Connector class for accessing HGMD data stored in an in-house database. More...

Collaboration diagram for cls.HGMDAnnotation.CHGMDAnnotation:

Public Member Functions
def	Initialize (self, config)
	Initialize module, establishing a connection to the database. More...

def	CloseConnection (self)
	Close the connection to the HGMD database. More...

def	GetMutationsByGeneID (self, geneID)
	Retrieves all disease-related mutations that are reported in HGMD for a certain gene. More...

def	GetMutationsByHGMD (self, hgmdAcc)
	Retrieves all disease-related mutations that are reported in HGMD for a certain HGMD accession number. More...

def	GetMutationsByUMLS (self, umlsId, includeChildren=False)
	Retrieves all disease-related mutations that are reported in HGMD for a certain UMLS identifier. More...

def	GetMutationsByCoordinateRange (self, startCoord, endCoord)
	Retrieve all disease-related mutations that are reported in HGMD for a given coordinate range. More...

def	GetMutationsByDisease (self, diseaseTokens, exact=True, operator="OR")
	Retrieve all disease-related mutations that are reported in HGMD for the given disease terms. More...

def	GetDiseases (self, diseaseTokens, operator="OR")
	Retrieve all HGMD disease terms from the database that contain the particular word tokens. More...

def	GetDiseaseSets (self)
	Get the predefined disease sets from the database. More...

def	GetConcepts (self, terms, op="OR")
	Get the disease concepts that are build from UMLS. More...

Public Attributes
	db

	coordSys

Static Public Attributes
tuple	MUTATION_DATA

string	GENERAL_QUERY_STUB

	config = None

	hgmd = CHGMDAnnotation()

int	geneID = 5071

def	mutations = hgmd.GetMutationsByGeneID(geneID)

string	pos = "GRCh37:6:10404798"

string	start = "GRCh37:6:10404798"

string	end = "GRCh37:6:10404898"

string	disease = "Parkinson disease"

list	disease = ["parkin", "dement"]

string	op = " AND "

def	diseases = hgmd.GetDiseases(disease ,op)

Detailed Description

Connector class for accessing HGMD data stored in an in-house database.

Member Function Documentation

◆ CloseConnection()

def cls.HGMDAnnotation.CHGMDAnnotation.CloseConnection ( self )

Close the connection to the HGMD database.

    @return @c True if all went ok, @c False, if there was an
    error (issued by @ref common.ErrorHandler).

◆ GetConcepts()

def cls.HGMDAnnotation.CHGMDAnnotation.GetConcepts	(	self,
		terms,
		op = `"OR"`
	)

Get the disease concepts that are build from UMLS.

    @param terms Query terms that should be containg in the concepts.
    If empty, all concepts will be returned
    @param op The logical operator that defines if the terms
    should be contained jointly in the concept (AND) or if any
    of them should be present (OR)
    @return The list of concepts. @c False if there was an
    error (issued by @ref common.ErrorHandler).

◆ GetDiseases()

def cls.HGMDAnnotation.CHGMDAnnotation.GetDiseases	(	self,
		diseaseTokens,
		operator = `"OR"`
	)

Retrieve all HGMD disease terms from the database that contain the particular word tokens.

Parameters

diseaseTokens	The disease term(s) that have to be present in the disease name. Can be either a single term or a list of terms.
operator	The logical operator that defines, if the disease tokens should be contained jointly in the HGMD disease string (AND) or if any of them should be present (OR)

Returns: The list of disease names from HGMD. False if there was an error (issued by common.ErrorHandler).

◆ GetDiseaseSets()

def cls.HGMDAnnotation.CHGMDAnnotation.GetDiseaseSets ( self )

Get the predefined disease sets from the database.

    @return A dictionary of predefined disease sets. The keys are the
    defined disease classes (like 'Alzheimer', 'Parkinson'), the values
    contain the exact HGMD disease terms (like 'Parkinson disease,
    early-onset'). @c False if an error occured (issued by @ref
    common.ErrorHandler).

◆ GetMutationsByCoordinateRange()

def cls.HGMDAnnotation.CHGMDAnnotation.GetMutationsByCoordinateRange	(	self,
		startCoord,
		endCoord
	)

Retrieve all disease-related mutations that are reported in HGMD for a given coordinate range.

Parameters

startCoord	The start coordinate of the range, specified as a string in the format Build:Chromosome:Start[-End]
endCoord	The end coordinate of the range specified as a string in the format Build:Chromosome:Start[-End]. Has to be greater or equal to startCoord.

Returns: The list of mutations stored in HGMD. False if there was an error when getting the data (issued by common.ErrorHandler).

◆ GetMutationsByDisease()

def cls.HGMDAnnotation.CHGMDAnnotation.GetMutationsByDisease	(	self,
		diseaseTokens,
		exact = `True`,
		operator = `"OR"`
	)

Retrieve all disease-related mutations that are reported in HGMD for the given disease terms.

Parameters

diseaseTokens	The disease term(s) that have to be present in the disease name. Can be either a single term or a list of terms.
exact	If `True`, only exact matches to the requested disease terms are returned, if `False`, also partial matched are considered.
operator	The logical operator that defines, if the disease tokens should be contained jointly in the HGMD string (AND) or if any of them should be present (OR)

Returns: The list of mutations known in HGMD. False, if there was an error (issued by common.ErrorHandler).

◆ GetMutationsByGeneID()

def cls.HGMDAnnotation.CHGMDAnnotation.GetMutationsByGeneID	(	self,
		geneID
	)

Retrieves all disease-related mutations that are reported in HGMD for a certain gene.

Parameters

geneID The Entrez Gene ID of the gene of interesest, e.g., 5071 for PARK2

Returns: The list of mutations stored in HGMD. False, if there was an error when getting the data (issued by common.ErrorHandler).

◆ GetMutationsByHGMD()

def cls.HGMDAnnotation.CHGMDAnnotation.GetMutationsByHGMD	(	self,
		hgmdAcc
	)

Retrieves all disease-related mutations that are reported in HGMD for a certain HGMD accession number.

Parameters

hgmdAcc The HGMD accession number

Returns: The list of mutations stored in HGMD. False, if there was an error when getting the data (issued by common.ErrorHandler).

◆ GetMutationsByUMLS()

def cls.HGMDAnnotation.CHGMDAnnotation.GetMutationsByUMLS	(	self,
		umlsId,
		includeChildren = `False`
	)

Retrieves all disease-related mutations that are reported in HGMD for a certain UMLS identifier.

Parameters

umlsId	The UMLS identifier
includeChildren	If true, will also include mutations that are annotated to descending terms.

Returns: The list of mutations stored in HGMD. False, if there was an error when getting the data (issued by common.ErrorHandler).

◆ Initialize()

def cls.HGMDAnnotation.CHGMDAnnotation.Initialize	(	self,
		config
	)

Initialize module, establishing a connection to the database.

    Prior to any use of this module, this initialization function needs to
    be called, as otherwise the database connection is not established.
    @param config  @ref common.Paths.CPaths object containing database
    access credentials
    @return @c True if all went ok. @c False if there was an error
    (issued by @ref common.ErrorHandler).

Member Data Documentation

◆ config

cls.HGMDAnnotation.CHGMDAnnotation.config = None

static

◆ coordSys

cls.HGMDAnnotation.CHGMDAnnotation.coordSys

◆ db

cls.HGMDAnnotation.CHGMDAnnotation.db

◆ disease [1/2]

list cls.HGMDAnnotation.CHGMDAnnotation.disease = "Parkinson disease"

static

◆ disease [2/2]

list cls.HGMDAnnotation.CHGMDAnnotation.disease = ["parkin", "dement"]

static

◆ diseases

def cls.HGMDAnnotation.CHGMDAnnotation.diseases = hgmd.GetDiseases(disease ,op)

static

◆ end

string cls.HGMDAnnotation.CHGMDAnnotation.end = "GRCh37:6:10404898"

static

◆ geneID

int cls.HGMDAnnotation.CHGMDAnnotation.geneID = 5071

static

◆ GENERAL_QUERY_STUB

string cls.HGMDAnnotation.CHGMDAnnotation.GENERAL_QUERY_STUB

static

◆ hgmd

cls.HGMDAnnotation.CHGMDAnnotation.hgmd = CHGMDAnnotation()

static

◆ MUTATION_DATA

tuple cls.HGMDAnnotation.CHGMDAnnotation.MUTATION_DATA

static

Initial value:

=  (
        ("gene", "", "allmut", "Gene symbol" ),
        ("base", "mutationCategory" "allmut", "Mutation category"))

◆ mutations

def cls.HGMDAnnotation.CHGMDAnnotation.mutations = hgmd.GetMutationsByGeneID(geneID)

static

◆ op

string cls.HGMDAnnotation.CHGMDAnnotation.op = " AND "

static

◆ pos

string cls.HGMDAnnotation.CHGMDAnnotation.pos = "GRCh37:6:10404798"

static

◆ start

string cls.HGMDAnnotation.CHGMDAnnotation.start = "GRCh37:6:10404798"

static

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

cls/HGMDAnnotation.py

Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description

Member Function Documentation

◆ CloseConnection()

◆ GetConcepts()

◆ GetDiseases()

◆ GetDiseaseSets()

◆ GetMutationsByCoordinateRange()

◆ GetMutationsByDisease()

◆ GetMutationsByGeneID()

◆ GetMutationsByHGMD()

◆ GetMutationsByUMLS()

◆ Initialize()

Member Data Documentation

◆ config

◆ coordSys

◆ db

◆ disease [1/2]

◆ disease [2/2]

◆ diseases

◆ end

◆ geneID

◆ GENERAL_QUERY_STUB

◆ hgmd

◆ MUTATION_DATA

◆ mutations

◆ op

◆ pos

◆ start