simplicity.evolution package

Submodules

simplicity.evolution.decoder module

simplicity.evolution.decoder.decode_genome(single_encoded_genome)

simplicity.evolution.mutations module

Created on Thu Jun 1 11:15:10 2023

@author: pietro

simplicity.evolution.mutations.assign_sub(unassigned_subst, sub_coord_dicmap)

Update the substitution coordinates to include the substitutions that will be included (assign the substitutions to lineages with the positions in their genome)

Parameters:

• unassigned_subst (dic) – dict with a list of substitutions for each nitrogenous base.

• sub_coord_dicmap (coordinates of the substitutions that will be introduced)

Returns:

• sub_coord_dicmap (list)

• UPDATED coordinates of substitution

• index of individual (in population.individuals) that hosts the lineage

• index of lineage inside the host

• position in the genome of lineage mutated

• nitrogenous base that will be introduced at that position

simplicity.evolution.mutations.fetch_bases(population, sub_coord_dicmap)

Add base to be substituted to subst_coord. First it checks if the position is already mutated, if so it takes the mutated base. Otherwise fetches the base from the reference genome.

Parameters:

• population (instance of population class)

• sub_coord_dicmap (list) – coordinates of substitution

Returns:

• sub_coord_dicmap (list)

• coordinates of substitution

• index of individual (in population.individuals) that hosts the lineage

• index of lineage inside the host

• position in the genome of lineage mutated

• nitrogenous base of the lineage at that position

simplicity.evolution.mutations.get_individuals_to_update(subst_coord)

simplicity.evolution.mutations.get_lineage_name(phylodots, lineage_name)

simplicity.evolution.mutations.get_subst_numbers(sub_coord_dicmap, sub_number)

Returns count of how many of each nitrogenous base will undergo substitution

Parameters:

• sub_coord_dicmap (list) – coordinates of substitutions

• sub_number (int) – number of substitution events

Raises:

ValueError – Raise error if the list of coordinates is not the same size as the number of substitution events

Returns:

dic that counts the number of bases to be substituted. e.g. 4 A, 3 T, 0 C, 5 G

Return type:

TYPE

simplicity.evolution.mutations.map_to_dic(mutating_lineages, positions, L_lin)

Map mutation positions onto dictionary of population.individuals

Parameters:

• mutating_lineages (list)

• lineages( (list of selected lineages that will mutate (subset of active) – coord map onto individuals

• positions (array) – positions that will undergo substitution

Returns:

• sub_coord_dicmap (list)

• coordinates of substitution

• index of individual (in population.individuals) that hosts the lineage

• index of lineage inside the host

• position in the genome of lineage to be mutated

simplicity.evolution.mutations.map_to_lin(positions, L)

Maps positions to be mutated onto active_lineages (lineages).

Parameters:

• positions (array) – positions that will undergo substitution

• L (int) – lenght of lineage genome

Returns:

sub_coord_linmap –

lineages mutation coordinates:

(LIST index of active_lineage to mutate,

position in the genome to mutate).

the index here does not refer to the index of the population.individuals dic

Return type:

tuple

simplicity.evolution.mutations.mutate(population, NSR, L, dt, phenotype_model, *args)

Mutation model, mutates the viruses in the population.

Parameters:

• NSR (float) – nucleotide substitution rate.

• dt (float) – delta t - extrande time step (in years)

simplicity.evolution.mutations.select_positions(population, L, NSR, dt)

Select genome positions to mutate using two parallel Poisson processes.

Returns:

array of pooled genome indices to mutate mutating_lineages : list of [individual_id, lineage_id] per mutation sub_number : number of mutations this time step

Return type:

positions

simplicity.evolution.mutations.sub_events(rng, NSR, L, dt, IH_lineages)

Choose the number of substitutions that happen in a time step dt,

drawing random number sampled from Poisson distribution.

Parameters:

• rng (numpy method) – Random number generator.

• NSR (float) – nucleotide substitution rate.

• dt (float) – delta t - extrande time step.

• IH_lineages (int) – number of active IH_lineages that can mutate in time step dt

Returns:

number of substitutions that happen in a time step dt.

Return type:

int

simplicity.evolution.mutations.sub_matrix()

Define substitution matrix. If you want to specify a different matrix, change the code here.

simplicity.evolution.mutations.substitution(M, bases_count, rng)

Generate substitutions for each base based on substitution matrix. These substitutions are not assigned to any genome position yet, the function returns a dict with a list of substitutions for each nitrogenous base.

Parameters:

• M (substitution matrix)

• bases_count (dic) – dictionary with count of bases to substitute

Returns:

dictionary that contain a list of substitutions for each base type. e.g A = [T,T,G,C,G,T,T,C,C,G]

Return type:

dic

simplicity.evolution.mutations.update_lineages(population, sub_coord_dicmap)

Update lineages genomes in population with the selected mutations from the coordinates.

Parameters:

• population (instance of population class)

• sub_coord_dicmap (substituions coordinates)

simplicity.evolution.reference module

@author: Pietro Gerletti

simplicity.evolution.reference.get_reference()

Module contents