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Variant annotation and effect prediction package.
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package org.snpeff.snpEffect.testCases.unity;
import java.util.HashSet;
import java.util.Set;
import org.junit.Assert;
import org.junit.Test;
import org.snpeff.interval.BioType;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Transcript;
import org.snpeff.interval.Variant;
import org.snpeff.interval.Variant.VariantType;
import org.snpeff.snpEffect.EffectType;
import org.snpeff.snpEffect.HgvsDna;
import org.snpeff.snpEffect.HgvsProtein;
import org.snpeff.snpEffect.VariantEffect;
import org.snpeff.snpEffect.VariantEffect.EffectImpact;
import org.snpeff.snpEffect.VariantEffects;
import org.snpeff.util.Gpr;
import org.snpeff.util.GprSeq;
import org.snpeff.vcf.EffFormatVersion;
import org.snpeff.vcf.VcfEffect;
/**
* Test cases for structural variants: Inversions
*
* Gene models used in these test cases:
*
* Gene: Gene_1:953-1216
* 1:957-1157, strand: +, id:transcript_0, Protein
* Exons:
* 1:957-988 'exon_0_0', rank: 1, frame: ., sequence: gttgcttgaatactgtatagccttgccattgt
* 1:1045-1057 'exon_0_1', rank: 2, frame: ., sequence: tgtgttgctaact
* 1:1148-1157 'exon_0_2', rank: 3, frame: ., sequence: agacatggac
* CDS : gttgcttgaatactgtatagccttgccattgttgtgttgctaactagacatggac
* Protein : VA*ILYSLAIVVLLTRHG?
*
* 1
* 0 1
* 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5
* 789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567
* gttgcttgaatactgtatagccttgccattgt........................................................tgtgttgctaact..........................................................................................agacatggac
* V A * I L Y S L A I V V L L T R H G
* 01201201201201201201201201201201 2012012012012 0120120120
* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------->>>>>>>>>>>>>------------------------------------------------------------------------------------------>>>>>>>>>>
* | | | | | |
* | | | | | ^1157
* | | | | ^1148
* | | | ^1057
* | | ^1045
* | ^988
* ^957
*
*
* Gene: Gene_1:2057-2157
* 1:2066-2141, strand: +, id:transcript_1, Protein
* Exons:
* 1:2066-2069 'exon_1_0', rank: 1, frame: ., sequence: actt
* 1:2084-2089 'exon_1_1', rank: 2, frame: ., sequence: cccttt
* 1:2116-2126 'exon_1_2', rank: 3, frame: ., sequence: tacgcccacgt
* 1:2133-2141 'exon_1_3', rank: 4, frame: ., sequence: ccgccgctg
* CDS : acttcccttttacgcccacgtccgccgctg
* Protein : TSLLRPRPPL
*
* 1
* 7 8 9 0 1 2 3 4
* 6789012345678901234567890123456789012345678901234567890123456789012345678901
* actt..............cccttt..........................tacgcccacgt......ccgccgctg
* T S L L R P R P P L
* 0120 120120 12012012012 012012012
* >>>>-------------->>>>>>-------------------------->>>>>>>>>>>------>>>>>>>>>
* | | | | | | | |
* | | | | | | | ^2141
* | | | | | | ^2133
* | | | | | ^2126
* | | | | ^2116
* | | | ^2089
* | | ^2084
* | ^2069
* ^2066
*
*/
public class TestCasesStructuralInv extends TestCasesBase {
EffFormatVersion formatVersion = EffFormatVersion.FORMAT_ANN;
public TestCasesStructuralInv() {
super();
}
Set arrayToSet(String array[]) {
Set set = new HashSet<>();
if (array != null) {
for (String h : array)
set.add(h);
}
return set;
}
protected void checkEffects(Variant variant, EffectType expEffs[], String expHgvsp[], String expHgvsc[], EffectImpact expectedImpact, String expAnns[]) {
checkEffects(variant, expEffs, expHgvsp, expHgvsc, expectedImpact, expAnns, null);
}
protected void checkEffects(Variant variant, EffectType expEffs[], String expHgvsp[], String expHgvsc[], EffectImpact expectedImpact, String expAnns[], Gene genesToAdd[]) {
// Convert to sets
Set expectedEffs = new HashSet<>();
if (expEffs != null) {
for (EffectType et : expEffs)
expectedEffs.add(et);
}
Set expectedHgvsp = arrayToSet(expHgvsp);
Set expectedHgvsc = arrayToSet(expHgvsc);
Set expectedAnns = arrayToSet(expAnns);
// Initialize
initSnpEffPredictor(genesToAdd);
if (verbose) {
Gpr.debug("Variant: " + variant);
for (Gene g : genome.getGenes()) {
Gpr.debug("\tGene: " + g.toStr());
for (Transcript tr : g)
Gpr.debug(tr + "\n\n" + tr.toStringAsciiArt(true));
}
}
// Calculate effects
VariantEffects effects = snpEffectPredictor.variantEffect(variant);
if (verbose) Gpr.debug("VariantEffects: " + effects);
// Checknumber of results
Assert.assertEquals(true, effects.size() >= 1);
Set effs = new HashSet<>();
Set hgvscs = new HashSet<>();
Set hgvsps = new HashSet<>();
Set anns = new HashSet<>();
boolean impactOk = false;
for (VariantEffect varEff : effects) {
effs.addAll(varEff.getEffectTypes());
HgvsDna hgvsc = new HgvsDna(varEff);
String hgvsDna = hgvsc.toString();
hgvscs.add(hgvsDna);
HgvsProtein hgvsp = new HgvsProtein(varEff);
String hgvsProt = hgvsp.toString();
hgvsps.add(hgvsProt);
impactOk |= (varEff.getEffectImpact() == expectedImpact);
// Create VcfEffect
VcfEffect vcfEffect = new VcfEffect(varEff, formatVersion);
String annField = vcfEffect.toString();
anns.add(annField);
if (verbose) Gpr.debug("Effect: " + varEff.toStr() //
+ "\n\tHGVS.c: " + hgvsDna //
+ "\n\tHGVS.p: " + hgvsProt //
+ "\n\tANN : " + annField //
);
}
// Check effects
Assert.assertTrue("Effects do not match" //
+ "\n\tExpected : " + expectedEffs //
+ "\n\tFound : " + effs//
, effs.containsAll(expectedEffs) //
);
// Check impact
Assert.assertTrue("Effect impact '" + expectedImpact + "' not found", impactOk);
// Check HGVS.c
Assert.assertTrue("HGVS.c do not match" //
+ "\n\tExpected : " + expectedHgvsc //
+ "\n\tFound : " + hgvscs//
, hgvscs.containsAll(expectedHgvsc) //
);
// Check HGVS.p
Assert.assertTrue("HGVS.p do not match" //
+ "\n\tExpected : " + expectedHgvsp //
+ "\n\tFound : " + hgvsps//
, hgvsps.containsAll(expectedHgvsp) //
);
// Check ANN fields
Assert.assertTrue("ANN fields do not match" //
+ "\n\tExpected : " + expectedAnns //
+ "\n\tFound : " + anns //
, anns.containsAll(expectedAnns) //
);
}
@Override
protected void init() {
randSeed = 20151205;
genomeName = "testCase";
addUtrs = false;
onlyPlusStrand = true;
onlyMinusStrand = false;
numGenes = 2;
maxGeneLen = 1000;
maxTranscripts = 1;
maxExons = 5;
minExons = 2;
shiftHgvs = false;
initRand();
}
/**
* Inversion: Whole gene
*/
@Test
public void test01_invGene() {
Gpr.debug("Test");
// Create variant
Variant variant = new Variant(chromosome, 950, 1250, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.GENE_INVERSION };
EffectImpact expectedImpact = EffectImpact.MODERATE;
checkEffects(variant, expEffs, null, null, expectedImpact, null);
}
/**
* Inversion: whole transcript
*/
@Test
public void test01_invTr() {
Gpr.debug("Test");
// Create variant
Variant variant = new Variant(chromosome, 950, 1200, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.TRANSCRIPT_INVERSION };
String expHgvsc[] = { "c.-7_*43inv" };
EffectImpact expectedImpact = EffectImpact.MODERATE;
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, null);
}
/**
* Inversion: One coding exon
*/
@Test
public void test02() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1040, 1100, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.EXON_INVERSION };
String expHgvsc[] = { "c.33-5_45+43inv" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, null);
}
/**
* Inversion: Two coding exons
*/
@Test
public void test03() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1040, 1160, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.EXON_INVERSION };
String expHgvsc[] = { "c.33-5_*3inv" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, null);
}
/**
* Inversion: Part of one coding exon
*/
@Test
public void test04() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1040, 1050, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.EXON_INVERSION_PARTIAL };
String expHgvsc[] = { "c.33-5_38inv" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, null);
}
/**
* Inversion: Part of two coding exon
*/
@Test
public void test05() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1050, 1150, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.EXON_INVERSION_PARTIAL };
String expHgvsc[] = { "c.38_48inv" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, null);
}
/**
* Inversion: Two genes
*/
@Test
public void test06() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1050, 2160, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.GENE_INVERSION };
String expHgvsc[] = { "n.1051_2161inv" };
EffectImpact expectedImpact = EffectImpact.MODERATE;
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, null);
}
/**
* Inversion: Part of two genes (fusions) cutting on introns
*/
@Test
public void test07() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1100, 2075, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "n.1101_2076inv" };
EffectImpact expectedImpact = EffectImpact.HIGH;
String expAnns[] = { "|bidirectional_gene_fusion|HIGH|geneName1&geneName2|geneId1&geneId2|gene_variant|geneId1|||n.1101_2076inv||||||" };
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, expAnns);
}
/**
* Inversion: Part of two genes (fusions) cutting exons
*/
@Test
public void test08() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1050, 2120, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "n.1051_2121inv" };
EffectImpact expectedImpact = EffectImpact.HIGH;
String expAnns[] = { "|bidirectional_gene_fusion|HIGH|geneName1&geneName2|geneId1&geneId2|gene_variant|geneId1|||n.1051_2121inv||||||" };
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, expAnns);
}
/**
* Inversion: Intron
*/
@Test
public void test09() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 991, 1020, "");
variant.setVariantType(VariantType.INV);
EffectType expEffs[] = { EffectType.INTRON };
String expHgvsc[] = { "c.32+3_33-25inv" };
EffectImpact expectedImpact = EffectImpact.MODIFIER;
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, null);
}
/**
* Inversion creating a fusion between two pairs (i.e. four genes)
*/
@Test
public void test10() {
Gpr.debug("Test");
Variant variant = new Variant(chromosome, 1050, 2120, "");
variant.setVariantType(VariantType.INV);
// Add another gene
boolean strandMinus = false;
Gene gene = new Gene(chromosome, 2000, 2200, strandMinus, "geneId3", "geneName3", BioType.protein_coding);
Transcript tr = new Transcript(gene, 2000, 2200, strandMinus, "tr3");
Exon ex = new Exon(tr, 2000, 2200, strandMinus, "ex1_tr3", 1);
String seq = chromoSequence.substring(ex.getStart(), ex.getEnd() - 1);
ex.setSequence(strandMinus ? GprSeq.reverseWc(seq) : seq);
tr.add(ex);
gene.add(tr);
Gene genesToAdd[] = { gene };
// Expected resutls
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "n.1051_2121inv" };
EffectImpact expectedImpact = EffectImpact.HIGH;
String expAnns[] = { "|bidirectional_gene_fusion|HIGH|geneName1&geneName2|geneId1&geneId2|gene_variant|geneId1|||n.1051_2121inv||||||" //
, "|bidirectional_gene_fusion|HIGH|geneName1&geneName3|geneId1&geneId3|gene_variant|geneId1|||n.1051_2121inv||||||" //
};
checkEffects(variant, expEffs, null, expHgvsc, expectedImpact, expAnns, genesToAdd);
}
}
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