Class TestCasesIntegrationBase
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- Direct Known Subclasses:
TestCasesIntegratioBuildPdb
,TestCasesIntegrationApply
,TestCasesIntegrationCancer
,TestCasesIntegrationCanonical
,TestCasesIntegrationCircularGenome
,TestCasesIntegrationDup
,TestCasesIntegrationEff
,TestCasesIntegrationEmbl
,TestCasesIntegrationGenBank
,TestCasesIntegrationGff3
,TestCasesIntegrationGtf22
,TestCasesIntegrationHgvsDel
,TestCasesIntegrationHgvsDnaDup
,TestCasesIntegrationHgvsFrameShift
,TestCasesIntegrationHgvsHard
,TestCasesIntegrationHgvsIns
,TestCasesIntegrationHgvsMnps
,TestCasesIntegrationHgvsUpDownStream
,TestCasesIntegrationInsVep
,TestCasesIntegrationLof
,TestCasesIntegrationMotif
,TestCasesIntegrationNextProt
,TestCasesIntegrationNmd
,TestCasesIntegrationNoChange
,TestCasesIntegrationProteinInteraction
,TestCasesIntegrationRefSeq
,TestCasesIntegrationSequenceOntology
,TestCasesIntegrationSpliceRegion
,TestCasesIntegrationTranscriptError
,TestCasesZzz
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 boolean
debug
protected boolean
ignoreErrors
protected boolean
shiftHgvs
static int
SHOW_EVERY
java.lang.String
testsDir
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
appyTranscript(java.lang.String genome, java.lang.String trId, java.lang.String vcfFileName)
Apply a variant to a transcriptSnpEffectPredictor
build(java.lang.String genome)
Build a genomeSnpEffectPredictor
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)
Build a genome from a genbank file and compare results to 'expected' resultsSnpEffectPredictor
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, VariantEffect.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
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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Method Detail
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appyTranscript
public Transcript appyTranscript(java.lang.String genome, java.lang.String trId, java.lang.String vcfFileName)
Apply a variant to a transcript
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build
public SnpEffectPredictor build(java.lang.String genome)
Build a genome
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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)
Build a genome from a genbank file and compare results to 'expected' results
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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, VariantEffect.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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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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