Package org.snpeff.snpEffect

Class SnpEffectPredictor

  • All Implemented Interfaces:
    java.io.Serializable
    public class SnpEffectPredictor
extends java.lang.Object
implements java.io.Serializable
    Predicts effects of SNPs

    Note: Actually tries to predict any kind of SeqChange, not only SNPs . It is called SnpEffectPredictor for 'historical reasons'.

    Author:
    pcingola
    See Also:
    Serialized Form

    • Field Detail

      • SMALL_VARIANT_SIZE_THRESHOLD

        public static final int SMALL_VARIANT_SIZE_THRESHOLD
        See Also:
        Constant Field Values

    • Constructor Detail

      • SnpEffectPredictor

        public SnpEffectPredictor​(Genome genome)

    • Method Detail

      • add

        public void add​(Gene gene)
        Add a gene interval

      • add

        public void add​(Marker marker)
        Add a marker

        Note: Markers have to be added BEFORE building the interval trees. Interval trees are built the first time you call snpEffect(snp) method.

      • addAll

        public void addAll​(Markers markersToAdd)
        Add a set of markers

      • buildForest

        public void buildForest()
        Create interval trees (forest)

      • countTranscripts

        public int countTranscripts()
        Count number of transcripts

      • createGenomicRegions

        public Markers createGenomicRegions()
        Create (and add) up-down stream, splice sites, intergenic, etc

      • filterTranscriptSupportLevel

        public void filterTranscriptSupportLevel​(TranscriptSupportLevel maxTsl)
        Filter transcripts by TSL

      • getGene

        public Gene getGene​(java.lang.String geneId)
        Obtain a gene by geneId

      • getGenome

        public Genome getGenome()

      • getMarkers

        public Markers getMarkers()

      • getSpliceRegionExonSize

        public int getSpliceRegionExonSize()

      • setSpliceRegionExonSize

        public void setSpliceRegionExonSize​(int spliceRegionExonSize)

      • getSpliceRegionIntronMax

        public int getSpliceRegionIntronMax()

      • setSpliceRegionIntronMax

        public void setSpliceRegionIntronMax​(int spliceRegionIntronMax)

      • getSpliceRegionIntronMin

        public int getSpliceRegionIntronMin()

      • setSpliceRegionIntronMin

        public void setSpliceRegionIntronMin​(int spliceRegionIntronMin)

      • getTranscript

        public Transcript getTranscript​(java.lang.String trId)

      • getUpDownStreamLength

        public int getUpDownStreamLength()

      • setUpDownStreamLength

        public void setUpDownStreamLength​(int upDownStreamLength)

      • keepTranscriptsProteinCoding

        public int keepTranscriptsProteinCoding()
        Remove all transcripts that are NOT in the list
        Returns:
        : Number of transcripts removed

      • print

        public void print()
        Dump to sdtout

      • query

        public Markers query​(Marker marker)
        Return a collection of intervals that intersect 'marker'

      • queryClosestGene

        public Gene queryClosestGene​(Marker inputInterval)
        Find closest gene to this marker

        In case more than one 'closest' gene is found (e.g. two or more genes at the same distance). The following rules apply:

        i) If many genes have the same 'closest distance', coding genes are preferred.

        ii) If more than one coding gene has the same 'closet distance', a random gene is returned.

      • queryDeep

        public Markers queryDeep​(Marker marker)
        Return a collection of intervals that intersect 'marker' Query resulting genes, transcripts and exons to get ALL types of intervals possible

      • regions

        public java.util.Set<java.lang.String> regions​(Marker marker,
                                               boolean showGeneDetails,
                                               boolean compareTemplate)
        Name of the regions hit by a marker
        Returns:
        A set of region names

      • regions

        public java.util.Set<java.lang.String> regions​(Marker marker,
                                               boolean showGeneDetails,
                                               boolean compareTemplate,
                                               java.lang.String id)
        Name of the regions hit by a marker
        Parameters:
        id - : Only use genes or transcripts matching this ID (null for any)

      • removeNonCanonical

        public void removeNonCanonical​(java.lang.String canonFile)
        Remove all non-canonical transcripts If a file is provided, read "Gene => canonical_transcript" mapping from file

      • removeUnverified

        public boolean removeUnverified()
        Remove all unverified transcripts
        Returns:
        true if ALL genes had ALL transcripts removed (i.e. something went wrong, like in cases where no transcript was checked during the building process)

      • retainAllTranscripts

        public int retainAllTranscripts​(java.util.Set<java.lang.String> trIds)
        Remove all transcripts that are NOT in the list
        Returns:
        : Number of transcripts removed

      • save

        public void save​(Config config)
        Save predictor to a binary file (specified by the configuration)

      • save

        public void save​(java.lang.String fileName)
        Save predictor to a binary file

      • setDebug

        public void setDebug​(boolean debug)

      • setSpliceSiteSize

        public void setSpliceSiteSize​(int spliceSiteSize)

      • setUseChromosomes

        public void setUseChromosomes​(boolean useChromosomes)

      • size

        public int size()

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • variantEffect

        public VariantEffects variantEffect​(Variant variant)
        Predict the effect of a variant

      • variantEffect

        protected void variantEffect​(Variant variant,
                             VariantEffects variantEffects,
                             Markers intersects)
        Calculate variant effect for each marker in 'intersect'