package jalview.io.vcf;
import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertTrue;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.List;
+import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class VCFLoaderTest
private static final String[] VCF = { "##fileformat=VCFv4.2",
"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
- "##reference=GRCh38",
+ "##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
// 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" };
+ @BeforeClass
+ public void setUp()
+ {
+ /*
+ * configure to capture all available VCF and VEP (CSQ) fields
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.setProperty("VCF_FIELDS", ".*");
+ Cache.setProperty("VEP_FIELDS", ".*");
+ }
+
@Test(groups = "Functional")
public void testDoLoad() throws IOException
{
SequenceI gene1 = alignment.findName("gene1");
int[] to = new int[] { 45051610, 45051634 };
int[] from = new int[] { gene1.getStart(), gene1.getEnd() };
- gene1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
+ gene1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+ 1, 1));
/*
* map 'transcript1' to chromosome via 'gene1'
to = new int[] { 45051612, 45051619, 45051624, 45051633 };
SequenceI transcript1 = alignment.findName("transcript1");
from = new int[] { transcript1.getStart(), transcript1.getEnd() };
- transcript1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+ transcript1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+ from, to,
1, 1));
/*
SequenceI gene2 = alignment.findName("gene2");
to = new int[] { 45051634, 45051610 };
from = new int[] { gene2.getStart(), gene2.getEnd() };
- gene2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
+ gene2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+ 1, 1));
/*
* map 'transcript2' to chromosome via 'gene2'
to = new int[] { 45051633, 45051624, 45051619, 45051612 };
SequenceI transcript2 = alignment.findName("transcript2");
from = new int[] { transcript2.getStart(), transcript2.getEnd() };
- transcript2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+ transcript2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+ from, to,
1, 1));
/*
SequenceI gene3 = alignment.findName("gene3");
to = new int[] { 45051610, 45051634 };
from = new int[] { gene3.getStart(), gene3.getEnd() };
- gene3.setGeneLoci("human", "GRCh38", "5", new MapList(from, to, 1, 1));
+ gene3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(from, to,
+ 1, 1));
/*
* map 'transcript3' to chromosome
SequenceI transcript3 = alignment.findName("transcript3");
to = new int[] { 45051612, 45051619, 45051624, 45051633 };
from = new int[] { transcript3.getStart(), transcript3.getEnd() };
- transcript3.setGeneLoci("human", "GRCh38", "5", new MapList(from, to,
+ transcript3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+ from, to,
1, 1));
/*
to = new int[] { 45051615, 45051617, 45051619, 45051632, 45051634,
45051634 };
from = new int[] { transcript4.getStart(), transcript4.getEnd() };
- transcript4.setGeneLoci("human", "GRCh38", "5", new MapList(from, to,
+ transcript4.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+ from, to,
1, 1));
/*
assertEquals(sf.getScore(), 0.1f, DELTA);
assertEquals(sf.getValue("alleles"), "C,A");
// gene features include Consequence for all transcripts
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+ Map map = (Map) sf.getValue("CSQ");
+ assertEquals(map.size(), 9);
sf = geneFeatures.get(1);
assertEquals(sf.getBegin(), 5);
assertEquals(sf.getEnd(), 5);
assertEquals(sf.getScore(), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+ 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.getValue("alleles"), "CGG,C");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+ 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.getValue("alleles"), "C,T");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+ 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.getValue("alleles"), "C,G");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+ 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.getValue("alleles"), "A,G");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+ 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.getValue("alleles"), "A,AC");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+ map = (Map) sf.getValue("CSQ");
+ assertEquals(map.size(), 9);
/*
* verify variant feature(s) added to transcript3
assertEquals(sf.getScore(), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
// transcript features only have Consequence for that transcripts
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
- assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+ map = (Map) sf.getValue("CSQ");
+ assertEquals(map.size(), 9);
+ assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
assertEquals(sf.getScore(), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
- assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+ 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.getValue("alleles"), "A,AC");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
- assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+ assertEquals(map.size(), 9);
+ assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
/*
* verify variants computed on protein product for transcript3
assertEquals(sf.getEnd(), 7);
assertEquals(sf.getScore(), 0.5f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
- assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+ 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.getValue("alleles"), "C,G");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
- assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+ 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.getValue("alleles"), "A,G");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
- assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+ 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.getValue("alleles"), "A,AC");
- assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
- assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+ assertEquals(map.size(), 9);
+ assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
}
}