BayesicSpace::ParseFASTA Class Reference

FASTA alignment parser. More...

#include <fastaParser.hpp>

Public Member Functions
	ParseFASTA ()=default
	Default constructor.
	ParseFASTA (const std::string &fastaFileName)
	Constructor from FASTA file.
	ParseFASTA (const ParseFASTA &toCopy)
	Copy constructor.
	ParseFASTA (ParseFASTA &&toMove) noexcept
	Move constructor.
ParseFASTA &	operator= (const ParseFASTA &toCopy)
	Copy assignment operator.
ParseFASTA &	operator= (ParseFASTA &&toMove) noexcept
	Move assignment operator.
	~ParseFASTA ()=default
	Destructor.
size_t	sequenceNumber () const noexcept
	Number of sequences in alignment.
size_t	alignmentLength () const
	Alignment length.
std::string	extractConsensusWindow (const size_t &startIdx, const size_t &windowLength) const
	Extract a consensus region.
std::vector< std::pair< size_t, std::vector< uint32_t > > >	diversityInWindows (const size_t &windowSize, const size_t &stepSize) const
	Sequence diversity in windows.
std::unordered_map< std::string, uint32_t >	extractWindow (const size_t &windowStartPosition, const size_t &windowSize) const
	Extract an alignment window.
std::vector< std::pair< std::string, uint32_t > >	extractWindowSorted (const size_t &windowStartPosition, const size_t &windowSize) const
	Extract an alignment window and sort.
AlignmentStatistics	extractSequence (const std::string &querySequence) const
	Extract a region matching a sequence.
void	imputeMissing ()
	Impute missing values.

Detailed Description

FASTA alignment parser.

Reads a FASTA alignment file, separates the sequences and headers, and provides analysis methods. The data are stored in memory, so users should pay attention to file sizes.

Constructor & Destructor Documentation

ParseFASTA() [1/4]

BayesicSpace::ParseFASTA::ParseFASTA ( )

default

Default constructor.

ParseFASTA() [2/4]

ParseFASTA::ParseFASTA

(

const std::string &

fastaFileName

)

Constructor from FASTA file.

Read data from a FASTA file.

Parameters

[in]

fastaFileName

input FASTA file name

ParseFASTA() [3/4]

ParseFASTA::ParseFASTA

(

const ParseFASTA &

toCopy

)

Copy constructor.

Parameters

[in]

toCopy

object to copy

ParseFASTA() [4/4]

ParseFASTA::ParseFASTA ( ParseFASTA &&  toMove )

noexcept

Move constructor.

Parameters

[in]

toMove

object to move

~ParseFASTA()

BayesicSpace::ParseFASTA::~ParseFASTA ( )

default

Destructor.

Member Function Documentation

alignmentLength()

size_t BayesicSpace::ParseFASTA::alignmentLength ( ) const

inline

Alignment length.

Returns

alignment length

diversityInWindows()

std::vector< std::pair< size_t, std::vector< uint32_t > > > ParseFASTA::diversityInWindows	(	const size_t &	windowSize,
		const size_t &	stepSize
	)		const

Sequence diversity in windows.

Calculate the number of different sequences in window sliding along a sequence alignment. Reports the number of times each unique sequence occurs by window position.

Parameters

[in]	windowSize	window size in base pairs
[in]	stepSize	window movement steps in base pairs

Returns

vector of pairs that contain window start positions and unique sequence counts

extractConsensusWindow()

std::string ParseFASTA::extractConsensusWindow	(	const size_t &	startIdx,
		const size_t &	windowLength
	)		const

Extract a consensus region.

Extract a window of the consensus sequence.

Parameters

[in]	startIdx	index of the window start
[in]	windowLength	number of nucleotides in the window

extractSequence()

AlignmentStatistics ParseFASTA::extractSequence

(

const std::string &

querySequence

)

const

Extract a region matching a sequence.

Report all unique sequences (and their counts) matching the query sequence. Matching performed using striped Smith-Waterman alignment.

Parameters

[in]

querySequence

the query sequence

Returns

matching window start and length

extractWindow()

std::unordered_map< std::string, uint32_t > ParseFASTA::extractWindow	(	const size_t &	windowStartPosition,
		const size_t &	windowSize
	)		const

Extract an alignment window.

Calculates the number of different sequences in a window. Reports the number of times each unique sequence occurs in the provided window.

Parameters

[in]	windowStartPosition	window start
[in]	windowSize	window size in base pairs

Returns

map of sequences to the number of times each occurs in the alignment

extractWindowSorted()

std::vector< std::pair< std::string, uint32_t > > ParseFASTA::extractWindowSorted	(	const size_t &	windowStartPosition,
		const size_t &	windowSize
	)		const

Extract an alignment window and sort.

Calculates the number of different sequences in a window. Reports the number of times each unique sequence occurs in the provided window. The output is sorted by the number of times a sequence is present, in descending order.

Parameters

[in]	windowStartPosition	window start
[in]	windowSize	window size in base pairs

Returns

map of sequences to the number of times each occurs in the alignment, sorted

imputeMissing()

void ParseFASTA::imputeMissing

(

)

Impute missing values.

Replaces missing (N or other variants, e.g. Y, S, etc.) nucleotides with the consensus value.

operator=() [1/2]

ParseFASTA & ParseFASTA::operator=

(

const ParseFASTA &

toCopy

)

Copy assignment operator.

Parameters

[in]

toCopy

object to copy

operator=() [2/2]

ParseFASTA & ParseFASTA::operator= ( ParseFASTA &&  toMove )

noexcept

Move assignment operator.

Parameters

[in]

toMove

object to move

sequenceNumber()

size_t BayesicSpace::ParseFASTA::sequenceNumber ( ) const

inlinenoexcept

Number of sequences in alignment.

Returns

number of sequences in the alignment

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

• include/fastaParser.hpp
• src/fastaParser.cpp