Utilitary function to manipulate PolymorphismSequenceContainer. More...

#include <Bpp/PopGen/PolymorphismSequenceContainerTools.h>

Public Member Functions
virtual	~PolymorphismSequenceContainerTools ()

Static Public Member Functions
static std::unique_ptr< PolymorphismSequenceContainer >	read (const std::string &path, std::shared_ptr< const Alphabet > alpha)
	Read a Mase+ file and return a PolymorphismSequenceContainer. Toggle Sequence when selection tag begin with OUTGROUP (see Polymorphix) More...

static std::unique_ptr< PolymorphismSequenceContainer >	extractIngroup (const PolymorphismSequenceContainer &psc)
	Extract ingroup sequences from a PolymorphismSequenceContainer and create a new one. More...

static std::unique_ptr< PolymorphismSequenceContainer >	extractOutgroup (const PolymorphismSequenceContainer &psc)
	Extract outgroup sequences from a PolymorphismSequenceContainer and create a new one. More...

static std::unique_ptr< PolymorphismSequenceContainer >	extractGroup (const PolymorphismSequenceContainer &psc, size_t groupId)
	Extract a special group from the PolymorphismSequenceContainer. More...

static std::unique_ptr< PolymorphismSequenceContainer >	getSelectedSequences (const PolymorphismSequenceContainer &psc, const SequenceSelection &ss)
	Extract selected sequences. More...

static std::unique_ptr< PolymorphismSequenceContainer >	sample (const PolymorphismSequenceContainer &psc, size_t n, bool replace=true)
	Get a random set of sequences. More...

static std::unique_ptr< PolymorphismSequenceContainer >	getSitesWithoutGaps (const PolymorphismSequenceContainer &psc)
	Retrieves sites without gaps from PolymorphismSequenceContainer. More...

static size_t	getNumberOfNonGapSites (const PolymorphismSequenceContainer &psc, bool ingroup)
	Return number of sites without gaps in a PolymorphismSequenceContainer. More...

static size_t	getNumberOfCompleteSites (const PolymorphismSequenceContainer &psc, bool ingroup)
	Return number of completely resolved sites in a PolymorphismSequenceContainer. More...

static std::unique_ptr< PolymorphismSequenceContainer >	getCompleteSites (const PolymorphismSequenceContainer &psc)
	Retrieves complete sites from a PolymorphismSequenceContainer. More...

static std::unique_ptr< PolymorphismSequenceContainer >	excludeFlankingGap (const PolymorphismSequenceContainer &psc)
	exclude flanking sites with gap but keep gap sites within the alignment More...

static std::unique_ptr< PolymorphismSequenceContainer >	getSelectedSites (const PolymorphismSequenceContainer &psc, const std::string &setName, bool phase)
	Get a PolymorphismSequenceContainer corresponding to a site selection annotated in the mase comments. More...

static std::unique_ptr< PolymorphismSequenceContainer >	getNonCodingSites (const PolymorphismSequenceContainer &psc, const std::string &setName)
	Retrieve non-coding sites defined in the mase file header. More...

static std::unique_ptr< PolymorphismSequenceContainer >	getOnePosition (const PolymorphismSequenceContainer &psc, const std::string &setName, size_t pos)
	Retrieve sites at one codon position (1,2,3) More...

static std::unique_ptr< PolymorphismSequenceContainer >	getIntrons (const PolymorphismSequenceContainer &psc, const std::string &setName, const GeneticCode &gCode)
	Retrieve intron sites. More...

static std::unique_ptr< PolymorphismSequenceContainer >	get5Prime (const PolymorphismSequenceContainer &psc, const std::string &setName)
	Retrieve 5' sites. More...

static std::unique_ptr< PolymorphismSequenceContainer >	get3Prime (const PolymorphismSequenceContainer &psc, const std::string &setName, const GeneticCode &gCode)
	Retrieve 3' sites. More...

static std::string	getIngroupSpeciesName (const PolymorphismSequenceContainer &psc)
	Get the species name of the ingroup. More...

static std::unique_ptr< PolymorphismSequenceContainer >	getSynonymousSites (const PolymorphismSequenceContainer &psc, const GeneticCode &gCode)
	Retrieve synonymous codon sites. More...

static std::unique_ptr< PolymorphismSequenceContainer >	getNonSynonymousSites (const PolymorphismSequenceContainer &psc, const GeneticCode &gCode)
	Retrieve non-synonymous codon sites. More...

Detailed Description

Utilitary function to manipulate PolymorphismSequenceContainer.

Author: Sylvain Gaillard

Definition at line 38 of file PolymorphismSequenceContainerTools.h.

Constructor & Destructor Documentation

◆ ~PolymorphismSequenceContainerTools()

PolymorphismSequenceContainerTools::~PolymorphismSequenceContainerTools ( )

virtual

Definition at line 12 of file PolymorphismSequenceContainerTools.cpp.

Member Function Documentation

◆ excludeFlankingGap()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::excludeFlankingGap ( const PolymorphismSequenceContainer & psc )

static

exclude flanking sites with gap but keep gap sites within the alignment

Parameters

psc	a PolymorphismSequenceContainer reference

Definition at line 257 of file PolymorphismSequenceContainerTools.cpp.

References bpp::SiteTools::hasGap().

◆ extractGroup()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::extractGroup	(	const PolymorphismSequenceContainer &	psc,
		size_t	groupId
	)

static

Extract a special group from the PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference.
groupId	the group identifier as an size_t.

Exceptions

GroupNotFoundException if group_id is not found.

Definition at line 89 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), and bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences().

◆ extractIngroup()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::extractIngroup ( const PolymorphismSequenceContainer & psc )

static

Extract ingroup sequences from a PolymorphismSequenceContainer and create a new one.

Parameters

psc	a PolymorphismSequenceContainer reference

Exceptions

Exception if there is no ingroup sequence

Definition at line 43 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and bpp::PolymorphismSequenceContainer::isIngroupMember().

◆ extractOutgroup()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::extractOutgroup ( const PolymorphismSequenceContainer & psc )

static

Extract outgroup sequences from a PolymorphismSequenceContainer and create a new one.

Parameters

psc	a PolymorphismSequenceContainer reference

Exceptions

Exception if there is no outgroup sequence

Definition at line 66 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and bpp::PolymorphismSequenceContainer::isIngroupMember().

◆ get3Prime()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::get3Prime	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		const GeneticCode &	gCode
	)

static

Retrieve 3' sites.

Parameters

psc	a PolymorphismSequenceContainer
setName	name of the CDS site selection
gCode	The genetic code to use

Definition at line 464 of file PolymorphismSequenceContainerTools.cpp.

References bpp::GeneticCode::codonAlphabet(), bpp::CodonAlphabet::getCodon(), bpp::TemplateVectorSiteContainer< class, class >::getComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::MaseTools::getSiteSet(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::GeneticCode::isStop(), and bpp::TemplateVectorSiteContainer< class, class >::site().

◆ get5Prime()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::get5Prime	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName
	)

static

Retrieve 5' sites.

Parameters

psc	a PolymorphismSequenceContainer
setName	name of the CDS site selection

Definition at line 425 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::MaseTools::getPhase(), bpp::SiteContainerTools::getSelectedSites(), bpp::MaseTools::getSiteSet(), bpp::PolymorphismSequenceContainer::isIngroupMember(), and bpp::TemplateVectorSiteContainer< class, class >::site().

◆ getCompleteSites()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getCompleteSites ( const PolymorphismSequenceContainer & psc )

static

Retrieves complete sites from a PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference

Definition at line 228 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::TemplateVectorSiteContainer< class, class >::getSequenceNames(), bpp::CompleteTemplateSiteContainerIterator< class, class, class >::hasMoreSites(), bpp::PolymorphismSequenceContainer::isIngroupMember(), and bpp::CompleteTemplateSiteContainerIterator< class, class, class >::nextSite().

◆ getIngroupSpeciesName()

string PolymorphismSequenceContainerTools::getIngroupSpeciesName ( const PolymorphismSequenceContainer & psc )

static

Get the species name of the ingroup.

Parameters

psc	a PolymorphismSequenceContainer.

Definition at line 503 of file PolymorphismSequenceContainerTools.cpp.

References bpp::MaseTools::getAvailableSequenceSelections(), bpp::TemplateVectorSiteContainer< class, class >::getComments(), and bpp::StringTokenizer::getToken().

◆ getIntrons()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getIntrons	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		const GeneticCode &	gCode
	)

static

Retrieve intron sites.

Same as getNonCodgingSites but exclude 5' and 3' flanking regions if there are

Parameters

psc	a PolymorphismSequenceContainer
setName	name of the CDS site selection
gCode	The genetic code to use

Definition at line 378 of file PolymorphismSequenceContainerTools.cpp.

References bpp::GeneticCode::codonAlphabet(), bpp::CodonAlphabet::getCodon(), bpp::TemplateVectorSiteContainer< class, class >::getComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), bpp::MaseTools::getPhase(), bpp::SiteContainerTools::getSelectedSites(), bpp::MaseTools::getSiteSet(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::GeneticCode::isStop(), and bpp::TemplateVectorSiteContainer< class, class >::site().

◆ getNonCodingSites()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getNonCodingSites	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName
	)

static

Retrieve non-coding sites defined in the mase file header.

Be careful: to use before excluding gap

Parameters

psc	a PolymorphismSequenceContainer reference
setName	name of the CDS site selection

Definition at line 306 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::MaseTools::getSiteSet(), and bpp::PolymorphismSequenceContainer::isIngroupMember().

◆ getNonSynonymousSites()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getNonSynonymousSites	(	const PolymorphismSequenceContainer &	psc,
		const GeneticCode &	gCode
	)

static

Retrieve non-synonymous codon sites.

Parameters

psc	a PolymorphismSequenceContainer.
gCode	The genetic code to use

Returns: A new PolymorphismSequenceContainer with only non-synonymous sites.

Definition at line 555 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::TemplateVectorSiteContainer< class, class >::getSequenceNames(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::CodonSiteTools::isSynonymousPolymorphic(), and bpp::TemplateVectorSiteContainer< class, class >::site().

◆ getNumberOfCompleteSites()

size_t PolymorphismSequenceContainerTools::getNumberOfCompleteSites	(	const PolymorphismSequenceContainer &	psc,
		bool	ingroup
	)

static

Return number of completely resolved sites in a PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference
ingroup	a boolean set to true if you want to take only ingroup sequences into account

Exceptions

Exception if there is no ingroup sequence

Definition at line 206 of file PolymorphismSequenceContainerTools.cpp.

References count(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), and bpp::SiteTools::isComplete().

◆ getNumberOfNonGapSites()

size_t PolymorphismSequenceContainerTools::getNumberOfNonGapSites	(	const PolymorphismSequenceContainer &	psc,
		bool	ingroup
	)

static

Return number of sites without gaps in a PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference
ingroup	a boolean set to true if you want to take only ingroup sequences into account

Exceptions

Exception if there is no ingroup sequence

Definition at line 184 of file PolymorphismSequenceContainerTools.cpp.

References count(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), and bpp::SiteTools::hasGap().

◆ getOnePosition()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getOnePosition	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		size_t	pos
	)

static

Retrieve sites at one codon position (1,2,3)

Be careful: to use before excluding gap Be careful: if there is no phase information, the method catch an exception and set the phase to 1 This allows to use this method for PolymorphismSequenceContainer generated by getSelectedSequence

Parameters

psc	a PolymorphismSequenceContainer reference
setName	name of the CDS site selection
pos	position index.

Definition at line 335 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), bpp::MaseTools::getPhase(), bpp::SiteContainerTools::getSelectedSites(), and bpp::PolymorphismSequenceContainer::isIngroupMember().

◆ getSelectedSequences()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getSelectedSequences	(	const PolymorphismSequenceContainer &	psc,
		const SequenceSelection &	ss
	)

static

Extract selected sequences.

Parameters

psc	a PolymorphismSequenceContainer reference.
ss	a sequence selection.

Definition at line 113 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getAlphabet(), bpp::TemplateVectorSiteContainer< class, class >::getComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::PolymorphismSequenceContainer::isIngroupMember(), and bpp::TemplateVectorSiteContainer< class, class >::sequence().

Referenced by sample().

◆ getSelectedSites()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getSelectedSites	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		bool	phase
	)

static

Get a PolymorphismSequenceContainer corresponding to a site selection annotated in the mase comments.

Warning: in the new PolymorphismSequenceContainer the mase comments are lost Information about cds positions and start codon is no more available

Parameters

psc	a PolymorphismSequenceContainer.
setName	The name of the set to retrieve.
phase	a boolean set to true if you want to take the phase into account during the extraction. It removes the useless sites.

Definition at line 275 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::MaseTools::getPhase(), bpp::MaseTools::getSelectedSites(), and bpp::PolymorphismSequenceContainer::isIngroupMember().

◆ getSitesWithoutGaps()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getSitesWithoutGaps ( const PolymorphismSequenceContainer & psc )

static

Retrieves sites without gaps from PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference

Definition at line 155 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::TemplateVectorSiteContainer< class, class >::getSequenceNames(), bpp::NoGapTemplateSiteContainerIterator< class, class, class >::hasMoreSites(), bpp::PolymorphismSequenceContainer::isIngroupMember(), and bpp::NoGapTemplateSiteContainerIterator< class, class, class >::nextSite().

◆ getSynonymousSites()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::getSynonymousSites	(	const PolymorphismSequenceContainer &	psc,
		const GeneticCode &	gCode
	)

static

Retrieve synonymous codon sites.

Parameters

psc	a PolymorphismSequenceContainer.
gCode	The genetic code to use

Returns: A new PolymorphismSequenceContainer with only synonymous sites.

Definition at line 525 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSites(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::TemplateVectorSiteContainer< class, class >::getSequenceNames(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::CodonSiteTools::isSynonymousPolymorphic(), and bpp::TemplateVectorSiteContainer< class, class >::site().

◆ read()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::read	(	const std::string &	path,
		std::shared_ptr< const Alphabet >	alpha
	)

static

Read a Mase+ file and return a PolymorphismSequenceContainer. Toggle Sequence when selection tag begin with OUTGROUP (see Polymorphix)

Parameters

path	Path to the Mase+ file
alpha	Sequence Alphabet

Exceptions

Exception if the file is not in the specified format

Definition at line 16 of file PolymorphismSequenceContainerTools.cpp.

References bpp::MaseTools::getAvailableSequenceSelections(), bpp::MaseTools::getSequenceSet(), and bpp::Mase::readSequences().

◆ sample()

unique_ptr< PolymorphismSequenceContainer > PolymorphismSequenceContainerTools::sample	(	const PolymorphismSequenceContainer &	psc,
		size_t	n,
		bool	replace = `true`
	)

static

Get a random set of sequences.

Parameters

psc	a PolymorphismSequenceContainer reference
n	the number of sequence to get
replace	a boolean flag true for sampling with replacement

Definition at line 136 of file PolymorphismSequenceContainerTools.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), bpp::RandomTools::getSample(), and getSelectedSequences().

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

Bpp/PopGen/PolymorphismSequenceContainerTools.h
Bpp/PopGen/PolymorphismSequenceContainerTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ~PolymorphismSequenceContainerTools()

Member Function Documentation

◆ excludeFlankingGap()

◆ extractGroup()

◆ extractIngroup()

◆ extractOutgroup()

◆ get3Prime()

◆ get5Prime()

◆ getCompleteSites()

◆ getIngroupSpeciesName()

◆ getIntrons()

◆ getNonCodingSites()

◆ getNonSynonymousSites()

◆ getNumberOfCompleteSites()

◆ getNumberOfNonGapSites()

◆ getOnePosition()

◆ getSelectedSequences()

◆ getSelectedSites()

◆ getSitesWithoutGaps()

◆ getSynonymousSites()

◆ read()

◆ sample()