package jalview.io.vcf;
+import static jalview.io.gff.SequenceOntologyI.SEQUENCE_VARIANT;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureAttributes;
+import jalview.datamodel.features.FeatureAttributes.Datatype;
import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
import java.util.Map;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
public class VCFLoaderTest
+ ">transcript4/1-18\n-----TGG-GGACGAGAGTGTGA-A\n";
private static final String[] VCF = { "##fileformat=VCFv4.2",
+ // fields other than AF are ignored when parsing as they have no INFO definition
"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
+ "##INFO=<ID=AC_Female,Number=A,Type=Integer,Description=\"Allele count in Female genotypes\"",
+ "##INFO=<ID=AF_AFR,Number=A,Type=Float,Description=\"Allele Frequency among African/African American genotypes\"",
"##reference=Homo_sapiens/GRCh38",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
// A/T,C variants in position 2 of gene sequence (precedes transcript)
- // should create 2 variant features with respective scores
- "17\t45051611\t.\tA\tT,C\t1666.64\tRF\tAC=15;AF=5.0e-03,4.0e-03",
+ // should create 2 variant features with respective AF values
+ // malformed values for AC_Female and AF_AFR should be ignored
+ "17\t45051611\t.\tA\tT,C\t1666.64\tRF\tAC=15;AF=5.0e-03,4.0e-03;AC_Female=12,3d;AF_AFR=low,2.3e-4",
// SNP G/C in position 4 of gene sequence, position 2 of transcript
// insertion G/GA is transferred to nucleotide but not to peptide
- "17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
+ "17\t45051613\t.\tG\tGA,C\t1666.65\tRF\tAC=15;AF=3.0e-03,2.0e-03",
+ // '.' in INFO field should be ignored
+ "17\t45051615\t.\tG\tC\t1666.66\tRF\tAC=16;AF=." };
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
/*
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.setProperty("VCF_FIELDS", ".*");
Cache.setProperty("VEP_FIELDS", ".*");
+ Cache.setProperty("VCF_ASSEMBLY", "GRCh38=GRCh38");
+ Cache.initLogger();
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public void setUpBeforeTest()
+ {
+ /*
+ * clear down feature attributes metadata
+ */
+ FeatureAttributes.getInstance().clear();
}
@Test(groups = "Functional")
public void testDoLoad() throws IOException
{
AlignmentI al = buildAlignment();
- VCFLoader loader = new VCFLoader(al);
- File f = makeVcf();
+ File f = makeVcfFile();
+ VCFLoader loader = new VCFLoader(f.getPath());
- loader.doLoad(f.getPath(), null);
+ loader.doLoad(al.getSequencesArray(), null);
/*
* verify variant feature(s) added to gene
List<SequenceFeature> geneFeatures = al.getSequenceAt(0)
.getSequenceFeatures();
SequenceFeatures.sortFeatures(geneFeatures, true);
- assertEquals(geneFeatures.size(), 4);
+ assertEquals(geneFeatures.size(), 5);
SequenceFeature sf = geneFeatures.get(0);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
- assertEquals(sf.getScore(), 4.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(sf.getValue("AF"), "4.0e-03");
+ assertEquals(sf.getValue("AF_AFR"), "2.3e-4");
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C");
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ // malformed integer for AC_Female is ignored (JAL-3375)
+ assertNull(sf.getValue("AC_Female"));
+
sf = geneFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 5.0e-03, DELTA);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+ DELTA);
+ assertEquals(sf.getValue("AC_Female"), "12");
+ // malformed float for AF_AFR is ignored (JAL-3375)
+ assertNull(sf.getValue("AC_AFR"));
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T");
sf = geneFeatures.get(2);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = geneFeatures.get(3);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+ sf = geneFeatures.get(4);
+ assertEquals(sf.getFeatureGroup(), "VCF");
+ assertEquals(sf.getBegin(), 6);
+ assertEquals(sf.getEnd(), 6);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ // AF=. should not have been captured
+ assertNull(sf.getValue("AF"));
+ assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
+
/*
* verify variant feature(s) added to transcript
*/
List<SequenceFeature> transcriptFeatures = al.getSequenceAt(1)
.getSequenceFeatures();
- assertEquals(transcriptFeatures.size(), 2);
+ assertEquals(transcriptFeatures.size(), 3);
sf = transcriptFeatures.get(0);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = transcriptFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
/*
}
}
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
- assertEquals(proteinFeatures.size(), 1);
+ assertEquals(proteinFeatures.size(), 3);
sf = proteinFeatures.get(0);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 1);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+ assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
assertEquals(sf.getDescription(), "p.Ser1Thr");
+
+ /*
+ * check that sequence_variant attribute AF has been clocked as
+ * numeric with correct min and max values
+ * (i.e. invalid values have been ignored - JAL-3375)
+ */
+ FeatureAttributes fa = FeatureAttributes.getInstance();
+ assertSame(fa.getDatatype(SEQUENCE_VARIANT, "AF"), Datatype.Number);
+ float[] minmax = fa.getMinMax(SEQUENCE_VARIANT, "AF");
+ assertEquals(minmax[0], 0.002f);
+ assertEquals(minmax[1], 0.005f);
}
- private File makeVcf() throws IOException
+ private File makeVcfFile() throws IOException
{
File f = File.createTempFile("Test", ".vcf");
f.deleteOnExit();
{
AlignmentI al = buildAlignment();
- VCFLoader loader = new VCFLoader(al);
+ File f = makeVcfFile();
- File f = makeVcf();
+ VCFLoader loader = new VCFLoader(f.getPath());
- loader.doLoad(f.getPath(), null);
+ loader.doLoad(al.getSequencesArray(), null);
/*
* verify variant feature(s) added to gene2
List<SequenceFeature> geneFeatures = al.getSequenceAt(2)
.getSequenceFeatures();
SequenceFeatures.sortFeatures(geneFeatures, true);
- assertEquals(geneFeatures.size(), 4);
+ assertEquals(geneFeatures.size(), 5);
+ SequenceFeature sf;
/*
- * variant A/T at 45051611 maps to T/A at gene position 24
+ * insertion G/GA at 45051613 maps to an insertion at
+ * the preceding position (21) on reverse strand gene
+ * reference: CAAGC -> GCTTG/21-25
+ * genomic variant: CAAGAC (G/GA)
+ * gene variant: GTCTTG (G/GT at 21)
*/
- SequenceFeature sf = geneFeatures.get(3);
+ sf = geneFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
- assertEquals(sf.getBegin(), 24);
- assertEquals(sf.getEnd(), 24);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 5.0e-03, DELTA);
- assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A");
+ assertEquals(sf.getBegin(), 21);
+ assertEquals(sf.getEnd(), 21);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
/*
- * variant A/C at 45051611 maps to T/G at gene position 24
+ * variant G/C at 45051613 maps to C/G at gene position 22
*/
sf = geneFeatures.get(2);
assertEquals(sf.getFeatureGroup(), "VCF");
- assertEquals(sf.getBegin(), 24);
- assertEquals(sf.getEnd(), 24);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 4.0e-03, DELTA);
- assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,G");
+ assertEquals(sf.getBegin(), 22);
+ assertEquals(sf.getEnd(), 22);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
/*
- * variant G/C at 45051613 maps to C/G at gene position 22
+ * variant A/C at 45051611 maps to T/G at gene position 24
*/
- sf = geneFeatures.get(1);
+ sf = geneFeatures.get(3);
assertEquals(sf.getFeatureGroup(), "VCF");
- assertEquals(sf.getBegin(), 22);
- assertEquals(sf.getEnd(), 22);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
- assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
+ assertEquals(sf.getBegin(), 24);
+ assertEquals(sf.getEnd(), 24);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,G");
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03,
+ DELTA);
/*
- * insertion G/GA at 45051613 maps to an insertion at
- * the preceding position (21) on reverse strand gene
- * reference: CAAGC -> GCTTG/21-25
- * genomic variant: CAAGAC (G/GA)
- * gene variant: GTCTTG (G/GT at 21)
+ * variant A/T at 45051611 maps to T/A at gene position 24
*/
- sf = geneFeatures.get(0);
+ sf = geneFeatures.get(4);
assertEquals(sf.getFeatureGroup(), "VCF");
- assertEquals(sf.getBegin(), 21);
- assertEquals(sf.getEnd(), 21);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
- assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
+ assertEquals(sf.getBegin(), 24);
+ assertEquals(sf.getEnd(), 24);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A");
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+ DELTA);
/*
- * verify 2 variant features added to transcript2
+ * verify 3 variant features added to transcript2
*/
List<SequenceFeature> transcriptFeatures = al.getSequenceAt(3)
.getSequenceFeatures();
- assertEquals(transcriptFeatures.size(), 2);
+ assertEquals(transcriptFeatures.size(), 3);
/*
* insertion G/GT at position 21 of gene maps to position 16 of transcript
*/
- sf = transcriptFeatures.get(0);
+ sf = transcriptFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 16);
assertEquals(sf.getEnd(), 16);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
/*
* SNP C/G at position 22 of gene maps to position 17 of transcript
*/
- sf = transcriptFeatures.get(1);
+ sf = transcriptFeatures.get(2);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getType(), SEQUENCE_VARIANT);
+ assertEquals(sf.getScore(), 0f);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
/*
* verify variant feature(s) computed and added to protein
}
}
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
- assertEquals(proteinFeatures.size(), 1);
+ assertEquals(proteinFeatures.size(), 3);
sf = proteinFeatures.get(0);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 6);
assertEquals(sf.getEnd(), 6);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+ assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
assertEquals(sf.getDescription(), "p.Ala6Gly");
}
{
AlignmentI al = buildAlignment();
- VCFLoader loader = new VCFLoader(al);
+ VCFLoader loader = new VCFLoader("test/jalview/io/vcf/testVcf.vcf");
/*
* VCF data file with variants at gene3 positions
* 13 C/G, C/T
* 17 A/AC (insertion), A/G
*/
- loader.doLoad("test/jalview/io/vcf/testVcf.dat", null);
+ loader.doLoad(al.getSequencesArray(), null);
/*
* verify variant feature(s) added to gene3
SequenceFeature sf = geneFeatures.get(0);
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 1);
- assertEquals(sf.getScore(), 0.1f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.1f, DELTA);
assertEquals(sf.getValue("alleles"), "C,A");
// gene features include Consequence for all transcripts
Map map = (Map) sf.getValue("CSQ");
sf = geneFeatures.get(1);
assertEquals(sf.getBegin(), 5);
assertEquals(sf.getEnd(), 5);
- assertEquals(sf.getScore(), 0.2f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 9);
assertEquals(sf.getEnd(), 11); // deletion over 3 positions
- assertEquals(sf.getScore(), 0.3f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.3f, DELTA);
assertEquals(sf.getValue("alleles"), "CGG,C");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(3);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
- assertEquals(sf.getScore(), 0.5f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(4);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
- assertEquals(sf.getScore(), 0.4f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
assertEquals(sf.getValue("alleles"), "C,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(5);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(6);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17); // insertion
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 3);
assertEquals(sf.getEnd(), 3);
- assertEquals(sf.getScore(), 0.2f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
// transcript features only have Consequence for that transcripts
map = (Map) sf.getValue("CSQ");
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
}
}
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
- assertEquals(proteinFeatures.size(), 1);
+ SequenceFeatures.sortFeatures(proteinFeatures, true);
+ assertEquals(proteinFeatures.size(), 2);
sf = proteinFeatures.get(0);
assertEquals(sf.getFeatureGroup(), "VCF");
+ assertEquals(sf.getBegin(), 1);
+ assertEquals(sf.getEnd(), 1);
+ assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT);
+ assertEquals(sf.getDescription(), "agC/agT");
+ sf = proteinFeatures.get(1);
+ assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+ assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
assertEquals(sf.getDescription(), "p.Glu4Gly");
/*
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
- assertEquals(sf.getScore(), 0.5f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
- assertEquals(sf.getScore(), 0.4f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
assertEquals(sf.getValue("alleles"), "C,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(3);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
}
-}
+
+ /**
+ * A test that demonstrates loading a contig sequence from an indexed sequence
+ * database which is the reference for a VCF file
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testLoadVCFContig() throws IOException
+ {
+ VCFLoader loader = new VCFLoader(
+ "test/jalview/io/vcf/testVcf2.vcf");
+
+ SequenceI seq = loader.loadVCFContig("contig123");
+ assertEquals(seq.getLength(), 15);
+ assertEquals(seq.getSequenceAsString(), "AAAAACCCCCGGGGG");
+ List<SequenceFeature> features = seq.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 2);
+ SequenceFeature sf = features.get(0);
+ assertEquals(sf.getBegin(), 8);
+ assertEquals(sf.getEnd(), 8);
+ assertEquals(sf.getDescription(), "C,A");
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 12);
+ assertEquals(sf.getEnd(), 12);
+ assertEquals(sf.getDescription(), "G,T");
+
+ seq = loader.loadVCFContig("contig789");
+ assertEquals(seq.getLength(), 25);
+ assertEquals(seq.getSequenceAsString(), "GGGGGTTTTTAAAAACCCCCGGGGG");
+ features = seq.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 2);
+ sf = features.get(0);
+ assertEquals(sf.getBegin(), 2);
+ assertEquals(sf.getEnd(), 2);
+ assertEquals(sf.getDescription(), "G,T");
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 21);
+ assertEquals(sf.getEnd(), 21);
+ assertEquals(sf.getDescription(), "G,A");
+
+ seq = loader.loadVCFContig("contig456");
+ assertEquals(seq.getLength(), 20);
+ assertEquals(seq.getSequenceAsString(), "CCCCCGGGGGTTTTTAAAAA");
+ features = seq.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 1);
+ sf = features.get(0);
+ assertEquals(sf.getBegin(), 15);
+ assertEquals(sf.getEnd(), 15);
+ assertEquals(sf.getDescription(), "T,C");
+ }
+}
\ No newline at end of file