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broad.pda.annotation.BEDFileParser Class Reference
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Public Member Functions

 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)
 

Static Public Member Functions

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
 

Protected Member Functions

void loadIsoformDataByChrToTree (File file) throws IOException
 
void loadIsoformDataByChrToTree (File file, String chr) throws IOException
 

Constructor & Destructor Documentation

broad.pda.annotation.BEDFileParser.BEDFileParser ( )

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broad.pda.annotation.BEDFileParser.BEDFileParser ( String  fileName) throws IOException

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broad.pda.annotation.BEDFileParser.BEDFileParser ( String  fileName,
int  ThreePrimeTrimSize 
) throws IOException
broad.pda.annotation.BEDFileParser.BEDFileParser ( String  fileName,
String  chr 
) throws IOException

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broad.pda.annotation.BEDFileParser.BEDFileParser ( Collection< Gene >  genes)

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broad.pda.annotation.BEDFileParser.BEDFileParser ( Map< String, Collection< Gene >>  transcripts)

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Member Function Documentation

void broad.pda.annotation.BEDFileParser.addRefSeq ( Gene  gene)

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void broad.pda.annotation.BEDFileParser.addRefSeq ( GeneWithIsoforms  gene)

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void broad.pda.annotation.BEDFileParser.addRefSeqSet ( Collection<?extends Gene >  collection)

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void broad.pda.annotation.BEDFileParser.bed2CuffGtf ( BufferedWriter  bw,
String  src,
boolean  useExtraFileds 
) throws Exception

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void broad.pda.annotation.BEDFileParser.bed2gtf ( BufferedWriter  bw,
String  src 
) throws Exception

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void broad.pda.annotation.BEDFileParser.bed2gtf_bundleOverlappers ( BufferedWriter  bw,
String  src,
BEDFileParser  mergedData 
) throws IOException

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void broad.pda.annotation.BEDFileParser.clear ( )
void broad.pda.annotation.BEDFileParser.collapseSingleExonTranscripts ( )

Merges all single exon transcripts

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boolean broad.pda.annotation.BEDFileParser.containChr ( String  chr)

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boolean broad.pda.annotation.BEDFileParser.contains ( String  geneName)
BEDFileParser broad.pda.annotation.BEDFileParser.copy ( )

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void broad.pda.annotation.BEDFileParser.dedup ( )
BEDFileParser broad.pda.annotation.BEDFileParser.differenceByGenomicRegion ( BEDFileParser  other,
String  considerOrientaion 
)
BEDFileParser broad.pda.annotation.BEDFileParser.equalizeTranscriptEnds ( BEDFileParser  other)
static BEDFileParser broad.pda.annotation.BEDFileParser.expanedUtrs ( BEDFileParser  bed,
Integer  utr1,
Integer  utr2 
)
static

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void broad.pda.annotation.BEDFileParser.filterByOverlap ( Collection< Gene >  genes)
GeneWithIsoforms broad.pda.annotation.BEDFileParser.get ( String  geneName)

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BEDReader broad.pda.annotation.BEDFileParser.get3PRegion ( int  toIn,
int  toOut 
)

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Map<String, IntervalTree<GeneWithIsoforms> > broad.pda.annotation.BEDFileParser.getAnnotationSetMap ( )
Iterator<String> broad.pda.annotation.BEDFileParser.getChromosomeIterator ( )

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IntervalTree<GeneWithIsoforms> broad.pda.annotation.BEDFileParser.getChrTree ( String  chr)

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GeneWithIsoforms broad.pda.annotation.BEDFileParser.getClosestDownstream ( Gene  annot)

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GeneWithIsoforms broad.pda.annotation.BEDFileParser.getClosestDownstream ( LightweightGenomicAnnotation  annot)

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GeneWithIsoforms broad.pda.annotation.BEDFileParser.getClosestUpstream ( Gene  annot)

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GeneWithIsoforms broad.pda.annotation.BEDFileParser.getClosestUpstream ( LightweightGenomicAnnotation  annot)

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Gene broad.pda.annotation.BEDFileParser.getExactIsoform ( GeneWithIsoforms  loci)
static Gene broad.pda.annotation.BEDFileParser.getGene ( String  geneFile,
String  geneName 
) throws IOException
static
static Gene broad.pda.annotation.BEDFileParser.getGeneByName ( String  geneName,
String  bedFile 
) throws IOException
static

Get gene from bed file by gene name

Parameters
geneNameGene name
bedFileBed file
Returns
Gene model described by the first line in the bed file with name field equal to gene name
Exceptions
IOException

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List<Gene> broad.pda.annotation.BEDFileParser.GetGenes ( )

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List<GeneWithIsoforms> broad.pda.annotation.BEDFileParser.GetGenesWithIsoforms ( )
Iterator<GeneWithIsoforms> broad.pda.annotation.BEDFileParser.getGenomicRegionOverlappers ( LightweightGenomicAnnotation  region)

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Map<String, IntervalTree<GeneWithIsoforms> > broad.pda.annotation.BEDFileParser.getIntervalTreeWithIsoforoms ( )
Map<String, IntervalTree<GeneWithIsoforms> > broad.pda.annotation.BEDFileParser.getMergedAnnotationMap ( double  minPctOverlapToMerge)

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Map<String, IntervalTree<GeneWithIsoforms> > broad.pda.annotation.BEDFileParser.getMergedAnnotationMap ( boolean  mergall)

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BEDFileParser broad.pda.annotation.BEDFileParser.getMergedCopy ( )

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HashMap<String, Gene> broad.pda.annotation.BEDFileParser.getNameGeneMap ( )

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int broad.pda.annotation.BEDFileParser.getNumberOfIsoforms ( String  chr)
int broad.pda.annotation.BEDFileParser.getNumberOfIsoforms ( )
Returns
Number of transcripts in the reader

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static double broad.pda.annotation.BEDFileParser.getNumberOfIsoforms ( IntervalTree< GeneWithIsoforms >  overlapTree)
static
IntervalTree<GeneWithIsoforms> broad.pda.annotation.BEDFileParser.getOverlappers ( Gene  gene)

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IntervalTree<GeneWithIsoforms> broad.pda.annotation.BEDFileParser.getOverlappers ( LightweightGenomicAnnotation  region)

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BEDReader broad.pda.annotation.BEDFileParser.getPromoters ( )
BEDReader broad.pda.annotation.BEDFileParser.getPromoters ( int  toIn,
int  toOut 
)

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void broad.pda.annotation.BEDFileParser.IncrementScoreIfOverlap ( BEDFileParser  bed,
int  setNumber,
Boolean  setToZero 
)

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void broad.pda.annotation.BEDFileParser.intersect ( BEDFileParser  bed)
boolean broad.pda.annotation.BEDFileParser.isEmpty ( )
static boolean broad.pda.annotation.BEDFileParser.isOverlapCompatible ( Gene  first,
Gene  second,
double  minPctOverlap 
)
static

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static Set<Annotation> broad.pda.annotation.BEDFileParser.loadAlignmentData ( File  file) throws IOException
static

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static Set<Annotation> broad.pda.annotation.BEDFileParser.loadAlignmentData ( BufferedReader  reader) throws IOException
static
static Set<Annotation> broad.pda.annotation.BEDFileParser.loadAlignmentData ( File  file,
boolean  ucscDownload 
) throws IOException
static

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static Map<String, Collection<Annotation> > broad.pda.annotation.BEDFileParser.loadAlignmentDataByChr ( File  file) throws IOException
static
static Map<String, Set<Alignments> > broad.pda.annotation.BEDFileParser.loadAlignmentDataByChr3Prime ( File  file,
int  extensionFactor 
) throws IOException
static
static Map<String, Set<Alignments> > broad.pda.annotation.BEDFileParser.loadAlignmentDataByChr5Prime ( File  file,
int  extensionFactor 
) throws IOException
static
static Map<String, List<Alignments> > broad.pda.annotation.BEDFileParser.loadAlignmentDataByChrArrayList ( File  file) throws IOException
static
static Map<String, IntervalTree<Alignments> > broad.pda.annotation.BEDFileParser.loadAlignmentDataToTree ( File  file) throws IOException
static
static Map<String, Integer> broad.pda.annotation.BEDFileParser.loadChrSizes ( String  file)
static

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static Set<Gene> broad.pda.annotation.BEDFileParser.loadData ( File  file) throws IOException
static

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static Set<Gene> broad.pda.annotation.BEDFileParser.loadData ( File  file,
Alignments  region 
) throws IOException
static

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static Map<String, Collection<Gene> > broad.pda.annotation.BEDFileParser.loadDataByChr ( String  file) throws IOException
static

Read genes from the bed file and get genes by chromosome

Parameters
fileName of bed file
Returns
Map of chromosome name to set of genes on chromosome
Exceptions
IOException

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static Map<String, Collection<Gene> > broad.pda.annotation.BEDFileParser.loadDataByChr ( File  file) throws IOException
static

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static Map<String, IntervalTree<Gene> > broad.pda.annotation.BEDFileParser.loadDataByChrToTree ( File  file) throws IOException
static

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static Map<String, Gene> broad.pda.annotation.BEDFileParser.loadDataByName ( File  file) throws IOException
static
static Map<Alignments, String> broad.pda.annotation.BEDFileParser.loadDataLine ( File  file) throws IOException
static
static Map<Alignments, String> broad.pda.annotation.BEDFileParser.loadDataLine ( BufferedReader  reader) throws IOException
static
void broad.pda.annotation.BEDFileParser.loadGTF ( File  file,
String  chr 
) throws IOException
void broad.pda.annotation.BEDFileParser.loadIsoformDataByChrToTree ( File  file) throws IOException
protected

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void broad.pda.annotation.BEDFileParser.loadIsoformDataByChrToTree ( File  file,
String  chr 
) throws IOException
protected
static List<String> broad.pda.annotation.BEDFileParser.loadList ( String  file) throws IOException
static
static List<String> broad.pda.annotation.BEDFileParser.loadList ( String  file,
boolean  skipFirstLine 
) throws IOException
static
static void broad.pda.annotation.BEDFileParser.main ( String[]  args) throws IOException
static

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void broad.pda.annotation.BEDFileParser.makeGenes ( )
void broad.pda.annotation.BEDFileParser.makeGenes ( double  minPctOverlapToMerge)

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static Map<String, IntervalTree<Gene> > broad.pda.annotation.BEDFileParser.makeIntervalTreeFor3Prime ( File  geneFile,
int  size 
) throws IOException
static

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void broad.pda.annotation.BEDFileParser.merge ( )

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BEDFileParser broad.pda.annotation.BEDFileParser.mergeByGtfGeneId ( )

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void broad.pda.annotation.BEDFileParser.minus ( Collection< Gene >  genes,
boolean  recursive 
)

Removes from this reader all elements that overlap the given list.

Parameters
recursive- if true not only transcripts overlapping the given set but also transcripts that overlap the overlappers will be removed

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BEDFileParser broad.pda.annotation.BEDFileParser.overlap_GenomicLevel ( BEDFileParser  other,
String  task,
String  considerOrientaion 
)

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BEDFileParser broad.pda.annotation.BEDFileParser.overlapByGenomicRegion ( BEDFileParser  other,
String  considerOrientaion 
)
static BEDFileParser broad.pda.annotation.BEDFileParser.readSiphyOutToBed ( String  siphyFile) throws NumberFormatException, IOException
static

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GeneWithIsoforms broad.pda.annotation.BEDFileParser.remove ( GeneWithIsoforms  record)

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BEDFileParser broad.pda.annotation.BEDFileParser.removeSingeleExon ( )

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BEDFileParser broad.pda.annotation.BEDFileParser.removeSmallTranscripts ( int  minExnNum,
int  minTranscriptLength 
)

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Map<String, Collection<Gene> > broad.pda.annotation.BEDFileParser.toConstituentIntroformMap ( )

Builds an artificial map of isoforms where "constituent" introns are the exons.

Returns
Map<String, Collection<Gene> > broad.pda.annotation.BEDFileParser.toConstituentIsoformMap ( )
Map<String, Collection<Gene> > broad.pda.annotation.BEDFileParser.toConstituentIsoformMap ( boolean  removeGenesWithoutConstituentIsoforms)
Map<String, Collection<Gene> > broad.pda.annotation.BEDFileParser.toMap ( )
void broad.pda.annotation.BEDFileParser.updateScrToBedScore ( double  score)
static Map<String, BEDFileParser> broad.pda.annotation.BEDFileParser.uploadSetOfFiles ( String  bedLst) throws IOException
static

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static void broad.pda.annotation.BEDFileParser.writeBED ( String  save,
Collection< Annotation >  regions 
) throws IOException
static

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static void broad.pda.annotation.BEDFileParser.writeBED ( String  save,
Map< Annotation, double[]>  scores 
) throws IOException
static

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static void broad.pda.annotation.BEDFileParser.writeBED ( String  save,
Collection< Annotation >  alignments,
boolean  sort 
) throws IOException
static

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static void broad.pda.annotation.BEDFileParser.writeBED ( String  save,
Map< Annotation, double[]>  scores,
boolean  withScores,
boolean  sort 
) throws IOException
static
static void broad.pda.annotation.BEDFileParser.writeBEDWithScores ( String  save,
Map< Annotation, double[]>  scores 
) throws IOException
static

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void broad.pda.annotation.BEDFileParser.writeFullBed ( String  save) throws IOException

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void broad.pda.annotation.BEDFileParser.writeFullBed ( String  save,
boolean  useExtraFields 
) throws IOException

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void broad.pda.annotation.BEDFileParser.writeFullBed ( BufferedWriter  bw) throws IOException

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void broad.pda.annotation.BEDFileParser.writeFullBed ( BufferedWriter  bw,
boolean  useExtraFields 
) throws IOException

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static void broad.pda.annotation.BEDFileParser.writeFullBED ( String  save,
Collection< Gene >  genes 
) throws IOException
static
static void broad.pda.annotation.BEDFileParser.writeFullBED ( String  save,
Map< Gene,?extends Object >  genes 
) throws IOException
static
static void broad.pda.annotation.BEDFileParser.writeSortedBED ( String  save,
Map< Annotation, double[]>  scores 
) throws IOException
static

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static void broad.pda.annotation.BEDFileParser.writeSortedBED ( String  save,
Collection< Annotation >  alignments 
) throws IOException
static

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static void broad.pda.annotation.BEDFileParser.writeSortedBEDWithScores ( String  save,
Map< Annotation, double[]>  scores 
) throws IOException
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The documentation for this class was generated from the following file:
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