RSEntry.RSEntry Class Reference

Classes
class	RSVar

Public Member Functions
def	__init__ (self, chrom, rsid, pos=None)
def	__add__ (self, rse)
def	__eq__ (self, rse)
def	__getitem__ (self, key)
def	__iadd__ (self, rse)
def	__len__ (self)
def	__repr__ (self)
def	__str__ (self)
def	add_var (self, var)
def	add_var_from_args (self, pos, ref, var, major=0, minor=0, clin=[], afs=[], var_type='', pop_afs={})
def	all_vars_empty (self)
def	get_major_alleles (self)
def	get_major_alleles_pop (self, pop)
def	pick_major_allele (self, var_list)
def	to_vcf (self, pop=None, cons=False, is_maj=False)

Public Attributes
	chrom
	rsid
	pos
	vars

Detailed Description

A class to hold all variants at a given position.

Attributes
--------------------
chrom : str
    Which chromosome the entry is on (1-22, X, Y)
rsid : int
    The RefSNP ID number for the entry
pos : int
    Base position of the entry (1-indexed)
vars : dict
    Dictionary that maps variant code strings to RSVariant objects

Methods
--------------------
add_var(var)
    Add a RSVariant object to the RSEntry
add_var_from_args(pos, ref, var, major=0, minor=0, clin=[], afs=[],
    var_type='', pop_afs={})
    Add a variant to the RSEntry based on the given arguments
all_vars_empty()
    Check if all variants in the RSEntry are empty
get_major_alleles()
    Return a list of major RSVariants
get_major_alleles_pop(pop)
    Return a list of major RSVariants for a given population
pick_major_allele(var_list)
    Reproducibly choose a representative variant
to_vcf(pop=None, cons=False, is_maj=False)
    Create a VCF record from variants

Constructor & Destructor Documentation

__init__()

def RSEntry.RSEntry.__init__	(		self,
			chrom,
			rsid,
			pos = None
	)

Initialize an instance of the RSEntry class. Requires a chromosome and
a RSID number. Base position is optional, and if not passed will be
inferred from the first added variant.

Parameters:
chrom: Chromosome of the entry
rsid: RefSNP ID number of the entry
pos: Position of the entry

Member Function Documentation

__add__()

def RSEntry.RSEntry.__add__	(		self,
			rse
	)

Implement addition for two RSEntry objects.

__eq__()

def RSEntry.RSEntry.__eq__	(		self,
			rse
	)

Implement equality checking for two RSEntry objects.

__getitem__()

def RSEntry.RSEntry.__getitem__	(		self,
			key
	)

Allow access to variants via the [] operator.

__iadd__()

def RSEntry.RSEntry.__iadd__	(		self,
			rse
	)

Implement incremental addition.

__len__()

def RSEntry.RSEntry.__len__

(

self

)

Implement len operator.

__repr__()

def RSEntry.RSEntry.__repr__

(

self

)

Implement repr operator.

__str__()

def RSEntry.RSEntry.__str__

(

self

)

Implement str operator.

add_var()

def RSEntry.RSEntry.add_var	(		self,
			var
	)

Add a variant by passing an RSVariant object. Note that this creates a
new RSVar object and doesn't use the passed object.
    
Parameters:
var: RSVar object to add

add_var_from_args()

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

Add a variant by passing all necessary information.

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

all_vars_empty()

def RSEntry.RSEntry.all_vars_empty

(

self

)

Check if all variants are empty.

get_major_alleles()

def RSEntry.RSEntry.get_major_alleles

(

self

)

Get a list of variants representing a major allele (AF >= 0.5).

get_major_alleles_pop()

def RSEntry.RSEntry.get_major_alleles_pop	(		self,
			pop
	)

Get a list of variants representing a major allele (AF >= 0.5) for the
given population.

Parameters:
pop: Population to use

pick_major_allele()

def RSEntry.RSEntry.pick_major_allele	(		self,
			var_list
	)

Reproducibly choose a representative variant.

Parameters:
var_list: List of RSVar objects to pick from

to_vcf()

def RSEntry.RSEntry.to_vcf	(		self,
			pop = None,
			cons = False,
			is_maj = False
	)

Create a VCF record from variants. If preparing a consensus VCF
file, makes sure that there is only one alternate allele per line.

Parameters:
pop: Population to use
cons: If this VCF file is a consensus VCF
is_maj: If this RSCollection object already contains only major alleles

---

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

• RSEntry.py