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 Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	FASTA_DELIMITER

Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory

MARK, MIN_TOTAL_FRAME_COUNT

Constructor Summary

Constructors

Constructor	Description
SnpEffPredictorFactoryGff(Config config)

Method Summary

Modifier and Type	Method	Description
protected Exon	addExon(Transcript tr, GffMarker gffMarker, java.lang.String exonId)	Create a new exon
protected java.util.List<Exon>	addExons(GffMarker gffMarker)	Create and add a new exon
protected Gene	addGene(GffMarker gffMarker)
protected Gene	addGene(GffMarker gffMarker, boolean findNextGeneId)	Create and add a gene based on GffMarker
protected IntergenicConserved	addIntergenicConserved(GffMarker gffMarker)	Add an intergenic conserved region
protected boolean	addInterval(GffMarker gffMarker)	Add interval based on GffMarker data
protected IntronConserved	addIntronConserved(GffMarker gffMarker)	Add an intron conserved region
protected java.util.List<Utr3prime>	addUtr3(GffMarker gffMarker)	Create new UTR3primes
protected java.util.List<Utr5prime>	addUtr5(GffMarker gffMarker)	Create UTR5primes
SnpEffectPredictor	create()
protected Exon	findOrCreateExon(java.lang.String parentId, GffMarker gffMarker)	Find an exon for a given parentId
protected Gene	findOrCreateGene(GffMarker gffMarker)	Find or create a gene based on GffMarker
protected Transcript	findOrCreateTranscript(GffMarker gffMarker)	Create and add a transcript based on GffMarker
protected boolean	parse(java.lang.String line)	Parse a line
protected void	readExonSequences()	Read exon sequences from a FASTA file
protected void	readExonSequencesGff(java.lang.String gffFileName)	Read chromosome sequence from GFF3 file and extract exons' sequences
protected 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FASTA_DELIMITER

public static final java.lang.String FASTA_DELIMITER

See Also:

Constant Field Values

Constructor Detail

SnpEffPredictorFactoryGff

public SnpEffPredictorFactoryGff(Config config)

Method Detail

addExon

protected Exon addExon(Transcript tr,
                       GffMarker gffMarker,
                       java.lang.String exonId)

Create a new exon

addExons

protected java.util.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 java.util.List<Utr3prime> addUtr3(GffMarker gffMarker)

Create new UTR3primes

addUtr5

protected java.util.List<Utr5prime> addUtr5(GffMarker gffMarker)

Create UTR5primes

create

public SnpEffectPredictor create()

Specified by:

create in class SnpEffPredictorFactory

findOrCreateExon

protected Exon findOrCreateExon(java.lang.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(java.lang.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(java.lang.String gffFileName)

Read chromosome sequence from GFF3 file and extract exons' sequences

readGff

protected void readGff()
                throws java.lang.Exception

Read GFF file from the beginning looking for 'typeToRead' elements

Throws:

java.lang.Exception