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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.Random;
import java.util.Set;
import org.junit.Test;
import org.snpeff.interval.BioType;
import org.snpeff.interval.Cds;
import org.snpeff.interval.Chromosome;
import org.snpeff.interval.CytoBands;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Marker;
import org.snpeff.interval.Transcript;
import org.snpeff.interval.Variant;
import org.snpeff.interval.VariantBnd;
import org.snpeff.snpEffect.Config;
import org.snpeff.snpEffect.EffectType;
import org.snpeff.snpEffect.HgvsDna;
import org.snpeff.snpEffect.HgvsProtein;
import org.snpeff.snpEffect.SnpEffectPredictor;
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;
import junit.framework.Assert;
/**
* Test case for structural variants: Translocation (fusions)
*
* We create two genes (one transcript each). Each gene is in one different chromosome
*
* Transcripts:
* 1:10-90, strand: +, id:tr1, Protein
* Exons:
* 1:10-30 'exon1', rank: 1, frame: ., sequence: tatttgtatgaggatttgagt
* 1:40-90 'exon2', rank: 2, frame: ., sequence: tactcagtgctgggcaatcccttagctgtcgcgccgcttaccctactattc
* CDS : tatttgtatgaggatttgagttactcagtgctgggcaatcccttagctgtcgcgccgcttaccctactattc
* Protein : YLYEDLSYSVLGNPLAVAPLTLLF
*
* 2:110-190, strand: +, id:tr2, Protein
* Exons:
* 2:110-125 'exon3', rank: 1, frame: ., sequence: gttaatgggatttcac
* 2:150-190 'exon4', rank: 2, frame: ., sequence: atgggaacggagtgtcgacagcaccttatggggagctatat
* CDS : gttaatgggatttcacatgggaacggagtgtcgacagcaccttatggggagctatat
* Protein : VNGISHGNGVSTAPYGELY
*
*
* Genes diagram:
*
* [ Chr1: Gene1 ]
* >>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
* | | | |
* ^10 ^30 ^40 ^90
*
*
* [ Chr2: Gene2 ]
* >>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
* | | | |
* ^110 ^125 ^150 ^190
*
*/
public class TestCasesStructuralTranslocations {
EffFormatVersion formatVersion = EffFormatVersion.FORMAT_ANN;
boolean debug = false;
boolean verbose = false || debug;
Random rand = new Random(20160229);
Config config;
String chr1Seq;
String chr2Seq;
Genome genome;
Chromosome chr1, chr2;
Gene gene1, gene2;
Transcript tr1, tr2;
SnpEffectPredictor snpEffectPredictor;
public TestCasesStructuralTranslocations() {
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[], EffectType notExpEffs[], String expHgvsp[], String expHgvsc[], EffectImpact expectedImpact, String expAnns[]) {
// Convert to sets
Set expectedEffs = new HashSet<>();
if (expEffs != null) {
for (EffectType et : expEffs)
expectedEffs.add(et);
}
Set notExpectedEffs = new HashSet<>();
if (notExpEffs != null) {
for (EffectType et : notExpEffs)
notExpectedEffs.add(et);
}
Set expectedHgvsp = arrayToSet(expHgvsp);
Set expectedHgvsc = arrayToSet(expHgvsc);
Set expectedAnns = arrayToSet(expAnns);
if (verbose) {
Gpr.debug("Variant: " + variant);
for (Gene g : genome.getGenes()) {
Gpr.debug("\tGene: " + g.getId() + "\t" + gene1.getStart() + " - " + gene1.getEnd());
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 effects that should NOT be present
Assert.assertFalse("Effects should NOT be present: " + notExpectedEffs //
, effs.removeAll(notExpectedEffs) // Returns true if the set has changed (i.e. there was an element removed)
);
// 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) //
);
}
public void init(boolean gene1NegativeStrand, boolean gene2NegativeStrand) {
config = new Config("test");
chr1Seq = "TGCTTGTCGATATTTGTATGAGGATTTGAGTACTACGCACTACTCAGTGCTGGGCAATCCCTTAGCTGTCGCGCCGCTTACCCTACTATTCAGGAGTAGGCCCTATCTCCACAGTGACTGTAGTACCAGCCATCTCTCTCGTTGCCGTCTGCGGTGCCGTCACACACGCTCCAGTCCCAGCTACGTTTCGCCAGGCTCAG";
chr2Seq = "GCGATTGGTTGAATAAGCATAAGGTAGTTATCCGCCTGCACCTTGTTGAAAGATTGGACTTAATCCACCCCGTTAACAAAGGAATCGATCATGTTGCGCATATCGTCTAGGTTAATGGGATTTCACCGCTTACCCACTTAGCGGGCTGGAATGGGAACGGAGTGTCGACAGCACCTTATGGGGAGCTATATTCCCCCTAT";
genome = new Genome("test");
chr1 = new Chromosome(genome, 0, chr1Seq.length() - 1, "1");
chr2 = new Chromosome(genome, 0, chr2Seq.length() - 1, "2");
chr1.setSequence(chr1Seq);
chr2.setSequence(chr2Seq);
genome.add(chr1);
genome.add(chr2);
gene1 = new Gene(chr1, 10, 90, gene1NegativeStrand, "gene1", "gene1", BioType.protein_coding);
gene2 = new Gene(chr2, 110, 190, gene2NegativeStrand, "gene2", "gene2", BioType.protein_coding);
tr1 = new Transcript(gene1, gene1.getStart(), gene1.getEnd(), gene1.isStrandMinus(), "tr1");
tr2 = new Transcript(gene2, gene2.getStart(), gene2.getEnd(), gene2.isStrandMinus(), "tr2");
gene1.add(tr1);
gene2.add(tr2);
tr1.setProteinCoding(true);
tr2.setProteinCoding(true);
Exon e11 = new Exon(tr1, 10, 30, tr1.isStrandMinus(), "exon1", 0);
Exon e12 = new Exon(tr1, 40, 90, tr1.isStrandMinus(), "exon2", 0);
Exon e21 = new Exon(tr2, 110, 125, tr2.isStrandMinus(), "exon3", 0);
Exon e22 = new Exon(tr2, 150, 190, tr2.isStrandMinus(), "exon4", 0);
Exon exons[] = { e11, e12, e21, e22 };
for (Exon e : exons) {
String seq = e.getChromosome().getSequence().substring(e.getStart(), e.getEnd() + 1);
if (e.isStrandMinus()) seq = GprSeq.reverseWc(seq);
e.setSequence(seq);
Transcript tr = (Transcript) e.getParent();
tr.add(e);
Cds cds = new Cds(tr, e.getStart(), e.getEnd(), e.isStrandMinus(), "");
tr.add(cds);
}
tr1.rankExons();
tr2.rankExons();
if (verbose) System.out.println("Transcripts:\n" + tr1 + "\n" + tr2);
snpEffectPredictor = new SnpEffectPredictor(genome);
snpEffectPredictor.setUpDownStreamLength(0);
snpEffectPredictor.add(gene1);
snpEffectPredictor.add(gene2);
snpEffectPredictor.buildForest();
// Create fake cytobands
CytoBands cytoBands = genome.getCytoBands();
cytoBands.add(new Marker(chr1, chr1.getStart(), 99, false, "p1"));
cytoBands.add(new Marker(chr1, 100, chr1.getEnd(), false, "q1"));
cytoBands.add(new Marker(chr2, chr2.getStart(), 99, false, "q2"));
cytoBands.add(new Marker(chr2, 100, chr2.getEnd(), false, "p2"));
cytoBands.build();
}
/**
* Translocation in the same direction (both genes in positive strand)
*
* #CHROM POS ID REF ALT
* chr1 35 . N N[chr2:140[
*
* gene1: >>>>>>>>>>>----
* |
* gene2 ---->>>>>>>>>
*
*/
@Test
public void test01_0() {
Gpr.debug("Test");
init(false, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, false);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr1_Ser7;tr2:His6_Tyr19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction (both genes in positive strand)
*
* #CHROM POS ID REF ALT
* chr1 35 . N N[chr2:140[
*
* gene1: >>>>>>>>>>>----
* |
* gene2 ---->>>>>>>>>>>>---
*
*/
@Test
public void test01_0_nonFs() {
Gpr.debug("Test");
init(false, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 152, false, false);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr1_Ser7;tr2:Gly7_Tyr19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in opposite directions
*
* #CHROM POS ID REF ALT
* chr1 35 . N N[chr2:140[
*
* gene1: >>>>>>>>>>>----
* |
* gene2 ----<<<<<<<<<<<<---
*
*/
@Test
public void test01_1() {
Gpr.debug("Test");
init(false, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, false);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr1_Ser7;tr2:Ile1_Met14)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in opposite directions
*
* #CHROM POS ID REF ALT
* chr1 35 . N N[chr2:140[
*
* gene1: <<<<<<<<<<<<----
* |
* gene2 ---->>>>>>>>>----
*
*/
@Test
public void test01_2() {
Gpr.debug("Test");
init(true, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, false);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Thr18_Ile24;tr2:His6_Tyr19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction (both genes in negative strand)
*
* #CHROM POS ID REF ALT
* chr1 35 . N N[chr2:140[
*
* gene1: <<<<<<<<<<<<----
* |
* gene2 ----<<<<<<<<<<<<---
*
*/
@Test
public void test01_3() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, false);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Thr18_Ile24;tr2:Ile1_Met14)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction (both genes in negative strand)
*
* #CHROM POS ID REF ALT
* chr1 35 . N N[chr2:140[
*
* gene1: <<<<<<<<<<<<----
* |
* gene2 --<<<<<<<<<<<<---
*
*/
@Test
public void test01_3_noFs() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 152, false, false);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Thr18_Ile24;tr2:Ile1_Pro13)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in opposite directions (both genes in positive strand)
*
* #CHROM POS ID REF ALT
* chr1 35 . N N]chr2:140]
*
* gene1: >>>>>>>>>>>----
* |
* gene2 >>>>>>>>>>>----
*
*/
@Test
public void test02_0() {
Gpr.debug("Test");
init(false, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, false);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr1_Ser7;tr2:Val1_His6)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N N]chr2:140]
*
* gene1: >>>>>>>>>>>----
* |
* gene2 <<<<<<<<<<<----
*
*/
@Test
public void test02_1() {
Gpr.debug("Test");
init(false, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, false);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr1_Ser7;tr2:Met14_Asn19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N N]chr2:140]
*
* gene1: >>>>>>>>>>>----
* |
* gene2 -----<<<<<<<<<<<----
*
*/
@Test
public void test02_1_nonFs() {
Gpr.debug("Test");
init(false, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 124, true, false);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr1_Ser7;tr2:Ter15_Asn19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N N]chr2:140]
*
* gene1: <<<<<<<<<<<----
* |
* gene2 >>>>>>>>>>>----
*
*/
@Test
public void test02_2() {
Gpr.debug("Test");
init(true, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, false);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Thr18_Ile24;tr2:Val1_His6)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N N]chr2:140]
*
* gene1: <<<<<<<<<<<----
* |
* gene2 ----->>>>>>>>>>>----
*
*/
@Test
public void test02_2_nonFs() {
Gpr.debug("Test");
init(true, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 124, true, false);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Thr18_Ile24;tr2:Val1_Ser5)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the opposite directions
*
* #CHROM POS ID REF ALT
* chr1 35 . N N]chr2:140]
*
* gene1: <<<<<<<<<<<----
* |
* gene2 <<<<<<<<<<<----
*
*/
@Test
public void test02_3() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, false);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Thr18_Ile24;tr2:Met14_Asn19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in opposite directions
*
* #CHROM POS ID REF ALT
* chr1 35 . N [chr2:140[N
*
* gene1: --->>>>>>>>>>>----
* |
* gene2 --->>>>>>>>>>>----
*
*/
@Test
public void test03_0() {
Gpr.debug("Test");
init(false, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, true);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr8_Phe24;tr2:His6_Tyr19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N [chr2:140[N
*
* gene1: --->>>>>>>>>>>----
* |
* gene2 ---<<<<<<<<<<----
*
*/
@Test
public void test03_1() {
Gpr.debug("Test");
init(false, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, true);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr8_Phe24;tr2:Ile1_Met14)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N [chr2:140[N
*
* gene1: --->>>>>>>>>>>----
* |
* gene2 ---<<<<<<<<<<----
*
*/
@Test
public void test03_1_nonFs() {
Gpr.debug("Test");
init(false, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 152, false, true);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr8_Phe24;tr2:Ile1_Pro13)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N [chr2:140[N
*
* gene1: ---<<<<<<<<<<<----
* |
* gene2 --->>>>>>>>>>>----
*
*/
@Test
public void test03_2() {
Gpr.debug("Test");
init(true, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, true);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Glu1_Val17;tr2:His6_Tyr19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N [chr2:140[N
*
* gene1: ---<<<<<<<<<<<----
* |
* gene2 >>>>>>>>>>>----
*
*/
@Test
public void test03_2_nonFs() {
Gpr.debug("Test");
init(true, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 152, false, true);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Glu1_Val17;tr2:Gly7_Tyr19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the opposite directions
*
* #CHROM POS ID REF ALT
* chr1 35 . N [chr2:140[N
*
* gene1: ---<<<<<<<<<<<----
* |
* gene2 ---<<<<<<<<<<<----
*
*/
@Test
public void test03_3() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, false, true);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Glu1_Val17;tr2:Ile1_Met14)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction (both genes in positive strand)
*
* #CHROM POS ID REF ALT
* chr1 35 . N ]chr2:140]N
*
* gene1: --->>>>>>>>>>>----
* |
* gene2 --->>>>>>>>>>>----
*
*/
@Test
public void test04_0() {
Gpr.debug("Test");
init(false, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr8_Phe24;tr2:Val1_His6)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction (both genes in positive strand)
*
* #CHROM POS ID REF ALT
* chr1 35 . N ]chr2:140]N
*
* gene1: --->>>>>>>>>>>----
* |
* gene2 --->>>>>>>>>>>
*
*/
@Test
public void test04_0_nonFs() {
Gpr.debug("Test");
init(false, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 124, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr8_Phe24;tr2:Val1_Ser5)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in opposite directions
*
* #CHROM POS ID REF ALT
* chr1 35 . N ]chr2:140]N
*
* gene1: --->>>>>>>>>>>----
* |
* gene2 ---<<<<<<<<<<<----
*
*/
@Test
public void test04_1() {
Gpr.debug("Test");
init(false, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.21+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Tyr8_Phe24;tr2:Met14_Asn19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in opposite directions
*
* #CHROM POS ID REF ALT
* chr1 35 . N ]chr2:140]N
*
* gene1: ---<<<<<<<<<<<<<<----
* |
* gene2 --->>>>>>>>>>>----
*
*/
@Test
public void test04_2() {
Gpr.debug("Test");
init(true, false);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION_REVERESE };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Glu1_Val17;tr2:Val1_His6)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N ]chr2:140]N
*
* gene1: ---<<<<<<<<<<<<----
* |
* gene2 ---<<<<<<<<<<<----
*
*/
@Test
public void test04_3() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 140, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION, EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Glu1_Val17;tr2:Met14_Asn19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, null, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation in the same direction
*
* #CHROM POS ID REF ALT
* chr1 35 . N ]chr2:140]N
*
* gene1: ---<<<<<<<<<<<<----
* |
* gene2 ---<<<<<<<<<<<----
*
*/
@Test
public void test04_3_nonFs() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 124, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION };
EffectType notExpEffs[] = { EffectType.FRAME_SHIFT };
String expHgvsc[] = { "t(1;2)(p1;p2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Glu1_Val17;tr2:Ter15_Asn19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation affecting a gene and an intergenic region
*
* [ Chr1: Gene1 ]
* ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..............................................................................................................
* ^10 ^30 | ^40 ^90 |
* |>
* ------------------
* <|
* | |
* ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........
* ^110 ^125 ^150 ^190
* [ Chr2: Gene2 ]
*/
@Test
public void test05_1_one_gene() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 35, "N", "N", chr2, 50, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION_HALF };
EffectType notExpEffs[] = {};
String expHgvsc[] = { "t(1;2)(p1;q2)(c.51+5)" };
String expHgvsp[] = { "t(1;2)(tr1:Glu1_Val17;)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation affecting a gene and an intergenic region
*
* [ Chr1: Gene1 ]
* ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..............................................................................................................
* ^10 ^30 ^40 ^90 |
* |>
* ------------
* <|
* |
* ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........
* ^110 ^125 ^150 ^190
* [ Chr2: Gene2 ]
*/
@Test
public void test05_2_one_gene() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 135, "N", "N", chr2, 124, true, true);
EffectType expEffs[] = { EffectType.GENE_FUSION_HALF };
EffectType notExpEffs[] = {};
String expHgvsc[] = { "t(1;2)(q1;p2)(c.42-10)" };
String expHgvsp[] = { "t(1;2)(;tr2:Ter15_Asn19)" };
EffectImpact expectedImpact = EffectImpact.HIGH;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
/**
* Translocation not affecting any gene (intergenic regions)
*
* [ Chr1: Gene1 ]
* ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..............................................................................................................
* ^10 ^30 ^40 ^90 |
* <|------------------------------------------------------------------------------------|>
* |
* ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........
* ^110 ^125 ^150 ^190
* [ Chr2: Gene2 ]
*/
@Test
public void test06_no_gene() {
Gpr.debug("Test");
init(true, true);
// Create variant
VariantBnd variant = new VariantBnd(chr1, 135, "N", "N", chr2, 50, true, true);
EffectType expEffs[] = { EffectType.FEATURE_FUSION };
EffectType notExpEffs[] = {};
String expHgvsc[] = { "t(1;2)(q1;q2)(n.136)" };
String expHgvsp[] = { "" };
EffectImpact expectedImpact = EffectImpact.LOW;
checkEffects(variant, expEffs, notExpEffs, expHgvsp, expHgvsc, expectedImpact, null);
}
}
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