Class SnpEffectPredictor

Method Details

• load

  public static SnpEffectPredictor load(Config config)

  Load predictor from a binary file

• 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

• filterTags

  public void filterTags(Set<String> tags, Set<String> tagsNo)

  Filter transcripts by tags

• filterTranscriptSupportLevel

  public void filterTranscriptSupportLevel(TranscriptSupportLevel maxTsl)

  Filter transcripts by TSL

• getGene

  public Gene getGene(String geneId)

  Obtain a gene by geneId

• getGenome

  public Genome getGenome()

• getIntervalForest

  public IntervalForest getIntervalForest()

• 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(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 Set<String> regions(Marker marker, boolean showGeneDetails, boolean compareTemplate)

  Name of the regions hit by a marker

  Returns:

  A set of region names

• regions

  public Set<String> regions(Marker marker, boolean showGeneDetails, boolean compareTemplate, 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(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(Set<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(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 String toString()

  Overrides:

  toString in class 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'