broad.core.sequence.TranscribedRegions Class Reference

Public Member Functions
	TranscribedRegions (String genomeFasta, String bedFile) throws IOException
Map< String, Collection< Gene > >	getGenes ()
int	shiftPosition (String chr, int pos, int offset)
Strand	getOrientation (String chr, int pos)
char	getTranscribedBase (String chr, int pos, Strand strand) throws IOException
char	getTranscribedBase (String chr, int pos) throws IOException

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

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.core.sequence.TranscribedRegions.TranscribedRegions	(	String	genomeFasta,
		String	bedFile
	)		throws IOException

Parameters

genomeFasta	Genome fasta file
bedFile	Bed gene annotation

Exceptions

IOException

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Member Function Documentation

Map<String, Collection<Gene> > broad.core.sequence.TranscribedRegions.getGenes

(

)

Get the genes

Returns

Genes by chromosome

Strand broad.core.sequence.TranscribedRegions.getOrientation	(	String	chr,
		int	pos
	)

Get the transcribed orientation of the position based on the gene set Returns unknown if the position does not overlap a gene or strand is ambiguous

Parameters

chr	Chromosome
pos	Position

Returns

The orientation

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char broad.core.sequence.TranscribedRegions.getTranscribedBase	(	String	chr,
		int	pos,
		Strand	strand
	)		throws IOException

Get the oriented transcribed base at the position based on orientation provided or based on orientation of overlapping exon if orientation provided is null

Parameters

chr	Chromosome
pos	Position
strand	Strand or null if get from annotation

Returns

The transcribed base

Exceptions

IOException

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char broad.core.sequence.TranscribedRegions.getTranscribedBase	(	String	chr,
		int	pos
	)		throws IOException

Get the oriented transcribed base at the position based on orientation of overlapping exon

Parameters

chr	Chromosome
pos	Position

Returns

The transcribed base

Exceptions

IOException

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static void broad.core.sequence.TranscribedRegions.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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int broad.core.sequence.TranscribedRegions.shiftPosition	(	String	chr,
		int	pos,
		int	offset
	)

Shift a position along the direction of transcription If the shifted position is not in the same block as the original position, this method currently throws an exception Throws an exception if the position is not in any transcribed interval

Parameters

chr	Chromosome
pos	Original position
offset	Offset along direction of transcription (can be negative)

Returns

Shifted position within the transcript

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

• java/broad/core/sequence/TranscribedRegions.java