Trio

class hail.genetics.Trio(s, fam_id=None, pat_id=None, mat_id=None, is_female=None)[source]

Class containing information about nuclear family relatedness and sex.

Parameters:
  • s (str) – Sample ID of proband.
  • fam_id (str or None) – Family ID.
  • pat_id (str or None) – Sample ID of father.
  • mat_id (str or None) – Sample ID of mother.
  • is_female (bool or None) – Sex of proband.

Attributes

fam_id Family ID.
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.
mat_id ID of mother in trio, may be missing.
pat_id ID of father in trio, may be missing.
s ID of proband in trio, never missing.

Methods

__init__ Initialize self.
is_complete Returns True if the trio has a defined mother and father.
fam_id

Family ID.

Return type:str or None
is_complete()[source]

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

The considered fields are mat_id() and pat_id(). Recall that s may never be missing. The fam_id() and is_female() fields 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
mat_id

ID of mother in trio, may be missing.

Return type:str or None
pat_id

ID of father in trio, may be missing.

Return type:str or None
s

ID of proband in trio, never missing.

Return type:str