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
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
FieldsFields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected Exon
addExon
(Transcript tr, GffMarker gffMarker, String exonId) Create a new exonCreate and add a new exonprotected Gene
protected Gene
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 regionCreate new UTR3primesCreate UTR5primescreate()
protected Exon
findOrCreateExon
(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 a lineprotected void
Read exon sequences from a FASTA fileprotected void
readExonSequencesGff
(String gffFileName) Read chromosome sequence from GFF3 file and extract exons' sequencesprotected void
readGff()
Read GFF file from the beginning looking for 'typeToRead' elementsMethods 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 Details
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FASTA_DELIMITER
- See Also:
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Constructor Details
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SnpEffPredictorFactoryGff
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Method Details
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addExon
Create a new exon -
addExons
Create and add a new exon -
addGene
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addGene
Create and add a gene based on GffMarker -
addIntergenicConserved
Add an intergenic conserved region -
addInterval
Add interval based on GffMarker data- Returns:
- true if on success
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addIntronConserved
Add an intron conserved region -
addUtr3
Create new UTR3primes -
addUtr5
Create UTR5primes -
create
- Specified by:
create
in classSnpEffPredictorFactory
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findOrCreateExon
Find an exon for a given parentId -
findOrCreateGene
Find or create a gene based on GffMarker -
findOrCreateTranscript
Create and add a transcript based on GffMarker -
parse
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
Read chromosome sequence from GFF3 file and extract exons' sequences -
readGff
Read GFF file from the beginning looking for 'typeToRead' elements- Throws:
Exception
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