cls.Variant.CCoordinateVariant Class Reference

Variant based on coordinates only. More...

Inheritance diagram for cls.Variant.CCoordinateVariant:

Public Member Functions
def	__init__ (s, dver, gc)
	Constructor. More...
def	__str__ (s)
def	__eq__ (s, obj)
	The equality operator. More...
def	IsValid (s)
	Is this a valid object? More...
def	GetChrom (s)
	Get the chromosome name. More...
def	GetStart (s)
	Get the start coordinate of the variant. More...
def	GetEnd (s)
	Get the end coordinate of the variant. More...
def	GetBuild (s)
	Get the build version. More...
def	GetCoordString (s)
	Get the coordinate string of the variant. More...

Detailed Description

Variant based on coordinates only.

This class stores the location of a variant and offers a comparison
operator.

Constructor & Destructor Documentation

__init__()

def cls.Variant.CCoordinateVariant.__init__	(		s,
			dver,
			gc
	)

Constructor.

Parameters

dver	Data version String for config file lookup.
gc	Genomic SNP coordinate.

Member Function Documentation

__eq__()

def cls.Variant.CCoordinateVariant.__eq__	(		s,
			obj
	)

The equality operator.

Reimplemented in cls.Variant.CAlleleVariant.

__str__()

def cls.Variant.CCoordinateVariant.__str__

(

s

)

Reimplemented in cls.Variant.CAlleleVariant.

GetBuild()

def cls.Variant.CCoordinateVariant.GetBuild

(

s

)

Get the build version.

GetChrom()

def cls.Variant.CCoordinateVariant.GetChrom

(

s

)

Get the chromosome name.

GetCoordString()

def cls.Variant.CCoordinateVariant.GetCoordString

(

s

)

Get the coordinate string of the variant.

    @return The coordinate string consisting of chromosome, start, end, and
    build. 

GetEnd()

def cls.Variant.CCoordinateVariant.GetEnd

(

s

)

Get the end coordinate of the variant.

GetStart()

def cls.Variant.CCoordinateVariant.GetStart

(

s

)

Get the start coordinate of the variant.

IsValid()

def cls.Variant.CCoordinateVariant.IsValid

(

s

)

Is this a valid object?

Returns

True The genomics coordinates were converted successfully, the object can be used.

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

• cls/Variant.py