Class SnpEffPredictorFactory

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      protected void add​(Cds cds)  
      protected void add​(Chromosome chromo)  
      protected void add​(Exon exon)  
      protected void add​(Gene gene)
      Add a Gene
      protected void add​(Marker marker)
      Add a generic Marker
      protected void add​(Transcript tr)
      Add a transcript
      protected void addMarker​(Marker marker, boolean unique)
      Add a marker to the collection
      protected void addSequences​(java.lang.String chr, java.lang.String chrSeq)
      Add genomic reference sequences
      protected void adjustChromosomes()
      Adjust chromosome length using gene information This is used when the sequence is not available (which makes sense on test-cases and debugging only)
      protected void adjustTranscripts()
      Adjust transcripts: recalculate start, end, strand, etc.
      protected void beforeExonSequences()
      Perform some actions before reading sequences
      protected void codingFromCds()
      Only coding transcripts have CDS: Make sure that transcripts having CDS are protein coding It might not be always "precise" though: $ grep CDS genes.gtf | cut -f 2 | ~/snpEff/scripts/uniqCount.pl 113 IG_C_gene 64 IG_D_gene 24 IG_J_gene 366 IG_V_gene 21 TR_C_gene 3 TR_D_gene 82 TR_J_gene 296 TR_V_gene 461 non_stop_decay 63322 nonsense_mediated_decay 905 polymorphic_pseudogene 34 processed_transcript 1340112 protein_coding
      protected void collapseZeroLenIntrons()
      Collapse exons having zero size introns between them
      abstract SnpEffectPredictor create()  
      protected void createRandSequences()
      Create random sequences for exons Note: This is only used for test cases!
      protected void deleteRedundant()
      Consolidate transcripts: If two exons are one right next to the other, join them E.g.
      protected void exonsFromCds()
      Create exons from CDS info
      protected void exonsFromCds​(Transcript tr)
      Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process
      protected Gene findGene​(java.lang.String id)  
      protected Gene findGene​(java.lang.String geneId, java.lang.String id)  
      protected Marker findMarker​(java.lang.String id)  
      protected Transcript findTranscript​(java.lang.String id)  
      protected Transcript findTranscript​(java.lang.String trId, java.lang.String id)  
      protected Chromosome getOrCreateChromosome​(java.lang.String chromoName)
      Get a chromosome.
      java.util.Map<java.lang.String,​java.lang.String> getProteinByTrId()  
      protected int parsePosition​(java.lang.String posStr)
      Parse a string as a 'position'.
      protected void readExonSequences()
      Read exon sequences from a FASTA file
      protected void replaceTranscript​(Transcript trOld, Transcript trNew)  
      void setCreateRandSequences​(boolean createRandSequences)  
      void setDebug​(boolean debug)  
      void setFastaFile​(java.lang.String fastaFile)  
      void setFileName​(java.lang.String fileName)  
      void setRandom​(java.util.Random random)  
      void setReadSequences​(boolean readSequences)
      Read sequences? Note: This is only used for debugging and testing
      void setStoreSequences​(boolean storeSequences)  
      void setVerbose​(boolean verbose)  
      protected java.lang.String showChromoNamesDifferences()
      Shw differences in chromosome names
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • MIN_TOTAL_FRAME_COUNT

        public static int MIN_TOTAL_FRAME_COUNT
    • Constructor Detail

      • SnpEffPredictorFactory

        public SnpEffPredictorFactory​(Config config,
                                      int inOffset)
    • Method Detail

      • add

        protected void add​(Cds cds)
      • add

        protected void add​(Exon exon)
      • add

        protected void add​(Gene gene)
        Add a Gene
      • add

        protected void add​(Marker marker)
        Add a generic Marker
      • add

        protected void add​(Transcript tr)
        Add a transcript
      • addMarker

        protected void addMarker​(Marker marker,
                                 boolean unique)
        Add a marker to the collection
      • addSequences

        protected void addSequences​(java.lang.String chr,
                                    java.lang.String chrSeq)
        Add genomic reference sequences
      • adjustChromosomes

        protected void adjustChromosomes()
        Adjust chromosome length using gene information This is used when the sequence is not available (which makes sense on test-cases and debugging only)
      • adjustTranscripts

        protected void adjustTranscripts()
        Adjust transcripts: recalculate start, end, strand, etc.
      • beforeExonSequences

        protected void beforeExonSequences()
        Perform some actions before reading sequences
      • codingFromCds

        protected void codingFromCds()
        Only coding transcripts have CDS: Make sure that transcripts having CDS are protein coding It might not be always "precise" though: $ grep CDS genes.gtf | cut -f 2 | ~/snpEff/scripts/uniqCount.pl 113 IG_C_gene 64 IG_D_gene 24 IG_J_gene 366 IG_V_gene 21 TR_C_gene 3 TR_D_gene 82 TR_J_gene 296 TR_V_gene 461 non_stop_decay 63322 nonsense_mediated_decay 905 polymorphic_pseudogene 34 processed_transcript 1340112 protein_coding
      • collapseZeroLenIntrons

        protected void collapseZeroLenIntrons()
        Collapse exons having zero size introns between them
      • createRandSequences

        protected void createRandSequences()
        Create random sequences for exons Note: This is only used for test cases!
      • deleteRedundant

        protected void deleteRedundant()
        Consolidate transcripts: If two exons are one right next to the other, join them E.g. exon1:1234-2345, exon2:2346-2400 => exon:1234-2400 This happens mostly in GTF files, where the stop-codon is specified separated from the exon info.
      • exonsFromCds

        protected void exonsFromCds()
        Create exons from CDS info
      • exonsFromCds

        protected void exonsFromCds​(Transcript tr)
        Create exons from CDS info WARNING: We might end up with redundant exons if some exons existed before this process
        Parameters:
        tr - : Transcript with CDS info, but no exons
      • findGene

        protected Gene findGene​(java.lang.String id)
      • findGene

        protected Gene findGene​(java.lang.String geneId,
                                java.lang.String id)
      • findMarker

        protected Marker findMarker​(java.lang.String id)
      • findTranscript

        protected Transcript findTranscript​(java.lang.String id)
      • findTranscript

        protected Transcript findTranscript​(java.lang.String trId,
                                            java.lang.String id)
      • getOrCreateChromosome

        protected Chromosome getOrCreateChromosome​(java.lang.String chromoName)
        Get a chromosome. If it doesn't exist, create it
      • getProteinByTrId

        public java.util.Map<java.lang.String,​java.lang.String> getProteinByTrId()
      • parsePosition

        protected int parsePosition​(java.lang.String posStr)
        Parse a string as a 'position'. Note: It subtracts 'inOffset' so that all coordinates are zero-based
      • readExonSequences

        protected void readExonSequences()
        Read exon sequences from a FASTA file
      • setCreateRandSequences

        public void setCreateRandSequences​(boolean createRandSequences)
      • setDebug

        public void setDebug​(boolean debug)
      • setFastaFile

        public void setFastaFile​(java.lang.String fastaFile)
      • setFileName

        public void setFileName​(java.lang.String fileName)
      • setRandom

        public void setRandom​(java.util.Random random)
      • setReadSequences

        public void setReadSequences​(boolean readSequences)
        Read sequences? Note: This is only used for debugging and testing
      • setStoreSequences

        public void setStoreSequences​(boolean storeSequences)
      • setVerbose

        public void setVerbose​(boolean verbose)
      • showChromoNamesDifferences

        protected java.lang.String showChromoNamesDifferences()
        Shw differences in chromosome names