Class TestCasesIntegrationBase
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- 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
public class TestCasesIntegrationBase extends java.lang.Object
Base class: Provides common methods used for testing
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
BASE_DIR
boolean
debug
protected boolean
ignoreErrors
protected java.util.List<java.lang.String>
prefixes
protected boolean
shiftHgvs
static int
SHOW_EVERY
java.lang.String
testsDir
protected java.lang.String
testType
boolean
verbose
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Constructor Summary
Constructors Constructor Description TestCasesIntegrationBase()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Transcript
applyTranscript(java.lang.String genome, java.lang.String trId, java.lang.String vcfFileName)
Apply a variant to a transcriptvoid
before()
SnpEffectPredictor
build(java.lang.String genome)
Build a genome, return SnpEffectPredictorSnpEffectPredictor
buildAndCompare(java.lang.String genome, java.lang.String refSeqFile, java.lang.String fastaFile, java.lang.String resultFile, boolean hideProtein)
Build a genome from a RefSeq file and compare results to 'expected' resultsSnpEffectPredictor
buildEmbl(java.lang.String genome, java.lang.String emblFile)
Build a genome from a embl file and compare results to 'expected' resultsSnpEffectPredictor
buildGeneBank(java.lang.String genome, java.lang.String genBankFile)
SnpEffectPredictor
buildGeneBank(java.lang.String genome, java.lang.String genBankFile, boolean circularCorrectlargeGap)
Build a genome from a genbank file and compare results to 'expected' resultsSnpEffCmdBuild
buildGetBuildCmd(java.lang.String genome)
Build a genome and return the build commandSnpEffectPredictor
buildGff3AndCompare(java.lang.String genome, java.lang.String gff3File, java.lang.String resultFile, boolean readSeqs, boolean createRandSequences)
Build a genome from a GFF3 file and compare results to 'expected' resultsvoid
buildGtfAndCompare(java.lang.String genome, java.lang.String gtf22, java.lang.String fastaFile, java.lang.String resultFile)
Build a genome from a GTF file and compare results to 'expected' resultsvoid
checkHgvs(java.lang.String genome, java.lang.String vcfFile, int minCheck)
Check HGVS annotationsvoid
checkNoChange(java.lang.String[] args)
void
checkTranscriptError(java.lang.String[] args, ErrorWarningType warningType)
Run a predictor and check if the expected warnings appearvoid
compareHgvs(java.lang.String genome, java.lang.String vcfFileName)
void
compareHgvs(java.lang.String genome, java.lang.String vcfFileName, boolean compareProt)
void
compareVep(java.lang.String genome, java.lang.String vcf, java.lang.String trId)
Compare with results from ENSEMBL's VEP on transcript ENST00000268124void
compareVepSO(java.lang.String genome, java.lang.String vcf, java.lang.String trId)
Benchmarking: Compare with results from ENSEMBL's VEPvoid
init()
SnpEffectPredictor
loadSnpEffectPredictor(java.lang.String genome, boolean build)
Load predictor and create interval forestjava.lang.String
path(java.lang.String fileName)
protected java.lang.String
pathClassName()
java.lang.String
pathMigrate(java.lang.String fileName)
Used to migrate test files in old pathjava.lang.String
showTranscripts(Genome genome)
java.lang.String
showTranscripts(Genome genome, boolean hideProtein)
Show a genome in a 'standard' wayjava.util.List<VcfEntry>
snpEffect(java.lang.String genome, java.lang.String vcfFile, java.lang.String[] otherArgs)
Calculate snp effect for an input VCF filejava.util.List<VcfEntry>
snpEffect(java.lang.String genome, java.lang.String vcfFile, java.lang.String[] otherArgs, EffFormatVersion effFormatVersion)
Calculate snp effect for an input VCF filevoid
snpEffectCancer(java.lang.String vcfFile, java.lang.String txtFile, java.lang.String genome, boolean classic, java.lang.String hgsvP, java.lang.String hgvsC, java.lang.String genotype, java.lang.String trId)
Calculate snp effect for a list of snps using cancer samples
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Field Detail
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BASE_DIR
public static final java.lang.String BASE_DIR
- See Also:
- Constant Field Values
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SHOW_EVERY
public static int SHOW_EVERY
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debug
public boolean debug
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verbose
public boolean verbose
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testsDir
public java.lang.String testsDir
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ignoreErrors
protected boolean ignoreErrors
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shiftHgvs
protected boolean shiftHgvs
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testType
protected java.lang.String testType
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prefixes
protected java.util.List<java.lang.String> prefixes
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Method Detail
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applyTranscript
public Transcript applyTranscript(java.lang.String genome, java.lang.String trId, java.lang.String vcfFileName)
Apply a variant to a transcript
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before
@BeforeEach public void before()
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build
public SnpEffectPredictor build(java.lang.String genome)
Build a genome, return SnpEffectPredictor
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buildAndCompare
public SnpEffectPredictor buildAndCompare(java.lang.String genome, java.lang.String refSeqFile, java.lang.String fastaFile, java.lang.String resultFile, boolean hideProtein)
Build a genome from a RefSeq file and compare results to 'expected' results
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buildEmbl
public SnpEffectPredictor buildEmbl(java.lang.String genome, java.lang.String emblFile)
Build a genome from a embl file and compare results to 'expected' results
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buildGeneBank
public SnpEffectPredictor buildGeneBank(java.lang.String genome, java.lang.String genBankFile)
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buildGeneBank
public SnpEffectPredictor buildGeneBank(java.lang.String genome, java.lang.String genBankFile, boolean circularCorrectlargeGap)
Build a genome from a genbank file and compare results to 'expected' results
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buildGetBuildCmd
public SnpEffCmdBuild buildGetBuildCmd(java.lang.String genome)
Build a genome and return the build command
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buildGff3AndCompare
public SnpEffectPredictor buildGff3AndCompare(java.lang.String genome, java.lang.String gff3File, java.lang.String resultFile, boolean readSeqs, boolean createRandSequences)
Build a genome from a GFF3 file and compare results to 'expected' results
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buildGtfAndCompare
public void buildGtfAndCompare(java.lang.String genome, java.lang.String gtf22, java.lang.String fastaFile, java.lang.String resultFile)
Build a genome from a GTF file and compare results to 'expected' results
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checkHgvs
public void checkHgvs(java.lang.String genome, java.lang.String vcfFile, int minCheck)
Check HGVS annotations
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checkNoChange
public void checkNoChange(java.lang.String[] args)
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checkTranscriptError
public void checkTranscriptError(java.lang.String[] args, ErrorWarningType warningType)
Run a predictor and check if the expected warnings appear
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compareHgvs
public void compareHgvs(java.lang.String genome, java.lang.String vcfFileName)
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compareHgvs
public void compareHgvs(java.lang.String genome, java.lang.String vcfFileName, boolean compareProt)
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compareVep
public void compareVep(java.lang.String genome, java.lang.String vcf, java.lang.String trId)
Compare with results from ENSEMBL's VEP on transcript ENST00000268124
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compareVepSO
public void compareVepSO(java.lang.String genome, java.lang.String vcf, java.lang.String trId)
Benchmarking: Compare with results from ENSEMBL's VEP
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init
public void init()
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loadSnpEffectPredictor
public SnpEffectPredictor loadSnpEffectPredictor(java.lang.String genome, boolean build)
Load predictor and create interval forest
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path
public java.lang.String path(java.lang.String fileName)
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pathClassName
protected java.lang.String pathClassName()
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pathMigrate
public java.lang.String pathMigrate(java.lang.String fileName)
Used to migrate test files in old path
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showTranscripts
public java.lang.String showTranscripts(Genome genome)
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showTranscripts
public java.lang.String showTranscripts(Genome genome, boolean hideProtein)
Show a genome in a 'standard' way
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snpEffect
public java.util.List<VcfEntry> snpEffect(java.lang.String genome, java.lang.String vcfFile, java.lang.String[] otherArgs)
Calculate snp effect for an input VCF file
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snpEffect
public java.util.List<VcfEntry> snpEffect(java.lang.String genome, java.lang.String vcfFile, java.lang.String[] otherArgs, EffFormatVersion effFormatVersion)
Calculate snp effect for an input VCF file
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snpEffectCancer
public void snpEffectCancer(java.lang.String vcfFile, java.lang.String txtFile, java.lang.String genome, boolean classic, java.lang.String hgsvP, java.lang.String hgvsC, java.lang.String genotype, java.lang.String trId)
Calculate snp effect for a list of snps using cancer samples
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