broad.pda.annotation.GTFFileParser Class Reference

Inheritance diagram for broad.pda.annotation.GTFFileParser:

Collaboration diagram for broad.pda.annotation.GTFFileParser:

Public Member Functions
	GTFFileParser ()
	GTFFileParser (String fileName) throws IOException
	GTFFileParser (String fileName, String chr) throws IOException
HashMap< String, ArrayList < String > >	getGTFGeneTranscriptMap ()
void	write (BufferedWriter bw, String source) throws IOException
void	GTFWrite (BufferedWriter bw, String Src, boolean UseExtraFields) throws Exception
HashMap< String, Locus >	getGeneIDIsoMap ()
Public Member Functions inherited from broad.pda.annotation.BEDFileParser
	BEDFileParser ()
	BEDFileParser (String fileName) throws IOException
	BEDFileParser (String fileName, int ThreePrimeTrimSize) throws IOException
	BEDFileParser (String fileName, String chr) throws IOException
	BEDFileParser (Collection< Gene > genes)
	BEDFileParser (Map< String, Collection< Gene >> transcripts)
GeneWithIsoforms	get (String geneName)
List< Gene >	GetGenes ()
List< GeneWithIsoforms >	GetGenesWithIsoforms ()
IntervalTree< GeneWithIsoforms >	getChrTree (String chr)
Map< String, IntervalTree < GeneWithIsoforms > >	getIntervalTreeWithIsoforoms ()
Iterator< String >	getChromosomeIterator ()
IntervalTree< GeneWithIsoforms >	getOverlappers (Gene gene)
IntervalTree< GeneWithIsoforms >	getOverlappers (LightweightGenomicAnnotation region)
Iterator< GeneWithIsoforms >	getGenomicRegionOverlappers (LightweightGenomicAnnotation region)
BEDFileParser	getMergedCopy ()
Map< String, IntervalTree < GeneWithIsoforms > >	getMergedAnnotationMap (double minPctOverlapToMerge)
Map< String, IntervalTree < GeneWithIsoforms > >	getMergedAnnotationMap (boolean mergall)
Map< String, IntervalTree < GeneWithIsoforms > >	getAnnotationSetMap ()
int	getNumberOfIsoforms (String chr)
int	getNumberOfIsoforms ()
Gene	getExactIsoform (GeneWithIsoforms loci)
HashMap< String, Gene >	getNameGeneMap ()
BEDReader	get3PRegion (int toIn, int toOut)
BEDReader	getPromoters ()
BEDReader	getPromoters (int toIn, int toOut)
void	loadGTF (File file, String chr) throws IOException
void	addRefSeq (Gene gene)
void	addRefSeq (GeneWithIsoforms gene)
void	addRefSeqSet (Collection<?extends Gene > collection)
void	writeFullBed (String save) throws IOException
void	writeFullBed (String save, boolean useExtraFields) throws IOException
void	writeFullBed (BufferedWriter bw) throws IOException
void	writeFullBed (BufferedWriter bw, boolean useExtraFields) throws IOException
void	makeGenes ()
void	makeGenes (double minPctOverlapToMerge)
boolean	isEmpty ()
boolean	contains (String geneName)
boolean	containChr (String chr)
void	clear ()
void	merge ()
void	collapseSingleExonTranscripts ()
void	IncrementScoreIfOverlap (BEDFileParser bed, int setNumber, Boolean setToZero)
void	updateScrToBedScore (double score)
void	filterByOverlap (Collection< Gene > genes)
void	intersect (BEDFileParser bed)
void	bed2gtf (BufferedWriter bw, String src) throws Exception
void	bed2CuffGtf (BufferedWriter bw, String src, boolean useExtraFileds) throws Exception
void	bed2gtf_bundleOverlappers (BufferedWriter bw, String src, BEDFileParser mergedData) throws IOException
void	dedup ()
void	minus (Collection< Gene > genes, boolean recursive)
GeneWithIsoforms	remove (GeneWithIsoforms record)
Map< String, Collection< Gene > >	toMap ()
Map< String, Collection< Gene > >	toConstituentIsoformMap ()
Map< String, Collection< Gene > >	toConstituentIsoformMap (boolean removeGenesWithoutConstituentIsoforms)
Map< String, Collection< Gene > >	toConstituentIntroformMap ()
BEDFileParser	copy ()
BEDFileParser	overlap_GenomicLevel (BEDFileParser other, String task, String considerOrientaion)
BEDFileParser	overlapByGenomicRegion (BEDFileParser other, String considerOrientaion)
BEDFileParser	mergeByGtfGeneId ()
BEDFileParser	equalizeTranscriptEnds (BEDFileParser other)
BEDFileParser	differenceByGenomicRegion (BEDFileParser other, String considerOrientaion)
BEDFileParser	removeSmallTranscripts (int minExnNum, int minTranscriptLength)
BEDFileParser	removeSingeleExon ()
GeneWithIsoforms	getClosestUpstream (Gene annot)
GeneWithIsoforms	getClosestDownstream (Gene annot)
GeneWithIsoforms	getClosestUpstream (LightweightGenomicAnnotation annot)
GeneWithIsoforms	getClosestDownstream (LightweightGenomicAnnotation annot)

Protected Member Functions
void	loadIsoformDataByChrToTree (File file, String chr) throws IOException
void	loadIsoformDataByChrToTree (File file) throws IOException
Protected Member Functions inherited from broad.pda.annotation.BEDFileParser
void	loadIsoformDataByChrToTree (File file) throws IOException
void	loadIsoformDataByChrToTree (File file, String chr) throws IOException

Additional Inherited Members
Static Public Member Functions inherited from broad.pda.annotation.BEDFileParser
static Gene	getGeneByName (String geneName, String bedFile) throws IOException
static double	getNumberOfIsoforms (IntervalTree< GeneWithIsoforms > overlapTree)
static Set< Gene >	loadData (File file) throws IOException
static Set< Gene >	loadData (File file, Alignments region) throws IOException
static Map< String, Gene >	loadDataByName (File file) throws IOException
static Map< String, Collection < Gene > >	loadDataByChr (String file) throws IOException
static Map< String, Collection < Gene > >	loadDataByChr (File file) throws IOException
static Map< String, IntervalTree< Gene > >	loadDataByChrToTree (File file) throws IOException
static Map< String, Integer >	loadChrSizes (String file)
static List< String >	loadList (String file) throws IOException
static List< String >	loadList (String file, boolean skipFirstLine) throws IOException
static Map< Alignments, String >	loadDataLine (File file) throws IOException
static Set< Annotation >	loadAlignmentData (File file) throws IOException
static Set< Annotation >	loadAlignmentData (BufferedReader reader) throws IOException
static Set< Annotation >	loadAlignmentData (File file, boolean ucscDownload) throws IOException
static Map< String, Collection < Annotation > >	loadAlignmentDataByChr (File file) throws IOException
static Map< String, IntervalTree< Alignments > >	loadAlignmentDataToTree (File file) throws IOException
static Map< String, List < Alignments > >	loadAlignmentDataByChrArrayList (File file) throws IOException
static Map< String, Set < Alignments > >	loadAlignmentDataByChr3Prime (File file, int extensionFactor) throws IOException
static Map< String, Set < Alignments > >	loadAlignmentDataByChr5Prime (File file, int extensionFactor) throws IOException
static Map< Alignments, String >	loadDataLine (BufferedReader reader) throws IOException
static void	writeBED (String save, Collection< Annotation > regions) throws IOException
static void	writeBED (String save, Map< Annotation, double[]> scores) throws IOException
static void	writeSortedBED (String save, Map< Annotation, double[]> scores) throws IOException
static void	writeSortedBED (String save, Collection< Annotation > alignments) throws IOException
static void	writeSortedBEDWithScores (String save, Map< Annotation, double[]> scores) throws IOException
static void	writeBEDWithScores (String save, Map< Annotation, double[]> scores) throws IOException
static void	writeBED (String save, Collection< Annotation > alignments, boolean sort) throws IOException
static void	writeBED (String save, Map< Annotation, double[]> scores, boolean withScores, boolean sort) throws IOException
static void	writeFullBED (String save, Collection< Gene > genes) throws IOException
static void	writeFullBED (String save, Map< Gene,?extends Object > genes) throws IOException
static Map< String, IntervalTree< Gene > >	makeIntervalTreeFor3Prime (File geneFile, int size) throws IOException
static boolean	isOverlapCompatible (Gene first, Gene second, double minPctOverlap)
static void	main (String[] args) throws IOException
static Map< String, BEDFileParser >	uploadSetOfFiles (String bedLst) throws IOException
static BEDFileParser	expanedUtrs (BEDFileParser bed, Integer utr1, Integer utr2)
static BEDFileParser	readSiphyOutToBed (String siphyFile) throws NumberFormatException, IOException
static Gene	getGene (String geneFile, String geneName) throws IOException

Constructor & Destructor Documentation

broad.pda.annotation.GTFFileParser.GTFFileParser

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broad.pda.annotation.GTFFileParser.GTFFileParser

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String

fileName

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throws IOException

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broad.pda.annotation.GTFFileParser.GTFFileParser	(	String	fileName,
		String	chr
	)		throws IOException

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Member Function Documentation

HashMap<String,Locus> broad.pda.annotation.GTFFileParser.getGeneIDIsoMap

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HashMap<String, ArrayList<String> > broad.pda.annotation.GTFFileParser.getGTFGeneTranscriptMap

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void broad.pda.annotation.GTFFileParser.GTFWrite	(	BufferedWriter	bw,
		String	Src,
		boolean	UseExtraFields
	)		throws Exception

Write a GTF using only the attributes in extraFields (not modifying the gene_id, transcript_id as GTF2BED does)

Parameters

bw	BufferedWriter
Src	string to annotate src field
UseExtraFields	- if false call gtf2bed ; if true assumes has gene id and transcript id as maybe others

Exceptions

Exception

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void broad.pda.annotation.GTFFileParser.loadIsoformDataByChrToTree ( File  file, String  chr  ) throws IOException

protected

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void broad.pda.annotation.GTFFileParser.loadIsoformDataByChrToTree ( File  file ) throws IOException

protected

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void broad.pda.annotation.GTFFileParser.write	(	BufferedWriter	bw,
		String	source
	)		throws IOException

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The documentation for this class was generated from the following file:

• java/broad/pda/annotation/GTFFileParser.java