Class TestCasesIntegrationBase
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
- Direct Known Subclasses:
IntegrationTest
,TestCasesIntegrationAlphaFold
,TestCasesIntegrationApply
,TestCasesIntegrationBuildPdb
,TestCasesIntegrationCancer
,TestCasesIntegrationCanonical
,TestCasesIntegrationCircularGenome
,TestCasesIntegrationCodingTag
,TestCasesIntegrationConfig
,TestCasesIntegrationCovid19
,TestCasesIntegrationCutsomIntervals
,TestCasesIntegrationDelEtc
,TestCasesIntegrationDup
,TestCasesIntegrationEff
,TestCasesIntegrationEmbl
,TestCasesIntegrationErrors
,TestCasesIntegrationExonFrame
,TestCasesIntegrationFilterTranscripts
,TestCasesIntegrationGenBank
,TestCasesIntegrationGff3
,TestCasesIntegrationGtf22
,TestCasesIntegrationHgvs
,TestCasesIntegrationHgvsDel
,TestCasesIntegrationHgvsDnaDup
,TestCasesIntegrationHgvsFrameShift
,TestCasesIntegrationHgvsHard
,TestCasesIntegrationHgvsIns
,TestCasesIntegrationHgvsLarge
,TestCasesIntegrationHgvsMnps
,TestCasesIntegrationHgvsUpDownStream
,TestCasesIntegrationInsEtc
,TestCasesIntegrationInsVep
,TestCasesIntegrationLargeDeletion
,TestCasesIntegrationLof
,TestCasesIntegrationMarkerSeq
,TestCasesIntegrationMissenseSilentRatio
,TestCasesIntegrationMixedVariants
,TestCasesIntegrationMnp
,TestCasesIntegrationMotif
,TestCasesIntegrationNextProt
,TestCasesIntegrationNmd
,TestCasesIntegrationNoChange
,TestCasesIntegrationProtein
,TestCasesIntegrationProteinInteraction
,TestCasesIntegrationRefSeq
,TestCasesIntegrationRegulation
,TestCasesIntegrationSequenceOntology
,TestCasesIntegrationSnp
,TestCasesIntegrationSnpEnsembl
,TestCasesIntegrationSpliceRegion
,TestCasesIntegrationStructural
,TestCasesIntegrationTranscriptError
,TestCasesIntegrationVariant
,TestCasesIntegrationVcfs
,TestCasesIntegrationZzz
Base class: Provides common methods used for testing
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionapplyTranscript
(String genome, String trId, String vcfFileName) Apply a variant to a transcriptvoid
before()
Build a genome, return SnpEffectPredictorbuildAndCompare
(String genome, String refSeqFile, String fastaFile, String resultFile, boolean hideProtein) Build a genome from a RefSeq file and compare results to 'expected' resultsBuild a genome from a embl file and compare results to 'expected' resultsbuildGeneBank
(String genome, String genBankFile) buildGeneBank
(String genome, String genBankFile, boolean circularCorrectlargeGap) Build a genome from a genbank file and compare results to 'expected' resultsbuildGetBuildCmd
(String genome) Build a genome and return the build commandbuildGff3AndCompare
(String genome, String gff3File, String resultFile, boolean readSeqs, boolean createRandSequences) Build a genome from a GFF3 file and compare results to 'expected' resultsvoid
buildGtfAndCompare
(String genome, String gtf22, String fastaFile, String resultFile) Build a genome from a GTF file and compare results to 'expected' resultsvoid
Check HGVS annotationsvoid
checkNoChange
(String[] args) void
checkTranscriptError
(String[] args, ErrorWarningType warningType) Run a predictor and check if the expected warnings appearvoid
compareHgvs
(String genome, String vcfFileName) void
compareHgvs
(String genome, String vcfFileName, boolean compareProt) void
compareVep
(String genome, String vcf, String trId) Compare with results from ENSEMBL's VEP on transcript ENST00000268124void
compareVepSO
(String genome, String vcf, String trId) Benchmarking: Compare with results from ENSEMBL's VEPvoid
init()
loadSnpEffectPredictor
(String genome, boolean build) Load predictor and create interval forestprotected String
pathMigrate
(String fileName) Used to migrate test files in old pathshowTranscripts
(Genome genome) showTranscripts
(Genome genome, boolean hideProtein) Show a genome in a 'standard' wayCalculate snp effect for an input VCF filesnpEffect
(String genome, String vcfFile, String[] otherArgs, EffFormatVersion effFormatVersion) Calculate snp effect for an input VCF filevoid
snpEffectCancer
(String vcfFile, String txtFile, String genome, boolean classic, String hgsvP, String hgvsC, String genotype, String trId) Calculate snp effect for a list of snps using cancer samples
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Field Details
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BASE_DIR
- See Also:
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SHOW_EVERY
public static int SHOW_EVERY -
debug
public boolean debug -
verbose
public boolean verbose -
testsDir
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ignoreErrors
protected boolean ignoreErrors -
shiftHgvs
protected boolean shiftHgvs -
testType
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prefixes
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Constructor Details
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TestCasesIntegrationBase
public TestCasesIntegrationBase()
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Method Details
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applyTranscript
Apply a variant to a transcript -
before
@BeforeEach public void before() -
build
Build a genome, return SnpEffectPredictor -
buildAndCompare
public SnpEffectPredictor buildAndCompare(String genome, String refSeqFile, String fastaFile, String resultFile, boolean hideProtein) Build a genome from a RefSeq file and compare results to 'expected' results -
buildEmbl
Build a genome from a embl file and compare results to 'expected' results -
buildGeneBank
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buildGeneBank
public SnpEffectPredictor buildGeneBank(String genome, String genBankFile, boolean circularCorrectlargeGap) Build a genome from a genbank file and compare results to 'expected' results -
buildGetBuildCmd
Build a genome and return the build command -
buildGff3AndCompare
public SnpEffectPredictor buildGff3AndCompare(String genome, String gff3File, String resultFile, boolean readSeqs, boolean createRandSequences) Build a genome from a GFF3 file and compare results to 'expected' results -
buildGtfAndCompare
Build a genome from a GTF file and compare results to 'expected' results -
checkHgvs
Check HGVS annotations -
checkNoChange
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checkTranscriptError
Run a predictor and check if the expected warnings appear -
compareHgvs
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compareHgvs
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compareVep
Compare with results from ENSEMBL's VEP on transcript ENST00000268124 -
compareVepSO
Benchmarking: Compare with results from ENSEMBL's VEP -
init
public void init() -
loadSnpEffectPredictor
Load predictor and create interval forest -
path
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pathClassName
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pathMigrate
Used to migrate test files in old path -
showTranscripts
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showTranscripts
Show a genome in a 'standard' way -
snpEffect
Calculate snp effect for an input VCF file -
snpEffect
public List<VcfEntry> snpEffect(String genome, String vcfFile, String[] otherArgs, EffFormatVersion effFormatVersion) Calculate snp effect for an input VCF file -
snpEffectCancer
public void snpEffectCancer(String vcfFile, String txtFile, String genome, boolean classic, String hgsvP, String hgvsC, String genotype, String trId) Calculate snp effect for a list of snps using cancer samples
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