cls.ClinVarData.CClinVarData Class Reference

Class for accessing the ClinVar data. More...

Public Member Functions
def	__init__ (s, pth, cvId, gcoords, addRefAlt, clnsig, clnorigin, clndbn, clnsrc, allOpt, noData)
	Constructor. More...
def	GetLen (s)
def	GetAnnotations (s)
def	GetData (s, variant)
	Returns the requested ClinVar annotations that match the variant. More...
def	GetDataRange (s, startVariant, endVariant)
	Returns the requested ClinVar annotations that are in the range of (startVariant, endVariant). More...

Static Public Attributes
list	AllInfoAnnotations = ["CLNSIG", "ORIGIN", "CLNDN", "CLNVI"]
list	AllFieldAnnotations = ["Id","Gcoords", "Ref", "Alt"]
dictionary	ClnoriginDic

Detailed Description

Class for accessing the ClinVar data.

This class should only be used by calling the GetData and GetDataRange functions. These functions return the requested ClinVar annotations for one position or for a range respectively.

Constructor & Destructor Documentation

__init__()

def cls.ClinVarData.CClinVarData.__init__	(		s,
			pth,
			cvId,
			gcoords,
			addRefAlt,
			clnsig,
			clnorigin,
			clndbn,
			clnsrc,
			allOpt,
			noData
	)

Constructor.

   Initialize a table with the requested ClinVar annotations. The order
   of parameter appearance corresponds to the order of the columns
   reported by the @ref GetData and @ref GetDataRange methods.
   @param pth  Initialized @ref common.Paths.CPaths instance.
   @param cvId True, if the ClinVar VCF id is to be appended.
   @param gcoords True, if the ClinVar gcoords are to be appended.
   @param addRefAlt True, if the ClinVar ref and alt allele are to be
           appended.
   @param clnsig True, if CLNSIG annotations are to be appended.
   @param clnorigin True, if CLNORIGIN annotations are to be appended.
   @param clndbn True, if CLNDBN annotations are to be appended.
   @param clnsrc True, if CLNSRC annotations are to be appended.
   @param allOpt True if all annotations listed above are to be appended.
   @param noData The empty value specifier.

Member Function Documentation

GetAnnotations()

def cls.ClinVarData.CClinVarData.GetAnnotations

(

s

)

GetData()

def cls.ClinVarData.CClinVarData.GetData	(		s,
			variant
	)

Returns the requested ClinVar annotations that match the variant.

   @param variant An instance either of CAlleleVariant or of
      CCoordinateVariant, depending if an exact ref-alt match was
      required. The variant for which to query ClinVar for annotations that
      match in coordiante and / or ref-alt allele.
   @return a list of lists of ClinVar annotations that match the variant.
   Each
       list element corresponds to one entry in ClinVar. Each list element
       is a list itself and holds the ClinVar annotations requested by the
       user in the order as they appear in the two lists
       s.AllFieldAnnotations + AllInfoAnnotations (which is equivalent to
      the order of the input flags of this class' constructor,
      @ref CClinVarData.__init__).

GetDataRange()

def cls.ClinVarData.CClinVarData.GetDataRange	(		s,
			startVariant,
			endVariant
	)

Returns the requested ClinVar annotations that are in the range of (startVariant, endVariant).

Parameters

startVariant	An instance of CCoordinateVariant. The beginning of the coordinate range for which to query ClinVar.
endVariant	An instance of CCoordinateVariant. The end of the coordinate range for which to query ClinVar.

Returns

A list of lists of ClinVar annotations that lie in the range specified by startVariant, endVariant. Each list element corresponds to one entry in ClinVar. Each list element is a list itself and holds the ClinVar annotations requested by the user in the order as they appear in the two lists s.AllFieldAnnotations + AllInfoAnnotations (which is equivalent to the order of the input flags of this class' constructor, CClinVarData.__init__).

GetLen()

def cls.ClinVarData.CClinVarData.GetLen

(

s

)

Member Data Documentation

AllFieldAnnotations

list cls.ClinVarData.CClinVarData.AllFieldAnnotations = ["Id","Gcoords", "Ref", "Alt"]

static

AllInfoAnnotations

list cls.ClinVarData.CClinVarData.AllInfoAnnotations = ["CLNSIG", "ORIGIN", "CLNDN", "CLNVI"]

static

ClnoriginDic

dictionary cls.ClinVarData.CClinVarData.ClnoriginDic

static

Initial value:

=  {"0":"unknown", "1":"germline", "2":"somatic",
                        "4":"inherited", "8":"paternal", "16":"maternal",
                        "32":"de-novo", "64":"biparental","128":"uniparental",
                        "256":"not-tested", "512":"tested-inconclusive",
                        "1073741824":"other", CELL_NO_DATA:CELL_NO_DATA}

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

• cls/ClinVarData.py