broad.pda.seq.clip.FastaExtendPeaks Class Reference

Public Member Functions
	FastaExtendPeaks (String genomeFasta, String bedFile, String peakFile, int windowSize) throws IOException
	FastaExtendPeaks (Map< String, Sequence > chrsByName, String bedFile, String peakFile, int windowSize) throws IOException
	FastaExtendPeaks (Map< String, Sequence > chrsByName, String bedFile) throws IOException
	FastaExtendPeaks (Map< String, Sequence > chrsByName, String bedFile, String peakFile) throws IOException
	FastaExtendPeaks (String genomeFasta, String bedFile) throws IOException
void	writeFasta (Map< String, Collection< Gene >> genesToWrite, String outFile) throws IOException

Static Public Member Functions
static void	main (String[] args) throws IOException

Detailed Description

Author

shari Extends peaks to standardized size (for probe design, etc.)

Constructor & Destructor Documentation

broad.pda.seq.clip.FastaExtendPeaks.FastaExtendPeaks	(	String	genomeFasta,
		String	bedFile,
		String	peakFile,
		int	windowSize
	)		throws IOException

Parameters

genomeFasta	Fasta file of sequences
bedFile	Bed file

Exceptions

IOException

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broad.pda.seq.clip.FastaExtendPeaks.FastaExtendPeaks	(	Map< String, Sequence >	chrsByName,
		String	bedFile,
		String	peakFile,
		int	windowSize
	)		throws IOException

Load sequences and annotations

Parameters

chrsByName	Chromosomes by name
bedFile	Genes in bed format
windowSize	size of return sequences

Exceptions

IOException

broad.pda.seq.clip.FastaExtendPeaks.FastaExtendPeaks	(	Map< String, Sequence >	chrsByName,
		String	bedFile
	)		throws IOException

Load sequences and annotations

Parameters

chrsByName	Chromosomes by name
bedFile	Genes in bed format

Exceptions

IOException

broad.pda.seq.clip.FastaExtendPeaks.FastaExtendPeaks	(	Map< String, Sequence >	chrsByName,
		String	bedFile,
		String	peakFile
	)		throws IOException

broad.pda.seq.clip.FastaExtendPeaks.FastaExtendPeaks	(	String	genomeFasta,
		String	bedFile
	)		throws IOException

Member Function Documentation

static void broad.pda.seq.clip.FastaExtendPeaks.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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void broad.pda.seq.clip.FastaExtendPeaks.writeFasta	(	Map< String, Collection< Gene >>	genesToWrite,
		String	outFile
	)		throws IOException

Parameters

outFile

Exceptions

IOException

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

• java/broad/pda/seq/clip/FastaExtendPeaks.java