Package org.snpeff.snpEffect.testCases.unity

Class TestCasesStructuralInv

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv

public class TestCasesStructuralInv
extends TestCasesBase

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

Field Summary

Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase

addUtrs, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, transcript, verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesStructuralInv()

Method Summary

Modifier and Type	Method	Description
protected void	checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void	checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns, Gene[] genesToAdd)
protected void	init()
void	test01_invGene()	Inversion: Whole gene
void	test01_invTr()	Inversion: whole transcript
void	test02()	Inversion: One coding exon
void	test03()	Inversion: Two coding exons
void	test04()	Inversion: Part of one coding exon
void	test05()	Inversion: Part of two coding exon
void	test06()	Inversion: Two genes
void	test07()	Inversion: Part of two genes (fusions) cutting on introns
void	test08()	Inversion: Part of two genes (fusions) cutting exons
void	test09()	Inversion: Intron
void	test10()	Inversion creating a fusion between two pairs (i.e.

Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase

after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, initRand, initSnpEffPredictor, initSnpEffPredictor, prependSequenceToFirstExon, showTranscripts

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TestCasesStructuralInv

public TestCasesStructuralInv()

Method Detail

checkEffects

protected void checkEffects(Variant variant,
                            EffectType[] expEffs,
                            java.lang.String[] expHgvsp,
                            java.lang.String[] expHgvsc,
                            VariantEffect.EffectImpact expectedImpact,
                            java.lang.String[] expAnns)

checkEffects

protected void checkEffects(Variant variant,
                            EffectType[] expEffs,
                            java.lang.String[] expHgvsp,
                            java.lang.String[] expHgvsc,
                            VariantEffect.EffectImpact expectedImpact,
                            java.lang.String[] expAnns,
                            Gene[] genesToAdd)

init

protected void init()

Overrides:

init in class TestCasesBase

test01_invGene

public void test01_invGene()

Inversion: Whole gene

test01_invTr

public void test01_invTr()

Inversion: whole transcript

test02

public void test02()

Inversion: One coding exon

test03

public void test03()

Inversion: Two coding exons

test04

public void test04()

Inversion: Part of one coding exon

test05

public void test05()

Inversion: Part of two coding exon

test06

public void test06()

Inversion: Two genes

test07

public void test07()

Inversion: Part of two genes (fusions) cutting on introns

test08

public void test08()

Inversion: Part of two genes (fusions) cutting exons

test09

public void test09()

Inversion: Intron

test10

public void test10()

Inversion creating a fusion between two pairs (i.e. four genes)