Class TestCasesStructuralInv
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
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public class TestCasesStructuralInv extends TestCasesBase
Test cases for structural variants: InversionsGene 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
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose
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Constructor Summary
Constructors Constructor Description TestCasesStructuralInv()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void
checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns, Gene[] genesToAdd)
protected void
init()
void
test01_invGene()
Inversion: Whole genevoid
test01_invTr()
Inversion: whole transcriptvoid
test02()
Inversion: One coding exonvoid
test03()
Inversion: Two coding exonsvoid
test04()
Inversion: Part of one coding exonvoid
test05()
Inversion: Part of two coding exonvoid
test06()
Inversion: Two genesvoid
test07()
Inversion: Part of two genes (fusions) cutting on intronsvoid
test08()
Inversion: Part of two genes (fusions) cutting exonsvoid
test09()
Inversion: Intronvoid
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, path, pathClassName, prependSequenceToFirstExon
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Method Detail
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checkEffects
protected void checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
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checkEffects
protected void checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns, Gene[] genesToAdd)
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init
protected void init()
- Overrides:
init
in classTestCasesBase
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test01_invGene
@Test public void test01_invGene()
Inversion: Whole gene
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test01_invTr
@Test public void test01_invTr()
Inversion: whole transcript
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test02
@Test public void test02()
Inversion: One coding exon
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test03
@Test public void test03()
Inversion: Two coding exons
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test04
@Test public void test04()
Inversion: Part of one coding exon
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test05
@Test public void test05()
Inversion: Part of two coding exon
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test06
@Test public void test06()
Inversion: Two genes
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test07
@Test public void test07()
Inversion: Part of two genes (fusions) cutting on introns
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test08
@Test public void test08()
Inversion: Part of two genes (fusions) cutting exons
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test09
@Test public void test09()
Inversion: Intron
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test10
@Test public void test10()
Inversion creating a fusion between two pairs (i.e. four genes)
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