Package org.snpeff.snpEffect.factory

Class SnpEffPredictorFactoryGff

java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
Direct Known Subclasses:
SnpEffPredictorFactoryGff2, SnpEffPredictorFactoryGff3, SnpEffPredictorFactoryGtf22, SnpEffPredictorFactoryRand
public abstract class SnpEffPredictorFactoryGff extends SnpEffPredictorFactory
This class creates a SnpEffectPredictor from a GFF file. This includes derived formats as GTF.

References: http://gmod.org/wiki/GFF3

Author:
pcingola

  • Field Details

  • Constructor Details

    • SnpEffPredictorFactoryGff

      public SnpEffPredictorFactoryGff(Config config)

  • Method Details

    • addExon

      protected Exon addExon(Transcript tr, GffMarker gffMarker, String exonId)
      Create a new exon

    • addExons

      protected List<Exon> addExons(GffMarker gffMarker)
      Create and add a new exon

    • addGene

      protected Gene addGene(GffMarker gffMarker)

    • addGene

      protected Gene addGene(GffMarker gffMarker, boolean findNextGeneId)
      Create and add a gene based on GffMarker

    • addIntergenicConserved

      protected IntergenicConserved addIntergenicConserved(GffMarker gffMarker)
      Add an intergenic conserved region

    • addInterval

      protected boolean addInterval(GffMarker gffMarker)
      Add interval based on GffMarker data
      Returns:
      true if on success

    • addIntronConserved

      protected IntronConserved addIntronConserved(GffMarker gffMarker)
      Add an intron conserved region

    • addUtr3

      protected List<Utr3prime> addUtr3(GffMarker gffMarker)
      Create new UTR3primes

    • addUtr5

      protected List<Utr5prime> addUtr5(GffMarker gffMarker)
      Create UTR5primes

    • create

      public SnpEffectPredictor create()
      Specified by:
      create in class SnpEffPredictorFactory

    • findOrCreateExon

      protected Exon findOrCreateExon(String parentId, GffMarker gffMarker)
      Find an exon for a given parentId

    • findOrCreateGene

      protected Gene findOrCreateGene(GffMarker gffMarker)
      Find or create a gene based on GffMarker

    • findOrCreateTranscript

      protected Transcript findOrCreateTranscript(GffMarker gffMarker)
      Create and add a transcript based on GffMarker

    • parse

      protected boolean parse(String line)
      Parse a line
      Returns:
      true if a line was parsed

    • readExonSequences

      protected void readExonSequences()
      Description copied from class: SnpEffPredictorFactory
      Read exon sequences from a FASTA file
      Overrides:
      readExonSequences in class SnpEffPredictorFactory

    • readExonSequencesGff

      protected void readExonSequencesGff(String gffFileName)
      Read chromosome sequence from GFF3 file and extract exons' sequences

    • readGff

      protected void readGff() throws Exception
      Read GFF file from the beginning looking for 'typeToRead' elements
      Throws:
      Exception