Class TestCasesIntegrationBase

    • 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 transcript
      SnpEffectPredictor build​(java.lang.String genome)
      Build a genome
      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)
      Build a genome from a genbank file and compare results to 'expected' results
      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, VariantEffect.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 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

      • SHOW_EVERY

        public static int SHOW_EVERY
      • debug

        public boolean debug
      • verbose

        public boolean verbose
      • ignoreErrors

        protected boolean ignoreErrors
      • shiftHgvs

        protected boolean shiftHgvs
      • testsDir

        public java.lang.String testsDir
    • Constructor Detail

      • TestCasesIntegrationBase

        public TestCasesIntegrationBase()
    • Method Detail

      • appyTranscript

        public Transcript appyTranscript​(java.lang.String genome,
                                         java.lang.String trId,
                                         java.lang.String vcfFileName)
        Apply a variant to a transcript
      • 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)
        Build a genome from a genbank file and compare results to 'expected' results
      • 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,
                                         VariantEffect.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
      • 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