Class TestCasesStructuralTranslocations
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- org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
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public class TestCasesStructuralTranslocations extends java.lang.Object
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
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Constructor Summary
Constructors Constructor Description TestCasesStructuralTranslocations()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
checkEffects(Variant variant, EffectType[] expEffs, EffectType[] notExpEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact)
void
init(boolean gene1NegativeStrand, boolean gene2NegativeStrand)
void
test01_0()
Translocation in the same direction (both genes in positive strand)void
test01_0_nonFs()
Translocation in the same direction (both genes in positive strand)void
test01_1()
Translocation in opposite directionsvoid
test01_2()
Translocation in opposite directionsvoid
test01_3()
Translocation in the same direction (both genes in negative strand)void
test01_3_noFs()
Translocation in the same direction (both genes in negative strand)void
test02_0()
Translocation in opposite directions (both genes in positive strand)void
test02_1()
Translocation in the same directionvoid
test02_1_nonFs()
Translocation in the same directionvoid
test02_2()
Translocation in the same directionvoid
test02_2_nonFs()
Translocation in the same directionvoid
test02_3()
Translocation in the opposite directionsvoid
test03_0()
Translocation in opposite directionsvoid
test03_1()
Translocation in the same directionvoid
test03_1_nonFs()
Translocation in the same directionvoid
test03_2()
Translocation in the same directionvoid
test03_2_nonFs()
Translocation in the same directionvoid
test03_3()
Translocation in the opposite directionsvoid
test04_0()
Translocation in the same direction (both genes in positive strand)void
test04_0_nonFs()
Translocation in the same direction (both genes in positive strand)void
test04_1()
Translocation in opposite directionsvoid
test04_2()
Translocation in opposite directionsvoid
test04_3()
Translocation in the same directionvoid
test04_3_nonFs()
Translocation in the same directionvoid
test05_1_one_gene()
Translocation affecting a gene and an intergenic regionvoid
test05_2_one_gene()
Translocation affecting a gene and an intergenic regionvoid
test06_no_gene()
Translocation not affecting any gene (intergenic regions)
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Method Detail
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checkEffects
protected void checkEffects(Variant variant, EffectType[] expEffs, EffectType[] notExpEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact)
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init
public void init(boolean gene1NegativeStrand, boolean gene2NegativeStrand)
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test01_0
@Test public void test01_0()
Translocation in the same direction (both genes in positive strand)#CHROM POS ID REF ALT chr1 35 . N N[chr2:140[
gene1: >>>>>>>>>>>---- | gene2 ---->>>>>>>>>
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test01_0_nonFs
@Test public void test01_0_nonFs()
Translocation in the same direction (both genes in positive strand)#CHROM POS ID REF ALT chr1 35 . N N[chr2:140[
gene1: >>>>>>>>>>>---- | gene2 ---->>>>>>>>>>>>---
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test01_1
@Test public void test01_1()
Translocation in opposite directions#CHROM POS ID REF ALT chr1 35 . N N[chr2:140[
gene1: >>>>>>>>>>>---- | gene2 ----<<<<<<<<<<<<---
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test01_2
@Test public void test01_2()
Translocation in opposite directions#CHROM POS ID REF ALT chr1 35 . N N[chr2:140[
gene1: <<<<<<<<<<<<---- | gene2 ---->>>>>>>>>----
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test01_3
@Test public void test01_3()
Translocation in the same direction (both genes in negative strand)#CHROM POS ID REF ALT chr1 35 . N N[chr2:140[
gene1: <<<<<<<<<<<<---- | gene2 ----<<<<<<<<<<<<---
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test01_3_noFs
@Test public void test01_3_noFs()
Translocation in the same direction (both genes in negative strand)#CHROM POS ID REF ALT chr1 35 . N N[chr2:140[
gene1: <<<<<<<<<<<<---- | gene2 --<<<<<<<<<<<<---
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test02_0
@Test public void test02_0()
Translocation in opposite directions (both genes in positive strand)#CHROM POS ID REF ALT chr1 35 . N N]chr2:140]
gene1: >>>>>>>>>>>---- | gene2 >>>>>>>>>>>----
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test02_1
@Test public void test02_1()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N N]chr2:140]
gene1: >>>>>>>>>>>---- | gene2 <<<<<<<<<<<----
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test02_1_nonFs
@Test public void test02_1_nonFs()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N N]chr2:140]
gene1: >>>>>>>>>>>---- | gene2 -----<<<<<<<<<<<----
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test02_2
@Test public void test02_2()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N N]chr2:140]
gene1: <<<<<<<<<<<---- | gene2 >>>>>>>>>>>----
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test02_2_nonFs
@Test public void test02_2_nonFs()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N N]chr2:140]
gene1: <<<<<<<<<<<---- | gene2 ----->>>>>>>>>>>----
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test02_3
@Test public void test02_3()
Translocation in the opposite directions#CHROM POS ID REF ALT chr1 35 . N N]chr2:140]
gene1: <<<<<<<<<<<---- | gene2 <<<<<<<<<<<----
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test03_0
@Test public void test03_0()
Translocation in opposite directions#CHROM POS ID REF ALT chr1 35 . N [chr2:140[N
gene1: --->>>>>>>>>>>---- | gene2 --->>>>>>>>>>>----
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test03_1
@Test public void test03_1()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N [chr2:140[N
gene1: --->>>>>>>>>>>---- | gene2 ---<<<<<<<<<<----
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test03_1_nonFs
@Test public void test03_1_nonFs()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N [chr2:140[N
gene1: --->>>>>>>>>>>---- | gene2 ---<<<<<<<<<<----
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test03_2
@Test public void test03_2()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N [chr2:140[N
gene1: ---<<<<<<<<<<<---- | gene2 --->>>>>>>>>>>----
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test03_2_nonFs
@Test public void test03_2_nonFs()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N [chr2:140[N
gene1: ---<<<<<<<<<<<---- | gene2 >>>>>>>>>>>----
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test03_3
@Test public void test03_3()
Translocation in the opposite directions#CHROM POS ID REF ALT chr1 35 . N [chr2:140[N
gene1: ---<<<<<<<<<<<---- | gene2 ---<<<<<<<<<<<----
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test04_0
@Test public void test04_0()
Translocation in the same direction (both genes in positive strand)#CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N
gene1: --->>>>>>>>>>>---- | gene2 --->>>>>>>>>>>----
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test04_0_nonFs
@Test public void test04_0_nonFs()
Translocation in the same direction (both genes in positive strand)#CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N
gene1: --->>>>>>>>>>>---- | gene2 --->>>>>>>>>>>
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test04_1
@Test public void test04_1()
Translocation in opposite directions#CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N
gene1: --->>>>>>>>>>>---- | gene2 ---<<<<<<<<<<<----
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test04_2
@Test public void test04_2()
Translocation in opposite directions#CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N
gene1: ---<<<<<<<<<<<<<<---- | gene2 --->>>>>>>>>>>----
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test04_3
@Test public void test04_3()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N
gene1: ---<<<<<<<<<<<<---- | gene2 ---<<<<<<<<<<<----
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test04_3_nonFs
@Test public void test04_3_nonFs()
Translocation in the same direction#CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N
gene1: ---<<<<<<<<<<<<---- | gene2 ---<<<<<<<<<<<----
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test05_1_one_gene
@Test public void test05_1_one_gene()
Translocation affecting a gene and an intergenic region[ Chr1: Gene1 ] ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.............................................................................................................. ^10 ^30 | ^40 ^90 | |> ------------------ <| | | ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......... ^110 ^125 ^150 ^190 [ Chr2: Gene2 ]
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test05_2_one_gene
@Test public void test05_2_one_gene()
Translocation affecting a gene and an intergenic region[ Chr1: Gene1 ] ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.............................................................................................................. ^10 ^30 ^40 ^90 | |> ------------ <| | ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......... ^110 ^125 ^150 ^190 [ Chr2: Gene2 ]
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test06_no_gene
@Test public void test06_no_gene()
Translocation not affecting any gene (intergenic regions)[ Chr1: Gene1 ] ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.............................................................................................................. ^10 ^30 ^40 ^90 | <|------------------------------------------------------------------------------------|> | ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......... ^110 ^125 ^150 ^190 [ Chr2: Gene2 ]
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