(), 7); |
526 |
1 |
SequenceFeature sf = geneFeatures.get(0); |
527 |
1 |
assertEquals(sf.getBegin(), 1); |
528 |
1 |
assertEquals(sf.getEnd(), 1); |
529 |
1 |
assertEquals(sf.getScore(), 0f); |
530 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.1f, DELTA); |
531 |
1 |
assertEquals(sf.getValue("alleles"), "C,A"); |
532 |
|
|
533 |
1 |
Map map = (Map) sf.getValue("CSQ"); |
534 |
1 |
assertEquals(map.size(), 9); |
535 |
1 |
assertEquals(map.get("PolyPhen"), "Bad"); |
536 |
|
|
537 |
1 |
sf = geneFeatures.get(1); |
538 |
1 |
assertEquals(sf.getBegin(), 5); |
539 |
1 |
assertEquals(sf.getEnd(), 5); |
540 |
1 |
assertEquals(sf.getScore(), 0f); |
541 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA); |
542 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
543 |
1 |
map = (Map) sf.getValue("CSQ"); |
544 |
1 |
assertEquals(map.size(), 9); |
545 |
1 |
assertEquals(map.get("PolyPhen"), "Bad;;"); |
546 |
|
|
547 |
1 |
sf = geneFeatures.get(2); |
548 |
1 |
assertEquals(sf.getBegin(), 9); |
549 |
1 |
assertEquals(sf.getEnd(), 11); |
550 |
1 |
assertEquals(sf.getScore(), 0f); |
551 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.3f, DELTA); |
552 |
1 |
assertEquals(sf.getValue("alleles"), "CGG,C"); |
553 |
1 |
map = (Map) sf.getValue("CSQ"); |
554 |
1 |
assertEquals(map.size(), 9); |
555 |
|
|
556 |
1 |
sf = geneFeatures.get(3); |
557 |
1 |
assertEquals(sf.getBegin(), 13); |
558 |
1 |
assertEquals(sf.getEnd(), 13); |
559 |
1 |
assertEquals(sf.getScore(), 0f); |
560 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA); |
561 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
562 |
1 |
map = (Map) sf.getValue("CSQ"); |
563 |
1 |
assertEquals(map.size(), 9); |
564 |
|
|
565 |
1 |
sf = geneFeatures.get(4); |
566 |
1 |
assertEquals(sf.getBegin(), 13); |
567 |
1 |
assertEquals(sf.getEnd(), 13); |
568 |
1 |
assertEquals(sf.getScore(), 0f); |
569 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA); |
570 |
1 |
assertEquals(sf.getValue("alleles"), "C,G"); |
571 |
1 |
map = (Map) sf.getValue("CSQ"); |
572 |
1 |
assertEquals(map.size(), 9); |
573 |
|
|
574 |
1 |
sf = geneFeatures.get(5); |
575 |
1 |
assertEquals(sf.getBegin(), 17); |
576 |
1 |
assertEquals(sf.getEnd(), 17); |
577 |
1 |
assertEquals(sf.getScore(), 0f); |
578 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA); |
579 |
1 |
assertEquals(sf.getValue("alleles"), "A,G"); |
580 |
1 |
map = (Map) sf.getValue("CSQ"); |
581 |
1 |
assertEquals(map.size(), 9); |
582 |
|
|
583 |
1 |
sf = geneFeatures.get(6); |
584 |
1 |
assertEquals(sf.getBegin(), 17); |
585 |
1 |
assertEquals(sf.getEnd(), 17); |
586 |
1 |
assertEquals(sf.getScore(), 0f); |
587 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA); |
588 |
1 |
assertEquals(sf.getValue("alleles"), "A,AC"); |
589 |
1 |
map = (Map) sf.getValue("CSQ"); |
590 |
1 |
assertEquals(map.size(), 9); |
591 |
|
|
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
|
598 |
1 |
List<SequenceFeature> transcriptFeatures = al.findName("transcript3") |
599 |
|
.getSequenceFeatures(); |
600 |
1 |
SequenceFeatures.sortFeatures(transcriptFeatures, true); |
601 |
1 |
assertEquals(transcriptFeatures.size(), 3); |
602 |
1 |
sf = transcriptFeatures.get(0); |
603 |
1 |
assertEquals(sf.getBegin(), 3); |
604 |
1 |
assertEquals(sf.getEnd(), 3); |
605 |
1 |
assertEquals(sf.getScore(), 0f); |
606 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA); |
607 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
608 |
|
|
609 |
1 |
map = (Map) sf.getValue("CSQ"); |
610 |
1 |
assertEquals(map.size(), 9); |
611 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3"); |
612 |
|
|
613 |
1 |
sf = transcriptFeatures.get(1); |
614 |
1 |
assertEquals(sf.getBegin(), 11); |
615 |
1 |
assertEquals(sf.getEnd(), 11); |
616 |
1 |
assertEquals(sf.getScore(), 0f); |
617 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA); |
618 |
1 |
assertEquals(sf.getValue("alleles"), "A,G"); |
619 |
1 |
assertEquals(map.size(), 9); |
620 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3"); |
621 |
|
|
622 |
1 |
sf = transcriptFeatures.get(2); |
623 |
1 |
assertEquals(sf.getBegin(), 11); |
624 |
1 |
assertEquals(sf.getEnd(), 11); |
625 |
1 |
assertEquals(sf.getScore(), 0f); |
626 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA); |
627 |
1 |
assertEquals(sf.getValue("alleles"), "A,AC"); |
628 |
1 |
assertEquals(map.size(), 9); |
629 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3"); |
630 |
|
|
631 |
|
|
632 |
|
|
633 |
|
|
634 |
|
|
635 |
|
|
636 |
|
|
637 |
|
|
638 |
1 |
List<DBRefEntry> dbRefs = al.findName("transcript3").getDBRefs(); |
639 |
1 |
SequenceI peptide = null; |
640 |
1 |
for (DBRefEntry dbref : dbRefs) |
641 |
|
{ |
642 |
2 |
if (dbref.getMap().getMap().getFromRatio() == 3) |
643 |
|
{ |
644 |
1 |
peptide = dbref.getMap().getTo(); |
645 |
|
} |
646 |
|
} |
647 |
1 |
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures(); |
648 |
|
|
649 |
|
|
650 |
|
|
651 |
1 |
assertTrue(proteinFeatures.isEmpty()); |
652 |
|
|
653 |
|
|
654 |
|
|
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
|
662 |
|
|
663 |
|
|
664 |
|
|
665 |
|
|
666 |
|
|
667 |
|
|
668 |
|
|
669 |
|
|
670 |
|
|
671 |
1 |
transcriptFeatures = al.findName("transcript4").getSequenceFeatures(); |
672 |
1 |
SequenceFeatures.sortFeatures(transcriptFeatures, true); |
673 |
1 |
assertEquals(transcriptFeatures.size(), 4); |
674 |
1 |
sf = transcriptFeatures.get(0); |
675 |
1 |
assertEquals(sf.getBegin(), 7); |
676 |
1 |
assertEquals(sf.getEnd(), 7); |
677 |
1 |
assertEquals(sf.getScore(), 0f); |
678 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA); |
679 |
1 |
assertEquals(sf.getValue("alleles"), "C,T"); |
680 |
1 |
assertEquals(map.size(), 9); |
681 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
682 |
|
|
683 |
1 |
sf = transcriptFeatures.get(1); |
684 |
1 |
assertEquals(sf.getBegin(), 7); |
685 |
1 |
assertEquals(sf.getEnd(), 7); |
686 |
1 |
assertEquals(sf.getScore(), 0f); |
687 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA); |
688 |
1 |
assertEquals(sf.getValue("alleles"), "C,G"); |
689 |
1 |
assertEquals(map.size(), 9); |
690 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
691 |
|
|
692 |
1 |
sf = transcriptFeatures.get(2); |
693 |
1 |
assertEquals(sf.getBegin(), 11); |
694 |
1 |
assertEquals(sf.getEnd(), 11); |
695 |
1 |
assertEquals(sf.getScore(), 0f); |
696 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA); |
697 |
1 |
assertEquals(sf.getValue("alleles"), "A,G"); |
698 |
1 |
assertEquals(map.size(), 9); |
699 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
700 |
|
|
701 |
1 |
sf = transcriptFeatures.get(3); |
702 |
1 |
assertEquals(sf.getBegin(), 11); |
703 |
1 |
assertEquals(sf.getEnd(), 11); |
704 |
1 |
assertEquals(sf.getScore(), 0f); |
705 |
1 |
assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA); |
706 |
1 |
assertEquals(sf.getValue("alleles"), "A,AC"); |
707 |
1 |
assertEquals(map.size(), 9); |
708 |
1 |
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4"); |
709 |
|
} |
710 |
|
|
711 |
|
|
712 |
|
|
713 |
|
|
714 |
|
|
715 |
|
@throws |
716 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (39) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
717 |
1 |
@Test(groups = "Functional")... |
718 |
|
public void testLoadVCFContig() throws IOException |
719 |
|
{ |
720 |
1 |
VCFLoader loader = new VCFLoader( |
721 |
|
"test/jalview/io/vcf/testVcf2.vcf"); |
722 |
|
|
723 |
1 |
SequenceI seq = loader.loadVCFContig("contig123"); |
724 |
1 |
assertEquals(seq.getLength(), 15); |
725 |
1 |
assertEquals(seq.getSequenceAsString(), "AAAAACCCCCGGGGG"); |
726 |
1 |
List<SequenceFeature> features = seq.getSequenceFeatures(); |
727 |
1 |
SequenceFeatures.sortFeatures(features, true); |
728 |
1 |
assertEquals(features.size(), 2); |
729 |
1 |
SequenceFeature sf = features.get(0); |
730 |
1 |
assertEquals(sf.getBegin(), 8); |
731 |
1 |
assertEquals(sf.getEnd(), 8); |
732 |
1 |
assertEquals(sf.getDescription(), "C,A"); |
733 |
1 |
sf = features.get(1); |
734 |
1 |
assertEquals(sf.getBegin(), 12); |
735 |
1 |
assertEquals(sf.getEnd(), 12); |
736 |
1 |
assertEquals(sf.getDescription(), "G,T"); |
737 |
|
|
738 |
1 |
seq = loader.loadVCFContig("contig789"); |
739 |
1 |
assertEquals(seq.getLength(), 25); |
740 |
1 |
assertEquals(seq.getSequenceAsString(), "GGGGGTTTTTAAAAACCCCCGGGGG"); |
741 |
1 |
features = seq.getSequenceFeatures(); |
742 |
1 |
SequenceFeatures.sortFeatures(features, true); |
743 |
1 |
assertEquals(features.size(), 2); |
744 |
1 |
sf = features.get(0); |
745 |
1 |
assertEquals(sf.getBegin(), 2); |
746 |
1 |
assertEquals(sf.getEnd(), 2); |
747 |
1 |
assertEquals(sf.getDescription(), "G,T"); |
748 |
1 |
sf = features.get(1); |
749 |
1 |
assertEquals(sf.getBegin(), 21); |
750 |
1 |
assertEquals(sf.getEnd(), 21); |
751 |
1 |
assertEquals(sf.getDescription(), "G,A"); |
752 |
|
|
753 |
1 |
seq = loader.loadVCFContig("contig456"); |
754 |
1 |
assertEquals(seq.getLength(), 20); |
755 |
1 |
assertEquals(seq.getSequenceAsString(), "CCCCCGGGGGTTTTTAAAAA"); |
756 |
1 |
features = seq.getSequenceFeatures(); |
757 |
1 |
SequenceFeatures.sortFeatures(features, true); |
758 |
1 |
assertEquals(features.size(), 1); |
759 |
1 |
sf = features.get(0); |
760 |
1 |
assertEquals(sf.getBegin(), 15); |
761 |
1 |
assertEquals(sf.getEnd(), 15); |
762 |
1 |
assertEquals(sf.getDescription(), "T,C"); |
763 |
|
} |
764 |
|
} |