ancIBD.transition

Class for calculating Transition Probabilities, i.e. infitesimal transition Matrices. Contains Sub-Classes, as well as factory Method. @ Author: Harald Ringbauer, 2021, All rights reserved

Module Contents

Classes

Transitions	Class for transition probabilities.
FiveStateTransitions	Implements the Model Transitions [units generally in Morgan]
FiveStateAsymmetric	A transition model for detecting IBD between ancient and modern sample pairs.
SevenStateTransitions	Implements the Model Transitions [units generally in Morgan]
TwoStateTransitions	Implements the Model Transitions [units generally in Morgan]
ThreeStateTransitions	Implements the Model Transitions [units generally in Morgan]
FiveStatGeneric	A transition model for detecting IBD. Same as FiveStateTransitions, except that the 3x3 speed-up is not implemented here.

Functions

load_transition_model([t_model])

Load the Transition Model

class ancIBD.transition.Transitions

Bases: object

Class for transition probabilities. Has methods to return them

trans_mat = []

r_map = []

output = True

abstract calc_transition_rate(n=0)

Calulate and return Transition Matrix

give_transition_rate()

Give the transition_matrix

set_params(**kwargs)

Set the Values.

class ancIBD.transition.FiveStateTransitions

Bases: Transitions

Implements the Model Transitions [units generally in Morgan]

ibd_in = 0.0005

ibd_out = 0.001

ibd_jump = 0.05

min_gap = 1e-10

max_gap = 0.05

calc_transition_rate(submat33=True, n=4)

Return Transition Rate Matrix [k,k] to exponate. n: Number of symetric IBD states. Usually four (2x2 copying possibilities) submat33: Whether to only fill in the first 3 states

full_transition_matrix(r_vec, t=[], n=4, submat33=True)

Compute and return the full transition Matrix. Calculates the first 3 states (not more needed by symmetry) t full Transition Matrix [k,k]. NO LOG STATE. If not given caluclate r_vec Map Length of Jumps [l] in Morgan n: Number of symmetric, non-background states

prep_3x3matrix(t, n)

Prepare and return the grouped 3x3 Matrix (grouped 3rd State: Everything in other IBD states) t: Origianl transition matrix (only first three entry important) n: Number of symmetric states

exponentiate_r(rates, rec_v)

Calculates exponentiation of the rates matrix with rec_v rates: 2D Matrix of transitions rec_v: Array of length l

rmap_to_gaps(r_map=[], cm=False)

Return the recombination map gaps [in Morgan] Input: Map Positions [l] (units see cm parameter below) Return: Rec. Distance Array [l] cm: Whether input is in centimorgan or morgan min_cap: Minimum Map Gap between Loci to cap max_cap: Maximum Mapg Gap between Loci to cap

class ancIBD.transition.FiveStateAsymmetric

Bases: FiveStateTransitions

A transition model for detecting IBD between ancient and modern sample pairs.

ibd_in = 1

ibd_out = 20

ibd_jump = 400

ibd_jump2 = 0.5

calc_transition_rate()

Return Transition Rate Matrix [k,k] to exponate.

full_transition_matrix(r_vec, t=[], n=4, submat33=True)

Compute and return the full transition Matrix. Calculates the first 3 states (not more needed by symmetry) t full Transition Matrix [k,k]. NO LOG STATE. If not given caluclate r_vec Map Length of Jumps [l] in Morgan n: Number of symmetric, non-background states, not used by this method, keeping it here to just keep function signature the same as that of the 5state HMM. submat33: also not used by this function, keeping it here just to keep consistency with the 5 state hmm Note: this is the only function called by outside code

class ancIBD.transition.SevenStateTransitions

Bases: FiveStateTransitions

Implements the Model Transitions [units generally in Morgan]

ibd_in = 1

ibd_out = 20

ibd_jump = 500

exponentiate_r(rates, rec_v)

Calculates exponentiation of the rates matrix with rec_v rates: 2D Matrix of transitions rec_v: Array of length l

calc_transition_rate()

Return Transition Rate Matrix [k,k] to exponate. n: Number of symetric IBD states. Usually four (2x2 copying possibilities) submat33: Whether to only fill in the first 3 states

full_transition_matrix(r_vec, t=[], n=4, submat33=True)

Compute and return the full transition Matrix. Calculates the first 3 states (not more needed by symmetry) t full Transition Matrix [k,k]. NO LOG STATE. If not given caluclate r_vec Map Length of Jumps [l] in Morgan n: Number of symmetric, non-background states, not used by this method, keeping it here to just keep function signature the same as that of the 5state HMM. submat33: also not used by this function, keeping it here just to keep consistency with the 5 state hmm Note: this is the only function called by outside code

class ancIBD.transition.TwoStateTransitions

Bases: FiveStateTransitions

Implements the Model Transitions [units generally in Morgan]

ibd_in = 1

ibd_out = 20

calc_transition_rate()

Return Transition Rate Matrix [k,k] to exponate. n: Number of symetric IBD states. Usually four (2x2 copying possibilities) submat33: Whether to only fill in the first 3 states

full_transition_matrix(r_vec, t=[], n=4, submat33=True)

The last two arguments n and submat33 are not used. They are retained just for compatibility with the one Harald wrote.

class ancIBD.transition.ThreeStateTransitions

Bases: FiveStateTransitions

Implements the Model Transitions [units generally in Morgan]

ibd_in = 1

ibd_out = 20

ibd_jump = 400

calc_transition_rate()

Return Transition Rate Matrix [k,k] to exponate. n: Number of symetric IBD states. Usually four (2x2 copying possibilities) submat33: Whether to only fill in the first 3 states

full_transition_matrix(r_vec, t=[], n=4, submat33=True)

The last two arguments n and submat33 are not used. They are retained just for compatibility with the one Harald wrote.

class ancIBD.transition.FiveStatGeneric

Bases: FiveStateTransitions

A transition model for detecting IBD. Same as FiveStateTransitions, except that the 3x3 speed-up is not implemented here.

ibd_in = 1

ibd_out = 20

ibd_jump = 400

calc_transition_rate()

Return Transition Rate Matrix [k,k] to exponate.

full_transition_matrix(r_vec, t=[], n=4, submat33=True)

Compute and return the full transition Matrix. Calculates the first 3 states (not more needed by symmetry) t full Transition Matrix [k,k]. NO LOG STATE. If not given caluclate r_vec Map Length of Jumps [l] in Morgan n: Number of symmetric, non-background states, not used by this method, keeping it here to just keep function signature the same as that of the 5state HMM. submat33: also not used by this function, keeping it here just to keep consistency with the 5 state hmm Note: this is the only function called by outside code

ancIBD.transition.load_transition_model(t_model='standard')

Load the Transition Model