Static Public Member Functions
static Map	getSequenceForGene (Collection< Gene > alignments, String genomeDirectory, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats) throws Exception

static Sequence	getFirstSequence (String fastaFile) throws IOException

static Map	splitByChr (Collection< Gene > genes)

static String	getSequenceForGene (Gene gene, Sequence chrom, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats, boolean stranded) throws Exception

static String	getSequenceForGene (Gene gene, Sequence chrom, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats) throws Exception

static String	getSequenceUnoriented (Alignments align, Sequence chrom, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats) throws Exception

static String	getSequenceUnoriented (Alignments align, Sequence chrom, boolean repeatMask) throws Exception

static String	getSequenceForGene (Gene gene, String genomeDirectory, boolean repeatMask) throws Exception

static String	getGenomeSequence (GenomicAnnotation annot, String genomeDirectory, boolean repeatMask) throws Exception

static String	getSequenceUnoriented (Alignments align, String genomeDirectory, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats) throws Exception

static String	reverseComplement (String seq)

static void	writeFasta (String save, Map< String, Collection< Gene >> genesByChr, String genomeDir, boolean repeatMask) throws Exception

static void	main (String[] args) throws Exception

Member Function Documentation

static Sequence broad.pda.rnai.ExtractSequence.getFirstSequence ( String fastaFile ) throws IOException

static

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static String broad.pda.rnai.ExtractSequence.getGenomeSequence	(	GenomicAnnotation	annot,
		String	genomeDirectory,
		boolean	repeatMask
	)		throws Exception

static

Suggestion: Use classes in net.sf.picard.reference instead, which are WAY faster because they use an indexed FASTA file

Parameters

annot
genomeDirectory
repeatMask

Returns

Exceptions

Exception

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static Map broad.pda.rnai.ExtractSequence.getSequenceForGene	(	Collection< Gene >	alignments,
		String	genomeDirectory,
		boolean	repeatMask,
		Map< String, IntervalTree< Alignments >>	okRepeats
	)		throws Exception

static

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static String broad.pda.rnai.ExtractSequence.getSequenceForGene	(	Gene	gene,
		Sequence	chrom,
		boolean	repeatMask,
		Map< String, IntervalTree< Alignments >>	okRepeats,
		boolean	stranded
	)		throws Exception

static

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static String broad.pda.rnai.ExtractSequence.getSequenceForGene	(	Gene	gene,
		Sequence	chrom,
		boolean	repeatMask,
		Map< String, IntervalTree< Alignments >>	okRepeats
	)		throws Exception

static

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static String broad.pda.rnai.ExtractSequence.getSequenceForGene	(	Gene	gene,
		String	genomeDirectory,
		boolean	repeatMask
	)		throws Exception

static

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static String broad.pda.rnai.ExtractSequence.getSequenceUnoriented	(	Alignments	align,
		Sequence	chrom,
		boolean	repeatMask,
		Map< String, IntervalTree< Alignments >>	okRepeats
	)		throws Exception

static

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static String broad.pda.rnai.ExtractSequence.getSequenceUnoriented	(	Alignments	align,
		Sequence	chrom,
		boolean	repeatMask
	)		throws Exception

static

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static String broad.pda.rnai.ExtractSequence.getSequenceUnoriented	(	Alignments	align,
		String	genomeDirectory,
		boolean	repeatMask,
		Map< String, IntervalTree< Alignments >>	okRepeats
	)		throws Exception

static

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static void broad.pda.rnai.ExtractSequence.main ( String[] args ) throws Exception

static

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static String broad.pda.rnai.ExtractSequence.reverseComplement ( String seq )

static

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static Map broad.pda.rnai.ExtractSequence.splitByChr ( Collection< Gene > genes )

static

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static void broad.pda.rnai.ExtractSequence.writeFasta	(	String	save,
		Map< String, Collection< Gene >>	genesByChr,
		String	genomeDir,
		boolean	repeatMask
	)		throws Exception

static

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

java/broad/pda/rnai/ExtractSequence.java

Static Public Member Functions

Member Function Documentation