RSEntry.RSEntry.RSVar Class Reference

Public Member Functions
def	__init__ (self, pos, ref, var, major=0, minor=0, clin=[], afs=[], var_type='', pop_afs={})
def	__add__ (self, v)
def	__eq__ (self, v)
def	__iadd__ (self, v)
def	__repr__ (self)
def	__str__ (self)
def	af (self)
def	calc_afs (self)
def	calc_pop_afs (self, pop)
def	is_major (self)
def	is_empty (self)
def	pop_af (self, pop)
def	var_code (self)

Public Attributes
	pos
	ref
	var
	major
	minor
	clin
	afs
	var_type
	pop_afs

Detailed Description

A sub-class to represent a variant.

Attributes
--------------------
pos : int
    Base position of the variant
ref : str
    Reference base(s)
var : str
    Variant base(s)
major : int
    Number of studies that show this variant with AF >= 0.5
minor : int
    Number of studies that show this variant with AF < 0.5
clin : list
    List of clinical relevances
afs : list
    List of allele frequencies, stores as tuples of 
    (# patients showing var, # patients in study)
var_type : str
    What type of variant (SNP, indel, or blank)
pop_afs : dict
    Dict containing population allele frequencies

Methods
--------------------
af()
    Get a representative allele frequency for the variant
calc_afs()
    Calculate float allele frequencies from afs list
calc_pop_afs(pop)
    Calculate float allele frequencies for the given population
is_major()
    Return if the variant represents a major allele
is_empty()
    Return if the variant has no studies supporting it
pop_af(pop)
    Get a representative population allele frequency for the variant
    and given population.
var_code()
    Get the representative variant code for the variant

Constructor & Destructor Documentation

__init__()

def RSEntry.RSEntry.RSVar.__init__	(		self,
			pos,
			ref,
			var,
			major = 0,
			minor = 0,
			clin = [],
			afs = [],
			var_type = '',
			pop_afs = {}
	)

Initialize an instance of the RSVar class. Requires a position,
reference allele, and variant allele. All other information is 
oprtional, and will either be left blank or inferred (in the case
of var_type).

Parameters:
pos: Variant position
ref: Reference sequence at the variant position
var: Variant sequence
major: Number of studies in dbSNP listing this variant as major
minor: Number of studies in dbSNP listing this variant as minor
clin: Clinical significance of this variant
afs: Allele frequency of this allele
var_type: Variant type (SNP or indel) of this allele
pop_afs: Population allele frequencies

Member Function Documentation

__add__()

def RSEntry.RSEntry.RSVar.__add__	(		self,
			v
	)

Implement addition for two RSVar objects.

__eq__()

def RSEntry.RSEntry.RSVar.__eq__	(		self,
			v
	)

Implement equality checking for two RSVar objects.

__iadd__()

def RSEntry.RSEntry.RSVar.__iadd__	(		self,
			v
	)

Implement incremental addition.

__repr__()

def RSEntry.RSEntry.RSVar.__repr__

(

self

)

Implement repr operator.

__str__()

def RSEntry.RSEntry.RSVar.__str__

(

self

)

Implement str operator.

af()

def RSEntry.RSEntry.RSVar.af

(

self

)

Get a representative allele frequency for the variant.

calc_afs()

def RSEntry.RSEntry.RSVar.calc_afs

(

self

)

Calculate float allele frequencies from afs list.

calc_pop_afs()

def RSEntry.RSEntry.RSVar.calc_pop_afs	(		self,
			pop
	)

Calculate float allele frequencies from afs list.

Parameters:
pop: Population to use

is_empty()

def RSEntry.RSEntry.RSVar.is_empty

(

self

)

Return if the variant has no studies supporting it.

is_major()

def RSEntry.RSEntry.RSVar.is_major

(

self

)

Return if the variant represents a major allele.

pop_af()

def RSEntry.RSEntry.RSVar.pop_af	(		self,
			pop
	)

Get a representative population allele frequency for the variant
and given population.

Parameters:
pop: Population to use

var_code()

def RSEntry.RSEntry.RSVar.var_code

(

self

)

Get the representative variant code for the variant.

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

• RSEntry.py