Trio

class hail.representation.Trio(proband, fam=None, father=None, mother=None, is_female=None)

Class containing information about nuclear family relatedness and sex.

Parameters:

• proband (str) – Sample ID of proband.
• fam (str or None) – Family ID.
• father (str or None) – Sample ID of father.
• mother (str or None) – Sample ID of mother.
• is_female (bool or None) – Sex of proband.

Attributes

fam	Family ID.
father	ID of father in trio, may be missing.
is_female	Returns True if the proband is a reported female, False if reported male, and None if no sex is defined.
is_male	Returns True if the proband is a reported male, False if reported female, and None if no sex is defined.
mother	ID of mother in trio, may be missing.
proband	ID of proband in trio, never missing.

Methods

__init__	x.__init__(…) initializes x; see help(type(x)) for signature
is_complete	Returns True if the trio has a defined mother, father, and sex.

fam

Family ID.

Return type:str or None

father

ID of father in trio, may be missing.

Return type:str or None

is_complete()

Returns True if the trio has a defined mother, father, and sex.

The considered fields are mother, father, and sex. Recall that proband may never be missing. The fam field may be missing in a complete trio.

Return type:bool

is_female

Returns True if the proband is a reported female, False if reported male, and None if no sex is defined.

Return type:bool or None

is_male

Returns True if the proband is a reported male, False if reported female, and None if no sex is defined.

Return type:bool or None

mother

ID of mother in trio, may be missing.

Return type:str or None

proband

ID of proband in trio, never missing.

Return type:str