cls.ClinVarAnnotation.CClinVarAnnotation Class Reference

Class for accessing ClinVar. More...

Public Member Functions
def	__init__ (s, pth, c, inType, cvData, noData, haveHeader, reader, coll, perm)
	Constructor. More...
def	InGcoords (s, exactRefAlt=False)
	Performs the annotations of variants for the input options gcoord and gcoord-ref-alt. More...
def	InRange (s)
	Performs the annotations of variants for the input option range-abs. More...

Detailed Description

Class for accessing ClinVar.

Constructor & Destructor Documentation

__init__()

def cls.ClinVarAnnotation.CClinVarAnnotation.__init__	(		s,
			pth,
			c,
			inType,
			cvData,
			noData,
			haveHeader,
			reader,
			coll,
			perm
	)

Constructor.

    @param pth  Initialized @ref common.Paths.CPaths instance.
    @param c A list of column indices that give the genomic coordinates in
           the input file
    @param inType The type of analysis to perform. One of gcoords,
           gcoords-ref-alt, range-abs
    @param cvData ClinVarData object through which to access the ClinVar
           data
    @param noData The empty value specifier
    @param haveHeader True, if the input file has a header

Member Function Documentation

InGcoords()

def cls.ClinVarAnnotation.CClinVarAnnotation.InGcoords	(		s,
			exactRefAlt = False
	)

Performs the annotations of variants for the input options gcoord and gcoord-ref-alt.

Performs the annotations of variants for the input options gcoord and gcoord-ref-alt

Parameters

exactRefAlt

True if exact ref-alt match is required by the user.

InRange()

def cls.ClinVarAnnotation.CClinVarAnnotation.InRange

(

s

)

Performs the annotations of variants for the input option range-abs.

   Performs the annotations of variants for the input option range-abs.

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

• cls/ClinVarAnnotation.py