Package org.snpeff.snpEffect.testCases.integration

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

public class TestCasesIntegrationBase
extends java.lang.Object

Base class: Provides common methods used for testing

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

Constructor Summary

Constructors

Constructor	Description
TestCasesIntegrationBase()

Method Summary

Modifier and Type	Method	Description
Transcript	applyTranscript(java.lang.String genome, java.lang.String trId, java.lang.String vcfFileName)	Apply a variant to a transcript
void	before()
SnpEffectPredictor	build(java.lang.String genome)	Build a genome, return SnpEffectPredictor
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
SnpEffectPredictor	buildEmbl(java.lang.String genome, java.lang.String emblFile)	Build a genome from a embl file and compare results to 'expected' results
SnpEffectPredictor	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' results
SnpEffCmdBuild	buildGetBuildCmd(java.lang.String genome)	Build a genome and return the build command
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
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
void	checkHgvs(java.lang.String genome, java.lang.String vcfFile, int minCheck)	Check HGVS annotations
void	checkNoChange(java.lang.String[] args)
void	checkTranscriptError(java.lang.String[] args, ErrorWarningType warningType)	Run a predictor and check if the expected warnings appear
void	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 ENST00000268124
void	compareVepSO(java.lang.String genome, java.lang.String vcf, java.lang.String trId)	Benchmarking: Compare with results from ENSEMBL's VEP
void	init()
SnpEffectPredictor	loadSnpEffectPredictor(java.lang.String genome, boolean build)	Load predictor and create interval forest
java.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 path
java.lang.String	showTranscripts(Genome genome)
java.lang.String	showTranscripts(Genome genome, boolean hideProtein)	Show a genome in a 'standard' way
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
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
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

Methods inherited from class java.lang.Object

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

Field Detail

BASE_DIR

public static final java.lang.String BASE_DIR

See Also:

Constant Field Values

SHOW_EVERY

public static int SHOW_EVERY

debug

public boolean debug

verbose

public boolean verbose

testsDir

public java.lang.String testsDir

ignoreErrors

protected boolean ignoreErrors

shiftHgvs

protected boolean shiftHgvs

testType

protected java.lang.String testType

prefixes

protected java.util.List<java.lang.String> prefixes

Constructor Detail

TestCasesIntegrationBase

public TestCasesIntegrationBase()

Method Detail

applyTranscript

public Transcript applyTranscript(java.lang.String genome,
                                  java.lang.String trId,
                                  java.lang.String vcfFileName)

Apply a variant to a transcript

before

@BeforeEach
public void before()

build

public SnpEffectPredictor build(java.lang.String genome)

Build a genome, return SnpEffectPredictor

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

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

buildGeneBank

public SnpEffectPredictor buildGeneBank(java.lang.String genome,
                                        java.lang.String genBankFile)

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

buildGetBuildCmd

public SnpEffCmdBuild buildGetBuildCmd(java.lang.String genome)

Build a genome and return the build command

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

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

checkHgvs

public void checkHgvs(java.lang.String genome,
                      java.lang.String vcfFile,
                      int minCheck)

Check HGVS annotations

checkNoChange

public void checkNoChange(java.lang.String[] args)

checkTranscriptError

public void checkTranscriptError(java.lang.String[] args,
                                 ErrorWarningType warningType)

Run a predictor and check if the expected warnings appear

compareHgvs

public void compareHgvs(java.lang.String genome,
                        java.lang.String vcfFileName)

compareHgvs

public void compareHgvs(java.lang.String genome,
                        java.lang.String vcfFileName,
                        boolean compareProt)

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

compareVepSO

public void compareVepSO(java.lang.String genome,
                         java.lang.String vcf,
                         java.lang.String trId)

Benchmarking: Compare with results from ENSEMBL's VEP

init

public void init()

loadSnpEffectPredictor

public SnpEffectPredictor loadSnpEffectPredictor(java.lang.String genome,
                                                 boolean build)

Load predictor and create interval forest

path

public java.lang.String path(java.lang.String fileName)

pathClassName

protected java.lang.String pathClassName()

pathMigrate

public java.lang.String pathMigrate(java.lang.String fileName)

Used to migrate test files in old path

showTranscripts

public java.lang.String showTranscripts(Genome genome)

showTranscripts

public java.lang.String showTranscripts(Genome genome,
                                        boolean hideProtein)

Show a genome in a 'standard' way

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

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

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