Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGff
- java.lang.Object
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
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- 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
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
FASTA_DELIMITER
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors Constructor Description SnpEffPredictorFactoryGff(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected Exon
addExon(Transcript tr, GffMarker gffMarker, java.lang.String exonId)
Create a new exonprotected java.util.List<Exon>
addExons(GffMarker gffMarker)
Create and add a new exonprotected Gene
addGene(GffMarker gffMarker)
protected Gene
addGene(GffMarker gffMarker, boolean findNextGeneId)
Create and add a gene based on GffMarkerprotected IntergenicConserved
addIntergenicConserved(GffMarker gffMarker)
Add an intergenic conserved regionprotected boolean
addInterval(GffMarker gffMarker)
Add interval based on GffMarker dataprotected IntronConserved
addIntronConserved(GffMarker gffMarker)
Add an intron conserved regionprotected java.util.List<Utr3prime>
addUtr3(GffMarker gffMarker)
Create new UTR3primesprotected java.util.List<Utr5prime>
addUtr5(GffMarker gffMarker)
Create UTR5primesSnpEffectPredictor
create()
protected Exon
findOrCreateExon(java.lang.String parentId, GffMarker gffMarker)
Find an exon for a given parentIdprotected Gene
findOrCreateGene(GffMarker gffMarker)
Find or create a gene based on GffMarkerprotected Transcript
findOrCreateTranscript(GffMarker gffMarker)
Create and add a transcript based on GffMarkerprotected boolean
parse(java.lang.String line)
Parse a lineprotected void
readExonSequences()
Read exon sequences from a FASTA fileprotected void
readExonSequencesGff(java.lang.String gffFileName)
Read chromosome sequence from GFF3 file and extract exons' sequencesprotected void
readGff()
Read GFF file from the beginning looking for 'typeToRead' elements-
Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
add, add, add, add, add, add, addMarker, addSequences, adjustChromosomes, adjustTranscripts, beforeExonSequences, codingFromCds, collapseZeroLenIntrons, createRandSequences, deleteRedundant, exonsFromCds, exonsFromCds, findGene, findGene, findMarker, findTranscript, findTranscript, getOrCreateChromosome, getProteinByTrId, parsePosition, replaceTranscript, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Field Detail
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FASTA_DELIMITER
public static final java.lang.String FASTA_DELIMITER
- See Also:
- Constant Field Values
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Constructor Detail
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SnpEffPredictorFactoryGff
public SnpEffPredictorFactoryGff(Config config)
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Method Detail
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addExon
protected Exon addExon(Transcript tr, GffMarker gffMarker, java.lang.String exonId)
Create a new exon
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addGene
protected Gene addGene(GffMarker gffMarker, boolean findNextGeneId)
Create and add a gene based on GffMarker
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addIntergenicConserved
protected IntergenicConserved addIntergenicConserved(GffMarker gffMarker)
Add an intergenic conserved region
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addInterval
protected boolean addInterval(GffMarker gffMarker)
Add interval based on GffMarker data- Returns:
- true if on success
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addIntronConserved
protected IntronConserved addIntronConserved(GffMarker gffMarker)
Add an intron conserved region
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create
public SnpEffectPredictor create()
- Specified by:
create
in classSnpEffPredictorFactory
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findOrCreateExon
protected Exon findOrCreateExon(java.lang.String parentId, GffMarker gffMarker)
Find an exon for a given parentId
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findOrCreateGene
protected Gene findOrCreateGene(GffMarker gffMarker)
Find or create a gene based on GffMarker
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findOrCreateTranscript
protected Transcript findOrCreateTranscript(GffMarker gffMarker)
Create and add a transcript based on GffMarker
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parse
protected boolean parse(java.lang.String line)
Parse a line- Returns:
- true if a line was parsed
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readExonSequences
protected void readExonSequences()
Description copied from class:SnpEffPredictorFactory
Read exon sequences from a FASTA file- Overrides:
readExonSequences
in classSnpEffPredictorFactory
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readExonSequencesGff
protected void readExonSequencesGff(java.lang.String gffFileName)
Read chromosome sequence from GFF3 file and extract exons' sequences
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readGff
protected void readGff() throws java.lang.Exception
Read GFF file from the beginning looking for 'typeToRead' elements- Throws:
java.lang.Exception
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