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 Object
Base class: Provides common methods used for testing
  • Field Details

    • BASE_DIR

      public static final String BASE_DIR
      See Also:
    • SHOW_EVERY

      public static int SHOW_EVERY
    • debug

      public boolean debug
    • verbose

      public boolean verbose
    • testsDir

      public String testsDir
    • ignoreErrors

      protected boolean ignoreErrors
    • shiftHgvs

      protected boolean shiftHgvs
    • testType

      protected String testType
    • prefixes

      protected List<String> prefixes
  • Constructor Details

    • TestCasesIntegrationBase

      public TestCasesIntegrationBase()
  • Method Details

    • applyTranscript

      public Transcript applyTranscript(String genome, String trId, String vcfFileName)
      Apply a variant to a transcript
    • before

      @BeforeEach public void before()
    • build

      public SnpEffectPredictor build(String genome)
      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

      public SnpEffectPredictor buildEmbl(String genome, String emblFile)
      Build a genome from a embl file and compare results to 'expected' results
    • buildGeneBank

      public SnpEffectPredictor buildGeneBank(String genome, String genBankFile)
    • buildGeneBank

      public SnpEffectPredictor buildGeneBank(String genome, String genBankFile, boolean circularCorrectlargeGap)
      Build a genome from a genbank file and compare results to 'expected' results
    • buildGetBuildCmd

      public SnpEffCmdBuild buildGetBuildCmd(String genome)
      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

      public void buildGtfAndCompare(String genome, String gtf22, String fastaFile, String resultFile)
      Build a genome from a GTF file and compare results to 'expected' results
    • checkHgvs

      public void checkHgvs(String genome, String vcfFile, int minCheck)
      Check HGVS annotations
    • checkNoChange

      public void checkNoChange(String[] args)
    • checkTranscriptError

      public void checkTranscriptError(String[] args, ErrorWarningType warningType)
      Run a predictor and check if the expected warnings appear
    • compareHgvs

      public void compareHgvs(String genome, String vcfFileName)
    • compareHgvs

      public void compareHgvs(String genome, String vcfFileName, boolean compareProt)
    • compareVep

      public void compareVep(String genome, String vcf, String trId)
      Compare with results from ENSEMBL's VEP on transcript ENST00000268124
    • compareVepSO

      public void compareVepSO(String genome, String vcf, String trId)
      Benchmarking: Compare with results from ENSEMBL's VEP
    • init

      public void init()
    • loadSnpEffectPredictor

      public SnpEffectPredictor loadSnpEffectPredictor(String genome, boolean build)
      Load predictor and create interval forest
    • path

      public String path(String fileName)
    • pathClassName

      protected String pathClassName()
    • pathMigrate

      public String pathMigrate(String fileName)
      Used to migrate test files in old path
    • showTranscripts

      public String showTranscripts(Genome genome)
    • showTranscripts

      public String showTranscripts(Genome genome, boolean hideProtein)
      Show a genome in a 'standard' way
    • snpEffect

      public List<VcfEntry> snpEffect(String genome, String vcfFile, String[] otherArgs)
      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