umms.core.alignment.FeatureSequenceAlignment Class Reference

Classes
class	UnorderedGenePair

Public Member Functions
	FeatureSequenceAlignment (String featureBedFile, String genomeFasta) throws IOException
	FeatureSequenceAlignment (Collection< Gene > genes, String genomeFasta) throws IOException
	FeatureSequenceAlignment (String featureBedFile, String genomeFasta, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty) throws IOException
	FeatureSequenceAlignment (Collection< Gene > genes, Map< String, broad.core.sequence.Sequence > chrs, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty) throws IOException
	FeatureSequenceAlignment (Collection< Gene > genes, String genomeFasta, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty) throws IOException
Map< UnorderedGenePair, jaligner.Alignment >	getAllPairwiseSenseAlignments (float minAlignLength, float minPctIdentity)
Map< UnorderedGenePair, jaligner.Alignment >	getAllPairwiseAntisenseAlignments (float minAlignLength, float minPctIdentity)
void	writeAllSenseAlignmentsToBed (String outBedFile, int minAlignLength, float minPctIdentity) throws IOException
void	writeAllAntisenseAlignmentsToBed (String outBedFile, int minAlignLength, float minPctIdentity) throws IOException
void	writeAllSenseAlignmentsToBed (String outBedFile, boolean append, int minAlignLength, float minPctIdentity) throws IOException
void	writeAllAntisenseAlignmentsToBed (String outBedFile, boolean append, int minAlignLength, float minPctIdentity) throws IOException

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

Static Public Attributes
static float	DEFAULT_MATCH_SCORE = 5
static float	DEFAULT_MISMATCH_SCORE = -4
static float	DEFAULT_GAP_OPEN_PENALTY = 8
static float	DEFAULT_GAP_EXTEND_PENALTY = 2

Detailed Description

Author

prussell

Constructor & Destructor Documentation

umms.core.alignment.FeatureSequenceAlignment.FeatureSequenceAlignment	(	String	featureBedFile,
		String	genomeFasta
	)		throws IOException

Parameters

featureBedFile	Bed file of features
genomeFasta	Genome fasta file

Exceptions

IOException

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umms.core.alignment.FeatureSequenceAlignment.FeatureSequenceAlignment	(	Collection< Gene >	genes,
		String	genomeFasta
	)		throws IOException

Parameters

genes	Set of features
genomeFasta	Genome fasta file

Exceptions

IOException

umms.core.alignment.FeatureSequenceAlignment.FeatureSequenceAlignment	(	String	featureBedFile,
		String	genomeFasta,
		float	matchScore,
		float	mismatchScore,
		float	gapOpenPenalty,
		float	gapExtendPenalty
	)		throws IOException

Parameters

featureBedFile	Bed file of features
genomeFasta	Genome fasta file
matchScore	Match score for Smith Waterman
mismatchScore	Mismatch score for Smith Waterman
gapOpenPenalty	Gap open penalty for Smith Waterman
gapExtendPenalty	Gap extend penalty for Smith Waterman

Exceptions

IOException

umms.core.alignment.FeatureSequenceAlignment.FeatureSequenceAlignment	(	Collection< Gene >	genes,
		Map< String, broad.core.sequence.Sequence >	chrs,
		float	matchScore,
		float	mismatchScore,
		float	gapOpenPenalty,
		float	gapExtendPenalty
	)		throws IOException

Parameters

genes	The features
chrs	Map of chromosome names to sequences
matchScore	Match score for Smith Waterman
mismatchScore	Mismatch score for Smith Waterman
gapOpenPenalty	Gap open penalty for Smith Waterman
gapExtendPenalty	Gap extend penalty for Smith Waterman

Exceptions

IOException

umms.core.alignment.FeatureSequenceAlignment.FeatureSequenceAlignment	(	Collection< Gene >	genes,
		String	genomeFasta,
		float	matchScore,
		float	mismatchScore,
		float	gapOpenPenalty,
		float	gapExtendPenalty
	)		throws IOException

Parameters

genes	Set of features
genomeFasta	Genome fasta file
matchScore	Match score for Smith Waterman
mismatchScore	Mismatch score for Smith Waterman
gapOpenPenalty	Gap open penalty for Smith Waterman
gapExtendPenalty	Gap extend penalty for Smith Waterman

Exceptions

IOException

Member Function Documentation

Map<UnorderedGenePair, jaligner.Alignment> umms.core.alignment.FeatureSequenceAlignment.getAllPairwiseAntisenseAlignments	(	float	minAlignLength,
		float	minPctIdentity
	)

Get all antisense direction alignments passing thresholds

Parameters

minAlignLength	Min alignment length
minPctIdentity	Min percent identity

Returns

All antisense alignments of unordered gene pair passing criteria

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Map<UnorderedGenePair, jaligner.Alignment> umms.core.alignment.FeatureSequenceAlignment.getAllPairwiseSenseAlignments	(	float	minAlignLength,
		float	minPctIdentity
	)

Get all sense direction alignments passing thresholds

Parameters

minAlignLength	Min alignment length
minPctIdentity	Min percent identity

Returns

All sense alignments of unordered gene pair passing criteria

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static void umms.core.alignment.FeatureSequenceAlignment.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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void umms.core.alignment.FeatureSequenceAlignment.writeAllAntisenseAlignmentsToBed	(	String	outBedFile,
		int	minAlignLength,
		float	minPctIdentity
	)		throws IOException

Write all pairwise alignments (antisense direction only) to bed file in genome coordinates

Parameters

outBedFile	Output bed file
minAlignLength	Min alignment length to keep
minPctIdentity	Min percent identity to keep

Exceptions

IOException

void umms.core.alignment.FeatureSequenceAlignment.writeAllAntisenseAlignmentsToBed	(	String	outBedFile,
		boolean	append,
		int	minAlignLength,
		float	minPctIdentity
	)		throws IOException

Write all pairwise alignments (antisense direction only) to bed file in genome coordinates

Parameters

outBedFile	Output bed file
append	Write to end of file rather than beginning
minAlignLength	Min alignment length to keep
minPctIdentity	Min percent identity to keep

Exceptions

IOException

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void umms.core.alignment.FeatureSequenceAlignment.writeAllSenseAlignmentsToBed	(	String	outBedFile,
		int	minAlignLength,
		float	minPctIdentity
	)		throws IOException

Write all pairwise alignments (sense direction only) to bed file in genome coordinates

Parameters

outBedFile	Output bed file
minAlignLength	Min alignment length to keep
minPctIdentity	Min percent identity to keep

Exceptions

IOException

void umms.core.alignment.FeatureSequenceAlignment.writeAllSenseAlignmentsToBed	(	String	outBedFile,
		boolean	append,
		int	minAlignLength,
		float	minPctIdentity
	)		throws IOException

Write all pairwise alignments (sense direction only) to bed file in genome coordinates

Parameters

outBedFile	Output bed file
append	Write to end of file rather than beginning
minAlignLength	Min alignment length to keep
minPctIdentity	Min percent identity to keep

Exceptions

IOException

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Member Data Documentation

float umms.core.alignment.FeatureSequenceAlignment.DEFAULT_GAP_EXTEND_PENALTY = 2

static

Default gap extend penalty for Smith Waterman

float umms.core.alignment.FeatureSequenceAlignment.DEFAULT_GAP_OPEN_PENALTY = 8

static

Default gap open penalty for Smith Waterman

float umms.core.alignment.FeatureSequenceAlignment.DEFAULT_MATCH_SCORE = 5

static

Default match score for Smith Waterman

float umms.core.alignment.FeatureSequenceAlignment.DEFAULT_MISMATCH_SCORE = -4

static

Default mismatch score for Smith Waterman

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

• java/umms/core/alignment/FeatureSequenceAlignment.java