AltAllele¶

class hail.representation.AltAllele(ref, alt)[source]¶

An object that represents an allele in a polymorphism deviating from the reference allele.

Parameters:	ref (str) – reference allele alt (str) – alternate allele

Attributes

`alt`	Alternate allele.
`ref`	Reference allele.

Methods

`__init__`	x.__init__(…) initializes x; see help(type(x)) for signature
`category`	Returns the type of alt, i.e one of SNP, Insertion, Deletion, Star, MNP, Complex
`is_MNP`	True if this alternate allele is a multiple nucleotide polymorphism (MNP)
`is_SNP`	True if this alternate allele is a single nucleotide polymorphism (SNP)
`is_complex`	True if this alternate allele does not fit into the categories of SNP, MNP, Insertion, or Deletion
`is_deletion`	True if this alternate allele is a deletion of one or more bases
`is_indel`	True if this alternate allele is either an insertion or deletion of one or more bases
`is_insertion`	True if this alternate allele is an insertion of one or more bases
`is_transition`	True if this alternate allele is a transition SNP.
`is_transversion`	True if this alternate allele is a transversion SNP.
`num_mismatch`	Returns the number of mismatched bases in this alternate allele.
`stripped_snp`	Returns the one-character reduced SNP.

alt¶

Alternate allele.

Return type:	str

category()[source]¶

Returns the type of alt, i.e one of: SNP, Insertion, Deletion, Star, MNP, Complex

Return type:	str

is_MNP()[source]¶

True if this alternate allele is a multiple nucleotide polymorphism (MNP)

Return type:	bool

is_SNP()[source]¶

True if this alternate allele is a single nucleotide polymorphism (SNP)

Return type:	bool

is_complex()[source]¶

True if this alternate allele does not fit into the categories of SNP, MNP, Insertion, or Deletion

Return type:	bool

is_deletion()[source]¶

True if this alternate allele is a deletion of one or more bases

Return type:	bool

is_indel()[source]¶

True if this alternate allele is either an insertion or deletion of one or more bases

Return type:	bool

is_insertion()[source]¶

True if this alternate allele is an insertion of one or more bases

Return type:	bool

is_transition()[source]¶

True if this alternate allele is a transition SNP.

This is true if the reference and alternate bases are both purine (A/G) or both pyrimidine (C/T). This method raises an exception if the polymorphism is not a SNP.

Return type:	bool

is_transversion()[source]¶

True if this alternate allele is a transversion SNP.

This is true if the reference and alternate bases contain one purine (A/G) and one pyrimidine (C/T). This method raises an exception if the polymorphism is not a SNP.

Return type:	bool

num_mismatch()[source]¶

Returns the number of mismatched bases in this alternate allele.

Fails if the ref and alt alleles are not the same length.

Return type:	int

ref¶

Reference allele.

Return type:	str

stripped_snp()[source]¶

Returns the one-character reduced SNP.

Fails if called on an alternate allele that is not a SNP.

Return type:	str, str